Disallowed Ramachandran conformations of amino acid residues in protein structures

Journal of Molecular Biology
K GunasekaranP Balaram

Abstract

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were characterized on the basis of their backbone dihedral angles (phi, psi). Residues falling outside the defined "broad allowed limits" on the Ramachandran map were chosen and the reported B-factor value of the alpha-carbon atom was used to further select well defined disallowed conformations. The conformations of the selected 66 disallowed residues clustered in distinct regions of the Ramachandran map indicating that specific phi, psi angle distortions are preferred under compulsions imposed by local constraints. The distribution of various amino acid residues in the disallowed residue data set showed a predominance of small polar/charged residues, with bulky hydrophobic residues being infrequent. As a further check, for all the 66 cases non-hydrogen van der Waals short contacts in the protein structures were evaluated and compared with th...Continue Reading

Citations

Jul 29, 2009·Antioxidants & Redox Signaling·Merridee A WoutersNaomi L Haworth
May 6, 2008·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Bagautdin BagautdinovNaoki Kunishima
Feb 24, 2001·Protein Science : a Publication of the Protein Society·M C VegaL Serrano
Jun 4, 2013·Amino Acids·Pierrick CraveurJoseph Rebehmed
Mar 15, 2014·Journal of Biomolecular Structure & Dynamics·K M Saravanan, S Krishnaswamy
Jan 26, 1999·Journal of Molecular Biology·M E FraserW T Wolodko
Nov 13, 1998·Journal of Molecular Biology·T H TahirovI Kato
Sep 8, 2001·Journal of Molecular Biology·M López de la PazL Serrano
Jan 19, 2017·International Journal of Biological Macromolecules·Karthe Ponnuraj, Konda Mani Saravanan
Jan 12, 2002·Biopolymers·Debnath Pal, Pinak Chakrabarti
Jul 16, 2017·Protein Science : a Publication of the Protein Society·Neha NandwaniShachi Gosavi
Feb 11, 2003·Proteins·John B O Mitchell, James Smith
Nov 26, 2015·Science Advances·Andrew E Brereton, P Andrew Karplus
Jul 12, 2007·Proteins·Tulika PrakashSamir K Brahmachari
Oct 27, 2007·Protein Science : a Publication of the Protein Society·Jannette CareySara Linse
Nov 9, 2007·Chembiochem : a European Journal of Chemical Biology·Eduardo Vázquez-FigueroaAndreas S Bommarius
Jul 16, 2005·Proteins·Robert J AndersonXuliang Jiang
Jul 31, 2013·Acta Crystallographica. Section D, Biological Crystallography·Oliviero Carugo, Kristina Djinovic-Carugo
Dec 22, 1999·The Journal of Peptide Research : Official Journal of the American Peptide Society·V KrishnakumariR Nagaraj
Sep 16, 2005·The Journal of Biological Chemistry·Henryk J Korza, Matthias Bochtler
Dec 21, 2016·The Journal of Biological Chemistry·Frederick W JacobsenKannan Gunasekaran
Jan 31, 2003·Proteins·Simon C LovellDavid C Richardson
Aug 16, 2005·Biochemistry. Biokhimii︠a︡·A E SerovV I Tishkov
Feb 7, 2013·Journal of Biomolecular Structure & Dynamics·Ivan Yu TorshinVladimir G Tumanyan
Mar 22, 2013·Journal of Physics. Condensed Matter : an Institute of Physics Journal·L Olivares-Quiroz
Jun 29, 2013·Chemical Society Reviews·Andreas S Bommarius, Mariétou F Paye
May 13, 2017·IUBMB Life·Dinakar M Salunke, Deepak T Nair
Jul 21, 2011·Chemical Communications : Chem Comm·Damodara N ReddyErode N Prabhakaran
Jun 4, 2017·Journal of Biological Physics·Konda Mani Saravanan, Samuel Selvaraj
Jun 8, 2001·Progress in Biophysics and Molecular Biology·P Chakrabarti, D Pal
Mar 6, 2021·The Journal of Physical Chemistry. B·Ashraya RavikumarNarayanaswamy Srinivasan

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