Experimentally observed conformation-dependent geometry and hidden strain in proteins
Experimentally observed conformation-dependent geometry and hidden strain in proteins
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DOI：
10.1002/pro.5560050719
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发表时间：
1996-07-01
期刊：
影响因子：
8
通讯作者：
Karplus, PA
中科院分区：
文献类型：
--
作者：
Karplus, PA
已经编制了一个数据库，记录了 70 种不同蛋白质（在 1.75 埃或更好的浓度下精炼）的肽构象和几何形状。对数据库中有序残基的分析表明，phi,psi 分布具有比通常观察到的更精细的结构。此外，有明确的证据表明，肽共价几何形状取决于构象，肽间 N-C α-C 键角与其标准值相差近 +/-5 度。观察到的与标准肽几何形状的偏差在人口稠密区域的边缘附近最大，这与这些构象中发生的应变一致。这种隐藏应变的最小化可能是蛋白质热稳定性的一个重要因素。这些描述平衡肽几何形状如何随构象变化的经验数据证实并扩展了量子力学计算，并且具有有助于蛋白质结构的理论和实验分析的预测价值。
A database has been compiled documenting the peptide conformations and geometries from 70 diverse proteins refined at 1.75 Angstrom or better. Analysis of the well-ordered residues within the database shows phi,psi-distributions that have more fine structure than is generally observed. Also, clear evidence is presented that the peptide covalent geometry depends on conformation, with the interpeptide N-C alpha-C bond angle varying by nearly +/-5 degrees from its standard value. The observed deviations from standard peptide geometry are greatest near the edges of well-populated regions, consistent with strain occurring in these conformations. Minimization of such hidden strain could be an important factor in thermostability of proteins. These empirical data describing how equilibrium peptide geometry varies as a function of conformation confirm and extend quantum mechanics calculations, and have predictive value that will aid both theoretical and experimental analyses of protein structure.