Introduction

Release Notes

v2.4.1 series come with new and improved sequence, structure, and dynamics analysis features. See release notes for details.

How to Cite

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics
Bioinformatics 2014 30(18):2681-2683.

Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinformatics 2021 37(20):3657-3659.

Introduction¶

This tutorial shows how to use cryo-EM electron density data to perform elastic network model analysis as in [YZ20]. Electron density maps can be provided by the user or retrieved from the EMDB.

Cryo-electron microscopy (cryo-EM) is a type of transmission electron microscopy where the studied sample, e.g. protein solution, is rapidly frozen. In structural biology, single particle cryo-EM is gaining more and more popularity due to its advantage of allowing the observation of protein under near-native conditions at ever-improving resolution, and as a result, the structures of numerous mega-Dalton biomolecules are captured and stored in the form of cryo-EM density maps, with resolutions ranging from 2 to 100 Å.

Fitting all-atom structures to a density map is time-consuming, and sometimes not feasible due to low resolution. In addition, for the purpose of studying the dynamics, MD simulations of supercomplexes with atomic details are extremely computationally expensive. It is thus desirable to apply coarse-grained methods, for example the Anisotropic Network Model (ANM), to such data to study the “big motions” of molecular machines beyond the atomic level.

ProDy can be used for constructing a bead-and-spring model from cryo-EM data using a previously published algorithm ([TM94]), which can be used for ANM.

Required Programs¶

Latest version of ProDy is required.

Recommended Programs¶

We recommend a visualization program too, such as VMD.

Getting Started¶

To follow this tutorial, you will need the following files:

 31M Feb 29 20:20 2680.map
 31M Feb 29 20:20 2688.map
1.1M Feb 29 20:20 4a0v.pdb.gz
383K Feb 29 20:20 4uqj.pdb.gz
 12M Feb 29 20:20 EMD-1961.map
225K Feb 29 20:20 EMD-1961_mapped.pdb
231K Feb 29 20:20 EMD-1961.pdb
 55K Feb 29 20:20 EMD-2680_mapped.pdb
 78K Feb 29 20:20 EMD-2680.pdb
 57K Feb 29 20:20 EMD-2680_protein.pdb

We recommend that you will follow this tutorial by typing commands in an IPython session, e.g.:

$ ipython

or with pylab environment:

$ ipython --pylab

First, we will make necessary imports from ProDy and Matplotlib packages.

In [1]: from prody import *

In [2]: from pylab import *

In [3]: ion()

We have included these imports in every part of the tutorial, so that code copied from the online pages is complete. You do not need to repeat imports in the same Python session.

[YZ20]

Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps, Prog. Biophys. Mol. Biol. In Press 10.1016/j.pbiomolbio.2020.08.006.