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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]
+ Show Author Affiliations
  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 Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1379533
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
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.
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Mannige, Ranjan V., Kundu, Joyjit, Whitelam, Stephen, & Permyakov, Eugene A. The Ramachandran Number: An Order Parameter for Protein Geometry. United States. https://doi.org/10.1371/journal.pone.0160023
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Mannige, Ranjan V., Kundu, Joyjit, Whitelam, Stephen, and Permyakov, Eugene A. Thu . "The Ramachandran Number: An Order Parameter for Protein Geometry". United States. https://doi.org/10.1371/journal.pone.0160023. https://www.osti.gov/servlets/purl/1379533.
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@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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https://doi.org/10.1371/journal.pone.0160023
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The structure of a centrosymmetric protein crystal
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Describing intrinsically disordered proteins at atomic resolution by NMR
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  • Current Opinion in Structural Biology, Vol. 23, Issue 3
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α-Sheet:  The Toxic Conformer in Amyloid Diseases?
journal, September 2006

  • Daggett, Valerie
  • Accounts of Chemical Research, Vol. 39, Issue 9
  • DOI: 10.1021/ar0500719

Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins
journal, June 2014

  • Mittal, Anuradha; Lyle, Nicholas; Harmon, Tyler S.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 8
  • DOI: 10.1021/ct5002297

Conformational Entropy of Intrinsically Disordered Protein
journal, April 2013

  • Chong, Song-Ho; Ham, Sihyun
  • The Journal of Physical Chemistry B, Vol. 117, Issue 18
  • DOI: 10.1021/jp401049h

Structure of Collagen
journal, August 1954

  • Ramachandran, G. N.; Kartha, G.
  • Nature, Vol. 174, Issue 4423
  • DOI: 10.1038/174269c0

The Structure of Collagen
journal, November 1955

  • Rich, Alexander; Crick, F. H. C.
  • Nature, Vol. 176, Issue 4489
  • DOI: 10.1038/176915a0

Peptoid nanosheets exhibit a new secondary-structure motif
journal, October 2015

  • Mannige, Ranjan V.; Haxton, Thomas K.; Proulx, Caroline
  • Nature, Vol. 526, Issue 7573
  • DOI: 10.1038/nature15363

Free-floating ultrathin two-dimensional crystals from sequence-specific peptoid polymers
journal, April 2010

  • Nam, Ki Tae; Shelby, Sarah A.; Choi, Philip H.
  • Nature Materials, Vol. 9, Issue 5
  • DOI: 10.1038/nmat2742

Targeted editing and evolution of engineered ribosomes in vivo by filtered editing
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Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads
journal, July 2015

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  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep11740

Structural characterization of intrinsically disordered proteins by the combined use of NMR and SAXS
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Exchange-correlation functional with broad accuracy for metallic and nonmetallic compounds, kinetics, and noncovalent interactions
journal, October 2005

  • Zhao, Yan; Schultz, Nathan E.; Truhlar, D. G.
  • The Journal of Chemical Physics, Vol. 123, Issue 16
  • DOI: 10.1063/1.2126975

Pauling and Corey's  -pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease
journal, July 2004

  • Armen, R. S.; DeMarco, M. L.; Alonso, D. O. V.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 32
  • DOI: 10.1073/pnas.0401781101

Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
journal, July 2013

  • Das, R. K.; Pappu, R. V.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 33
  • DOI: 10.1073/pnas.1304749110

The discovery of the  -helix and  -sheet, the principal structural features of proteins
journal, September 2003

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

The Pleated Sheet, A New Layer Configuration of Polypeptide Chains
journal, May 1951

  • Pauling, L.; Corey, R. B.
  • Proceedings of the National Academy of Sciences, Vol. 37, Issue 5
  • DOI: 10.1073/pnas.37.5.251

Objectively judging the quality of a protein structure from a Ramachandran plot
journal, January 1997

Biopython: freely available Python tools for computational molecular biology and bioinformatics
journal, March 2009

PolyprOnline: polyproline helix II and secondary structure assignment database
journal, January 2014

A series of PDB related databases for everyday needs
journal, November 2010

  • Joosten, R. P.; te Beek, T. A. H.; Krieger, E.
  • Nucleic Acids Research, Vol. 39, Issue Database
  • DOI: 10.1093/nar/gkq1105

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures
journal, December 2013

  • Fox, Naomi K.; Brenner, Steven E.; Chandonia, John-Marc
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1240

Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution
journal, October 1994

Data and computation transformations for multiprocessors
conference, January 1995

  • Anderson, Jennifer M.; Amarasinghe, Saman P.; Lam, Monica S.
  • Proceedings of the fifth ACM SIGPLAN symposium on Principles and practice of parallel programming - PPOPP '95
  • DOI: 10.1145/209936.209954

Protein Folds in the All-β and All-α Classes
journal, June 1997

Phosphorylated peptide of G protein-coupled receptor induces dimerization in activated arrestin
text, January 2020

Structural Characterization of Intrinsically Disordered Proteins by NMR Spectroscopy
journal, September 2013

Dynamic New World: Refining Our View of Protein Structure, Function and Evolution
journal, March 2014

What’s in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered
journal, January 2013

  • Dunker, A. Keith; Babu, M. Madan; Barbar, Elisar
  • Intrinsically Disordered Proteins, Vol. 1, Issue 1
  • DOI: 10.4161/idp.24157

PeptideBuilder: A simple Python library to generate model peptides
journal, January 2013

  • Tien, Matthew Z.; Sydykova, Dariya K.; Meyer, Austin G.
  • PeerJ, Vol. 1
  • DOI: 10.7717/peerj.80
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