理解β-发夹结构的形成。
Understanding beta-hairpin formation.
作者信息
Dinner A R, Lazaridis T, Karplus M
机构信息
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
出版信息
Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9068-73. doi: 10.1073/pnas.96.16.9068.
Abstract
The kinetics of formation of protein structural motifs (e.g., alpha-helices and beta-hairpins) can provide information about the early events in protein folding. A recent study has used fluorescence measurements to monitor the folding thermodynamics and kinetics of a 16-residue beta-hairpin. In the present paper, we obtain the free energy surface and conformations involved in the folding of an atomistic model for the beta-hairpin from multicanonical Monte Carlo simulations. The results suggest that folding proceeds by a collapse that is downhill in free energy, followed by rearrangement to form a structure with part of the hydrophobic cluster; the hairpin hydrogen bonds propagate outwards in both directions from the partial cluster. Such a folding mechanism differs from the published interpretation of the experimental results, which is based on a helix-coil-type phenomenological model.
摘要
蛋白质结构基序（如α-螺旋和β-发夹）的形成动力学可以提供有关蛋白质折叠早期事件的信息。最近的一项研究使用荧光测量来监测一个16残基β-发夹的折叠热力学和动力学。在本文中，我们通过多正则蒙特卡罗模拟获得了β-发夹原子模型折叠过程中涉及的自由能面和构象。结果表明，折叠过程通过自由能下降的塌缩进行，随后重排形成具有部分疏水簇的结构；发夹氢键从部分簇向两个方向向外传播。这种折叠机制与基于螺旋-卷曲型唯象模型对实验结果的已发表解释不同。
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本文引用的文献
1
Protein Folding: A Perspective from Theory and Experiment.蛋白质折叠：理论与实验视角
Angew Chem Int Ed Engl. 1998 Apr 20;37(7):868-893. doi: 10.1002/(SICI)1521-3773(19980420)37:7<868::AID-ANIE868>3.0.CO;2-H.
2
Discrimination of the native from misfolded protein models with an energy function including implicit solvation.利用包含隐式溶剂化的能量函数区分天然蛋白质模型与错误折叠的蛋白质模型。
J Mol Biol. 1999 May 7;288(3):477-87. doi: 10.1006/jmbi.1999.2685.
3
Effective energy function for proteins in solution.溶液中蛋白质的有效能量函数。
Proteins. 1999 May 1;35(2):133-52. doi: 10.1002/(sici)1097-0134(19990501)35:2<133::aid-prot1>3.0.co;2-n.
4
Multicanonical ensemble: A new approach to simulate first-order phase transitions.多正则系综：一种模拟一级相变的新方法。
Phys Rev Lett. 1992 Jan 6;68(1):9-12. doi: 10.1103/PhysRevLett.68.9.
5
Fast events in protein folding: the time evolution of primary processes.蛋白质折叠中的快速事件：初级过程的时间演化
Annu Rev Phys Chem. 1998;49:173-202. doi: 10.1146/annurev.physchem.49.1.173.
6
Reversible peptide folding in solution by molecular dynamics simulation.通过分子动力学模拟实现溶液中可逆肽折叠
J Mol Biol. 1998 Jul 31;280(5):925-32. doi: 10.1006/jmbi.1998.1885.
7
A statistical mechanical model for beta-hairpin kinetics.一种用于β-发夹动力学的统计力学模型。
Proc Natl Acad Sci U S A. 1998 May 26;95(11):5872-9. doi: 10.1073/pnas.95.11.5872.
8
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Science. 1997 Dec 12;278(5345):1928-31. doi: 10.1126/science.278.5345.1928.
9
Folding dynamics and mechanism of beta-hairpin formation.β-发夹形成的折叠动力学与机制
Nature. 1997 Nov 13;390(6656):196-9. doi: 10.1038/36626.
10
The Levinthal paradox: yesterday and today.莱文索尔悖论：过去与现在。
Fold Des. 1997;2(4):S69-75. doi: 10.1016/s1359-0278(97)00067-9.
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