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Publications 2024
NCBI LIST CITATIONS
J385.
James M Krieger, Frane Doljanin, Anthony T Bogetti, Feng Zhang, Thiliban Manivarma, Ivet Bahar, Karolina Mikulska-Ruminska
WatFinder: A ProDy tool for protein-water interactions
Bioinformatics, btae516 (2024)
J384.
Ariel Leyte-Vidal, RosaAnna DeFilippis, Ian R Outhwaite, Isabelle Kwan, Ji Young Lee, Carlyn Leavitt, Kaeli B Miller, Delphine Rea, Aziz M Rangwala, Kevin Lou, Suhana Patel, Ailin Alvarez, Kevan M Shokat, Ivet Bahar, Markus A Seeliger, Neil P Shah
Absence of ABL1 exon 2-encoded SH3 residues in BCR::ABL1 destabilizes the autoinhibited kinase conformation and confers resistance to asciminib
Leukemia, 1-5 (2024)
J383.
Rommie Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Daniel Beltran, Philip C Biggin, Massimiliano Bonomi, Gregory R Bowman, Richard Bryce, Giovanni Bussi, Paolo Carloni, David Case, Andrea Cavalli, Chie-En A Chang, Thomas E Cheatham III, Margaret S Cheung, Cris Chipot, Lillian T Chong, Preeti Choudhary, Cecilia Clementi, Rosana Collepardo-Guevara, Peter Coveney, T Daniel Crawford, Matteo Dal Peraro, Bert de Groot, Lucie Delemotte, Marco De Vivo, Jonathan Essex, Franca Fraternali, Jiali Gao, Josep Lluís Gelpí, Francesco Luigi Gervasio, Fernando Danilo Gonzalez-Nilo, Helmut Grubmüller, Marina Guenza, Horacio V Guzman, Sarah Harris, Teresa Head-Gordon, Rigoberto Hernandez, Adam Hospital, Niu Huang, Xuhui Huang, Gerhard Hummer, Javier Iglesias-Fernández, Jan H Jensen, Shantenu Jha, Wanting Jiao, Shina Caroline Lynn Kamerlin, Syma Khalid, Charles Laughton, Michael Levitt, Vittorio Limongelli, Erik Lindahl, Kersten Lindorff-Larsen, Sharon Loverde, Magnus Lundborg, Yun Lina Luo, Francisco Javier Luque, Charlotte I Lynch, Alexander MacKerell, Alessandra Magistrato, Siewert J Marrink, Hugh Martin, J Andrew McCammon, Kenneth Merz, Vicent Moliner, Adrian Mulholland, Sohail Murad, Athi N Naganathan, Shikha Nangia, Frank Noe, Agnes Noy, Julianna Oláh, Megan O'Mara, Mary Jo Ondrechen, José N Onuchic, Alexey Onufriev, Silvia Osuna, Anna R Panchenko, Sergio Pantano, Michele Parrinello, Alberto Perez, Tomas Perez-Acle, Juan R Perilla, B Montgomery Pettitt, Adriana Pietropalo, Jean-Philip Piquemal, Adolfo Poma, Matej Praprotnik, Maria J Ramos, Pengyu Ren, Nathalie Reuter, Adrian Roitberg, Edina Rosta, Carme Rovira, Benoit Roux, Ursula Röthlisberger, Karissa Y Sanbonmatsu, Tamar Schlick, Alexey K Shaytan, Carlos Simmerling, Jeremy C Smith, Yuji Sugita, Katarzyna Swiderek, Makoto Taiji, Peng Tao, Julian Tirado-Rives, Inaki Tunón, Marc W Van Der Kamp, David Van der Spoel, Sameer Velankar, Gregory A Voth, Rebecca Wade, Ariel Warshel, Valerie Vaissier Welborn, Stacey Wetmore, Chung F Wong, Lee-Wei Yang, Martin Zacharias, Modesto Orozco (2024)
The need to implement FAIR principles in biomolecular simulations arXiv preprint arXiv:2407.16584
J382.
Nga H Nguyen, Shaohu Sheng, Anupam Banerjee, Christopher J Guerriero, Jingxin Chen, Xueqi Wang, Timothy D Mackie, Paul A Welling, Thomas R Kleyman, Ivet Bahar Anne E Carlson, Jeffrey L Brodsky (2024)
Characterization of hyperactive mutations in the renal potassium channel ROMK uncovers unique effects on channel biogenesis and ion conductance. Molecular Biology of the Cell, mbc. E23-12-0494
J381.
Veerpal Kaur, Demelza Wright, Samuel Mathew, Matthew Peters, Maria Zacharopoulou, Shang-Hua Yang, Laura Itzhaki, Ivet Bahar Reuven Gordon (2024)
Portable fiber-based double nanohole optical tweezer for trapping small proteins . Journal of Physics: Photonics 6, 035023
J380.
Banerjee A, Mathew S, Naqvi MM, Yilmaz SZ, Zacharopoulou M, Doruker P, Kumita JR, Yang SH, Gur M, Itzhaki LS, Gordon R, Bahar I (2024)
Influence of point mutations on PR65 conformational adaptability: Insights from molecular simulations and nanoaperture optical tweezers
. Science Advances, 10(22):eadn2208.
J379.
A Banerjee, S Zhang, I Bahar (2024)
Genome structural dynamics: insights from Gaussian network analysis of Hi-C data
. Briefings in Functional Genomics, 23(5), 525–537,
J378.
Lloyd D Harvey, Mona Alotaibi, Hee-Jung Janice Kim, Yi-Yin Tai, Ying Tang, Wei Sun, Wadih El Khoury, Chen-Shan C Woodcock, Yassmin Al Aaraj, Claudette M St. Croix, Donna B Stolz, Jiyoung Lee, Mary Hongying Cheng, Tae-Hwi Schwantes-An, Ankit A Desai, Michael W Pauciulo, William C Nichols, Amy Webb, Robert Lafyatis, Mehdi Nouraie, Haodi Wu, Jeffrey G McDonald, Caroline Chauvet, Susan Cheng, Ivet Bahar, Thomas Bertero, Raymond L Benza, Mohit Jain, Stephen Y Chan (2024)
Genetic regulation and targeted reversal of lysosomal dysfunction and inflammatory sterol metabolism in pulmonary arterial hypertension
. BioRxiv, 2024.02. 26.582142
J377.
Andreia CK Fontana, Adi NR Poli, Jitendra Gour, Yellamelli VV Srikanth, Nicholas Anastasi, Devipriya Ashok, Apeksha Khatiwada, Katelyn L Reeb, Mary Hongying Cheng, Ivet Bahar, Scott M Rawls, Joseph M Salvino (2024)
Synthesis and Structure¿Activity Relationships for Glutamate Transporter Allosteric Modulators
. Journal of Medicinal Chemistry, 67, 8, 6119¿6143
P4. I Sutkeviciute, JP Vilardaga, J Lee, I Bahar, B Kaynak (2024)
Small molecule allosteric modulators of class B GPCR, the PTHR, and method to identify them. US Patent App. 18/277,765
P3. Mark E Schurdak, Andreas Vogt, Andrew Michael Stern, Douglass Lansing Taylor, CHEN Fangyuan, PEI Fen, Hongying Cheng, Ivet Bahar, SHI Qingya, Moshe Arditi (2024)
Compounds for the treatment of a disease or disorder, methods for identifying said compounds
. US Patent App. 18/273,161
J376. Hoang Nguyen, Mary Hongying Cheng, JiYoung Lee, S Aggarwal, Ole V Mortensen, Ivet Bahar (2024). Allosteric modulation of serotonin and dopamine transporters: New insights from computations and experiments. Current Research in Physiology, 10012
J375. Yueming Zhu, Anupam Banerjee, Ping Xie, Andrey A Ivanov, Amad Uddin, Qiao Jiao, Junlong J Chi, Lidan Zeng, Ji Young Lee, Yifan Xue, Xinghua Lu, Massimo Cristofanilli, William J Gradishar, Curtis J Henry, Theresa W Gillespie, Manali Ajay Bhave, Kevin Kalinsky, Haian Fu, Ivet Bahar, Bin Zhang, Yong Wan (2024)
A Pharmacological suppression of the OTUD4-CD73 proteolytic axis revives antitumor immunity against immune-suppressive breast cancers. Journal of Clinical Investigation, 134(10): e176390.
J374. JiYoung Lee, Emma Gebauer, Markus A. Seeliger, Ivet Bahar (2024)
Allo-targeting of the kinase domain: Insights from in silico studies and comparison with experiments. Curr Opin Struct Biol Volume 84, 102770
J373. Carlos Ventura, Anupam Banerjee, Maria Zacharopoulou, Laura S Itzhaki, Ivet Bahar (2024)
Tandem-repeat proteins conformational mechanics are optimized to facilitate functional interactions and complexations. Curr Opin Struct Biol 84, 102744
J372. Svetlana N Samovich, Karolina Mikulska-Ruminska, Haider H Dar, Yulia Y
Tyurina, Vladimir A Tyurin, Austin B Souryavong, Alexander A Kapralov,
Andrew A Amoscato, Ofer Beharier, S Ananth Karumanchi, Claudette M St Croix,
Xin Yang, Theodore R Holman, Andrew P VanDemark, Yoel Sadovsky, Rama K
Mallampalli, Sally E Wenzel, Wei Gu, Yuri L Bunimovich, Ivet Bahar, Valerian
E Kagan, Hülya Bayir (2024) Strikingly High Activity of 15-Lipoxygenase
Towards Di-Polyunsaturated Arachidonoyl/Adrenoyl-Phosphatidylethanolamines
Generates Peroxidation Signals of Ferroptotic Cell Death. Angewandte
Chemie International Edition, e202314710
J371. MGS Costa, M Gur, JM Krieger, Bahar I (2024)
Computational biophysics meets cryo-EM revolution in the search for the functional dynamics of biomolecular systems. Wiley Interdisciplinary Reviews: Computational Molecular Science 14, e1689
J370.
MP Dalton, MH Cheng, Bahar I, JA Coleman (2024)
Structural Mechanisms
for VMAT2 inhibition by tetrabenazine
. Elife Mar 22:12:RP91973
Publications 2023
J369. Valerian E Kagan, Yulia Y Tyurina, Karolina Mikulska-Ruminska, Deena Damschroder, Eduardo Vieira Neto, Alessia Lasorsa, Alexander A Kapralov, Vladimir A Tyurin, Andrew A Amoscato, Svetlana N Samovich, Austin B Souryavong, Haider H Dar, Abu Ramim, Zhuqing Liang, Pablo Lazcano, Jiajia Ji, Michael W Schmidtke, Kirill Kiselyov, Aybike Korkmaz, Georgy K Vladimirov, Margarita A Artyukhova, Pushpa Rampratap, Laura K Cole, Ammanamanchi Niyatie, Emma-Kate Baker, Jim Peterson, Grant M Hatch, Jeffrey Atkinson, Jerry Vockley, Bernhard Kühn, Robert Wessells, Patrick CA van der Wel, Bahar I, Hülya Bayir, Miriam L Greenberg (2023)
Anomalous peroxidase activity of cytochrome c is the primary pathogenic target in Barth syndrome. Nature Metabolism 5, 2184-2205
J368. Denys Bondar, Olga Bragina, Ji Young Lee, Ivan Semenyuta, Ivar Järving, Volodymyr Brovarets, Peter Wipf, Bahar I, Yevgen Karpichev (2023)
Hydroxamic Acids as PARP-1 Inhibitors: Molecular Design and Anticancer Activity of Novel Phenanthridinones. Helvetica Chimica Acta 106 (10), e202300133
J367. Yan Zhang, Xiaojie Qiu, Jonathan S Weissman, Ivet Bahar, Jianhua Xing (2023)
Graph-Dynamo: Learning stochastic cellular state transition dynamics from single cell data. BioRxiv, 2023.09.24.559170
P2.
Bahar I, H Cheng, S Zhang, R Porritt, M Arditi (2023)
Compositions and
methods for treating a COVID-19 infection
. US Patent 11,746,144
J366. Dar HH, Mikulska-Ruminska K, Tyurina YY, Luci DK, Yasgar A, Samovich SN, Kapralov AA, Souryavong AB, Tyurin VA, Amoscato AA, Epperly MW, Shurin GV, Standley M, Holman TR, St. Croix CM, Watkins SC, VanDemark AP, Rana S, Zakharov AV, Simeonov A, Marugan J, Mallampalli RK, Wenzel SE, Greenberger JS, Rai G, Bayir H, Bahar I, Kagan VE (2023) Discovering selective antiferroptotic inhibitors of the 15LOX/PEBP1 complex noninterfering with biosynthesis of lipid mediators. Proc Natl Acad Sci (USA) 120, e2218896120
J365. Zhang X, Weiß T, Cheng MH, Chen S, Ambrosius CK, Czerniak AS, Li K, Feng M, Bahar I, Beck-Sickinger AG, Zhang C (2023) Structural basis of G protein-Coupled receptor CMKLR1 activation and signaling induced by a chemerin-derived agonist. PLoS Biol. Dec 6;21(12) :e3002188.; first appeared as: Zhang C, Zhang X, Weiß T, Cheng MH, Chen S, Ambrosius CK, Czerniak AS, Li K, Feng M, Bahar I, Beck-Sickinger AG (2023) Structural basis of CMKLR1 signaling induced by chemerin9. BioRxiv , 2023.06. 09.544295
J364. Amoscato AA, Anthonymuthu T, Kapralov O, Sparvero LJ, Shrivastava IH, Mikulska-Ruminska K, Tyurin VA, Shvedova AA, Tyurina YY, Bahar I, Wenzel S, Bayir H, Kagan VE (2023) Formation of protein adducts with hydroperoxy-PE electrophilic cleavage products during ferroptosis. Redox Biology 63, 1-17, 102758
J363. Banerjee A, Bahar I (2023) Structural Dynamics Predominantly Determine the Adaptability of Proteins to Amino Acid Deletions. International Journal of Molecular Sciences 24 (9), 8450
J362. Kaynak BT, Dahmani ZL, Doruker P, Banerjee A, Yang SH, Gordon R, Itzhaki LS, Bahar I (2023) Cooperative mechanics of PR65 scaffold underlies the allosteric regulation of the phosphatase PP2A. Structure 31, 607-618.
