Effects of compact volume and chain stiffness on the conformations of native proteins.
Effects of compact volume and chain stiffness on the conformations of native proteins.
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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
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发表时间：
1992
影响因子：
11.1
通讯作者：
Scheraga,HA
中科院分区：
文献类型：
--
作者：
Hao,MH;Rackovsky,S;Liwo,A;Pincus,MR;Scheraga,HA
报道了从晶体结构观察到的蛋白质天然构象统计特性的研究。根据键向量相关函数和分子体积分析蛋白质构象。据观察，虽然蛋白质结构的体积随残基数量几乎呈线性变化，但键向量相关函数对所有大小的蛋白质表现出普遍特征。为了定量解释天然蛋白质结构的键向量相关函数的性质，对特定但任意氨基酸序列的真实多肽链进行了蒙特卡罗模拟。该分子被限制在由其链长决定的椭圆体体积中，并且排除了不同氨基酸残基之间具有不可接受的非键接触的构象。通过对其 phi-psi 空间进行能量偏置采样，考虑了末端封闭的单个残基内的相互作用，该残基将链中两个最近邻的肽基相关联。发现模拟的链相关函数与长度相似的β-折叠型和混合型（α+β）蛋白质的晶体结构非常一致。基于这些计算，得出的结论是，观察到的这些天然蛋白质的构象可能源于两个基本因素：疏水相互作用下结构的紧密性和由于每个末端封闭残基内的相互作用而导致的多肽链的内在刚性。
An investigation of the statistical properties of the native conformations of proteins, observed from crystal structures, is reported. Protein conformations were analyzed in terms of a bond vector correlation function and molecular volume. It was observed that, while the volume of a protein structure varies nearly linearly with the number of residues, the bond vector correlation function exhibits a universal feature for all sizes of proteins. To interpret the nature of the bond vector correlation function of native protein structures quantitatively, Monte Carlo simulations of realistic polypeptide chains of specific but arbitrary amino acid sequence were carried out. The molecule was constrained in an ellipsoidal volume determined by its chain length, and conformations with unacceptable nonbonded contacts between different amino acid residues were excluded. The interactions within a terminally blocked single residue, which correlate two nearest-neighbor peptide groups in a chain, were taken into account by an energetically biased sampling of its phi-psi space. The simulated chain correlation functions were found to be in good agreement with those of the crystal structures of beta-sheet-type and mixed-type (alpha+beta) proteins of similar length. On the basis of these calculations, it is concluded that the observed conformations of these native proteins may arise from two basic factors: the compactness of structures under hydrophobic interactions and the intrinsic stiffness of polypeptide chains due to the interactions within each terminally blocked residue.