Literature DB >> 21538644

Revisiting the Ramachandran plot from a new angle.

Alice Qinhua Zhou1, Corey S O'Hern, Lynne Regan.   

Abstract

The pioneering work of Ramachandran and colleagues emphasized the dominance of steric constraints in specifying the structure of polypeptides. The ubiquitous Ramachandran plot of backbone dihedral angles (ϕ and ψ) defined the allowed regions of conformational space. These predictions were subsequently confirmed in proteins of known structure. Ramachandran and colleagues also investigated the influence of the backbone angle τ on the distribution of allowed ϕ/ψ combinations. The "bridge region" (ϕ ≤ 0° and -20° ≤ ψ ≤ 40°) was predicted to be particularly sensitive to the value of τ. Here we present an analysis of the distribution of ϕ/ψ angles in 850 non-homologous proteins whose structures are known to a resolution of 1.7 Å or less and sidechain B-factor less than 30 Ų. We show that the distribution of ϕ/ψ angles for all 87,000 residues in these proteins shows the same dependence on τ as predicted by Ramachandran and colleagues. Our results are important because they make clear that steric constraints alone are sufficient to explain the backbone dihedral angle distributions observed in proteins. Contrary to recent suggestions, no additional energetic contributions, such as hydrogen bonding, need be invoked.
Copyright © 2011 The Protein Society.

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Year:  2011        PMID: 21538644      PMCID: PMC3149190          DOI: 10.1002/pro.644

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  8 in total

1.  The Xplor-NIH NMR molecular structure determination package.

Authors:  Charles D Schwieters; John J Kuszewski; Nico Tjandra; G Marius Clore
Journal:  J Magn Reson       Date:  2003-01       Impact factor: 2.229

2.  Stereochemistry of polypeptide chain configurations.

Authors:  G N RAMACHANDRAN; C RAMAKRISHNAN; V SASISEKHARAN
Journal:  J Mol Biol       Date:  1963-07       Impact factor: 5.469

3.  Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints.

Authors:  Lauren L Porter; George D Rose
Journal:  Proc Natl Acad Sci U S A       Date:  2010-12-08       Impact factor: 11.205

4.  Role of amino acid properties to determine backbone tau(N-Calpha-C') stretching angle in peptides and proteins.

Authors:  S M Malathy Sony; K Saraboji; N Sukumar; M N Ponnuswamy
Journal:  Biophys Chem       Date:  2005-11-02       Impact factor: 2.352

5.  Bayesian statistical analysis of protein side-chain rotamer preferences.

Authors:  R L Dunbrack; F E Cohen
Journal:  Protein Sci       Date:  1997-08       Impact factor: 6.725

6.  Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units.

Authors:  C Ramakrishnan; G N Ramachandran
Journal:  Biophys J       Date:  1965-11       Impact factor: 4.033

7.  Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.

Authors:  J M Word; S C Lovell; J S Richardson; D C Richardson
Journal:  J Mol Biol       Date:  1999-01-29       Impact factor: 5.469

8.  Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

Authors:  J M Word; S C Lovell; T H LaBean; H C Taylor; M E Zalis; B K Presley; J S Richardson; D C Richardson
Journal:  J Mol Biol       Date:  1999-01-29       Impact factor: 5.469

  8 in total
  27 in total

1.  The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val.

Authors:  Alice Qinhua Zhou; Corey S O'Hern; Lynne Regan
Journal:  Biophys J       Date:  2012-05-15       Impact factor: 4.033

2.  Targeting the ubiquitin-conjugating enzyme E2D4 for cancer drug discovery-a structure-based approach.

Authors:  Vishwanath Ramatenki; Ramakrishna Dumpati; Rajender Vadija; Santhiprada Vellanki; Sarita Rajender Potlapally; Rohini Rondla; Uma Vuruputuri
Journal:  J Chem Biol       Date:  2016-12-24

3.  Parameterization and Analysis of Peptide-Based Catalysts for the Atroposelective Bromination of 3-Arylquinazolin-4(3H)-ones.

Authors:  Jennifer M Crawford; Elizabeth A Stone; Anthony J Metrano; Scott J Miller; Matthew S Sigman
Journal:  J Am Chem Soc       Date:  2018-01-10       Impact factor: 15.419

4.  Comment on "Revisiting the Ramachandran plot from a new angle".

Authors:  Lauren L Porter; George D Rose
Journal:  Protein Sci       Date:  2011-10-13       Impact factor: 6.725

5.  Intrinsic α-helical and β-sheet conformational preferences: a computational case study of alanine.

Authors:  Diego Caballero; Jukka Määttä; Alice Qinhua Zhou; Maria Sammalkorpi; Corey S O'Hern; Lynne Regan
Journal:  Protein Sci       Date:  2014-05-09       Impact factor: 6.725

6.  Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

Authors:  J C Gaines; S Acebes; A Virrueta; M Butler; L Regan; C S O'Hern
Journal:  Proteins       Date:  2018-02-26

7.  Natural selection based on coordination chemistry: computational assessment of [4Fe-4S]-maquettes with non-coded amino acids.

Authors:  Robert K Szilagyi; Rebecca Hanscam; Eric M Shepard; Shawn E McGlynn
Journal:  Interface Focus       Date:  2019-10-18       Impact factor: 3.906

Review 8.  Asymmetric Catalysis Mediated by Synthetic Peptides, Version 2.0: Expansion of Scope and Mechanisms.

Authors:  Anthony J Metrano; Alex J Chinn; Christopher R Shugrue; Elizabeth A Stone; Byoungmoo Kim; Scott J Miller
Journal:  Chem Rev       Date:  2020-09-24       Impact factor: 60.622

9.  New insights into the interdependence between amino acid stereochemistry and protein structure.

Authors:  Alice Qinhua Zhou; Diego Caballero; Corey S O'Hern; Lynne Regan
Journal:  Biophys J       Date:  2013-11-19       Impact factor: 4.033

10.  The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design.

Authors:  Matthew Carter Childers; Clare-Louise Towse; Valerie Daggett
Journal:  Protein Eng Des Sel       Date:  2016-06-09       Impact factor: 1.650

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