J361. Banerjee A, Saha S, Tvedt NC, Yang LW, Bahar I (2023) Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods. Current Opinion in Structural Biology 78, 102517
J360. Shekar A, Mabry SJ, Cheng MH, Aguilar JI, Patel S, Zanella D, Saleeby DP, Zhu Y, Romanazzi T, Ulery-Reynolds P, Bahar I, Angela M Carter, Heinrich JG Matthies, Aurelio Galli (2023) Syntaxin 1 Ser14 phosphorylation is required for nonvesicular dopamine release
Science Advances, 9(2), eadd8417
J359. Vilardaga JP, Clark LJ, White AD, Sutkeviciute I, Lee JY, Bahar I (2023) Molecular Mechanisms of PTH/PTHrP class B GPCR Signaling and Pharmacological Implications. Endocrine Reviews, 44, 474-491. https://doi.org/10.1210/endrev/bnac032
Publications 2022
J358. Noval Rivas M, Porritt RA, Cheng MH, Bahar I M Arditi (2022) Multisystem inflammatory syndrome in children and long COVID: the SARS-CoV-2 viral superantigen hypothesis. Frontiers in Immunology, 3480
J357. Smith IN, Dawson JE, Krieger J, Thacker S, Bahar I, Eng C (2022) Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation. J Chem Inf Model. 62(17):4175-4190. PMID: 36001481
J356. Abram A, Jakubiec M, Reeb K, Cheng MH, Gedschold R, Rapacz A, Mogilski S, Socala K, Nieoczym D, Szafarz M, Latacz G, Szulczyk B, Kalinowska-Tluscik J, Gawel K, Esguerra CV, Wyska E, Müller CE, Bahar I, Fontana ACK, Wlaz P, Kaminski RM, Kaminski K (2022) Discovery of (R)-N-Benzyl-2-(2,5-dioxopyrrolidin-1-yl)propanamide [(R)-AS-1], a Novel Orally Bioavailable EAAT2 Modulator with Drug-like Properties and Potent Antiseizure Activity In Vivo. J. Med. Chem. 65, 17, 11703-11725
J355. Todd NK, Huang Y, Lee JY, Doruker P, Krieger JM, Salisbury R, MacDonald M, Bahar I, Thathiah A (2022) GPCR kinases generate an APH1A phosphorylation barcode to regulate amyloid-β generation Cell Reports 40 (3), 111110
J354. Wingert B, Doruker P, Bahar I (2022). Activation and Speciation Mechanisms in Class A GPCRs. J Mol Biol. 434 (17), 167690.
J353. Lefever DE, Miedel MT, Pei F, DiStefano JK, Debiasio R, Shun TY, Saydmohammed M, Chikina M, Vernetti LA, Soto-Gutierrez A, Monga SP, Bataller RA, Behari J, Yechoor VK, Bahar I, Gough A, Stern AM, Taylor DL (2022) A Quantitative Systems Pharmacology Platform Reveals NAFLD Pathophysiological States and Targeting Strategies. Metabolites 12(6), 528
J352. Acar O, Zhang S, Bahar I, Carvunis AR (2022) Elastic Network Modeling of Cellular Networks Unveils Sensor and Effector Genes that Control Information Flow. PLOS Computational Biology 18 (5), e1010181. PMID: 35639793
J351. Krieger JM, Sorzano COS, Carazo JM, Bahar I (2022) Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0. Acta Crystallographica Section D: Structural Biology 78 (4) PMID: 35362464 PMCID: PMC8972803
J350. Colas C, Bahar I, Shi L, Font Sadurni J (2022) Editorial: Targeting Membrane Proteins: Structure-Function-Dynamics Relationships. Frontiers in Chemistry, 126PMID: 35308796
J349. Refai O, Aggarwal S, Cheng MH, Gichi Z, Salvino JM, Bahar I, Blakely RD, Mortensen OV (2022) Allosteric Modulator KM822 Attenuates Behavioral Actions of Amphetamine in Caenorhabditis elegans through Interactions with the Dopamine Transporter DAT-1. Molecular Pharmacology 101 (3) 123-131. PMID: 34906999 PMCID: PMC8969146
J348. Sang Z, Xiang Y, Bahar I, Shi Y. (2022) Llamanade : an open-source computational pipeline for robust nanobody humanization.. Structure, 30(3):418-429.e3. PMID: 34373858 PMCID: PMC8351782
J347. Sutkeviciuta I, Lee JY, White AD, Maria CS, Peña KA, Savransky S, Doruker P, Li H, Lei S, Kaynak B, Tu C, Clark LJ, Sanker S, Gardella TJ, Chang W, Bahar I* and Vilardaga JP*. (2022) Precise druggability of the PTH type 1 receptor. Nature Chem Biol. 18(3):272-280. PMID: 34949836 PMCID: PMC8891041
J346. Cheng MH, Krieger JM, Banerjee A, Xiang Y, Kaynak B, Shi Y, Arditi M, Bahar I (2022) Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions. iScience 25(3):103939. PMID: 35194576 PMCID: PMC8851820
J345. Chen C, Saville JW, Marti MM, Schäfer A, Cheng MH, Mannar D, Zhu X, Berezuk AM, Banerjee A, Sobolewski MD, Kim A, Treat BR, Da Silva Castanha PM, Enick N, McCormick KD, Liu X, Adams C, Hines MG, Sun Z, Chen W, Jacobs JL, Barratt-Boyes SM, Mellors JW, Baric RS, Bahar I, Dimitrov DS, Subramaniam S, Martinez DR, Li W (2022) Potent and Broad Neutralization of SARS-CoV-2 Variants of Concern (VOCs) including Omicron Sub-lineages BA. 1 and BA. 2 by Biparatopic Human VH Domains. iScience 25(8), 104798
J344. Qiu X, Zhang Y, Martin-Rufino JD, Weng C, Hosseinzadeh S, Yang D, Pogson AN, Hein MY, Hoi Joseph Min K, Wang L, Grody EI, Shurtleff MJ, Yuan R, Xu S, Ma Y, Replogle JM, Lander ES, Darmanis S, Bahar I, Sankaran VG, Xing J, Weissman JS (2022) Mapping transcriptomic vector fields of single cells. Cell 185:690-711. PMID: 35108499
J343. Lamade AM, Wu L, Dar H, Mentrup HL, Shrivastava IH, Epperly MW, St Croix CM, Tyurina YY, Anthonymuthu TS, Yang Q, Kapralov AA, Huang Z, Mao G, Amoscato AA, Hier ZE, Artyukova MA, Shurin G, Rosenbaum JC, Gough PJ, Bertin J, VanDemark AP, Watkins SC, Mollen KP, Bahar I, Greenberger JS, Kagan VE, Whalen MJ, Bayιr H. (2022) Inactivation of RIP3 kinase sensitizes to 15LOX/PEBP1-mediated ferroptotic death. Redox Biology 50, 102232 PMID: 35101798 PMCID: PMC8804265
J342. Kaynak BT, Krieger JM, Dudas B, Dahmani ZL, Costa MGS, Balog E, Scott AL, Doruker P, Perahia D, Bahar I. (2022) Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods. Front Mol Biosci., 9:832847 PMID: 35187088 PMCID: PMC8855042
Publications 2021
J341. Calero DH, Lederman R, Krieger J, Myška D, Strelak D, Filipovic J, Bahar I, Carazo JM, Sorzano CO. (2021) Continuous heterogeneity analysis of CryoEM images through Zernike polynomials and spherical harmonics. Microscopy and Microanalysis, 27 (S1), 1680-1682
J340. Romanazzi T, Zanella D, Cheng MH, Smith B, Carter AM, Galli A, Bahar I, Bossi E. (2021) Bile acids gate dopamine transporter mediated currents. Frontiers in Chemistry 9 PMID: 34957043 PMCID: PMC8702627
J339. Herreros D, Lederman RR, Krieger J, Jiménez-Moreno A, Martínez M, Myška D, Strelak D, Filipovic J, Bahar I, Carazo JM, Sanchez COS. (2021) Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials. IUCrJ 8(Pt 6):992-1005. PMID: 34804551 PMCID: PMC8562670
J338. White AD, Pena KA, Clark LJ, Maria CS, Liu S, Jean-Alphonse FG, Lee JY, Lei S, Cheng Z, Tu CL, Fang F, Szeto N, Gardella TJ, Xiao K, Gellman SH, Bahar I, Sutkeviciute I, Chang W, Vilardaga JP. (2021) Spatial Bias in cAMP Generation Determines Biological Responses to PTH type 1 Receptor Activation. Sci Signal. 14(703):eabc5944. PMID: 34609896 PMCID: PMC8682804
J337. Chen F, Shi Q, Pei F, Vogt A, Porritt RA, Garcia G, Gomez AC, Cheng MH, Schurdak ME, Liu B, Chan SY, Arumugaswami V, Stern AM, Taylor DL, Arditi M, Bahar I. (2021) A Systems-level Study Reveals Host-targeted Repurposable Drugs Against SARS-CoV2 Infection. Molecular Systems Biol. 17:e10239 PMID: 34339582 PMCID: PMC8328275
J336. Kaynak BT, Zhang S, Bahar I, Doruker P (2021) ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution. Bioinformatics 37:3956-8. PMID: 34240100 PMCID: PMC8570821
J335. Zhang Y, Zhang S, Xing J, Bahar I (2021) Normal mode analysis of membrane protein dynamics using the vibrational subsystem analysis. J Chem Phys 154, 195102 PMID: 34240914 PMCID: PMC8131107
J334. Mikulska-Ruminska K, Anthonymuthu TS, Levkina A, Shrivastava IH, Kapralov AA, Bayir H, Kagan VE, Bahar I. (2021) NO● Represses the Oxygenation of Arachidonoyl PE by 15LOX/PEBP1: Mechanism and Role in Ferroptosis. Int J Mol Sci. 22(10): 5253. PMID: 34067535 PMCID: PMC8156958
J333. Aggarwal J, Cheng MH, Salvino JM, Bahar I, Mortensen OV. (2021) Functional Characterization of the Dopaminergic Psychostimulant Sydnocarb as an Allosteric Modulator of the Human Dopamine Transporter. Biomedicines, 9(6), 634; https://doi.org/10.3390/biomedicines9060634 PMID: 34199621 PMCID: PMC8227285
J332. Aguilar JI, Cheng MH, Font J, Schwartz AC, Ledwitch K, Duran A, Mabry SJ, Belovich AN, Zhu Y, Carter AM, Shi L, Kurian MA, Fenollar-Ferrer C, Meiler J, Ryan RM, Mchaourab HS, Bahar I, Matthies HJG, Galli A. (2021) Psychomotor impairments and therapeutic implications revealed by a mutation associated with infantile Parkinsonism-Dystonia. ELife, 10, e68039 PMID: 34002696 PMCID: PMC8131106
J331. Cheng MH, Porritt RA, Rivas MN, Krieger JM, Ozdemir AB, Garcia G Jr, Arumugaswami V, Fries BC, Arditi M, Bahar I. (2021) A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro. Structure. 29(9):951-962 PMID: 33269352 PMCID: PMC7709177
J330. Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I. (2021) ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python. Bioinformatics 37:3657-9 PMID: 33822884 PMCID: PMC8545336
J329. Pei F, Shi Q, Zhang H, Bahar I (2021) Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. J Chem Inf Model 61:1670-1682. PMID: 33831302 PMCID: PMC8253547
J328. Porritt RA, Paschold L, Noval Rivas M, Cheng MH, Yonker LM, Chandnani H, Lopez M, Simnica D, Schultheiß C, Santiskulvong C, van Eyk J, McCormick JK, Fasano A, Bahar I, Binder M, Arditi M (2021) HLA class I-associated expansion of TRBV11-2 T cells in Multisystem Inflammatory Syndrome in Children. J Clin Invest. 131(10). PMID: 33705359 PMCID: PMC8121516 Link to article /commentary
J327. Sorkina T, Cheng MH, Bagalkot TR, Wallace C, Watkins SC, Bahar I, Sorkin A. (2021) Direct coupling of oligomerization and oligomerization-driven endocytosis of the dopamine transporter to its conformational mechanics and activity. J Biol Chem. Feb 18:100430. PMID: 33610553 PMCID: PMC8010718
J326. Wang H, Pei F, Vanyukov MM, Bahar I, Wu W, Xing EP. (2021) Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets. BMC Bioinformatics 22(1):50. PMID: 33546598 PMCID: PMC7866684
J325. Sun WY, Tyurin VA, Mikulska-Ruminska K, Shrivastava IH, Anthonymuthu TS, Zhai YJ, Pan MH, Gong HB, Lu DH, Sun J, Duan WJ, Korolev S, Abramov AY, Angelova PR, Miller I, Beharier O, Mao GW, Dar HH, Kapralov AA, Amoscato AA, Hastings TG, Greenamyre TJ, Chu CT, Sadovsky Y, Bahar I, Bayir H, Tyurina YY, He RR, Kagan VE. (2021) Phospholipase iPLA2ß averts ferroptosis by eliminating a redox lipid death signal. Nat Chem Biol 17(4):465-476. PMID: 33542532 PMCID: PMC8152680
J324. Meirovitch H, Bahar I. (2021) Harold A. Scheraga (10/18/1921—8/1/2020): A pioneering scientist who laid the foundations of protein science in the 20th century. Proc Natl Acad Sci USA 118(8):e2026796118. PMID: 33547253 PMCID: PMC7923550.
