Cargando…

A global map of the protein shape universe

Proteins are involved in almost all functions in a living cell, and functions of proteins are realized by their tertiary structures. Obtaining a global perspective of the variety and distribution of protein structures lays a foundation for our understanding of the building principle of protein struc...

Descripción completa

Detalles Bibliográficos
Autores principales: Han, Xusi, Sit, Atilla, Christoffer, Charles, Chen, Siyang, Kihara, Daisuke
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6481876/
https://www.ncbi.nlm.nih.gov/pubmed/30978181
http://dx.doi.org/10.1371/journal.pcbi.1006969
_version_ 1783413805673349120
author Han, Xusi
Sit, Atilla
Christoffer, Charles
Chen, Siyang
Kihara, Daisuke
author_facet Han, Xusi
Sit, Atilla
Christoffer, Charles
Chen, Siyang
Kihara, Daisuke
author_sort Han, Xusi
collection PubMed
description Proteins are involved in almost all functions in a living cell, and functions of proteins are realized by their tertiary structures. Obtaining a global perspective of the variety and distribution of protein structures lays a foundation for our understanding of the building principle of protein structures. In light of the rapid accumulation of low-resolution structure data from electron tomography and cryo-electron microscopy, here we map and classify three-dimensional (3D) surface shapes of proteins into a similarity space. Surface shapes of proteins were represented with 3D Zernike descriptors, mathematical moment-based invariants, which have previously been demonstrated effective for biomolecular structure similarity search. In addition to single chains of proteins, we have also analyzed the shape space occupied by protein complexes. From the mapping, we have obtained various new insights into the relationship between shapes, main-chain folds, and complex formation. The unique view obtained from shape mapping opens up new ways to understand design principles, functions, and evolution of proteins.
format Online
Article
Text
id pubmed-6481876
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-64818762019-05-07 A global map of the protein shape universe Han, Xusi Sit, Atilla Christoffer, Charles Chen, Siyang Kihara, Daisuke PLoS Comput Biol Research Article Proteins are involved in almost all functions in a living cell, and functions of proteins are realized by their tertiary structures. Obtaining a global perspective of the variety and distribution of protein structures lays a foundation for our understanding of the building principle of protein structures. In light of the rapid accumulation of low-resolution structure data from electron tomography and cryo-electron microscopy, here we map and classify three-dimensional (3D) surface shapes of proteins into a similarity space. Surface shapes of proteins were represented with 3D Zernike descriptors, mathematical moment-based invariants, which have previously been demonstrated effective for biomolecular structure similarity search. In addition to single chains of proteins, we have also analyzed the shape space occupied by protein complexes. From the mapping, we have obtained various new insights into the relationship between shapes, main-chain folds, and complex formation. The unique view obtained from shape mapping opens up new ways to understand design principles, functions, and evolution of proteins. Public Library of Science 2019-04-12 /pmc/articles/PMC6481876/ /pubmed/30978181 http://dx.doi.org/10.1371/journal.pcbi.1006969 Text en © 2019 Han et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Han, Xusi
Sit, Atilla
Christoffer, Charles
Chen, Siyang
Kihara, Daisuke
A global map of the protein shape universe
title A global map of the protein shape universe
title_full A global map of the protein shape universe
title_fullStr A global map of the protein shape universe
title_full_unstemmed A global map of the protein shape universe
title_short A global map of the protein shape universe
title_sort global map of the protein shape universe
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6481876/
https://www.ncbi.nlm.nih.gov/pubmed/30978181
http://dx.doi.org/10.1371/journal.pcbi.1006969
work_keys_str_mv AT hanxusi aglobalmapoftheproteinshapeuniverse
AT sitatilla aglobalmapoftheproteinshapeuniverse
AT christoffercharles aglobalmapoftheproteinshapeuniverse
AT chensiyang aglobalmapoftheproteinshapeuniverse
AT kiharadaisuke aglobalmapoftheproteinshapeuniverse
AT hanxusi globalmapoftheproteinshapeuniverse
AT sitatilla globalmapoftheproteinshapeuniverse
AT christoffercharles globalmapoftheproteinshapeuniverse
AT chensiyang globalmapoftheproteinshapeuniverse
AT kiharadaisuke globalmapoftheproteinshapeuniverse