THE J-COUPLING RESTRAINED MOLECULAR MECHANICS (JRMM) PROTOCOL - AN EFFICIENT ALTERNATIVE FOR DERIVING DNA ENDOCYCLIC TORSION ANGLE CONSTRAINTS .1. CORRELATION OF ENDOCYCLIC TORSION ANGLES AND VICINAL TORSION ANGLE PHI(1'2')
Sl. Lam et Scf. Auyeung, THE J-COUPLING RESTRAINED MOLECULAR MECHANICS (JRMM) PROTOCOL - AN EFFICIENT ALTERNATIVE FOR DERIVING DNA ENDOCYCLIC TORSION ANGLE CONSTRAINTS .1. CORRELATION OF ENDOCYCLIC TORSION ANGLES AND VICINAL TORSION ANGLE PHI(1'2'), Journal of biomolecular structure & dynamics, 13(5), 1996, pp. 803-814
An efficient alternative which makes use of the reliable 3J(1) (2) val
ue to derive the endocyclic torsion angle constraints is proposed in t
his study. Based on the information embedded in the two plots, (i) the
vicinal proton-proton J-couplings, 3J(1'2'), 3J(1'2 ''), 3J(2'3'), 3J
(2 '' 3') and 3J(3'4') against the pseudorotation phase angle, and (ii
) 3J(1'2 ''), 3J(2'3'), 3J(2 '' 3') and 3J(3'4') against 3J(1'2'); usi
ng 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 3J(1'2') possesses structural information other than
the vicinal torsion angle phi(1'2'). This study is divided into two pa
rts. In Part I, a correlation diagram between the endocyclic torsion a
ngles nu(i), (i=0,1,2,3,4) and the restrained vicinal torsion angle ph
i(1'2') is obtained through the use of the J-coupling restrained molec
ular mechanics (JrMM) protocol. The established phi(1'2')-nu(i) correl
ation shows nu(i) can be deduced from the reliable 3J(1'2') value and
it forms the basis for developing an alternative protocol to derive en
docyclic torsion angle constraints. In Part II of this series, extensi
ve testing demonstrating the validity of the JrMM protocol to derive n
u(i) for defining the sugar geometry of solution DNA molecules is pres
ented.