DynDom: A Program to Determine Domains, Hinges Axes, and Hinge Bending Residues

Steven Hayward(steve@chem.rug.nl) Biophysical Chemistry, Department of Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

Introduction

DynDom is a program that determines protein domains, hinge axes and amino acid residues involved in the hinge bending.

You can use DynDom if you have two conformations of the same protein. These may be two X-ray structures, or structures generated from NMR distant contraints, or structures derived from simulation techniques such as molecular dynamics or normal mode analysis.

The application of DynDom provides a view of the conformational change that is easily understood. The conformational change may be quite complicated in detail, but by using DynDom you can visualize it as involving the movement of domains as quasi-rigid bodies.

DynDom allows you to visualize the domain motion in terms of the rotation of one domain relative to another. The program's output is designed for display with RasMol, although it is easy to alter for display with other molecular graphics software. Figure 1 depicts the domain motion that occurs upon substrate binding in citrate synthase as determined by DynDom.

Methodology

DynDom determines domains by looking for clusters of rotation vectors that describe the rotational aspect of the conformational change. These rotation vectors can also be viewed using RasMol as seen in Figure2 for bacteriophage T4 lysozyme. Clusters form dynamic domains which are then analysed for their interdomain motions to give hinges axes. Finally the residues involved in the hinge bending are deterimined.

Usage

DynDom is easy to use requiring the setting of basically only three parameters. Default values exist which have proved to give good results in a number of cases. It is fast, usually taking no more than a few seconds on a Silicon Graphics O2. More information can be found at the DynDom home page where also you can see some results from the application of DynDom to a number of cases. Although the name implies that it can only be applied to domain proteins, it can be applied equally well to smaller regions of proteins such as loops.

References

Main References:

S.Hayward, H.J.C.Berendsen,"Systematic Analysis of Domain Motions in Proteins from Conformational Change; New Results on Citrate Synthase and T4 Lysozyme" Proteins, 30, 144, 1998.

S.Hayward, A.Kitao, H.J.C.Berendsen,"Model-Free Methods of Analyzing Domain Motions in Proteins from Simulation: A Comparison of Normal Mode Analysis and Molecular Dynamics Simulation of Lysozyme"Proteins, 27, 425, 1997.

Application:

B.L.de Groot, S.Hayward, D.van Aalten, A.Amadei, H.J.C.Berendsen, "Domain Motions in Bacteriophage T4 Lysozyme; A Comparison between Molecular Dynamics and Crystallographic Data " Proteins, 31, 116, 1998.

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