J323. Cheng MH, Krieger JM, Kaynak B, Arditi M, Bahar I. (2021) Impact of South African 501.V2 Variant on SARS-CoV-2 Spike Infectivity and Neutralization: A Structure-based Computational Assessment. BioRxiv [Online ahead of print].
J322. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T (2021) HiDeF: Identifying Persistent Structures in Multiscale 'Omics Data. Genome Biol. 22: 21. PMID: 33413539 PMCID: PMC7789082
J321. Dagvadorj J, Mikulska-Ruminska K, Tumurkhuu G, Ratsimandresy RA, Carriere J, Andres AM, Marek-Iannucci S, Song Y, Chen S, Lane M, Dorfleutner A, Gottlieb RA, Stehlik C, Cassel S, Sutterwala FS, Bahar I, Crother TR, Arditi M (2021) Recruitment of pro-IL-1a to Mitochondrial Cardiolipin, via Shared LC3 Binding Domain, Inhibits Mitophagy and Drives Maximal NLRP3 Activation. Proc Natl Acad Sci USA 118:e2015632118 PMID: 33361152 PMCID: PMC7817159
J320. Rivas MN, Porritt RA, Cheng MH, Bahar I, Arditi M. (2021) COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): A Novel Disease that Mimics Toxic Shock Syndrome. The Superantigen Hypothesis. J Allergy Clin Immunol. 147: 57-59. PMID: 33075409 PMCID: PMC7564502
J319. Anthonymuthu TS, Tyurina YY, Sun WY, Mikulska-Ruminska K, Shrivastava IH, Tyurin VA, Cinemre FB, Dar HH, VanDemark AP, Holman TR, Sadovsky YS, Stockwell BR, He RR, Bahar I, Bayir H, Kagan VE. (2021) Resolving the Paradox of Ferroptotic Cell Death: Ferrostatin-1 Binds to 15LOX/PEBP1 Complex, Suppresses Generation of Peroxidized ETE-PE, and Protects against Ferroptosis. Redox Biol. 38: 101744 PMID: 33126055 PMCID: PMC7596334 .
J318. Wingert B, Krieger JM, Li H, Bahar I (2021) Adaptability and Specificity: How Do Proteins Balance Opposing Needs to Achieve Function? Curr Opin Struct Biol 67:25-32. PMID: 33053463 PMCID: PMC8036234
J317. Zhang Y, Krieger JM, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I (2021) State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Prog Biophys Mol Biol S0079-6107(20)30082-1. PMID: 32866476 PMCID: PMC7914283
J316. Belovich AN, Aguilar JI, Mabry SJ, Cheng MH, Zanella D, Hamilton PJ, Stanislowski DJ, Shekar A, Foster JD, Bahar I, Matthies HJG, Galli A. (2021) A network of phosphatidylinositol (4, 5)-bisphosphate (PIP 2) binding sites on the dopamine transporter regulates amphetamine behavior in Drosophila Melanogaster. Molecular Psychiatry 26, 4417-4430. PMID: 31796894 PMCID: PMC7266731
Publications 2020
J315. Porritt RA, Paschold L, Rivas MN, Cheng MH, Yonker LM, Chandnani H, Lopez M, Simnica D, Schultheiβ C, Santiskulvong C, Van Eyk J, Fasano A, Bahar I, Binder M, Arditi M. (2020) Identification of a Unique TCR Repertoire, Consistent with a Superantigen Selection Process in Children with Multi-system Inflammatory Syndrome. BioRxiv doi: https://doi.org/10.1101/2020.11.09.372169
J314. Cheng MH, Porritt RA, Rivas MN, Krieger JM, Ozdemir AB, Garcia G, Arumugaswami V, Fries BC, Arditi M, Bahar I. (2020) A Monoclonal Antibody Against Staphylococcal Enterotoxin B Superantigen Inhibits SARS-CoV-2 entry in vitro. BioRxiv doi: https://doi.org/10.1101/2020.11.24.395079
J313. Zhou Z, Huang F, Shrivastava IH, Zhu R, Luo A, Hottiger M, Bahar I, Liu Z, Cristofanilli M, Wan Y (2020) New Insight into the Significance of KLF4 PARylation in Genome Stability, Carcinogenesis, and Therapy. EMBO Molecular Medicine, 12(12): e12391.
J312. Song X, Zhou Z, Li H, Xue Y, Lu X, Bahar I, Kepp O, Hung MC, Kroemer G, Wan Y (2020) Pharmacological Suppression of B7-H4 Glycosylation Restores Antitumor Immunity in Immune-Cold Breast Cancers. Cancer Discov 10:1872-1893. doi: 10.1158/2159-8290.CD-20-0402. [Online ahead of print]. PMID: 32938586 PMCID: 7710601
J311. Cheng MH, Zhang S, Porritt RA, Rivas MN, Paschold L, Willscher E, Binder M, Arditi M*, Bahar I* (2020) Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. Proc Natl Acad Sci USA 117: 25254-25262 PMID: 32989130 PMCID: PMC7568239
US Patent application: Compositions and methods for treating a covid-19 infection I Bahar, H Cheng, S Zhang, R Porritt, M Arditi US Patent App. 17/375,601
J310. Clark LJ, Krieger J, White AD, Bondarenko V, Lei S, Fang F, Lee JY, Doruker P, Böttke T, Jean-Alphonse F, Tang P, Gardella TJ, Xiao K, Sutkeviciute I, Coin I, Bahar I, Vilardaga JP (2020) Allosteric interactions in the parathyroid hormone GPCR-arrestin complex formation. Nat Chem Biol 16(10):1096-1104 PMID: 32632293 PMCID: PMC7502484 (available on 2021-01-06)
J309. Kaynak BT,* Bahar I,* Doruker P. (2020) Essential Site Scanning Analysis: a new approach for detecting sites that modulate the dispersion of protein global motions. Comp Struct Biotech J 18:1577-1586. PMID: 32637054 PMCID: PMC7330491
J308. Krieger JM, Doruker P, Scott AL, Perahia D, Bahar I. (2020) Towards Gaining Sight of Multiscale Events: Utilizing Network Models and Normal Modes in Hybrid Methods. Curr Opin Struct Biol 64:34-41. PMID: 32622329 PMCID: PMC7666066 (available on 2021-10-01)
J307. Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. (2020) Decoding of persistent multiscale structures in complex biological networks. bioRxiv. PMID: 32587977 PMCID: PMC7310637
J306. Zhao J, Dar HH, Deng Y, St. Croix CM, Li Z, Minami Y, Shrivastava IH, Tyurina YY, Etling E, Rosenbaum JC, Nagasaki T, Trudeau JB, Watkins SC, Bahar I, Bayir H, VanDemark AP, Kagan VE, Wenzel SE. (2020) PEBP1 Acts as a Rheostat Between Prosurvival Autophagy and Ferroptotic Death in Asthmatic Epithelial Cells. Proc Natl Acad Sci (USA) 117:14376-14385. PMID: 32513718 PMCID: PMC7321965
J305. Kim Y, Jun I, Shin DH, Yoon JG, Piao H, Jung J, Park HW, Cheng MH, Bahar I, Whitcomb DC, Lee MG (2020) Regulation of CFTR Bicarbonate Channel Activity by WNK1: Implications for Pancreatitis and CFTR-Related Disorders. Cell Mol Gastroenterol Hepatol 9:71-103. PMID: 31561038 PMCID: PMC6889609
J304. Shi Q, Pei F, Silverman GA, Pak SC, Perlmutter DH, Liu B*, Bahar I*. (2020) Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis. Int. J. Mol. Sci 21:2855. PMID: 32325894 PMCID: PMC7215584
J303. Ponzoni L, Nguyen NH, Bahar I*, Brodsky JL*. (2020) Complementary Computational and Experimental Evaluation of Missense Variants in the ROMK Potassium Channel. PLOS Comp Biol 16, e1007749. PMID: 32251469 PMCID: PMC7162551
J302. Li H, Doruker P, Hu G, Bahar I. (2020) Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding. Biophys J 118: 1782-1794. PMID: 32130874 PMCID: 7136436
J301. Li H, Pei F, Taylor DL, Bahar I. (2020) QuartataWeb: Integrated Chemical-protein-pathway Mapping for Polypharmacology and Chemogenomics. Bioinformatics 36:3935-3937. PMID: 32221612 PMCID: PMC7320630
J300. Zhou Z, Zhou H, Ponzoni L, Luo A, Zhu R, He M, Huang Y, Guan KL, Bahar I, Liu Z, Wan Y. (2020) EIF3H Orchestrates Hippo Pathway-mediated Oncogenesis Through an Unexpected Catalytic Control of YAP Stability. Cancer Res 80:2550-2563. PMID: 32269044 PMCID: PMC7316131
J299. Cheng MH, Zhang S, Porritt RA, Arditi M, Bahar I. (2020) An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations. BioRxiv. 2020 May 21:2020.05.21.109272. PMID: 32511374 PMCID: PMC7263503
J298. Thermozier S, Hou W, Zhang X, Shields D, Fisher R, Bayir H, Kagan V, Yu J, Liu B, Bahar I, Epperly MW, Wipf P, Wang H, Huq MS, and Greenberger JS. (2020) Anti-Ferroptosis Drug Enhances Total-Body Irradiation Mitigation by Drugs that Block Apoptosis and Necroptosis. Radiat Res 193:435-450. PMID: 32134361 PMCID: PMC7299160
J297. Ponzoni L, Penaherrera DA, Oltvai ZN, and Bahar I (2020) Rhapsody: Predicting the pathogenicity of human missense variants. Bioinformatics 36:3084-3092.PMID: 32101277 PMCID: PMC7214033
J296. Kapralov AA, Yang Q, Dar HH, Tyurina YY, Anthonymuthu TS?, Kim R, St. Croix CM, Mikulska-Ruminska K, Liu B, Shrivastava IH, Tyurin VA, Ting HC, Wu YL, Gao Y, Shurin GV, Artyukhova MA, Ponomareva LA, Timashev8 PS, Domingues RM, Stoyanovsky DA, Greenberger JS, Mallampalli RK, Bahar I, Gabrilovich DI, Bayir H, Kagan VE. (2020) Redox Lipid Reprogramming Commands Susceptibility of Macrophages and Microglia to Ferroptotic Death. Nat Chem Biol 16:278-290. PMID: 32080625 PMCID: PMC7233108
B18. Shrivastava IH, Liu C, Dutta A, Bakan A, Bahar I. (2020) Allostery as Structure-Encoded Collective Dynamics: Significance in Drug Design. Structural Biology in Drug Discovery: Methods, Techniques, and Practices. Eds Jean-Paul Renaud. Chapter 6, p125-141, John Wiley & Sons, NY.
J295. Lee JY, Krieger JM, Li H, Bahar I. (2020) Pharmmaker: Pharmacophore Modeling and Hit Identification Based on Druggability Simulations. Protein Sci 29:76-86 PMID: 31576621 PMCID: 6933858
J294. Zhang S, Chen F, Bahar I. (2020) Differences in the Intrinsic Spatial Dynamics of the Chromatin Contribute to Cell Differentiation. Nucleic Acids Res 48, 1131-1145. PMID: 31828312 PMCID: 7026660
J293. Zhang Y, Doruker P, Kaynak B, Zhang S, Krieger JM, Li H, Bahar I. (2020) Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior. Curr Opin Struct Biol 62:14-21. PMID: 31785465 PMCID: PMC7250723
Publications 2019
J292. Chi J, Li H, Zhou Z, Izquierdo-Ferrer J, Xue Y, Wavelet CM, Schiltz GE, Zhang B, Cristofanilli M, Lu X, Bahar I, Wan Y. (2019) A Novel Strategy to Block Mitotic Progression for Targeted Therapy. EBioMedicine 49:40-54 PMID:31669221 PMCID: 6945239
J291. Cheng MH, Bahar I. (2019) Monoamine transporters: structure, intrinsic dynamics and allosteric regulation. Nat Struct. & Molec. Biol 26: 545-556. PMID: 31270469 PMCID: 6712983
J290. Thermozier S, Zhang X, Hou W, Fisher R, Epperly MW, Liu B, Bahar I, Wang H, Greenberger JS. (2019) Radioresistance of Serpinb3a-/- Mice and Derived Hematopoietic and Marrow Stromal Cell Lines. Radiat Res. 192: 267-281. PMID: 31295086 PMCID: 6759811
B18. Taylor DL, Gough A, Schurdak ME, Vernetti L, Chennubhotla CS, Lefever D, Pei F, Faeder JR, Lezon TR, Stern AM, Bahar I. (2019) "Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology" in Handb Exp Pharmacol, 260:327-367 PMID: 31201557 PMCID: 6911651
J289. Cheng MH, Ponzoni L, Sorkina T, Lee JY, Zhang S, Sorkin A, Bahar I. (2019) Trimerization of Dopamine Transporter Triggered by AIM-100 Binding: Molecular Mechanisms and Effect of Mutations. Neuropharmacology 161:107676 PMID: 31228486 PMCID: 6917874 DOI: 10.1016/j.neuropharm.2019.107676
J288. Zhou Z, Feng Z, Hu D, Yang P, Gur M, Bahar I, Cristofanilli M, Gradishar WJ, Xie XQ, Wan Y. (2019) ) A novel small-molecule antagonizes PRMT5-mediated KLF4 methylation for targeted therapy. EBioMedicine 44: 98-111. PMID: 31101597 PMCID: 6604046
J287. Zhang S, Li H, Krieger JM, Bahar I. (2019) Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity. Mol Biol Evol 36: 2053-2068. PMID: 31028708 PMCID: 6736388
J286. Pei F, Li H, Liu, B, Bahar I. (2019) Quantitative systems pharmacological analysis of drugs of abuse reveals the pleiotropy of their targets and the effector role of mTORC1. Front Pharmacol 10: 191. PMID: 30906261 PMCID: 6418047
J285. Mikulska-Ruminska K, Shrivastava IH, Krieger JM, Zhang S, Li H, Bayir H, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. (2019) Characterization of differential dynamics, specificity, and allostery of lipoxygenase family members. J Chem Inf Model 59: 2496-2508. PMID: 30762363 PMCID: 6541894
J284. Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux J, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai C, Jang H, Padhorny D, Kozakov D, McLeish T (2019) Allostery in Its Many
Disguises: From Theory to Applications Structure 27(4): 566-578. PMID: 30744993 PMCID: 6688844
J283. Wang Y, Cobanoglu MC, Li J, Hidvegi T, Hale P, Ewing M, Chu AS, Gong Z, Muzumdar R, Pak SC, Silverman GA, Bahar I, Perlmutter DH (2019) An analog of glibenclamide selectively enhances autophagic degradation of misfolded α1-antitrypsin Z PloS One 14: e0209748. PMID: 30673724 PMCID: 6343872
J282. COS Sorzano, A Jiménez, J Mota, JL Vilas, D Maluenda, M Martínez, E Ramírez-Aportela, T Majtner, J Segura, R Sánchez-García, Y Rancel, L del Caño, P Conesa, R Melero, S Jonic, J Vargas, F Cazals, Z Freyberg, J Krieger, I Bahar, R Marabini, JM Carazo (2019) Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy. Acta Crystallog F Struct Biol Commun 75: 19-32. PMID: 30605122 PMCID: 6317454
J281. Lee JY, Krieger J, Herguedas B, García-Nafría J, Dutta A, Shaikh SA, Greger IH, Bahar I. (2019) Druggability Simulations and X-ray Crystallography Reveal a Ligand-binding Site in the GluA3 AMPA Receptor N-terminal Domain. Structure 27: 241-252. PMID: 30528594 PMCID: 6365164
J280.
