Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-α transforming growth factor
Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-α transforming growth factor
复制标题
人α型转化生长因子分子动力学模拟中多肽骨架的曲轴运动
作者：
Addi Fadel;Danqing Jin;G. Montelione;R. Levy
通过分子动力学（MD）模拟人α型转化生长因子在水溶剂中的150 ps的分子动力学过程，计算了主链N−H和Cα−H键矢的序参量.两种“曲轴运动”的多肽骨架中观察到的MD轨迹。第一种是由于主链二面角φ i−1和φi的相关变化，刚性肽键发生小幅摇摆。与Cα−H键矢量相比，这些高频的“自由曲轴”运动与骨架N-H键矢量的运动序参数系统较小的值相关。此外，罕见的“曲轴翻转”的肽键从一个局部最小值到另一个观察到的几个氨基酸残基。这些分子动力学模拟表明，N-H和Cα-H序参数的比较提供了一个有用的方法来识别曲柄轴的蛋白质的librational运动。
SummaryOrder parameters for the backbone N−H and Cα−H bond vectors have been calculated from a 150 ps molecular dynamics (MD) simulation of human type-α transforming growth factor in H2O solvent. Two kinds of ‘crankshaft motions’ of the polypeptide backbone are observed in this MD trajectory. The first involves small-amplitude rocking of the rigid peptide bond due to correlated changes in the backbone dihedral angles ψi−1 and φi. These high-frequency ‘librational crankshaft’ motions are correlated with systematically smaller values of motional order parameters for backbone N−H bond vectors compared to Cα−H bond vectors. In addition, infrequent ‘crankshaft flips’ of the peptide bond from one local minimum to another are observed for several amino acid residues. These MD simulations demonstrate that comparisons of N−H and Cα−H order parameters provide a useful approach for identifying crank-shaft librational motions in proteins.
影响因子：
2.9
作者：
NICHOLSON, LK;KAY, LE;TORCHIA, DA
通讯作者：
TORCHIA, DA