computer modeling in molecular biology.pdf

128 E. WesthoL C. Rubin-Carrez, and K Fritschtacts, etc. insures at least that the structural model is precise. The accuracy of a modelcan only be assessed either by X-ray crystallography or a posteriori by the incentivesand new ideas it gave rise to, since energetical and stereochemical considerationsalone cannot be taken as proof. Whatever the approach, modelling has to be complementedby extensive directed mutagenesis for testing first its structural validityand, if a functional test is available, for appraising the structure-function relationshipsit suggests [52].Recently, Rippe et al. [53] presented experimental evidence for the formation ofa parallel-stranded double helix for the alternating sequence d(A, G). By gel electrophoresis,UV absorption and vacuum UV circular dichroism, they havedemonstrated the formation of a double helix with a parallel orientation for suchan alternating sequence. This experimental study was suggested by a model built onthe basis of molecular mechanics and dynamics calculations [54]. Minimizationresults displayed a pronounced dependence on the electrostatic parameters and leadto structures with several internal H-bonds between amino groups and anionicphosphate oxygens. The only ones conserved after a 50 ps molecular dynamics trajectorycorrespond to the guanine intrastrand H-bonds HN2 (G) . . . OP (G), alsopresent in the initial model. As discussed above, we tend to think that several (if notall) of the intra-residue (for G) or inter-residue (for A) H-bonds between aminogroups and anionic phosphate oxygens are artefacts of the force field and that, incase such interactions do exist, they are mediated instead by water bridges. This studyillustrates the difficulties resulting from a proper treatment of localized and bridgingwater molecules involving at least one charged group during minimization andmolecular dynamics simulations when using an implicit treatment of the solvent. Itis not yet clear whether the problem will be solved by using an explicit representationof the solvent.5.1 5 ConclusionsEven with the simplified representations presently used in molecular mechanics anddynamics simulations, detailed treatments at the atomic level are, for the time being,ruled out for handling the global folding of large nucleic acid molecules (above 100nucleotides). As discussed above, in programs based on force field calculations, themain problems reside in proper handling of the electrostatics and the solvation ofnucleic acids. Indeed, in all forms of nucleic acids, water molecules should be consideredas an integral part of the structure, since intra- and inter-residue waterbridges fulfill the hydrogen bonding capacity of the polar atoms, forming strings,spines, or filaments in which water molecules have enough reorientational mobilityfor additional screening of the phosphate charges [16]. However, molecular dynamics