The J-coupling restrained molecular mechanics (JrMM) protocol--an efficient alternative for deriving DNA endocyclic torsion angle constraints. Part I: Correlation of endocyclic torsion angles and vicinal torsion angle phi 1'2'.
An efficient alternative which makes use of the reliable 3J1'2' value to derive the endocyclic torsion angle constraints is proposed in this study. Based on the information embedded in the two plots, (i) the vicinal proton-proton J-couplings, 3J1'2', 3J1'2", 3J2'3', 3J2"3' and 3J3'4' against the pseudorotation phase angle, and (ii) 3J1'2", 3J2'3', 3J2"3' and 3J3'4' against 3J1'2'; using the calculated J-couplings obtained for a range of sugar geometries of deoxyribose ring in nucleosides and nucleotides encountered along the pseudorotation itinerary [J. van Wijk, B.D. Huckriede, J.H. Ippel and C. Altona, Methods Enzymol. 211, 286-306 (1992)], it is suggested that the vicinal 3J1'2' possesses structural information other than the vicinal torsion angle phi 1'2'. This study is divided into two parts. In Part I, a correlation diagram between the endocyclic torsion angles nu(i) (i = 0,1,2,3,4) and the restrained vicinal torsion angle phi 1'2' is obtained through the use of the J-coupling restrained molecular mechanics (JrMM) protocol. The established phi 1'2'-nu(i) correlation shows nu(i) can be deduced from the reliable 3J1'2' value and it forms the basis for developing an alternative protocol to derive endocyclic torsion angle constraints. In Part II of this series, extensive testing demonstrating the validity of the JrMM protocol to derive nu(i) for defining the sugar geometry of solution DNA molecules is presented.
Lam
S L
SL
Department of Chemistry, Chinese University of Hong Kong, Shatin, N.T., Hong Kong.
Au-Yeung
S C
SC
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D003853:Deoxyribonucleosides / Q000737:chemistry; D003855:Deoxyribose / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
D003853:Deoxyribonucleosides; D003855:Deoxyribose; D004247:DNA