Bahar Lab Spotlight, Publications, and Research news archive

James Krieger received the DCSB Best Postdoctoral Associate Award of the Year 2019. He was nominated by his mentor, Dr. Ivet Bahar. James is the one of three first authors in a seminal paper on the signature dynamics of proteins, Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity, published in Mol Biol Evol. Please click here for more information.

Dr. Luca Ponzoni received the "Best Postdoc Award at the Department of Computational & Systems Biology — Year 2018" at the Annual Departmental Retreat in recognition of his outstanding work on the evaluation of the functional impact of missense variants (see Ponzoni & Bahar, Proc Natl Acad Sci USA 2018)

(L Ponzoni & I Bahar, Carnegie Museum of Nat History, Retreat, 6/15/2018 )

She (John) Zhang has been selected to represent Pitt's graduate students during the 2018 Pitt Day in Harrisburg, PA. She will present a poster (pictured below) to state lawmakers.

She (John) Zhang has received the Best DCSB Student Award for 2017, for his structure-based study of chromosomal dynamics using elastic network models. Below is a photo during his speech, after receiving the award, at the annual CSB Retreat Banquet.

Cihan received the Best DCSB Student Award for 2016 for his work on developing multi-scale models and simulations for dopaminergic signaling. He aims at understanding the effect of spatial complexity and heterogeneity in the efficiency of dopamine (DA) reuptake. Below is a snapshot from his simulations, displaying the release of DA (red dots) from active zones on DA neurons (green).

John received the best poster award in the DCSB retreat in June 2016 for his work on the ENM analysis of chromosome contact maps determined by Hi-C experiment.

Hongchun received the Best DCSB Postdoc Award for 2016 for developing the iGNM database and oGNM server, published in Nucleic Acids Research. The upgraded iGNM 2.0 database provides a user-friendly interface for retrieving information on the dynamics of 95% of Protein Data Bank (PDB) structures as well as their biological assemblies. It helps assess which structural elements undergo large correlated fluctuations, and enable conformational changes that may be relevant to function.

An interview with Assistant Professor Mary Cheng, on her recent work on dopamine transporter dynamics, was published by Cell Press, highlighting her recent paper paper published in Structure (see Cheng MH, Bahar I (2015) Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter Structure pii: S0969-2126).

Dr. Bing Liu gave a poster presentation at the Postdoctoral Data & Dine Symposium on Tuesday, May 19, 2015 and won a $500 travel award. He presented his work on "TLR3-TLR7 pathway crosswalk confers innate immune memory and homeostasis."

Two outstanding Tsinghua University Research Scholars, Feizhuo Kaitlyn Hu and Wenzhi Mao have returned to their home institutions after successfully completing extensive research, resulting in several publications in the Bahar Lab. We wish them continued success on their scientific journeys!

Anindita Dutta's recent award for the "Outstanding Student Researcher in the Department of Computational & Systems Biology of 2012".

Congratulations to Lidio Meireles, Ying Liu, and Lin Liu on their successful defenses!

Lidio was first author on the Protein Science article that became the cover of the September 2011 issue, "Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins", along with lab members Dr. Mert Gur, Dr. Ahmet Bakan, and Dr. Ivet Bahar.

Ahmet Bakan's recent PNAS paper on drug binding mechanisms vs. intrinsic changes in shape(PDF).

and related commentaries: " Small molecule inhibitors: Another one bites the Dusp."

Zheng Yang's study on GroEL machinery became the cover illustration for Molecular Biosystems

Dr. Lee Wei Yang, a former graduate student has recieved the Stephen L. Phillips Award

...read interview

(click to see full image) "2007 Outstanding Student Researcher Award" : Basak Isin

Former student Lee-Wei Yang published article in Pitt magazine " Investigations: Explorations and revalations taking place in the medical school"

...view article

Publications 2019

The hybrid methodology, coMD, that we have recently developed [1] has been recently extended to construct the energy landscape near the functional states of LeuT (Fig 1) [2]. This is the first energy landscape constructed for this NSS family member.

The work of Mary Cheng and collaborators shed light into the modulation of dopaminergic signaling by targeting human dopamine transporter (hDAT). The comparison of the effects of binding dopamine (DA), amphetamine (AMPH), orphenadrine (ORPH) (repurposable drug) and cocaine to (DAT) showed that DA or AMPH drive a structural transition towards a functional form predisposed to translocate the ligand. In contrast, ORPH inhibits DAT function by arresting it in the outward-facing open conformation. Further assays show that that ORPH, like cocaine, alters DAT uptake and endocytosis.

Most recent study of Dr Gur. published in Biophys J is highlighted in Ricardo Baron's News & Notable, "Fast sampling of A-to-B Protein Global Conformational Transitions: From Galileo Galilei to Monte Carlo Anisotropic Network Modeling The new methodology, coMD, introduced by Gur et al is stated to "surely prompt new exciting routes to rapidly connect A to B, and vice versa."

"Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL." Yang, Z., Majek, P., & Bahar, I. (2009). PLoS Comput Biol. 5: e100360. PMID: 19381265.

"Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter." Gu, Y., Shrivastava, I. H., Amara, S. G., & Bahar, I. (2009). Proc Natl Acad Sci U.S.A.. 106: 2589-94. PMID: 19202063.

"Signal propagation in proteins and relation to equilibrium fluctuations." Chennubhotla C, Bahar I. PLoS Comput Biol. 2007 Sep 21;3(9):1716-26.

Normal Mode Analysis Book "Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation." Chennubhotla C, Bahar I., Tobi D. (2007) Curr Opin Struct Biol. 17:633-40.

Recent applications have shown the applicability of normal mode analysis (NMA) to macromolecular assemblies...

...find out more

Book Review in Briefings in Bioinformatics

"A Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter."

We focused on the dopamine-binding and –unbinding free energies of human dopamine transporter (hDAT) using advanced molecular dynamics methods and characterized the conformational spectrum of hDAT. Transition of apo hDAT from outward-facing to inward-facing state, and vice versa was studied, permitting us to generate for the first time a first estimate of the energy landscape of hDAT.

"Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies" Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar ISci Rep (2014) 4:6245. PMID: 25175563

Controlling ionizing radiation (IR)-induced cell death mitigates radiation damage. Examining tumor suppressor protein p53 network dynamics in response to IR damage found that the strength of p53 transcriptional activity and its coupling (or timing with respect) to mitochondrial pore opening are major determinants of cell fate.

"Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis" LaRusch J et al.PLoS Genetics (2014) 10:e1004376. PMID: 2503378

Bahar research featured in winter 2014/2015 issue of Pitt Med.

"Coupled Global and Local Changes Direct Substrate Translocation by Neurotransmitter-Sodium Symporter Ortholog LeuT" Cheng MH, Bahar I (2013) Biophys J. 105:630-639. PMID: 23931311

This is a first attempt to complete the molecular description of all steps involved in LeuT transport cycle. Notably, the secondary substrate-binding site S2, the functional relevance of which has been debated, appears to stably bind an alanine only when the transporter assumes an intermediate conformer close to inward-facing state.

Coupling between the translocation of alanines bound to S1 and S2

Cover Image Elia "Protonation of Glutamate-208 Induces the Release of Agmatine in an Outward-Facing Conformation of Arginine/Agmatine Antiporter." Zomot E, Bahar I. (2011) J Biol Chem. 286:19693-701. PMID: 21487006

Protein Science cover "Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter." Gu Y, Shrivastava IH, Amara SG, Bahar I. (2009) Proc Natl Acad Sci U S A. 106:2589-94