Stoyanovsky D, Shrivastava I, Tyurina Y, Bahar I, Tyurin U, Protchenko O, Jadhav S, Bolevich S, Kozlov A, Vladimirov Y, Shvedova A, Philpott C, Bayir H, Kagan V. (2019) Iron catalysis of lipid peroxidation in ferroptosis: Regulated enzymatic or random free radical reaction? Free Radic Biol Med, 133: 153-161. PMID: 30217775 PMCID: 6555767
J279.
Krieger J, Lee JY, Greger IH, Bahar I. (2019) Activation and Desensitization of Ionotropic Glutamate Receptors by Selectively Triggering Pre-existing Motions. Neurosci Lett 700: 22-29 PMID: 29481851 PMCID: 6107436
Publications 2018
J278.
Anthonymuthu T, Kenny E, Shrivastava I, Tyurina YY, Hier Z, Ting H-C, Dar H, Tyurin V, Nesterova A, Amoscato A, Mikulska-Ruminska K, Rosenbaum J, Mao G, Jinming Z, Conrad M, Kellum J, Wenzel S, VanDemark A, Bahar I, Kagan V, Bayir H (2018) Empowerment of 15-lipoxygenase catalytic competence in selective oxidation of membrane ETE-PE to ferroptotic death signals, HpETE-PE. J Am Chem Soc 140: 17835-17839. PMID: 30525572 PMCID: 6622169
J277.
Wang K, Steer E, Otero PA, Bateman N, Cheng MH, Scott A, Wu C, Bahar I, Shih Y-T, Hsueh Y-P, Chu C (2018) PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons. eNeuro 5(6) ENEURO.0466-18.2018 eCollec PMID: 30783609 PMCID: 6377406
J276.
Van Dijk L, Giladi M, Refaeli B, Hiller R, Cheng MH, Bahar I, Khananshvili D. (2018) Key residues controlling bidirectional ion movements in Na+/Ca2+ exchanger. Cell Calcium 76: 10-22. PMID: 30248574 PMCID: 6688843
J275.
Dar HH, Tyurina YY, Mikulska-Ruminska K, Shrivastava I, Ting HC, Tyurin VA, Krieger J, St Croix CM, Watkins S, Bayir E, Mao G, Ambruster C, Kapralov A, Wang H, Parsek MH, Anthonymuthu TS, Ogunsola AF, Flitter BA, Freedman CJ, Gaston JR, Holman TR, Pilewski JM, Greenberger JS, Mallampalli RK, Doi Y, Lee JS, Bahar I, Bomberger JM, Bayir H, Kagan VE. (2018) Pseudomonas aeruginosa utilizes host polyunsaturated phosphatidylethanolamines to trigger theft-ferroptosis in bronchial epithelium. J Clin Invest. 128: 4639-4653 PMID: 3018910 PMCID: 6159971
J274.
Ponzoni L, Zhang S, Cheng MH, Bahar I. (2018) Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization. Philos Trans R Soc Lond B Biol Sci 373: pii: 20170177 PMID: 29735731 PMCID: 5941172
J273.
Ponzoni L, Bahar I. (2018) Structural dynamics is a determinant of the functional significance of missense variants. Proc Natl Acad Sci USA 115: 4164-4169 PMID: 29610305 PMCID: 5910821
J272.
Kaya C, Cheng MH, Block ER, Bartol TM, Sejnowski TJ, Sorkin A, Faeder JR, Bahar I. (2018) Heterogeneities in Axonal Structure and Transporter Distribution Lower Dopamine Reuptake Efficiency eNeuro 5: ENEURO.0298-17.2017 PMID: 29430519 PMCID: 5804147
J271.
Cheng MH, Kaya C, Bahar I. (2018)
A Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter. J Phys Chem B 122: 5336-5346 PMID: 29232131 PMCID: 5991911
J270.
Steinman J, Epperly M, Hou W, Willis J, Wang H, Fisher R, Liu B, Bahar I, McCaw T, Kagan V, Bayir H, Yu J, Wipf P, Li S, Huq MS, Greenberger JS. (2018)
Improved Total-Body Irradiation Survival by Delivery of Two Radiation Mitigators that Target Distinct Cell Death Pathways. Radiat Res. J 189: 68-83 PMID: 29140165 PMCID: 5808408
J269.
Tyurina YY, Shrivastava I, Tyurin VA, Mao G, Dar HH, Watkins S, Epperly M, Bahar I, Shvedova AA, Pitt B, Wenzel SE, Mallampalli RK, Sadovsky Y, Gabrilovich D, Greenberger JS, Bayir H, Kagan VE. (2018)
"Only a life lived for others is worth living:" Redox Signaling by Oxygenated Phospholipids in Cell Fate Decisions. Antioxid Redox Signal 29: 1333-1358 PMID: 28835115 PMCID: 6157439
Publications 2017
J268.
Lee JY, Feng Z, Xie XQ, Bahar I. (2017)
Allosteric Modulation of Intact γ-Secretase Structural Dynamics. Biophys J 113: 2634-2649 PMID: 29262358 PMCID: 5770568
J267.
Pei F, Li H, Henderson MJ, Titus SA, Jadhav A, Simeonov A, Cobanoglu MC, Mousavi SH, Shun T, McDermott L, Iyer P, Fioravanti M, Carlisle D, Friedlander RM, Bahar I, Taylor DL, Lezon TR, Stern AM, Schurdak ME. (2017)
Connecting Neuronal Cell Protective Pathways and Drug Combinations in a Huntington's Disease Model through the Application of Quantitative Systems Pharmacology. Sci Rep 7: 17803 PMID: 29259176 PMCID:5736652
J266.
Liu B, Oltvai ZN, Bayir H, Silverman GA, Pak SC, Perlmutter DH, Bahar I. (2017)
Quantitative assessment of cell fate decision between autophagy and apoptosis. Sci Rep 7: 17605 PMID: 29242632 PMCID: 5730598
J265.
Wenzel SE, Tyurina YY, Zhao J, St Croix CM, Dar HH, Mao G, Tyurin VA, Anthonymuthu TS, Kapralov AA, Amoscato AA, Mikulska-Ruminska K, Shrivastava IH, Kenny EM, Yang Q, Rosenbaum JC, Sparvero LJ, Emlet DR, Wen X, Minami Y, Qu F, Watkins SC, Holman TR, VanDemark AP, Kellum JA, Bahar I, Bayir H, Kagan VE. (2017)
PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals. Cell 171: 628-641 PMID: 29053969 PMCID: 5683852
J264.
Mikulska-Ruminska K, Kulik AJ, Benadiba C, Bahar I, Dietler G, Nowak W. (2017)
Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD. Sci Rep 7: 8852
PMID: 28821864 PMCID: 5562865
J263.
Ma S, Cheng MH, Guthrie DA, Newman AH, Bahar I, Sorkin A. (2017)
Targeting of dopamine transporter to filopodia requires an outward-facing conformation of the transporter. Sci Rep 7: 5399 PMID: 28710426 PMCID: 5511133
J262.
Li H, Sharma N, General IJ, Schreiber G, Bahar I. (2017)
Dynamic Modulation of Binding Affinity as a Mechanism for Regulating Interferon Signaling. J Mol Biol 429: 2571-2589 PMID: 28648616 PMCID: 5545807
J261.
Cheng MH, Garcia-Olivares J, Wasserman S, DiPietro J, Bahar I. (2017)
Allosteric Modulation of Human Dopamine Transporter Activity under Conditions Promoting its Dimerization. J Biol Chem 292: 12471-12482 PMID: 28584050 PMCID: 5535022
J260.
Cheng MH, Torres-Salazar D, Gonzalez-Suarez AD, Amara SG, Bahar I. (2017)
Substrate transport and anion permeation proceed through distinct pathways in glutamate transporters. ELife 6: pii: e25850 PMID: 28569666 PMCID: 5472439
J259.
Li H, Chang YY, Lee JY, Bahar I, Yang LW. (2017)
DynOmics: dynamics of structural proteome and beyond Nucleic Acids Res 45(W1): W374-W380 PMID: 28472330 PMCID: 5793847
J258.
Sauerwald N, Zhang S, Kingsford C, Bahar I. (2017)
Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings Nucleic Acids Res 45: 3663-3673 PMID: 28334818 PMCID: 5397156
J257.
Gur M, Cheng MH, Zomot E, Bahar I. (2017)
Effect of Dimerization on the Dynamics of Neurotransmitter:Sodium Symporters J Phys Chem B 121: 3657-3666 PMID: 28118712 PMCID: 5402697
T1.
Bahar I, Jernigan R, Dill K. (2017)
Protein Actions: Principles & Modeling. New York, NY: Garland Science, Taylor & Francis Group ISBN: 9780815341772
J256.
Zhou Z, Luo A, Shrivastava I, He M, Huang Y, Bahar I, Liu Z, Wan Y. (2017)
Regulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis EBioMedicine 15: 48-61 PMID: 28040451 PMCID: 5233825
J255.
Kagan VE, Mao G, Qu F, Angeli JP, Doll S, Croix CS, Dar HH, Liu B, Tyurin VA, Ritov VB, Kapralov AA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli RK, Stockwell BR, Tyurina YY, Conrad M, Bayir H (2017)
Oxidized Arachidonic and Adrenic Phosphatidylethanolamines Navigate Cells to Ferroptosis Nature Chem Biol 13: 81-90 PMID: 27842066 PMCID: 5506843
Publications 2016
J254.
Kurkcuoglu Z, Bahar I, Doruker P (2016) ClustENM: ENM-based sampling of essential conformational space at full atomic resolution
J Chem Theory Comput 12: 4549-62 PMID: 27494295 PMCID: 5088496
J253.
Liu B, Liu Q, Yang L, Palaniappan SK, Bahar I, Thiagarajan PS, Ding JL (2016) Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways
Sci Signal 9: ra70 PMID: 27405980 PMCID: 5087126
J252.
Stern AM, Schurdak ME, Bahar I, Berg JM, Taylor DL (2016) A perspective on implementing a quantitative systems pharmacology platform for drug discovery and the
advancement of personalized medicine J of Biomolecular Screening 21: 521-34 PMID: 26962875, PMC4917453
J251.
Li H, Chang YY, Yang LW, Bahar I (2016) iGNM 2.0: the Gaussian network model database for bimolecular structural dynamics Nucleic Acids Res 44: D415-422 PMID: 26582920; PMC4702874
J250.
Jun I, Cheng MH, Sim E, Jung J, Suh BL, Kim Y, Son H, Park K, Kim CH, Yoon J-H, Whitcomb DC, Bahar I, Lee MG (2016)
Pore Dilation Increases the Bicarbonate Permeability of CFTR, ANO1, and Glycine Receptor Anion Channels J of Physiology 594: 2929-55 PMID:26663196 PMCID: 4887682
Publications 2015
J249.
Gur M, Zomot E, Cheng MH, Bahar I (2015) Energy landscape of LeuT from molecular simulations J Chem Phys 143: 243134 PMID: 26723619; PMC4662675
J248.
Cheng MH, Bahar I (2015) Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter Structure 23: 2171-81PMID: 26481814; PMC4635030
J247.
Hu D, Gur M, Zhou Z, Gamper A, Hung MC, Fujita N, Lan L, Bahar I, Wan Y (2015) Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis Nat Commun 6: 8419PMID: 26420673; PMC4598737
J246.
Keskin O, Dyson HJ, Bahar I (2015) Biomolecular Systems Interactions, Dynamics, and Allostery: Reflections and New Directions Biophys J 109: E01-2PMID: 26377787; PMC4576319
J245.
Krieger J, Bahar I, Greger IH (2015) Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains Biophys J 109: 1136-48PMID: 26255587; PMC4576161
J244.
