THE J-COUPLING RESTRAINED MOLECULAR MECHANICS (JRMM) PROTOCOL - AN EFFICIENT ALTERNATIVE FOR DERIVING DNA ENDOCYCLIC TORSION ANGLE CONSTRAINTS .2. EXPERIMENTAL APPLICATION OF THE JRMM PROTOCOL
Sl. Lam et Scf. Anyeung, THE J-COUPLING RESTRAINED MOLECULAR MECHANICS (JRMM) PROTOCOL - AN EFFICIENT ALTERNATIVE FOR DERIVING DNA ENDOCYCLIC TORSION ANGLE CONSTRAINTS .2. EXPERIMENTAL APPLICATION OF THE JRMM PROTOCOL, Journal of biomolecular structure & dynamics, 13(5), 1996, pp. 815-825
The J-coupling restrained molecular mechanics (JrMM) protocol, which c
orrelates deoxyribose endocyclic torsion angles and vicinal proton-pro
ton torsion angle phi(1'2') in Part I of this study, is demonstrated t
o be a viable alternative to efficiently derive the endocyclic torsion
angle constraints for the determination of the solution structures of
DNA molecules. Extensive testing demonstrating the validity of the Jr
MM-derived torsion angle constraints in the restrained molecular dynam
ics and energy minimization structural refinement processes is perform
ed theoretically using an energy-minimized B-DNA model and experimenta
lly using a DNA hexamer d(CGTACG)(2). The results show that only a 0.2
Angstrom difference exists between the RMSD values of the refined str
uctures using the ideal and the JrMM-derived endocyclic torsion angle
constraints. The JrMM-derived torsion angles are also determined to be
in good agreement with the torsion angles derived through the use of
the vicinal J-derived torsion angles. These results show that through
the use of reliably measured J(1'2') values and computer simulation me
thod, the endocyclic torsion angle constraints can be derived reliably
and efficiently. Thus the JrMM method serves as an alternative strate
gy to generate endocyclic torsion angle constraints for the determinat
ion of the solution structures of DNA molecules.