FLEXIBLE-GEOMETRY CONFORMATIONAL ENERGY MAPS FOR THE AMINO-ACID RESIDUE PRECEDING A PROLINE
FLEXIBLE-GEOMETRY CONFORMATIONAL ENERGY MAPS FOR THE AMINO-ACID RESIDUE PRECEDING A PROLINE
复制标题
DOI：
10.1002/bip.360321104
复制
发表时间：
1992-11-01
期刊：
影响因子：
2.9
通讯作者：
MATTHEWS, BW
中科院分区：
文献类型：
--
作者：
HURLEY, JH;MASON, DA;MATTHEWS, BW
先前计算的构象能量图表明，脯氨酸之前的残基的α-螺旋构象是不利的，相对于超过7千卡/摩尔的扩展构象。然而，在已知的蛋白质结构中，观察到约9%的脯氨酸发生这种构象。此外，在蛋白质和肽中理论上不利的位置处引入或去除脯氨酸可以对稳定性和结构具有适度的影响。为了研究计算和实验之间的差异，我们确定了脯氨酸的构象如何影响计算的能量。我们还探讨了键长和键角弛豫对构象能图的影响。发现前一个残基的构象能不受脯氨酸构象的影响，但允许共价键松弛的效果是戏剧性的。如果键长和角度，和二面角内的吡咯烷环，被允许放松，α和β构象之间的计算能量差为1.1千卡/摩尔，在合理的协议与实验。计算的能量表面的详细形状也与已知蛋白质结构中观察到的构象分布非常一致。
Previously calculated conformational energy maps suggest that the alpha-helical conformation for the residue preceding a proline is disfavored relative to the extended conformation by more than 7 kcal/mol. In known protein structures this conformation is observed, however, to occur for about 9% of all prolines. In addition, introduction or removal of prolines at theoretically unfavorable positions in proteins and peptides can have modest effects on stability and structure. To investigate the discrepancy between calculation and experiment, we have determined how the conformation of the proline affects the calculated energy. We have also explored the effect of bond length and bond angle relaxation on the conformational energy map. The conformational energy of the preceding residue is found to be unaffected by the conformation of the proline, but the effect of allowing covalent bond relaxation is dramatic. If bond lengths and angles, and dihedral angles within the pyrrolidine ring, are allowed to relax, a calculated energy difference between the alpha and beta conformations of 1.1 kcal/mol is obtained, in reasonable agreement with experiment. The detailed shape of the calculated energy surface is also in excellent agreement with the observed conformational distributions in known protein structures.