ENZYME SPECIFICITY USING NORMAL MODE ANALYSIS

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We calculate normal modes of alpha-lytic protease, both for the wild type and for the M190A mutant, in order to investigate how internal vibrations in the enzyme might contribute to a characteristic feature of its catalytic specificity. While the wild type is highly specific for small substrates in its primary specificity pocket, the M190A mutant has a much broader specificity, catalyzing both large and small substrates. We hypothesize that for the atoms lining the walls of the specificity pocket, the wild-type normal modes have a more symmetric character, with the walls vibrating in phase, and the size of the pocket remaining relatively fixed. This is in agreement with previous X-ray crystallographic results. In contrast, we expect that the mutant modes have a more antiymmetric character, with the walls vibrating out of phase, and the pocket able to expand and contract. These results would suggest that the internal vibrations of a molecule may play a role in determining both binding and catalytic specificity. The use of resources has been very important for the detailed graphical analyses of our normal-mode results. An example of the types of calculations we make is that of the changes in active-site volume and surface area that take place as the protein structure is perturbed along each of its normal modes. These computationally-intensive calculations are made using an algorithm included in the Computer Graphics Labroatory's MidasPlus package. In addition to such calculations, we have used the CGL extensively for detailed three-dimensional rendering of both our crystallographic and modeled protein structures.