Dutta A, Krieger J, Lee JY, Garcia-Nafria J, Greger IH, Bahar I (2015) Cooperative Dynamics of Intact AMPA and NMDA Glutamate Receptors: Similarities and Subfamily-Specific Differences Structure 23: 1692-1704PMID: 26256538; PMC4558295
J243.
Haliloglu, T, Bahar I (2015) Adaptability of protein structures to enable functional interactions and evolutionary implications Curr Opin in Struct Biol 35: 17-23PMID: 26254902; PMC4688206
J242.
Bahar I, Cheng MH, Lee JY, Kaya C, Zhang S (2015) Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions Biophys J 109: 1101-9PMID: 26143655; PMC4576147
J241.
Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, the Center for Causal Discovery team (2015) Center for Causal Discovery of Biomedical Knowledge from Big Data J Am Med Inform Assoc 22: 1132-6PMID: 26138794 PMCID: 5009908
J240.
Cheng MH, Block E, Hu F, Cobanoglu MC, Sorkin A, Bahar I (2015) Insights into the modulation of dopamine transporter function by amphetamine, orphenadrine, and cocaine binding Front Neurol 6: 134PMID: 26106364; PMC4460958
J239.
Bakan A, Kapralov AA, Bayir H, Hu F, Kagan VE, Bahar I (2015) Inhibition of Peroxidase Activity of Cytochrome c: De Novo Compound Discovery and Validation Mol Pharmacol 88: 421-7PMID: 26078313; PMC: 4551054
J238.
Mao W, Kaya C, Dutta A, Horovitz A, Bahar I (2015) Comparative Study of the Effectiveness and Limitations of Current Methods for Detecting Sequence Coevolution Bioinformatics 31: 1929-37 PMID: 25697822; PMC4481699
J237.
Eyal E, Lum G, Bahar I (2015) The Anisotropic Network Model web server at 2015 (ANM 2.0) Bioinformatics 31: 1487-9 PMID: 25568280; PMC4410662
J236.
Zomot E, Gur M, Bahar I (2015) Microseconds Simulations Reveal a New Sodium-Binding Site and the Mechanism of Sodium-Coupled Substrate Uptake by LeuT J Biol Chem 290: 544-55 PMID: 25381247; PMC4281755
J235.
Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I (2015) BalestraWeb: Efficient, online evaluation of drug-target interactions Bioinformatics 31:131-3 PMID: 25192741; PMC4271144
Publications 2014
J234.
Cheng MH, Bahar I (2014) Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle PLoS Comput Biol 10: e1003879 PMID: 25299050; PMC4191883
J233.
Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar I (2014) Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies Sci Rep 4: 6245 PMID: 25175563; PMC4150106
J232.
Bahar I (2014) Coupling between Neurotransmitter Translocation and Protonation State of a Titratable Residue during Na(+)-Coupled Transport Biophys J 106: 2547-8 PMID: 24940770; PMC4070272
J231.
Bakan A,* Dutta A,* Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I (2014) Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics Bioinformatics 30: 2681-3 PMID: 24849577; PMC4155247
J230.
O'Reilly LP,* Long OS,* Cobanoglu MC,* Benson JA, Luke CJ, Miedel MT, Hale P, Perlmutter DH, Bahar I, Silverman GA, Pak SC (2014) A genome-wide RNAi screen identifies potential drug targets in a C. elegans model of α1-antitrypsin deficiency Hum Mol Genet 23: 5123-32 PMID: 24838285; PMC4159156
J229.
LaRusch J, Jung J, General IJ, Lewis MD, Park HW, Brand RE, Gelrud A, Anderson MA, Banks PA, Conwell D, Lawrence C, Romagnuolo J, Baillie J, Alkaade S, Cote' G, Gardner TB, Amann ST, Slivka A, Sandhu B, Aloe A, Kienholz ML, Yadav D, Barmada MM, Bahar I, Lee MG, Whitcomb DC, North American Pancreatitis Study Group (2014) Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis PLoS Genetics 10: e1004376 PMID: 25033378; PMC4102440
J228.
General IJ, Liu Y, Blackburn M, Mao W, Gierasch LM, Bahar I (2014) ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones PLoS Comp Bio 10: e1003624 PMID: 24831085; PMC4022485
J227.
Korotchenko VN, Saydmohammed M, Vollmer LL, Bakan A, Sheetz K, Debiec KT, Greene KA, Agliori CS, Bahar I, Day BW, Vogt A, Tsang M (2014) In Vivo Structure-Activity Relationship Studies Support Allosteric Targeting of a
Dual Specificity Phosphatase ChemBioChem 15: 1436-1445 PMID: 24909879; PMC4118675
J226.
Das A, Gur M,* Cheng MH,* Jo S, Bahar I, Roux B (2014) Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model PLoS Comput Biol 10: e1003521 PMID: 24699246; PMC3974643
J225.
Jiang J, Bakan A, Kapralov AA, Ishara Silva KI, Huang Z, Amoscato AA, Peterson J, Krishna Garapati VK, Saxena S, Bayir H, Atkinson J, Bahar I, Kagan VE (2014) Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: mitochondria-targeted imidazole-substituted fatty acids Free Radic Biol Med 71C: 221-230 PMID: 24631490; PMC4216591
J224.
Lui VW, Peyser ND, Ng PK, Hritz J, Zeng Y, Lu Y, Li H, Wang L, Gilbert BR, General IJ, Bahar I, Ju Z, Wang Z, Pendleton KP, Xiao X, Du Y, Vries JK, Hammerman PS, Garraway LA, Mills GB, Johnson DE, Grandis JR (2014) Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer Proc Natl Acad Sci USA 111: 1114-9 PMID: 24395800; PMC3903220
Publications 2013
J223.
Cobanoglu MC, Liu C, Hu F, Oltvai ZN, Bahar I (2013) Predicting drug-target interactions using probabilistic matrix factorization J Chem Inf Model 53: 3399-409 PMID: 24289468; PMC3871285
J222.
Chu CT, Ji J, Dagda RK, Jiang JF, Tyurina YY, Kapralov AA, Tyurin VA, Yanamala N, Shrivastava IH, Mohammadyani D, Qiang Wang KZ, Zhu J, Klein-Seetharaman J, Balasubramanian K, Amoscato AA, Borisenko G, Huang Z, Gusdon AM, Cheikhi A, Steer EK, Wang R, Baty C, Watkins S, Bahar I, Bayir H, Kagan VE (2013) Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells Nature Cell Biology 15: 1197-1205 PMID: 24036476; PMC3806088
J221.
Gur M, Madura JD, Bahar I (2013) Global transitions of proteins explored by a multiscale hybrid methodology: Application to adenylate kinase Biophys J 105: 1643-1652 PMID: 24094405; PMC3791301
J220.
Gur M, Zomot E, Bahar I (2013) Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions J Chem Phys 139: 121912. PMID: 24089724; PMC3739829
J219.
Cheng MH, Bahar I (2013) Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT Biophys J 105: 630-639. PMID: 23931311; PMC3736663
J218.
Zomot E, Bahar I (2013) Intracellular gating in an inward-facing state of aspartate transporter GltPh is regulated by the movements of the helical hairpin HP2 J Biol Chem 288: 8231-8237. PMID: 23386619; PMC3605641
Publications 2012
J217.
Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL (2012) FlexE: Using elastic network models to compare models of protein structure J Chem Theor Comp 8: 3985-3991. PMID: 25530735 PMCID: PMC4269272
J216.
Kurkcuoglu Z, Bakan A, Kocaman D, Bahar I, Doruker P (2012) Coupling between catalytic loop motions and enzyme global dynamics PLoS Comput Biol 8: e1002705. PMID: 23028297; PMC3459879
J215.
Bhatt D, Bahar I (2012) An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates J Chem Phys 137: 104101. PMID: 22979844; PMC3460967
J214.
Dutta A, Shrivastava IH, Sukumaran M, Greger IH, Bahar I (2012) Comparative dynamics of NMDA- and AMPA-Glutamate receptor N-terminal domains Structure 20: 1838-49. PMID: 22959625; PMC3496038
J213.
Isin B, Tirupula KC, Oltvai ZN, Klein-Seetharaman J, Bahar I (2012) Identification of motions in membrane proteins by elastic network models and their experimental validation Methods Mol Biol 914: 285-317. PMID: 22976035
J212.
Zomot E, Bahar I (2012) A conformational switch in a partially unwound helix selectively determines the pathway for substrate release from the carnitine/-butyrobetaine antiporter CaiT J Biol Chem 287: 31823-32. PMID: 22843728; PMC3442516
J211.
Bakan A, Nevins N, Lakdawala AS, Bahar I (2012) Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules J Chem Theory Comput 8: 2435-2447. PMID: 22798729; PMC3392909
J210.
Liu Y, Bahar I (2012) Sequence evolution correlates with structural dynamics Mol Biol Evol 29: 2253-63.PMID: 22427707; PMC3424413
J209.
Lezon TR, Bahar I (2012) Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh Biophys J 102: 1331-40. PMID: 22455916; PMC3309413
J208.
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjolander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S (2012) The interface of protein structure, protein biophysics, and molecular evolution Protein Science 21: 769-85. PMID: 22528593; PMC3403413
B17. Doruker P, Liu Y, Yang Z, Bahar I. (2012) In Silico Coarse-Grained Approaches to Structural Dynamics and Function of Proteins and their Assemblies in Comprehensive Biophysics. Editor-in-Chief: EH Egelman, vol 9, chapter 9.3, pp 27-52, Academic Press, Elsevier.
J207.
Liu L, Byeon IJ, Bahar I, Gronenborn AM (2012) Domain swapping proceeds via complete unfolding: A 19F- and 1H- NMR study of the cyanovirin-N protein J Am Chem Soc 134: 4229-35. PMID: 22296296; PMC3326405
Publications 2011
B16. Zomot E, Bakan A, Shrivastava IH, DeChancie J, Lezon TR, Bahar I. (2011) Sodium-coupled secondary transporters: Insights from Stucture-based computations in Molecular Machines. Edited by Benoit Roux World Scientific, NY.
J206.
Liu L, Gronenborn AM, Bahar I (2011) Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion Proteins 80: 616-625. PMID: 22105881; PMC3290687
J205.
Marcos E, Crehuet R, Bahar I (2011) Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members PLoS Comput Biol 9: e1002201. PMID: 21980279; PMC3182869
J204.
Jiang J, Shrivastava IH, Watts SD, Bahar I, Amara SG (2011) Large collective motions regulate the functional properties of glutamate transporter trimers Proc Natl Acad Sci USA 108: 15141-6. PMID: 21876140; PMC3174670
J203.
Meireles L, Gur M, Bakan A, Bahar I (2011) Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins Protein Science 20: 1645-58. PMID: 21826755; PMC3218357
J202.
Morel PA, Srinivas M, Turner MS, Fuschiotti P, Munshi R, Bahar I, Feili-Hariri M, Ahrens ET (2011) Gene expression analysis of dendritic cells that prevent diabetes in NOD mice: analysis of chemokines and costimulatory molecules J Leukoc Biol 90: 539-50. PMID: 21628331; PMC3157898
J201.
Eyal E, Dutta A, Bahar I (2011) Cooperative dynamics of proteins unraveled by network models WIREs Computational Molecular Science 1: 426-439.
J200.
Zomot E, Bahar I (2011) Protonation of glutamate-208 induces the release of agmatine in an outward-facing conformation of arginine/agmatine antiporter J Biol Chem 286: 19693-701. PMID: 21487006; PMC3103348
J199.
Bakan A, Meireles LM, Bahar I (2011) ProDy: Protein dynamics inferred from theory and experiments
Bioinformatics 27: 1575-1577. PMID: 21471012; PMC3102222
J198.
Sukumaran M, Rossmann M, Shrivastava I, Dutta A, Bahar I, Greger IH (2011)
Dynamics and allosteric potential of the AMPA receptor N-terminal domain EMBO J 30: 972-82. PMID: 21317871; PMC3049213
J197.
DeChancie J, Shrivastava
IH, Bahar I (2011)
Mechanism of substrate release by the aspartate transporter
GltPh: Insights from simulations Mol. BioSyst 7:832-842. PMID: 21161089; PMC3227142
J196.
Bakan A, Bahar I (2011)
Computational generation inhibitor-bound conformers of p38 map kinase and comparison with experiments Pac Symp Biocomput 2011: 181-92. PMID: 21121046
J195.
Mustata G, Li M, Zevola N, Bakan A, Zhang L, Epperly M, Greenberger JS,
Yu J, Bahar I (2011) Development of small-molecule PUMA inhibitors for mitigating radiation-induced
cell death Curr Top Med Chem 11: 281-90. PMID: 21320058; PMC3086011
Publications 2010
J194. Liu Y, Gierasch LM, Bahar I (2010) Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs
PLoS Comput Biol 6: e1000931. PMID: 20862304; PMC2940730
J193. Dutta A, Bahar I (2010) Metal-binding sites are designed to achieve optimal mechanical and signaling
properties Structure 18: 1140-8. PMID: 20826340; PMC2937013
J192. Lezon TR, Bahar I (2010) Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology PLoS Comput Biol 6: e:1000816. PMID: 20585542; PMC2887458
J191. Bahar I (2010) On the functional significance of soft modes predicted by coarse-grained models for membrane proteins J Gen Physiol 135: 563-73. PMID: 20513758; PMC2888054
J190. Zomot E, Bahar I (2010) The sodium/galactose symporter crystal structure is a dynamic, not so occluded state Mol Biosyst 6: 1040 -1046. PMID: 20358053; PMC2938171
J189. Marcos E, Crehuet R, Bahar I (2010) On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm PLoS Comput Biol 6: e1000738. PMID: 20386738; PMC2851564
J188. Bahar I, Lezon TR, Yang LW, Eyal E (2010) Global Dynamics of Proteins: Bridging Between Structure and Function Annu Rev Biophys 39: 23-42. PMID: 20192781; PMC2938190
J187. Liu Y, Bahar I (2010) Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones Pac Symp Biocomput 2010: 269-80. PMID: 19908379; PMC2938181
J186. Bahar I, Lezon T, Bakan A, Shrivastava IH (2010) Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins Chem Rev 110: 1463-1497. PMID: 19785456; PMC2836427
Publications 2009
B15. Lezon TR, Shrivastava IH, Yang Z, Bahar I. in Handbook on Biological Networks. Edited by Boccaletti S, Latora V, Moreno Y (2009) Elastic network models for biomolecular dynamics: Theory and application to membrane proteins and viruses World Scientific.
