Knowledge Resource Center for Ecological Environment in Arid Area
DOI | 10.1002/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
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ISSN | 0887-3585 |
EISSN | 1097-0134 |
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 |
推荐引用方式 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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