Molecular Dynamics Simulations in Protein-Protein Docking.

Autor:	Cieślak D; Laboratory of Plant Protein Phosphorylation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland., Kabelka I; Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden., Bartuzi D; Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden. damian.bartuzi@icm.uu.se.; Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland. damian.bartuzi@icm.uu.se.
Jazyk:	angličtina
Zdroj:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2024; Vol. 2780, pp. 91-106.
DOI:	10.1007/978-1-0716-3985-6_6
Abstrakt:	Concerted interactions between all the cell components form the basis of biological processes. Protein-protein interactions (PPIs) constitute a tremendous part of this interaction network. Deeper insight into PPIs can help us better understand numerous diseases and lead to the development of new diagnostic and therapeutic strategies. PPI interfaces, until recently, were considered undruggable. However, it is now believed that the interfaces contain "hot spots," which could be targeted by small molecules. Such a strategy would require high-quality structural data of PPIs, which are difficult to obtain experimentally. Therefore, in silico modeling can complement or be an alternative to in vitro approaches. There are several computational methods for analyzing the structural data of the binding partners and modeling of the protein-protein dimer/oligomer structure. The major problem with in silico structure prediction of protein assemblies is obtaining sufficient sampling of protein dynamics. One of the methods that can take protein flexibility and the effects of the environment into account is Molecular Dynamics (MD). While sampling of the whole protein-protein association process with plain MD would be computationally expensive, there are several strategies to harness the method to PPI studies while maintaining reasonable use of resources. This chapter reviews known applications of MD in the PPI investigation workflows. (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze:	MEDLINE
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