Flexibility of the furanose ring in nucleic acids: a compilation of crystal data

Binding of 2'-amino-2'-deoxycytidine-5'-triphosphate to norovirus polymerase induces rearrangement of the active site

Crystal structures of a genogroup II.4 human norovirus polymerase bound to an RNA primer-template duplex and the substrate analogue 2'-amino-2'-deoxycytidine-5'-triphosphate have been determined to 1.8 A resolution. The alteration of the substrate-binding site that is required to accommodate the 2'-amino group leads to a rearrangement of the polymerase active site and a disruption of the coordination shells of the active-site metal ions. The mode of binding seen for 2'-amino-2'-deoxycytidine-5'-triphosphate suggests a novel molecular mechanism of inhibition that may be exploited for the design of inhibitors targeting viral RNA polymerases.

Conformational studies of nucleic acids. II. The conformational energetics of commonly occurring nucleosides

We have examined the conformational energetics of the eight most commonly occurring nucleosides--A, U, G, C, dA, dT, dG, dC--as monitored by a semi-empirical energy force field. These are the first reported calculations to completely explore the entire conformational spaces available to all eight major nucleosides using experimentally consistent furanose geometries and an appropriate force field. Central to our approach is the ability to model an experimentally reasonable furanose for each nucleoside directly from only one parameter, the phase angle of pseudorotation P, as described in the previous paper (D.A. Pearlman, and S.-H. Kim, preceeding paper in this issue). This allows us to specify the conformation of a nucleoside by three variables: torsion angle gamma (O5'-C5'-C4'-C3'); torsion angle chi (O4'-C1'-N9/N1-C4/C2); and P. In our study each of these parameters was allowed to vary independently and in small increments over the range 0-360 degrees. The empirically observed preferences for C3'-endo and C2'-endo sugar conformations, for anti and syn values of chi and for staggered (g+, t, g-) values of gamma can be explained on the basis of the energy maps so obtained. Finer details, such as the different conformational preferences of ribonucleosides and deoxyribonucleosides and of purines and pyrimidines, can also be extracted from these maps and are consistent with experiment. The calculations support previous descriptions of pseudorotation as hindered. Statistical Boltzmann population factors for different conformational ranges in gamma, chi, and P, as predicted by the calculations, are consistent with factors obtained from crystallographic data. The excellent results here provide additional support for the suitability of the new sugar modeling technique used.

Flexibility of 3',5' deoxyribonucleoside diphosphates

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.