Statistical Thermodynamics of Protein Folding: Comparison of a Mean-Field Theory with Monte Carlo Simulations
Statistical Thermodynamics of Protein Folding: Comparison of a Mean-Field Theory with Monte Carlo Simulations
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蛋白质折叠的统计热力学：平均场理论与蒙特卡罗模拟的比较
DOI：
10.1063/1.468920
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发表时间：
1994
影响因子：
4.4
通讯作者：
H. Scheraga
中科院分区：
文献类型：
--
作者：
M. Hao;H. Scheraga
报道了分别用解析理论和计算机模拟对蛋白质折叠进行的比较研究。该理论基于一种改进的平均场形式，除了通常的平均场近似外，它还考虑了构象态子集中的能量分布。蛋白质序列特有的性质在理论上由两组变量参数化，一组用于平均场相互作用的能量学，另一组用于能量分布。对具有不同序列、不同链长和不同相互作用势的模型多肽进行了模拟，范围从对某些局部链态(键角和扭转角)的强烈偏向到完全没有局部构象偏好。对模型多肽的模拟结果的理论分析揭示了从统计卷曲状态到致密球状状态的折叠转变中的三种不同类型的行为，包括合作双态转变、连续折叠和玻璃样转变。结果表明，在不同电势下，通过对不同多肽的理论参数进行拟合，平均场理论可以较准确地描述不同多肽的热力学性质和折叠行为。通过比较理论描述和模拟结果，我们验证了理论的基本假设，从而对蛋白质的折叠跃迁有了新的认识。研究发现，模型多肽的一阶折叠转变的协同性主要由长程相互作用决定，特别是偶极取向；局部相互作用(如键角和扭角势)对折叠的协同特性影响很小，但对蛋白质折叠的最低能结构和未折叠构象之间的能量差有很大影响。
A comparative study of protein folding with an analytical theory and computer simulations, respectively, is reported. The theory is based on an improved mean-field formalism which, in addition to the usual mean-field approximations, takes into account the distributions of energies in the subsets of conformational states. Sequence-specific properties of proteins are parameterized in the theory by two sets of variables, one for the energetics of mean-field interactions and one for the distribution of energies. Simulations are carried out on model polypeptides with different sequences, with different chain lengths, and with different interaction potentials, ranging from strong biases towards certain local chain states (bond angles and torsional angles) to complete absence of local conformational preferences. Theoretical analysis of the simulation results for the model polypeptides reveals three different types of behavior in the folding transition from the statistical coiled state to the compact globular state; these include a cooperative two-state transition, a continuous folding, and a glass-like transition. It is found that, with the fitted theoretical parameters which are specific for each polypeptide under a different potential, the mean-fields theory can describe the thermodynamic properties and folding behavior of the different polypeptides accurately. By comparing the theoretical descriptions with simulation results, we verify the basic assumptions of the theory and, thereby, obtain new insights about the folding transitions of proteins. It is found that the cooperativity of the first-order folding transition of the model polypeptides is determined mainly by long-range interactions, in particular the dipolar orientation; the local interactions (e.g. bond-angle and torsion-angle potentials) have only a marginal effect on the cooperative characteristic of the folding, but have a large impact on the difference in energy between the folded lowest-energy structure and the unfolded conformations of a protein.
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。
影响因子：
5.6
作者：
Skolnick,J;Kolinski,A
通讯作者：
Kolinski,A
紧凑体积和链刚度对天然蛋白质构象的影响。
DOI：
10.1073/pnas.89.14.6614
发表时间：
1992
影响因子：
11.1
作者：
Hao,MH;Rackovsky,S;Liwo,A;Pincus,MR;Scheraga,HA
通讯作者：
Scheraga,HA
DOI：
10.1073/pnas.89.19.9029
发表时间：
1992-10-01
影响因子：
11.1
作者：
GOLDSTEIN, RA;LUTHEYSCHULTEN, ZA;WOLYNES, PG
通讯作者：
WOLYNES, PG