Introduction

This tutorial describes how to calculate the mechanical stiffness map for a given protein structure, using the coordinates in the native state as input. The map provides a measure of the effective resistance of all pairs of residues to increasing their inter-residue separation, in the context of the entire network.

This methodology can be successfully used for interpreting data from single molecule manipulation techniques results such as Single Molecule Force Spectroscopy (AFM) or optical tweezers. It may also be used for predicting the response to tension without performing expensive steered molecular dynamics simulations.

Theory and example of usage has been described in [EB08] and [MRK17].

Required Programs

Besides ProDy, the Matplotlib library and VMD program are required for some steps in this tutorial. IPython is highly recommended for interactive usage.

Getting Started

To follow this tutorial, you will not need any additional files.

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.

How to Cite

If you benefited from Mechanical Stiffness Calculations in your research, please cite the following paper:

[EB08]

Eyal E, Bahar I. Toward a Molecular Understanding of the Anisotropic Response of Proteins to External Forces: Insights from Elastic Network Models. Biophys. J. 2008 94:3424-34355.

[MRK17]

Mikulska-Ruminska K, Kulik A, Benadiba C, Bahar I, Dietler G, Nowak W. Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD. Sci. Rep. 2017 7:8852.