Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

TitleDeciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.
Publication TypeJournal Article
Year of Publication2014
AuthorsKoromyslova, A. D., A. O. Chugunov, and R. G. Efremov
JournalJ Chem Inf Model
Volume54
Issue4
Pagination1189-99
Date Published2014 Apr 28
ISSN1549-960X
KeywordsHydrophobic and Hydrophilic Interactions, Protein Conformation, Proteins, Static Electricity, Structure-Activity Relationship
Abstract

Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

DOI10.1021/ci500158y
Alternate JournalJ Chem Inf Model
PubMed ID24689707
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