Joint-based description of protein structure: its application to the geometric characterization of membrane proteins

Abstract A macroscopic description of a protein structure allows an understanding of the protein conformations in a more simplistic manner. Here, a new macroscopic approach that utilizes the joints of the protein secondary structures as a basic descriptor for the protein structure is proposed and ap...

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Autores principales:	Jayaraman Thangappan, Sangwook Wu, Sun-Gu Lee
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7443853ae4814ebda5ff6b535c720161
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spelling	oai:doaj.org-article:7443853ae4814ebda5ff6b535c7201612021-12-02T15:05:08ZJoint-based description of protein structure: its application to the geometric characterization of membrane proteins10.1038/s41598-017-01011-z2045-2322https://doaj.org/article/7443853ae4814ebda5ff6b535c7201612017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-01011-zhttps://doaj.org/toc/2045-2322Abstract A macroscopic description of a protein structure allows an understanding of the protein conformations in a more simplistic manner. Here, a new macroscopic approach that utilizes the joints of the protein secondary structures as a basic descriptor for the protein structure is proposed and applied to study the arrangement of secondary structures in helical membrane proteins. Two types of dihedral angle, Ω and λ, were defined based on the joint points of the transmembrane (TM) helices and loops, and employed to analyze 103 non-homologous membrane proteins with 3 to 14 TM helices. The Ω-λ plot, which is a distribution plot of the dihedral angles of the joint points, identified the allowed and disallowed regions of helical arrangement. Analyses of consecutive dihedral angle patterns indicated that there are preferred patterns in the helical alignment and extension of TM proteins, and helical extension pattern in TM proteins is varied as the size of TM proteins increases. Finally, we could identify some symmetric protein pairs in TM proteins under the joint-based coordinate and 3-dimensional coordinates. The joint-based approach is expected to help better understand and model the overall conformational features of complicated large-scale proteins, such as membrane proteins.Jayaraman ThangappanSangwook WuSun-Gu LeeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jayaraman Thangappan Sangwook Wu Sun-Gu Lee Joint-based description of protein structure: its application to the geometric characterization of membrane proteins
description	Abstract A macroscopic description of a protein structure allows an understanding of the protein conformations in a more simplistic manner. Here, a new macroscopic approach that utilizes the joints of the protein secondary structures as a basic descriptor for the protein structure is proposed and applied to study the arrangement of secondary structures in helical membrane proteins. Two types of dihedral angle, Ω and λ, were defined based on the joint points of the transmembrane (TM) helices and loops, and employed to analyze 103 non-homologous membrane proteins with 3 to 14 TM helices. The Ω-λ plot, which is a distribution plot of the dihedral angles of the joint points, identified the allowed and disallowed regions of helical arrangement. Analyses of consecutive dihedral angle patterns indicated that there are preferred patterns in the helical alignment and extension of TM proteins, and helical extension pattern in TM proteins is varied as the size of TM proteins increases. Finally, we could identify some symmetric protein pairs in TM proteins under the joint-based coordinate and 3-dimensional coordinates. The joint-based approach is expected to help better understand and model the overall conformational features of complicated large-scale proteins, such as membrane proteins.
format	article
author	Jayaraman Thangappan Sangwook Wu Sun-Gu Lee
author_facet	Jayaraman Thangappan Sangwook Wu Sun-Gu Lee
author_sort	Jayaraman Thangappan
title	Joint-based description of protein structure: its application to the geometric characterization of membrane proteins
title_short	Joint-based description of protein structure: its application to the geometric characterization of membrane proteins
title_full	Joint-based description of protein structure: its application to the geometric characterization of membrane proteins
title_fullStr	Joint-based description of protein structure: its application to the geometric characterization of membrane proteins
title_full_unstemmed	Joint-based description of protein structure: its application to the geometric characterization of membrane proteins
title_sort	joint-based description of protein structure: its application to the geometric characterization of membrane proteins
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/7443853ae4814ebda5ff6b535c720161
work_keys_str_mv	AT jayaramanthangappan jointbaseddescriptionofproteinstructureitsapplicationtothegeometriccharacterizationofmembraneproteins AT sangwookwu jointbaseddescriptionofproteinstructureitsapplicationtothegeometriccharacterizationofmembraneproteins AT sungulee jointbaseddescriptionofproteinstructureitsapplicationtothegeometriccharacterizationofmembraneproteins
_version_	1718388897032962048

Joint-based description of protein structure: its application to the geometric characterization of membrane proteins

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