J185. Yang Z, Bahar I, Widom M (2009) Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity Biophys J 96: 4438-48. PMID: 19486668; PMC2711457
J184. Molina G,* Vogt A,* Bakan A,* Dai W, Queiroz de Oliveira P, Znosko W, Smithgall TE, Bahar I, Lazo JS, Day BW, Tsang M (2009) Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages Nature Chem Biol 5: 680-7. PMID: 19578332; PMC2771339
J183. Liu L, Koharudin LM, Gronenborn AM, Bahar I (2009) A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations Proteins 77: 927-939. PMID: 19688820; PMC2767477
J182.
Lezon TR, Sali A, Bahar I
(2009) Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models PLoS Comput Biol 9: e1000496. PMID: 19730674; PMC2725293
J181.
Bakan A, Bahar I (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci USA 106: 14349-14354. PMID: 19706521; PMC2728110
J180.
Yang Z, Majek P, Bahar I (2009) Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL PLoS Comput Biol 5: e1000360. PMID: 19381265; PMC2664929
J179.
Yang LW, Eyal E, Bahar I, Kitao A (2009) Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics Bioinformatics 25: 606-614. PMID: 19147661; PMC2647834
J178. Mustata G, Follis AV, Hammoudeh DI, Metallo SJ, Wang H, Prochownik EV, Lazo JS, Bahar I (2009) Discovery of Novel Myc-Max Heterodimer Disruptors with a Three-Dimensional Pharmacophore Model J Med Chem 52: 1247-1250. PMID: 19215087; PMC2765518
J177. Gu Y, Shrivastava IH, Amara SG, Bahar I (2009) Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter Proc Natl Acad Sci U S A 106: 2589-94. PMID: 19202063; PMC2637273
Publications 2008
J176. Bakan A, Lazo JS, Wipf P, Brummond KM, Bahar I (2008) Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening Curr Med Chem 15: 2536-44. PMID: 18855677; PMC2764859
J175.
Shrivastava IH, Jiang J, Amara SG, Bahar I (2008)
Time-resolved mechanism of extracellular gate opening and
substrate binding in glutamate transporter J Biol Chem 283: 28680-28690. PMID: 18678877; PMC2568915 (Supplementary Material)
J174.
Engen
JR, Wales TE, Hochrein JM, Meyn MA III, Ozkan SB, Bahar I,
Smithgall TE (2008)
Structure and dynamic regulation of Src-family kinases Cell Mol Life Sci 65: 3058-73.
J173.
Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I (2008) Computational Insights on the Competing Effects of Nitric Oxide in Regulating Apoptosis PLoS ONE 3:
e2249. PMID: 18509469; PMC2386238
J172.
Isin B, Schulten K, Tajkhorshid E, Bahar I (2008) Mechanism of Signal Propagation upon Retinal Isomerization: Insights from Molecular Dynamics Simulations of Rhodopsin Restrained by Normal Modes Biophysical J
95: 789-803. PMID: 18390613; PMC2440475
J171.
Liu Y, Eyal E, Bahar I (2008) Analysis of correlated mutations in HIV-1 protease using spectral clustering
Bioinformatics 24:
1243-50. PMID: 18375964
J170.
Chennubhotla C, Yang Z, Bahar I (2008) Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL
Mol. BioSyst 4: 287-292. PMID: 18354781
J169.
Eyal E, Bahar I (2008) Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models Biophys J
94: 3424-35. PMID: 18223005; PMC2292382
Publications 2007
J168. Bahar I, Chennubhotla C, Tobi D (2007) Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation Curr Opin Struct Biol 17: 633-40. PMID: 18024008; PMC2197162
J167. Chennubhotla C, Bahar I (2007) Signal propagation in proteins and relation to equilibrium fluctuations
PLoS Comput Biol 3,
17: 16-26. PMID: 17892319; PMC1988854
J166. Chennubhotla C, Bahar I
(2007) Markov methods for hierarchical coarse-graining of large protein dynamics J Comput Biol 14: 765-76. PMID: 17691893
J165.
Tobi D, Bahar I (2007) Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity? BMC Bioinformatics
8: 226. PMID: 17598909
J164.
Eyal E, Chennubhotla C, Yang L-W, Bahar I (2007) Anisotropic Fluctuations of Amino Acids in Protein Structures: Insights from X-Ray Crystallography and Elastic Network Models Bioinformatics 23: i175-i184. PMID: 17646294 (Supplementary Materials)
J163.Eyal E, Pietrokovski S, Bahar I (2007) Rapid Assessment of Correlated Amino Acids from Pair-to-Pair (P2P) Substitution Matrices Bioinformatics 23: 1837-1839. PMID: 17496318
J162. Yang L-W, Eyal E, Chennubhotla C, JunGoo J, Gronenborn AM, Bahar I (2007) Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-ray Data with Computational Predictions Structure 15: 741-749. PMID: 17562320; PMC2760440
J161. Lazo JS, Skoko JJ, Werner S, Mitasev B, Bakan A, Koizumi F, Yellow-Duke A, Bahar I, Brummond KM (2007) Structurally Unique Inhibitors of Human Mitogen-activated Protein Kinase Phosphatase-1 Identified in a Pyrrole Carboxamide Library J Pharmacol Exp Ther 322: 940-947. PMID: 17538006
J160. Vries JK, Liu X, Bahar I (2007) The relationship between N-gram patterns and protein secondary structure Proteins 68: 830-838. PMID: 17523186
J159. Iyer, AK, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells AJ (2007) Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity
J Cell Physiol 211: 748-58. PMID: 17311283
B13.
Chennubhotla C,
Bahar I (2007) Markov Methods for Hierarchical Coarse-Graining
of Large Protein Dynamics Lect Notes in Comp Sci 3909: 379-393.
Publications 2006
E1. “Normal Mode Analysis. Theory and Applications to Biological and Chemical Systems”, Eds Cui Q, Bahar I (2006) Math & Comp Biology Series, Chapman & Hall CRC Press, Taylor & Francis.
J158.
Eyal E, Yang LW, Bahar I (2006) Anisotropic network model: systematic evaluation and a new web interface
Bioinformatics 22: 2619-27. PMID: 16928735
J157. Isin B, Rader AJ, Dhiman HK, Klein-Seetharaman J, Bahar I (2006) Predisposition of the dark state of rhodopsin to functional changes in structure
Proteins 65: 970-83. PMID: 17009319
J156.
Farkas IJ, Wu C, Chennubhotla C, Bahar I, Oltvai ZN (2006) Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae
BMC Bioinformatics 7: 478. PMID: 17069658; PMC1643839
J155.
Chennubhotla C,
Bahar I (2006) Markov propagation of allosteric effects in biomolecular
systems: application to GroEL-GroES Mol Syst Biol 2: 36. PMID: 16820777; PMC1681507
J154.
Yang LW, Rader AJ,
X Liu, CJ Jursa, SC Chen, HA Karimi, Bahar I (2006) oGNM: online computation of structural dynamics
using the Gaussian Network Model Nucleic
Acids Res 34: W24-31. PMID: 16845002; 16845002
J153. Shrivastava IH,
Bahar I (2006) Common Mechanism of Pore Opening Shared by Five
Different Potassium Channels Biophys J 90: 3929-3940. PMID: 16533848; PMC1459499
B14.
Rader AJ, Chennubhotla C, Yang L-W, Bahar I Eds Cui Q, Bahar I (2006) The Gaussian Network Model: Theory and Applications
in Normal Mode Analysis. Theory and Applications to Biological
and Chemical Systems Math
& Comp Biology Series, Chapman & Hall CRC Press, Taylor & Francis Group, 41-64.
J152. Munshi R,
Coalson RD, Ermentrout GB, Madura JD,
Meirovitch H, Stiles JR, Bahar I (2006) An Introduction to Simulation and Visualization
of Biological Systems at Multiple Scales: A Summer Training
Program for Interdisciplinary Research Biotechnology Progress
22: 179-185. PMID: 16454509
J151.
Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout GB,
Bahar I (2006) Bistability in Apoptosis: Roles of Bax, Bcl-2,
and Mitochondrial Permeability Transition Pores Biophys J 90: 1546-1559.
J150. Tobi D, Bahar I
(2006) Optimal
Design of Protein Docking Potentials: Efficiency and Limitations Proteins:
Structure, Function, and Bioinformatics 62: 970-981. PMID: 16385562
Publications 2005
J149. Chennubhotla C, Rader AJ, Yang L-W, Bahar I (2005) Elastic network models for understanding biomolecular
machinery: from enzymes to supramolecular assemblies CPhysical
Biology 2: S173-S180. PMID: 16280623
J148. Tobi D, Bahar I (2005) Structural Changes Involved in Protein Binding Correlate with intrinsic Motions of Proteins in the Unbound State Proc Natl Acad Sci (USA) 102: 18908-18913. PMID: 16354836; PMC1323175
J147. Bahar I, Rader AJ (2005) Coarse-grained normal mode analysis in structural
biology Curr
Opin Struct Biology 15: 1-7. PMID: 16143512; PMC1482533
J146. Yang L-W, Liu X,
Jursa CJ, Holliman M, Rader AJ, Karimi H,
Bahar I (2005) iGNM: A Database of Protein Functional Motions
Based on Gaussian Network Model Bioinformatics 21: 2978 -
2987. PMID: 15860562; PMC1752228
J145. Yang L-W, Bahar I (2005) Coupling between Catalytic Site and Collective Dynamics: A requirement for Mechanochemical Activity of Enzymes Structure 13: 893-904. PMID: 15939021; PMC1489920
J144. Berberich J, Yang L-W,
Madura J, Bahar I, Russell AJ (2005) A stable three enzyme creatinine biosensor. 1. Impact
of structure, function and environment on PEGylated and immobilized
sarcosine oxidase ACTA Biomaterialia 1(2): 173-181. PMID: 16701794
J143. Berberich J, Yang L-W,
Bahar I, Russell AJ (2005) A stable three enzyme creatinine biosensor. 2. Analysis of the impact of silver ions on creatine
amidinohydrolase ACTA Biomaterialia 1(2): 183-191. PMID: 16701795
J142. Ramaswamy A, Bahar I, Ioshikhes I (2005) Structural Dynamics of Nucleosome Core Particle:
Comparison with Nucleosomes Containing Histone Variants Proteins:
Structure, Function and Bioinformatics 58: 683-696. PMID: 15624215
J141. Rader AJ, Vlad D, Bahar I (2005) Maturation Dynamics of Bacteriophage HK97 Capsid
RStructure
13: 413-21. PMID: 15766543
Publications 2004
J140. Vodovotz Y, Kim P, Bagci EZ, Ermentrout GB,
Chow CC, Bahar I, Billiar TR (2004) Inflammatory Modulation of Hepatocyte Apoptosis
by Nitric Oxide: In Vivo, In Vitro, and In Silico Studies Current Molecular
Medicine 4: 753-762. PMID: 15579022
J139. Rader AJ, Bahar I (2004) Folding Core Predictions from Network Models of
Proteins Polymer 45: 659-668.
B11. Liu X, Karimi H, Yang L-W, Bahar I (2004) Protein Functional Motion Query and Visualization IEEE Proceedings, 28th Annual International Computer Software and Applications
Conference - (COMPSAC'04).
J138. Seki M, Masutani C,
Yang L-W, Schuffert A, Iwai S, Bahar I,
Wood RD (2004) High efficiency bypass of DNA damage by a single
human DNA polymerase EMBO J 10: 4484-94. PMID: 15496986; PMC526458
J137. Vries JK, Munshi R, Tobi D,
Klein-Seetharaman J, Benos PV, Bahar I (2004)A Sequence Alignment-Independent Method For Protein
Classification Applied
Bioinformatics 3: 137-48. PMID: 15693739
J136. Brisson M, Nguyen T, Vogt A, Yalowich J, Giorgianni A,
Tobi D, Bahar I, Stephenson CRJ, Wipf P, Lazo JS (2004) Discovery and characterization of novel small molecule
inhibitors of human Cdc25B dual specificity phosphatase Mol Pharmacology 66: 824-833. PMID: 15231869
J135. Sluis-Cremer N, Temiz NA, Bahar I (2004)Conformational changes in HIV-1 reverse transcriptase
induced by nonnucleoside reverse transcriptase inhibitor binding Current
HIV Research 2: 323-32. PMID: 15544453; PMC1298242
J134. Temiz NA, Meirovitch E, Bahar I (2004) Escherichia coli Adenylate Kinase Dynamics: Comparison of
Elastic Network Model Modes with Mode-Coupling 15N-NMR Relaxation
Data Proteins, Structure,
Function and Bioinformatics 57: 468-480. PMID: 15382240; PMC1752299
J133. Chen S-C, Bahar I (2004) Mining frequent patterns in proteins: A study of
serine proteinases Bioinformatics 20: i77-i85. PMID: 15262784
J132. Rader AJ, Anderson G, Isin B,
Khorana HG, Bahar I, Klein-Seetharaman J (2004) Identification of core amino acids stabilizing
rhodopsin Proc Natl Acad Sci USA 101: 7246-7251. PMID: 15123809; PMC409904
J131. Wang Y, Rader AJ, Bahar I, Jernigan RL
(2004) Global Ribosome Motions Revealed with Elastic Network
Model J Struct Biol 147: 302-314. PMID: 15450299
Publications 2003
Publications 2002
J127. Temiz NA,
Bahar I (2002) Inhibitor binding alters the directions of domain
motions in HIV-1 reverse transcriptase Proteins: Structure, Function and Genetics 49: 61-70.
