A new structural arrangement in proteins involving lysine NH3 + group and carbonyl

Abstract Screening of the Protein Data Bank led to identification of a recurring structural motif where lysine NH3 + group interacts with backbone carbonyl. This interaction is characterized by linear atom arrangement, with carbonyl O atom positioned on the three-fold symmetry axis of the NH3 + grou...

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Autores principales:	Olga N. Rogacheva, Sergei A. Izmailov, Lyudmila V. Slipchenko, Nikolai R. Skrynnikov
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b03b52b537194b319fa791b26d34bbf8
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spelling	oai:doaj.org-article:b03b52b537194b319fa791b26d34bbf82021-12-02T15:05:42ZA new structural arrangement in proteins involving lysine NH3 + group and carbonyl10.1038/s41598-017-16584-y2045-2322https://doaj.org/article/b03b52b537194b319fa791b26d34bbf82017-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-16584-yhttps://doaj.org/toc/2045-2322Abstract Screening of the Protein Data Bank led to identification of a recurring structural motif where lysine NH3 + group interacts with backbone carbonyl. This interaction is characterized by linear atom arrangement, with carbonyl O atom positioned on the three-fold symmetry axis of the NH3 + group (angle Cε-Nζ-O close to 180°, distance Nζ-O ca. 2.7-3.0 Å). Typically, this linear arrangement coexists with three regular hydrogen bonds formed by lysine NH3 + group (angle Cε-Nζ-acceptor atom close to 109°, distance Nζ-acceptor atom ca. 2.7-3.0 Å). Our DFT calculations using polarizable continuum environment suggest that this newly identified linear interaction makes an appreciable contribution to protein’s energy balance, up to 2 kcal/mol. In the context of protein structure, linear interactions play a role in capping the C-termini of α-helices and 310-helices. Of note, linear interaction involving conserved lysine is consistently found in the P-loop of numerous NTPase domains, where it stabilizes the substrate-binding conformation of the P-loop. Linear interaction NH3 + – carbonyl represents an interesting example of ion-dipole interactions that has so far received little attention compared to ion-ion interactions (salt bridges) and dipole-dipole interactions (hydrogen bonds), but nevertheless represents a distinctive element of protein architecture.Olga N. RogachevaSergei A. IzmailovLyudmila V. SlipchenkoNikolai R. SkrynnikovNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-8 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Olga N. Rogacheva Sergei A. Izmailov Lyudmila V. Slipchenko Nikolai R. Skrynnikov A new structural arrangement in proteins involving lysine NH3 + group and carbonyl
description	Abstract Screening of the Protein Data Bank led to identification of a recurring structural motif where lysine NH3 + group interacts with backbone carbonyl. This interaction is characterized by linear atom arrangement, with carbonyl O atom positioned on the three-fold symmetry axis of the NH3 + group (angle Cε-Nζ-O close to 180°, distance Nζ-O ca. 2.7-3.0 Å). Typically, this linear arrangement coexists with three regular hydrogen bonds formed by lysine NH3 + group (angle Cε-Nζ-acceptor atom close to 109°, distance Nζ-acceptor atom ca. 2.7-3.0 Å). Our DFT calculations using polarizable continuum environment suggest that this newly identified linear interaction makes an appreciable contribution to protein’s energy balance, up to 2 kcal/mol. In the context of protein structure, linear interactions play a role in capping the C-termini of α-helices and 310-helices. Of note, linear interaction involving conserved lysine is consistently found in the P-loop of numerous NTPase domains, where it stabilizes the substrate-binding conformation of the P-loop. Linear interaction NH3 + – carbonyl represents an interesting example of ion-dipole interactions that has so far received little attention compared to ion-ion interactions (salt bridges) and dipole-dipole interactions (hydrogen bonds), but nevertheless represents a distinctive element of protein architecture.
format	article
author	Olga N. Rogacheva Sergei A. Izmailov Lyudmila V. Slipchenko Nikolai R. Skrynnikov
author_facet	Olga N. Rogacheva Sergei A. Izmailov Lyudmila V. Slipchenko Nikolai R. Skrynnikov
author_sort	Olga N. Rogacheva
title	A new structural arrangement in proteins involving lysine NH3 + group and carbonyl
title_short	A new structural arrangement in proteins involving lysine NH3 + group and carbonyl
title_full	A new structural arrangement in proteins involving lysine NH3 + group and carbonyl
title_fullStr	A new structural arrangement in proteins involving lysine NH3 + group and carbonyl
title_full_unstemmed	A new structural arrangement in proteins involving lysine NH3 + group and carbonyl
title_sort	new structural arrangement in proteins involving lysine nh3 + group and carbonyl
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/b03b52b537194b319fa791b26d34bbf8
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A new structural arrangement in proteins involving lysine NH3 + group and carbonyl

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