Case D A
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
J Biomol NMR. 1999 Oct;15(2):95-102. doi: 10.1023/a:1008349812613.
Ab initio MP2 and density functional quantum chemistry calculations are used to explore geometries and vibrational properties of N-methylacetamide and of the alanine dipeptide with backbone angles characteristic of helix and sheet regions in proteins. The results are used to explore one-bond direct dipolar couplings for the N-H, C alpha-H alpha, C'-N, and C alpha-C' bonds, as well as for the two-bond C'-H interaction. Vibrational averaging affects these dipolar couplings, and these effects can be expressed as effective bond lengths that are 0.5-3% larger than the true bond lengths; bending and torsion vibrations have a bigger influence on the effective coupling than do stretching vibrations. Because of zero-point motion, these effects are important even at low temperature. Hydrogen bonding interactions at the amide group also increase the N-H effective bond length. Although vibrational contributions to effective bond lengths are small, they can have a significant influence on the extraction of order parameters from relaxation data, and a knowledge of relative bond lengths is needed when several types of dipolar couplings are to be simultaneously used for refinement. The present computational results are compared to both solid- and liquid-state NMR experiments. The analysis suggests that secondary structural elements in many proteins may be more rigid than is commonly thought.
从头算MP2和密度泛函量子化学计算被用于探索N-甲基乙酰胺以及具有蛋白质中螺旋和折叠区域特征主链角的丙氨酸二肽的几何结构和振动性质。结果被用于探索N-H、Cα-Hα、C'-N和Cα-C'键以及两键C'-H相互作用的一键直接偶极耦合。振动平均化会影响这些偶极耦合，并且这些影响可以表示为比真实键长大约0.5%-3%的有效键长；弯曲和扭转振动对有效耦合的影响比拉伸振动更大。由于零点运动，即使在低温下这些影响也很重要。酰胺基团处的氢键相互作用也会增加N-H有效键长。尽管振动对有效键长的贡献很小，但它们可能对从弛豫数据中提取序参量有显著影响，并且当要同时使用几种偶极耦合进行精修时，需要了解相对键长。将目前的计算结果与固态和液态核磁共振实验进行了比较。分析表明许多蛋白质中的二级结构元件可能比通常认为的更刚性。
