Pattabiraman N, Langridge R
Computer Graphics Laboratory, School of Pharmacy, University of California 94143.
J Biomol Struct Dyn. 1985 Feb;2(4):683-92. doi: 10.1080/07391102.1985.10506316.
In 3',5' deoxyribonucleoside diphosphates, in addition to the nature of the base and the sugar puckering, there are six single bond rotations. However, from the analysis of crystal structure data on the constituents of nucleic acids, only three rotational angles, that are about glycosyl bond, about C4'-C5' and about C3'-O3' bonds, are flexible. For a given sugar puckering and a base, potential energy calculations using non-bonded, electrostatic and torsional functions were carried out by varying the three torsion angles. The energies are represented as isopotential energy surfaces. Since the availability of the real-time color graphics, it is possible to analyse these isopotential energy surfaces. The calculations were carried out for C3' exo and C3' endo puckerings for deoxyribose and also for four bases. These calculations throw more light not only on the allowed regions for the three rotational angles but also on the relationships among them. The dependence of base and the puckering of the sugar on these rotational angles and thereby the flexibility of the 3',5' deoxyribonucleoside diphosphates is discussed. From our calculations, it is now possible to follow minimum energy path for interconversion among various conformers.
在3'，5' - 脱氧核糖核苷二磷酸中，除了碱基的性质和糖的构象外，还有六个单键旋转。然而，通过对核酸成分的晶体结构数据进行分析，只有三个旋转角度是灵活的，即围绕糖苷键、围绕C4'-C5'键和围绕C3'-O3'键的旋转角度。对于给定的糖构象和碱基，通过改变这三个扭转角，利用非键合、静电和扭转函数进行了势能计算。能量以等势能面表示。由于有实时彩色图形，因此可以分析这些等势能面。对脱氧核糖的C3'外式和C3'内式构象以及四种碱基都进行了计算。这些计算不仅揭示了三个旋转角度的允许区域，还揭示了它们之间的关系。讨论了碱基和糖的构象对这些旋转角度的依赖性，从而讨论了3'，5' - 脱氧核糖核苷二磷酸的灵活性。根据我们的计算，现在可以追踪各种构象异构体之间相互转化的最低能量路径。
