Arid
DOI10.1002/prot.24384
Sparsely populated residue conformations in protein structures: Revisiting "experimental" Ramachandran maps
Kalmankar, Neha V.1,2; Ramakrishnan, C.1; Balaram, P.1
通讯作者Balaram, P.
来源期刊PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
ISSN0887-3585
EISSN1097-0134
出版年2014
卷号82期号:7页码:1101-1112
英文摘要

The Ramachandran map clearly delineates the regions of accessible conformational (phi-) space for amino acid residues in proteins. Experimental distributions of phi, values in high-resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely arid, fully allowed region in the top left quadrant establishes that side-chain and backbone interactions may provide the energetic compensation necessary for populating this region of phi- space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12) and the i + 1 position of Type II turns (Bin 13). Of the 516 non-Gly residues in Bin 13, 384 occupied the i + 1 position of Type II turns. Further examination of these turn segments revealed a high propensity to occur at the N-terminus of helices and as a tight turn in hairpins. The strand-helix motif with the Type II turn as a connecting element was also found in as many as 57 examples. Proteins 2014; 82:1101-1112. (c) 2013 Wiley Periodicals, Inc.


英文关键词Ramachandran map protein conformation secondary structural motifs amino acid conformational propensities Type II ’ beta turn
类型Article
语种英语
国家India
收录类别SCI-E
WOS记录号WOS:000337474700001
WOS关键词AMINO-ACIDS ; STEREOCHEMICAL CRITERIA ; GLOBULAR-PROTEINS ; PEPTIDE UNITS ; COIL-LIBRARY ; DATA-BANK ; PROPENSITIES ; POLYPEPTIDE ; BACKBONE ; PLOT
WOS类目Biochemistry & Molecular Biology ; Biophysics
WOS研究方向Biochemistry & Molecular Biology ; Biophysics
资源类型期刊论文
条目标识符http://119.78.100.177/qdio/handle/2XILL650/184495
作者单位1.Indian Inst Sci, Mol Biophys Unit, Bangalore 560012, Karnataka, India;
2.Tata Inst Fundamental Res, Natl Ctr Biol Sci, Bangalore 560065, Karnataka, India
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GB/T 7714
Kalmankar, Neha V.,Ramakrishnan, C.,Balaram, P.. Sparsely populated residue conformations in protein structures: Revisiting "experimental" Ramachandran maps[J],2014,82(7):1101-1112.
APA Kalmankar, Neha V.,Ramakrishnan, C.,&Balaram, P..(2014).Sparsely populated residue conformations in protein structures: Revisiting "experimental" Ramachandran maps.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,82(7),1101-1112.
MLA Kalmankar, Neha V.,et al."Sparsely populated residue conformations in protein structures: Revisiting "experimental" Ramachandran maps".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 82.7(2014):1101-1112.
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