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Title: The Ramachandran Number: An Order Parameter for Protein Geometry

Abstract

Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as α-helices and β-sheets. Secondary structure is characterized by the local rotational state of the protein backbone, quantified by two dihedral angles called Øand Ψ. Particular types of secondary structure can generally be described by a single (diffuse) location on a two-dimensional plot drawn in the space of the angles Ø andΨ, called a Ramachandran plot. By contrast, a recently-discovered nanomaterial made from peptoids, structural isomers of peptides, displays a secondary-structure motif corresponding to two regions on the Ramachandran plot [Mannige et al., Nature 526, 415 (2015)]. In order to describe such 'higher-order' secondary structure in a compact way we introduce here a means of describing regions on the Ramachandran plot in terms of a single Ramachandran number, R, which is a structurally meaningful combination of Ø andΨ. We show that the potential applications of R are numerous: it can be used to describe the geometric content of protein structures, and can be used to draw diagrams that reveal, at a glance, the frequency of occurrence of regular secondary structures and disordered regions in large protein datasets. We propose that R might be used as an ordermore » parameter for protein geometry for a wide range of applications.« less

Authors:
 [1];  [1];  [1];  [2]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Foundry
  2. Russian Academy of Sciences (RAS), Moscow (Russian Federation). Inst. for Biological Instrumentation
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1379533
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 11; Journal Issue: 8; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Mannige, Ranjan V., Kundu, Joyjit, Whitelam, Stephen, and Permyakov, Eugene A. The Ramachandran Number: An Order Parameter for Protein Geometry. United States: N. p., 2016. Web. doi:10.1371/journal.pone.0160023.
Mannige, Ranjan V., Kundu, Joyjit, Whitelam, Stephen, & Permyakov, Eugene A. The Ramachandran Number: An Order Parameter for Protein Geometry. United States. doi:10.1371/journal.pone.0160023.
Mannige, Ranjan V., Kundu, Joyjit, Whitelam, Stephen, and Permyakov, Eugene A. Thu . "The Ramachandran Number: An Order Parameter for Protein Geometry". United States. doi:10.1371/journal.pone.0160023. https://www.osti.gov/servlets/purl/1379533.
@article{osti_1379533,
title = {The Ramachandran Number: An Order Parameter for Protein Geometry},
author = {Mannige, Ranjan V. and Kundu, Joyjit and Whitelam, Stephen and Permyakov, Eugene A.},
abstractNote = {Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as α-helices and β-sheets. Secondary structure is characterized by the local rotational state of the protein backbone, quantified by two dihedral angles called Øand Ψ. Particular types of secondary structure can generally be described by a single (diffuse) location on a two-dimensional plot drawn in the space of the angles Ø andΨ, called a Ramachandran plot. By contrast, a recently-discovered nanomaterial made from peptoids, structural isomers of peptides, displays a secondary-structure motif corresponding to two regions on the Ramachandran plot [Mannige et al., Nature 526, 415 (2015)]. In order to describe such 'higher-order' secondary structure in a compact way we introduce here a means of describing regions on the Ramachandran plot in terms of a single Ramachandran number, R, which is a structurally meaningful combination of Ø andΨ. We show that the potential applications of R are numerous: it can be used to describe the geometric content of protein structures, and can be used to draw diagrams that reveal, at a glance, the frequency of occurrence of regular secondary structures and disordered regions in large protein datasets. We propose that R might be used as an order parameter for protein geometry for a wide range of applications.},
doi = {10.1371/journal.pone.0160023},
journal = {PLoS ONE},
number = 8,
volume = 11,
place = {United States},
year = {Thu Aug 04 00:00:00 EDT 2016},
month = {Thu Aug 04 00:00:00 EDT 2016}
}

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Cited by: 2 works
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Works referenced in this record:

The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain
journal, April 1951

  • Pauling, L.; Corey, R. B.; Branson, H. R.
  • Proceedings of the National Academy of Sciences, Vol. 37, Issue 4, p. 205-211
  • DOI: 10.1073/pnas.37.4.205