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Geometric and statistical properties of the mean-field hydrophobic-polar model, the large-small model, and real protein sequences
Shih, CT; Su, ZY; Gwan, JF; Hao, BL; Hsieh, CH; Lo, JL; Lee, HC; Shih, CT , Natl Ctr High Performance Comp, Hsinchu, Taiwan.
2002
发表期刊PHYSICAL REVIEW E
ISSN1539-3755
卷号65期号:4页码:-
摘要Lattice models, for their coarse-grained nature, are best suited for the study of the "designability problem," the phenomenon in which most of the about 16 000 proteins of known structure have their native conformations concentrated in a relatively small number of about 500 topological classes of conformations. Here it is shown that on a lattice the most highly designable simulated protein structures are those that have the largest number of surface-core switchbacks. A combination of physical, mathematical, and biological reasons that causes the phenomenon is given. By comparing the most foldable model peptides with protein sequences in the Protein Data Bank, it is shown that whereas different models may yield similar designabilities, predicted foldable peptides will simulate natural proteins only when the model incorporates the correct physics and biology, in this case if the main folding force arises from the differing hydrophobicity of the residues, but does not originate, say, from the steric hindrance effect caused by the differing sizes of the residues.
部门归属Natl Ctr High Performance Comp, Hsinchu, Taiwan; Forschungszentrum Julich, Forum Modellierung, D-52425 Julich, Germany; Acad Sinica, Inst Theoret Phys, Beijing 100080, Peoples R China; Natl Cent Univ, Dept Phys, Chungli 32054, Taiwan; Natl Cent Univ, Dept Life Sci, Chungli 32054, Taiwan; Stanford Univ, Dept Phys, Stanford, CA 94305 USA; Tunghai Univ, Dept Phys, Taichung 40704, Taiwan
关键词Globular-proteins Aqueous-solution Folding Funnels Amino-acids Designability Transition Stability Polymers Peptide Design
学科领域Physics
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收录类别SCI
WOS记录号WOS:000175146400097
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被引频次:12[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/13562
专题理论物理所1978-2010年知识产出
通讯作者Shih, CT , Natl Ctr High Performance Comp, Hsinchu, Taiwan.
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Shih, CT,Su, ZY,Gwan, JF,et al. Geometric and statistical properties of the mean-field hydrophobic-polar model, the large-small model, and real protein sequences[J]. PHYSICAL REVIEW E,2002,65(4):-.
APA Shih, CT.,Su, ZY.,Gwan, JF.,Hao, BL.,Hsieh, CH.,...&Shih, CT , Natl Ctr High Performance Comp, Hsinchu, Taiwan..(2002).Geometric and statistical properties of the mean-field hydrophobic-polar model, the large-small model, and real protein sequences.PHYSICAL REVIEW E,65(4),-.
MLA Shih, CT,et al."Geometric and statistical properties of the mean-field hydrophobic-polar model, the large-small model, and real protein sequences".PHYSICAL REVIEW E 65.4(2002):-.
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