J126. Keskin O, Durell SR, Bahar I, Jernigan
RL, Covell DG (2002) Relating molecular flexibility to function: A case
study of tubulin Biophys J 83: 663-680. PMID: 12124255; PMC1302177
J125. Bagci Z, Jernigan RL, Bahar
I (2002) Residue packing in proteins: Uniform distribution
on a coarse-grained scale J Chem Physics 116: 2269-2276. (selected for the February
1, 2002 issue of the Virtual Journal of Biological Physics Research
in http://www.vjbio.org)
J124. Keskin O, Bahar I, Flatow D, Covell DG, Jernigan
RL (2002) Molecular mechanisms of chaperonin GroEL/GroES
function Biochemistry 41: 491-501.
J123. Bagci Z, Jernigan RL,
Bahar I (2002) Residue coordination in proteins conforms to the
closest packing of spheres Polymer 43: 451-459.
J122. Isin B, Doruker
P, Bahar I (2002) Functional motions of influenza virus hemagglutinin:
A structure-based analytical approach Biophys J 82: 569-581. PMID: 11806902; PMC1301869
J121. Doruker P, Bahar I, Baysal C, Erman B (2002) Collective deformations in proteins determined
by a mode analysis of molecular dynamics trajectories Polymer 43: 431-439.
J120. Ozkan SB, Dill
KA, Bahar I (2002) Fast-folding protein kinetics, hidden intermediates
and the sequential stabilization model Protein Science 11: 1958-1970. PMID: 12142450; PMC2373683
J119. Doruker P, Jernigan
RL, Bahar I (2002) Dynamics of large proteins through hierarchical
levels of coarse-grained structures J Comp Chem 23: 119-12. PMID: 11913377
Publications 2001
P1. (Patent 1) Erman B, Mark JE, Paterson BZ,
Bahar I, Kloczkowski A (2001) High Performance of Biodegradable Materials from
Oriented Starch Derivatives US Patent #6,218,532 B1.
J118. Ozkan B, Bahar I,
Dill KA (2001) Transition states and the meaning of F-values in
protein folding kinetics Nature Struct Biol 8: 765-769.
J117. Konuklar FAS, Aviyente
V, Sen TZ, Bahar I (2001)Modeling the deamidation of asparagine residues
via succinimide intermediates J Mol Model 7: 147-160.
J116. Atilgan AR, Durrell SR,
Jernigan RL, Demirel MC, Keskin O, Bahar I (2001) Anisotropy of fluctuation dynamics of proteins
with an elastic network model Biophys
J 80: 505-515.
Publications 2000
J115. Jernigan RL, Bahar I, Covell DG,
Atilgan AR, Erman B, Flatow D (2000) Relating the structure of HIV-1 reverse transcriptase
to its processing step J Biomol Structure
& Dynamics 1: 49-55.
J114. Doruker P, Atilgan AR, Bahar I (2000) Dynamics of proteins predicted by molecular dynamics
simulations and analytical approaches: Application to a-amylase
inhibitor Proteins:
Structure, Function & Genetics 40: 512-524.
J113. Duman G, Keskin O, Bahar I, Robinson JR (2000) Stabilization of the molten globule state of hen
egg white lysozyme with solutions containing polyvinyl pyrrolidone J Controlled
Release 64: 331-333.
J112. Haliloglu T, Bahar I,
Jernigan RL (2000) Collective dynamics of class I MHC/peptide complexes
and binding to T cell receptors Biophys J 78: 34A.
J111. Keskin O, Bahar I, Jernigan RL,
Myers TG, Beutler JA, Shoemaker RH, Sausville EA, Covell DG
(2000) Characterization of anticancer agents by their
growth inhibitory activity and relationships to mechanism of
action and structure Anticancer Drug Design 15: 79-98. PMID: 10901296
J110. Keskin O, Jernigan RL, Bahar I (2000) Proteins with similar architecture exhibit similar
large-scale dynamic behavior. Specificity resides in local differences
Biophysical Journal 78: 2093-2106.
Publications 1999
J109. Bahar I (1999) Dynamics of proteins and biomolecular complexes.
Inferring functional motions from structure Reviews in Chemical Engineering 15: 319-349.
B10. Jernigan RL, Bahar I (1999) Geometric Regularities among bonded and nonbonded
residues in proteins In
Perspectives in Structural Biology (GN Ramachandran Volume) Vijayan M, Yathindra N, Kolaskar AS Eds., Indian Academy
of Sciences, Universities Press, Hyderabad, pp 209-225.
J108. Haliloglu T, Bahar I (1999) Structure-based analysis of protein dynamics. Comparison
of theoretical results for hen lysozyme with X-ray diffraction
and NMR relaxation data Proteins:
Structure, Function & Genetics 37: 654-667.
J107. Jernigan RL,
Demirel MC, Bahar I (1999) Relating structure to function through the dominant
slow modes of motion of DNA topoisomerase II Int J Quantum Chem 75: 301-312.
J106. Bahar I, Jernigan RL (1999) Cooperative fluctuations and subunit communication
in tryptophan synthase Biochemistry 38: 3478-3490.
J105. Sen TZ, Bahar I, Erman B, Laupretre F,
Monnerie L (1999) Local dynamics of cis-polybutadiene and cis-polyisoprene.
A comparative study based on cooperative kinematics theory and
NMR experiments Macromolecules 32: 3017-3024.
J104. Bahar I,
Erman B, Jernigan RL, Atilgan AR, Covell D (1999) Collective motions of HIV-1 reverse transcriptase.
Examination of Flexibility and Enzyme Function J
Mol Biol 285: 1023-1037.
Publications 1998
B9. Erman B,
Bahar I Eds Inan E,
Markov KZ (1998) Simulation of polymeric systems in Continuum Models and Discrete Systems, pp 297-303, World Scientific Publishing.
J103. Keskin O, Bahar I, Badredtinov A, Ptitsyn O,
Jernigan RL (1998) Empirical solvent-mediated potentials hold for
both intramolecular and inter-molecular inter-residue interactions Protein Science 7: 2578-2586.
J102. Erman B, Bahar I (1998) Local chain dynamics and glass transition Makromolekulare Chem Makromol Symp. 133: 33-46.
J101. Lustig B, Bahar I, Jernigan RL (1998) RNA bulge entropies are correlated with peptide
binding strengths for HIV-1 and BIV TAR RNA because of improved
conformational access Nucleic Acids Res 26: 5212-5217.
J100. Demirel MC, Atilgan AR, Jernigan RL, Erman B,
Bahar I (1998) Identification of kinetically hot residues in proteins Protein Science 7: 2522-2532.
J99. Keskin O, Bahar I (1998) Packing of sidechains in low resolution models for
proteins Folding & Design 3: 469-479.
J98. Bahar I, Atilgan AR, Demirel MC, Erman B (1998)Vibrational dynamics of folded proteins: Significance of
slow and fast motions in relation to function and stability Phys.
Rev Lett 80: 2733-2736.
J97. Erdal S, Bahar I,
Erman B (1998) Swelling of sodium chloride filled polybutadiene
networks in aqueous environment Polymer 39, 2035-2041.
J96. Atilgan AR, Haliloglu T, Bahar I, & Erman B (1998) Correlated fluctuations in polymer networks Comput
Theor Polym Sci 8: 55-59.
J95. Bahar I, Jernigan RL (1998) Vibrational dynamics of transfer RNAs. Comparison of the
free and enzyme-bound forms J
Mol Biol 281: 871-884.
J94. Ozkan B,
Bahar I (1998) Recognition of native structure from complete enumeration
of low resolution models with constraints Proteins: Structure, Function and Genetics 32: 211-222.
J93. Haliloglu T,
Bahar I (1998) Coarse-grained simulations of conformational dynamics
of proteins Application to apomyoglobin Proteins: Structure, Function and Genetics 3:
271-281.
B8. Jernigan RL, Bahar I Eds Schleyer P vR, Allinger NL, Clark T, Gasteiger
J, Kollman PA, Schaefer III HF, Schreiner PR (1998) Coarse Grained Searches over Protein Conformations Encyclopedia of Computational
Chemistry &Sons: Chichester.
J92. Bahar I, Wallqvist A, Covell DG, Jernigan RL (1998) Correlation between native state hydrogen exchange
and cooperative residue fluctuations from a simple model
Biochemistry 37: 1067-1075.
Publications 1997
J91. Bahar I, Erman B, Haliloglu T, Jernigan RL
(1997) Efficient characterization of collective motions
and interresidue correlations in proteins by low-resolution
simulations Biochemistry 36: 13512-13523.
J90. Baysal C, Erman B, Bahar I, Laupretre L, Monnerie L
(1997) Local dynamics of bulk polybutadiene of various
microstructures: Comparison of Theory with NMR Measurements Macromolecules 30: 2058-2066.
J89. Haliloglu
T, Bahar I, Erman B (1997) Gaussian dynamics of folded proteins Phys. Rev. Lett. 79: 3090-3093.
J88. Bahar I (1997) Local relaxation in dense media: cooperative kinematics
theory and applications Macromol Theory &
Simulations 6: 881-906.
J87. Bahar I, Kaplan M, Jernigan RL (1997) Short-range conformational energies, secondary structure
propensities, and recognition of correct sequence-structure
matches Proteins 29: 292-308.
J86. Bahar I, Atilgan AR,
Jernigan RL, Erman B (1997) Understanding the recognition of protein structural
classes by amino acid composition Proteins 29: 172-185. PMID: 9329082
J85. Erman B,
Bahar I, Jernigan RL (1997) Equilibrium states of rigid bodies with multiple
interaction sites. Application to protein helices J Chem Phys 107: 2046-2059.
J84. Fakirov S, Sarac
Z, Anbar T, Boz B, Bahar I, Evstatiev M, Apostolov A,
Mark JE, Kloczkowski A (1997) Mechanical properties and transition temperatures
of crosslinked-oriented gelatin: II. Effect of orientation and
water content on transition temperatures Colloid Polym Sci 275:
307-314.
J83. Bahar I,
Cho J, Doruker P, Erman B, Haliloglu T, Kim E-G,
Mattice WL, Monnerie L, Rapold RF (1997) Three approaches that permit more efficient simulation
of the dynamics of atomistic models of polymers Trends in Polymer Science 5: 155-160.
J82. Doruker P,
Bahar I (1997) Role of water on unfolding kinetics of polypeptides
studied by molecular dynamics simulations Biophys J 72: 2445-2456. (Abstract)
J81. Bahar I,
Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in protein Folding & Design 2: 173-181.
J80. Bahar I, Jernigan RL (1997) Inter-residue potentials in globular proteins and
the dominance of highly specific hydrophilic interactions at
close separations J Mol
Biol 266: 195-214.
Publications 1996
J79. Zhao WY, Kloczkowski A, Mark JE, Erman B, Bahar I (1996) Make tough plastic films from gelatin Chemtech 26: 32-38.
J78. Haliloglu T, Bahar I, Erman B, Mattice WL (1996) Relative contributions of coupled rotations and small
amplitude torsions to conformational relaxation in polymers Macromolecules 29: 8942-8947.
J77. Bahar I, Jernigan RL (1996) Coordination geometry of non-bonded residues in
globular proteins Folding &
Design 1: 357-370.
J76. Haliloglu
T, Bahar I, Erman B (1996) The Response of a Single Grafted Chain to Shear
Flow. A Brownian Dynamics Simulation Study J Chemical Physics 105: 2919-2926.
J75. Zhao WV, Kloczkowski A, Mark JE, Erman B, Bahar
I (1996) Main-Chain Lyotropic Liquid-Crystalline Elastomers. 2. Orientation and Mechanical Properties of Polyisocyanate Films" Macromolecules 29: 2805-2812.
J74. Zhao WV, Kloczkowski
A, Mark JE, Erman B, Bahar I (1996) Main-Chain Lyotropic Liquid-Crystalline Elastomers.
1. Syntheses of Cross-Linked Polyisocyanate Gels Acquiring Liquid-Crystalline
Behavior in the Swollen State Macromolecules 29:
2796-2804.
J73. Haliloglu T,
Bahar I, Erman B, Mattice WL (1996) Mechanisms of the Exchange of Diblock Copolymers
between Micelles at Dynamic Equilibrium Macromolecules 29:
4764-4771.
J72. Baysal C, Erman B, Bahar I, Monnerie L (1996) Kinematics of Polymer Chains in Dense Medium. 4.
Effect of Backbone Geometry and Application to Polybutadiene Macromolecules 29: 2980-2988.
B7. Bahar I, Erman B Ed Fakirov S (1996) Segmental Orientation in Deformed Rubbery Networks Oriented Polymer Materials Huthig & Webf Verlag, Oxford, p467-481.
J71. Baysal C, Atilgan AR, Erman B, Bahar I (1996) A Molecular Dynamics Analysis of Coupling between
Librational Motions and Isomeric Jumps in Chain Molecules Macromolecules 29: 2510-2514.
J70. Jernigan RL, Bahar I (1996) Structure-Derived Potentials and Protein Simulations Current Opinion in Structural
Biology 6: 195-209.
J69. Zhao WV, Kloczkowski A, Mark JE, Erman B,
Bahar I (1996) Oriented Gelatin- A New Source for High-Performance
Macromol Sci Pure Appl ChemA33, 525-540.
