Scaling laws for folding native protein structures
文献类型：期刊论文
| 作者 | Jiang, F |
| 刊名 | SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS
 |
| 出版日期 | 2005 |
| 卷号 | 6期号:7页码:860 |
| 关键词 | SECONDARY STRUCTURE DATABASE PREDICTION SCOP |
| ISSN号 | 1468-6996 |
| 通讯作者 | Jiang, F (reprint author), Chinese Acad Sci, Inst Phys, Beijing Natl Lab Condensed Matter Phys, POB 603, Beijing 100080, Peoples R China. |
| 中文摘要 | We propose a nucleation hypothesis for protein folding. Based on this hypothesis, we have designed a new nearest-neighbor method for the prediction of protein secondary structures, in which the reliability of each prediction is estimated based on sequence conservation and clustering in the databases of known structures. We have found that predictions with higher reliability scores were indeed correlated with a higher predictive accuracy. We also found that by selecting the top 20% of residues based on reliability scores as nucleation residues, a clear pattern emerged where hydrophobic amino acids were largely buried and hydrophilic amino acids were more exposed. This was consistent with the widely accepted HP-model for protein folding. These results were true for several databases, such as PDBSELECT (< 25% sequence homology), SCOP-ASTRAL (< 25% sequence homology), and SCOP-ASTRAL unique fold classes, with 1300, 3956, and 762 proteins, respectively. Therefore, it is conceivable that the nucleation residues function not only as initiation sites for folding, but also as the core residues playing a primary role in determining the protein (thermodynamic) stability. The occurrence of these two functions on one set of amino acid residues in a protein is perhaps from the result of biological evolution. Finally, we have found power law behaviors in our results, whose scaling properties were modeled using polymer physics and critical phenomena. It is concluded that proteins behave like a real chain. A new physical picture for protein folding derived from our nucleation hypothesis has been described, in which there are two continuous phase transitions corresponding to the two stages of protein folding: one is nucleation and the other collapse. By determining the critical exponents of these two-phase transitions, it has been found that the nucleation process has a spatial dimension of d=3 while the collapse process of d=2. (c) 2005 Elsevier Ltd. All rights reserved. |
| 收录类别 | SCI |
| 语种 | 英语 |
| 公开日期 | 2013-09-24 |
| 源URL | [http://ir.iphy.ac.cn/handle/311004/52317]  |
| 专题 | 物理研究所_物理所公开发表论文_物理所公开发表论文_期刊论文 |
| 推荐引用方式 GB/T 7714 | Jiang, F. Scaling laws for folding native protein structures[J]. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS,2005,6(7):860. |
| APA | Jiang, F.(2005).Scaling laws for folding native protein structures.SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS,6(7),860. |
| MLA | Jiang, F."Scaling laws for folding native protein structures".SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 6.7(2005):860. |
入库方式： OAI收割
来源：物理研究所
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