Beta atomic contacts: identifying critical specific contacts in protein binding interfaces.

Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous studi...

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Autores principales:	Qian Liu, Chee Keong Kwoh, Steven C H Hoi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/97a5a867c3234637b2fe14e3edb6eb83
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id	oai:doaj.org-article:97a5a867c3234637b2fe14e3edb6eb83
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spelling	oai:doaj.org-article:97a5a867c3234637b2fe14e3edb6eb832021-11-18T07:48:36ZBeta atomic contacts: identifying critical specific contacts in protein binding interfaces.1932-620310.1371/journal.pone.0059737https://doaj.org/article/97a5a867c3234637b2fe14e3edb6eb832013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23630569/?tool=EBIhttps://doaj.org/toc/1932-6203Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous studies. These definitions neglect the nearby atomic organization of contact atoms, and thus detect predominant contacts which are interrupted by other atoms. It is questionable whether such kinds of interrupted contacts are as important as other contacts in protein binding. To tackle this challenge, we propose a new definition called beta (β) atomic contacts. Our definition, founded on the β-skeletons in computational geometry, requires that there is no other atom in the contact spheres defined by two contact atoms; this sphere is similar to the van der Waals spheres of atoms. The statistical analysis on a large dataset shows that β contacts are only a small fraction of conventional distance-based contacts. To empirically quantify the importance of β contacts, we design βACV, an SVM classifier with β contacts as input, to classify homodimers from crystal packing. We found that our βACV is able to achieve the state-of-the-art classification performance superior to SVM classifiers with distance-based contacts as input. Our βACV also outperforms several existing methods when being evaluated on several datasets in previous works. The promising empirical performance suggests that β contacts can truly identify critical specific contacts in protein binding interfaces. β contacts thus provide a new model for more precise description of atomic organization in protein quaternary structures than distance-based contacts.Qian LiuChee Keong KwohSteven C H HoiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 4, p e59737 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Qian Liu Chee Keong Kwoh Steven C H Hoi Beta atomic contacts: identifying critical specific contacts in protein binding interfaces.
description	Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous studies. These definitions neglect the nearby atomic organization of contact atoms, and thus detect predominant contacts which are interrupted by other atoms. It is questionable whether such kinds of interrupted contacts are as important as other contacts in protein binding. To tackle this challenge, we propose a new definition called beta (β) atomic contacts. Our definition, founded on the β-skeletons in computational geometry, requires that there is no other atom in the contact spheres defined by two contact atoms; this sphere is similar to the van der Waals spheres of atoms. The statistical analysis on a large dataset shows that β contacts are only a small fraction of conventional distance-based contacts. To empirically quantify the importance of β contacts, we design βACV, an SVM classifier with β contacts as input, to classify homodimers from crystal packing. We found that our βACV is able to achieve the state-of-the-art classification performance superior to SVM classifiers with distance-based contacts as input. Our βACV also outperforms several existing methods when being evaluated on several datasets in previous works. The promising empirical performance suggests that β contacts can truly identify critical specific contacts in protein binding interfaces. β contacts thus provide a new model for more precise description of atomic organization in protein quaternary structures than distance-based contacts.
format	article
author	Qian Liu Chee Keong Kwoh Steven C H Hoi
author_facet	Qian Liu Chee Keong Kwoh Steven C H Hoi
author_sort	Qian Liu
title	Beta atomic contacts: identifying critical specific contacts in protein binding interfaces.
title_short	Beta atomic contacts: identifying critical specific contacts in protein binding interfaces.
title_full	Beta atomic contacts: identifying critical specific contacts in protein binding interfaces.
title_fullStr	Beta atomic contacts: identifying critical specific contacts in protein binding interfaces.
title_full_unstemmed	Beta atomic contacts: identifying critical specific contacts in protein binding interfaces.
title_sort	beta atomic contacts: identifying critical specific contacts in protein binding interfaces.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/97a5a867c3234637b2fe14e3edb6eb83
work_keys_str_mv	AT qianliu betaatomiccontactsidentifyingcriticalspecificcontactsinproteinbindinginterfaces AT cheekeongkwoh betaatomiccontactsidentifyingcriticalspecificcontactsinproteinbindinginterfaces AT stevenchhoi betaatomiccontactsidentifyingcriticalspecificcontactsinproteinbindinginterfaces
_version_	1718422926980546560

Beta atomic contacts: identifying critical specific contacts in protein binding interfaces.

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