Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics.
Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics.
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球状蛋白质折叠、结构和动力学的新晶格模型的动态蒙特卡罗模拟。
DOI：
10.1016/0022-2836(91)80070-b
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发表时间：
1991
影响因子：
5.6
通讯作者：
Kolinski,A
中科院分区：
文献类型：
--
作者：
Skolnick,J;Kolinski,A
一个长期存在的分子生物学问题是从一级序列预测球状蛋白质的三级结构。在一个新的同时包括α和β-碳原子的24近邻蛋白质晶格模型的背景下，探索了折叠成独特的四元β桶、四螺旋束和模型α/β束的要求。研究了许多不同的情况，但形成独特的天然构象的共同要求是三级相互作用加上相对较小(但不是无关)的内在转动偏好的存在，该偏好从众多紧凑状态中选择出天然构象。当显式包含侧链时，许多构象具有与天然构象相同或略多的侧链接触数，正是局部固有的转动偏好产生了构象坍塌时的构象选择性。螺旋或β-Sheet二级结构的局部偏好可能与最终在天然构象中发现的二级结构不一致。β-蛋白、混合α/β-蛋白和螺旋束所需的内源转角密度分别为0.3%、2%和6%。此外，还考察了变构构象转变的理想化模型。折叠主要通过连续的现场组装机制进行，折叠要么在一个转角处开始，要么从孤立的螺旋或β链(在适当的情况下)开始。对于螺旋和β-蛋白质模型，使用完全不同的局部蒙特卡罗运动，在钻石晶格模拟中获得了类似的折叠路径。这有力地证明了这些结果是普遍的；也就是说，它们与晶格、蛋白质模型或蒙特卡罗动力学的特定实现无关。总体而言，这些同时表明，所有已知蛋白质基序的折叠可以在包括现实主干结构和理想化侧链的单一类型的晶格模型的背景下实现。
A long-standing problem of molecular biology is the prediction of globular protein tertiary structure from the primary sequence. In the context of a new, 24-nearest-neighbor lattice model of proteins that includes both α and β-carbon atoms, the requirements for folding to a unique four-member β-barrel, four-helix bundles and a model α/β-bundle have been explored. A number of distinct situations are examined, but the common requirements for the formation of a unique native conformation are tertiary interactions plus the presence of relatively small (but not irrelevant) intrinsic turn preferences that select out the native conformer from a manifold of compact states. When side-chains are explicitly included, there are many conformations having the same or a slightly greater number of side-chain contacts as in the native conformation, and it is the local intrinsic turn preferences that produce the conformational selectivity on collapse. The local preference for helix or β-sheet secondary structure may be at odds with the secondary structure ultimately found in the native conformation. The requisite intrinsic turn populations are about 0·3% for β-proteins, 2% for mixed α/β-proteins and 6% for helix bundles. In addition, an idealized model of an allosteric conformational transition has been examined. Folding occurs predominantly by a sequential on-site assembly mechanism with folding initiating either at a turn or from an isolated helix or β-strand (where appropriate). For helical and β-protein models, similar folding pathways were obtained in diamond lattice simulations, using an entirely different set of local Monte Carlo moves. This argues strongly that the results are universal; that is, they are independent of lattice, protein model or the particular realization of Monte Carlo dynamics. Overall, these simultaneous demonstrate that the folding of all known protein motifs can be achieved in the context of a single class of lattice models that includes realistic backbone structures and idealized side-chains.
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球状蛋白质折叠/展开途径的动态蒙特卡罗模拟。
影响因子：
5.6
作者：
Skolnick,J;Kolinski,A
通讯作者：
Kolinski,A
水溶液中蛋白质肽片段的构象：对蛋白质折叠起始的影响。
影响因子：
2.9
作者：
Wright,PE;Dyson,HJ;Lerner,RA
通讯作者：
Lerner,RA
影响因子：
5.6
作者：
DYSON, HJ;RANCE, M;WRIGHT, PE
通讯作者：
WRIGHT, PE
DOI：
--
发表时间：
1988
影响因子：
11.1
作者：
T. Creighton
通讯作者：
T. Creighton
配位数对聚合物链晶格模型动力学的影响
影响因子：
5.5
作者：
J. Downey;J. Kovac
通讯作者：
J. Kovac