J68. Haliloglu
T, Bahar I, Erman B, Kim EG, Mattice WL (1996) A Dynamic Rotational Isomeric State Approach for
Extension of the Time Scale of the Local Dynamics Observed in
Fully Atomistic Molecular Dynamics Simulations J
Chem Phys 104: 4828-4834.
Publications 1995
J67. Baysal C,
Atilgan AR, Erman B, Bahar I (1995) Coupling Between Different Modes in Local Chain
Dynamics: A Modal Correlation Analysis J Chem Soc Faraday Trans 91: 2483-2490.
J66. Haliloglu T, Bahar I,
Erman B (1995) Dependence of Segmental Orientation on Polymer
Conformational Characteristics Polymer 36: 4131-4134.
J65. Sarac Z, Erman B,
Bahar I (1995) Segmental Orientation in Deformed Networks. 2. Molecular
Theory of Biaxial Deformation Macromolecules 28: 582-588.
J64. Bahar I, Baysal N, Erman B, Monnerie L (1995) Kinematics of Polymer Chains in Dense Medium. 3.
Influence of Intramolecular Conformational Potentials Macromolecules 28: 1038-1048.
J63. Serhatkulu T,
Erman B, Bahar I, Fakirov S, Evstatiev M, Sapundjieva D
(1995) Dynamic-Mechanical Study of Amorphous Phases in
Poly(ethylene terephtalate)/Nylon-6 Blends Polymer 36, 2371-2377.
J62. Besbes S, Bokobza L,
Monnerie L, Bahar I, Erman B (1995) Molecular Orientation in Deformed Bimodal Networks.
2. Fourier Transform Infrared Measurements on PDMS Networks
and Comparison with Theory Macromolecules 28: 231-235.
J61. Bahar I, Erman B, Bokobza L, Monnerie L
(1995) Molecular Orientation in Deformed Bimodal Networks.
1. Theory Macromolecules 28: 225-230.
Publications 1994
J60. Mark JE, Yang Y, Kloczkowski A,
Erman B, Bahar I (1994) A Novel Orientation Technique for Semi-rigid Polymers.
2. Mechanical Properties of the Cellulose Acetate and Hydroxypropyl
cellulose Films Colloid & Polym Sci 272: 393.
J59. Bahar I, Erman B,
Fytas G, Steffen W (1994) Intramolecular Contributions to Stretched Exponential
Relaxation Behavior in Polymers Macromolecules 27: 5200-5205.
J58. Baysal C, Erman B, Bahar I (1994) Contribution of Bond Rotational Interdependence
to Local Chain Dynamics: A Brownian Dynamics Study Macromolecules 27, 3650-2657.
J57. Jernigan RL, Raghunathan G,
Bahar I (1994) Characterization of Interactions and Metal Ion
Binding Sites in Proteins Current Opinion in Structural Biology 4: 256-263.
J56. Apostolov AA,
Fakirov S, Sezen B, Bahar I, Kloczkowski A (1994) Structural and Mechanical Studies of a Blend of
Poly(butylene terephtalate) and Poly(ether ester) Based on Poly(butylene
terephtalate) and Poly(ethylene glycol) Polymer 35:
5247-5256.
J55. Yang Y, Kloczkowski A, Mark JE, Erman B, Bahar I (1994) A Novel Orientation Technique for Semi-Rigid Polymers.
1. Preparation of Cross-linked Cellulose Acetate and Hydroxypropylcellulose
Films Having Permanent Anisotropy in the Swollen State Colloid & Polym Sci 272: 284.
J54. Bahar I, Haliloglu T, Erman B (1994) Role of Structural Heterogeneities on Segmental
Orientation in Deformed Chains: Application to Alternating Copolymers Macromolecules 27: 1703.
J53. Bahar
I, Erman B, Monnerie L (1994) Effect of Molecular Structures on Local Chain Dynamics:
Analytical Approaches and Computational Methods Adv Polymer Sciences 116: 145-206,
Springer-Verlag Berlin Heidelberg.
J52. Sakrak G, Bahar I, Erman B (1994) Computer Simulation of Two-Dimensional Trifunctional
Bimodal Networks Macromol
Theory Simul 3: 151.
J51. Bahar I, Jernigan RL (1994) Cooperative Structural Reorganizations Induced
by Nonhomogeneous Intramolecular Interactions in Compact Globular
Proteins Biophysical Journal 66: 467. (Abstract)
J50. Bahar I, Jernigan RL (1994) Stabilization of Intermediate Density States in
Globular Proteins by Homogeneous Intramolecular Attractive Interactions
Biophysical Journal 66: 454.
(Abstract)
Publications 1993
J49. Kanberoglu C, Bahar I,
Erman B (1993) Stress-Strain-Molecular Orientation in Highly Cross-Linked
cis- Polyisoprene Networks Polymer 34: 4997.
J48. Doruker P,
Bahar I (1993) Effect of Intrachain Constraints and Polymer-Solvent
Interactions on Chain Statistics and Dynamics Comp Polymer Science 3: 87.
J47. Bahar I, Badur B, Doruker
P (1993) Solvent Effect on Translational Diffusivity and
Segmental Orientational Mobility of Polymers in Dilute Solution:
A Molecular Dynamics Study J Chem Phys 99: 2235.
J46. Erman B, Bahar I, Besbes S, Bokobza L, Monnerie L
(1993) Interpretation of Segmental Orientation in Deformed
Networks in Terms of Constrained Junction Model of Rubber Elasticity Polymer 34: 1858.
J45. Haliloglu T,
Erman B, Bahar I (1993) Orientational Mobility of Uniaxially Deformed Polymer
Chains: A Brownian Dynamics Simulation Study Polymer Communications 34: 440.
J44. Besbes S, Bokobza I, Monnerie L, Bahar I,
Erman B (1993) An Infrared Dichroism Investigation of Segmental
Orientation in Dry and Swollen Poly(dimethyl siloxane) Networks Polymer 34: 1179.
J43. Bahar I,
Erman B, Kremer F, Fischer EW (1993) Dynamic Rotational Isomeric State Approach for Segmental
Motions of cis-Polyisoprene in the Bulk State Colloid Polym
Sci 91: 1.
J42. Erman B, Bahar I (1993) Local Dynamics of Freely Rotating Chains in Dense
Systems Colloid Polym
Sci 91: 16.
Publications 1992
B6. Erman B,
Bahar I, Kloczkowski A, Mark JE Ed Aharoni SM (1992) Networks with Semi-Flexible Chains, in Synthesis,
Characterization, and Theory of Polymeric Networks and Gels Plenum Press, New York, p.113-126.
B5. Kloczkowski A,
Mark JE, Erman B, Bahar I Eds Noda I, Rubingh DN (1992) Isotropic-Nematic Phase Transitions in Polymer Networks
Deformed in the Dry and Swollen States in Polymer Solution, Blends
and Interfaces Elsevier Science
Publishers B V, p 221.
B4. Erman B, Bahar I, Yang Y, Kloczkowski
A, Mark JE Eds Noda I, Rubingh DN (1992) Novel Orientation Techniques for the Preparation
of High- Performance Materials from Semi-Flexible Polymers such
as Cellulosics in Polymer Solution, Blends and Interfaces,
Elsevier Science Publishers
B V, p 209.
B3. Erman B, Bahar I Eds Noda I, Rubingh DN (1992) Local Dynamics of Polymers in Restrictive Environment in Polymer Solution, Blends and Interfaces, Elsevier Science Publishers
B. V., p 197.
J41. Bahar I, Erman B, Monnerie L (1992) Kinematics of Polymer Chains with Freely Rotating
Bonds in Restrictive Environment. 2. Conformational and Orientational
Correlations Macromolecules 25: 6315.
J40. Bahar I,
Erman B, Monnerie L (1992) Kinematics of Polymer Chains with Freely Rotating
Bonds in Restrictive Environment. 1. Theory Macromolecules 25: 6309.
J39. Akcasu AZ, Bahar I, Erman B, Feng Y,
Han C (1992) Theoretical and Experimental Study of Dissolution
of Inhomogeneities Formed During Spinodal Decomposition in Polymer
Mixtures J Chem Phys 97: 5782.
J38. Akcasu AZ, Erman B, Bahar
I (1992) Nonlinear Kinetics of Spinodal Decomposition and
Dissolution of Inhomogeneities formed by Spinodal Decomposition
in Polymer Blends Makromolekulare Chemie Makromol Symp 62: 43.
J37. Haliloglu T, Erman B, Bahar I (1992) Time-Dependent Probability Distribution Functions
for Orientational Motions of Segments in Polymer Chains J Chem Phys 97:
4438.
J36. Haliloglu T,
Bahar I, Erman B (1992) Orientational and Conformational Correlations in
Deformed Polymer Chains with Fixed End-to-End Separation: A
Brownian Dynamics Simulation Study J Chem Phys 97: 4428.
J35. Bahar I, Neuburger
N, Mattice WL (1992) Mechanism of Local Conformational Transitions in
Poly(dialkyl Siloxanes). Molecular Dynamics Simulation and Dynamic
Rotational Isomeric State Approach Macromolecules 25: 4619.
J34. Neuburger N, Bahar I, Mattice WL (1992) Molecular Dynamics Simulations of Poly (dialkylsiloxanes).
Equilibrium Statistics and Unperturbed Chain Dimensions Macromolecules 25: 2447.
J33. Besbes S, Cermelli I,
Bokobza L, Monnerie L, Bahar I, Erman B, Herz
J (1992) Segmental Orientation in Model Networks of Poly(dimethyl
siloxane): Fourier Transform Infrared Dichroism Measurements
and Theoretical Interpretation Macromolecules 25: 1949.
B2. Erman B, Bahar I, Kloczkowski
A, Mark JE Eds Mark JE, Erman B (1992) Stresss-Strain and Segmental Orientation in Networks
with Semirigid Chains in Elastomeric Polymer Networks Prentice Hall Polymer Science
and Engineering Series Prentice Hall, Inc. New Jersey,
p142.
J32. Bahar
I, Erman B, Kremer F, Fischer EW (1992) Segmental Motions of cis-Polyisoprene in the Bulk
State: Interpretation of Dielectric Relaxation Data Macromolecules
25: 816.
Publications 1991
J31. Zuniga I, Bahar I, Dodge R, Mattice WL
(1991) Molecular Dynamics Analysis of Transitions Between
Rotational Isomers in Polymethylene with Discrete Hydrogen Atoms J Chem Phys 95: 5348.
J30. Haliloglu T, Bahar I, Erman B (1991) Segmental Orientation in Poly(oxyethylene) Networks Comp
Polymer Science 1, 151.
J29. Bahar I,
Erman B, Monnerie L (1991) A Stochastic Treatment of Conformational Transitions
of Polymer Chains in the Sub-Rouse Regime Macromolecules 24: 3618.
J28. Bahar I,
Dodge R, Zuniga I, Mattice WL (1991) Configurational Statistics of Poly(dimethyl siloxane).
II. A New Rotational Isomeric State Approach Macromolecules 24:
2993,.
J27. Bahar I, Zuniga I, Dodge R,
Mattice WL (1991) Conformational Statistics of Poly (dimethyl siloxane).
I. Probability Distribution of Rotational Isomers from Molecular
Dynamics Simulations Macromolecules 24: 2986.
J26. Mattice WL, Zuniga
I, Dodge R, Bahar I (1991) Use of Molecular Dynamics Trajectories for the
Formulation of Statistical Weight Matrices for Chains with Symmetric
Threefold Rotation Potentials Comp Polymer Science 1, 35:
.
J25. Bahar I,
Mattice WL (1991) Bimodal Distribution of Relaxational Modes for the
Helix-Coil Transition in Poly(oxymethylene) Macromolecules 24: 877.
J24. Erman B, Haliloglu T, Bahar I, Mark JE
(1991) Segmental Orientation in Uniaxially Deformed Networks:
A Higher Order Approximation for Finite Chains at Large Deformations Macromolecules 24: 901.
Publications 1990
J23. Bahar I, Erman B, Kloczkowski A,
Mark JE (1990) A Lattice Model for Segmental Orientation in Deformed
Polymeric Networks.2. Effect of Chain Stiffness and Thermotropic
Interactions Macromolecules 23: 5341.
J22. Erman B, Bahar I, Kloczkowski A, Mark JE
(1990) A Lattice Model for Segmental Orientation in Deformed
Polymeric Networks.1. Contribution of Intermolecular Correlations Macromolecules 23: 5335.
J21. Kuntman
A, Baysal B, Bahar I (1990) Conformational Characteristics of Poly(ethyl methacrylate).
Dipole Moment Measurements and Calculations Macromolecules 23: 4959.
J20. Bahar I, Erman B,
Monnerie L (1990) Effect of Surrounding Medium on Intramolecular Conformational
Changes in Probe Molecules Macromolecules 23: 3805.
J19. Bahar I, Mattice WL
(1990) Efficient Calculation of the Intramolecular Contribution
to Orientational Autocorrelation Functions Using Dynamic Rotational
Isomeric State Theory Macromolecules 23: 2719.
J18. Bahar I, Erman B, Monnerie L (1990) Local Orientational Motions in Flexible Polymeric
Chains Macromolecules 23: 1174.
J17. Kloczkowski A, Mark JE, Bahar I, Erman
B (1990) A Closed Form Solution for the Internal Dynamics
of Polymer Chains: I. Bonds with Independent Rotational Potentials J Chem Phys 92: 4513.
Publications 1989
Publications 1988
Publications 1987
Publications 1986
Publications 1985
B1. Bahar I. (1985) Thermodynamics of Compatibility in Binary Polymeric
Mixtures in Polymer Blends and Mixtures, NATO
ASI Series E: 89, Martinus Nijhoff Publishers, Dordrecht, p.349.
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