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A novel approach to computer simulation of protein-protein complex formation

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Published in:Doklady. Biochemistry and Biophysics vol. 427, no. 1 (Aug 2009), p. 215
Main Author: Kovalenko, I B
Other Authors: Abaturova, A M, Riznichenko, G Yu, Rubin, A B
Published:
Springer Nature B.V.
Subjects:
Computer Simulation
Diffusion
Models, Molecular
Probability
Protein Binding
Proteins > chemistry
Proteins > metabolism
Static Electricity
Molecules
Simulation
Molecular biology
Studies
Online Access:Citation/Abstract
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Abstract:  In this work, the authors developed a new method for determination of binding areas in proteins and precomplex structure with allowance for the Brownian diffusion and electrostatic interactions of proteins that occur when proteins approach one another. This method significantly simplies subsequent precise simulation and prediction of the final complex structure. The Brownian dynamics method, which can be used for predicting the structure of protein complexes, considers the interaction of only two molecules in solution. A characteristic feature and novelty of the method, as is shown below, is the possibility to use it for studying interaction of several protein molecules simultaneously. This makes it possible to simulate the formation of a large number of complexes, which takes place in solution or cell compartments and to monitor the real-time kinetics of this process.
ISSN:1607-6729
1608-3091
DOI:10.1134/S1607672909040127
Source:Science Database