computer modeling in molecular biology.pdf

104 E. Westhof; C. Rubin-Carrez, and K Fritsch5.1 IntroductionAn understanding of the functional mechanism of a biological macromolecule requiresthe knowledge not only of its precise molecular organization in space but alsoof its internal dynamics. Molecular modelling attempts to construct the three-dimensionalstructure of a macromolecule on the basis of the experimental as well astheoretical data available on a particular macromolecule and on the family to whichit belongs. The validity, the scope, and the predictive power of the model obtainedwill depend on the nature of the experimental observations collected (X-ray diffraction,sequence data, biochemical and chemical information, . . .). High-resolutionX-ray crystallographic analysis (diffraction data at 1.5 to 1.0 A resolution) yields awealth of unequalled structural information on the crystallized macromolecule.However, this requires not only the crystallization of the macromolecule but also thesolution to the phase problem. Generally, with biological macromolecules, the problemis compounded by their size and complexity. Besides, nucleic acids are very difficultto crystallize, since they are highly charged macromolecules which, in case ofRNA molecules, can undergo spontaneous cleavages, In addition, when large,nucleic acids, especially RNAs, often exchange between various base pairings andfoldings.5.2 Relevance of Molecular DynamicsSimulationsThe very fact that X-ray crystallography produces well-defined structures, characterizedby a set of coordinates, fosters a rather rigid and static view of macromolecules.On the other hand, various spectroscopic methods (especially nuclear magneticresonance and fluorescence methods) and hydrogen exchange studies provide ampleevidence for motions of various frequencies and amplitudes in macromolecules insolution. Nevertheless, X-ray diffraction can contribute to our knowledge of smallscaledynamic properties of proteins and nucleic acids. This advance was made possibleby the development of refinement methods [l], which allow the precise determinationof atomic coordinates and of the atomic Debye-Waller factors (B-factorsor thermal parameters). Indeed, atoms with thermal motions have their contributionsto the intensities of the diffracted X-rays reduced by an exponential factorwhich depends on the Debye-Waller parameter and on the resolution. This Debye-Waller parameter itself depends on the mean-square displacement of the atom, i. e.the mean of the squares of the differences between all positions occupied by the atom