Molecular dynamics as a tool to help design mutants

A 200 ps MD trajectory of wild type PCI and a 120 ps one for the Pro36Gly putative mutant are studied and compared with the structure of PCI in its complex with carboxypeptidase A (CPA). It is first established that the structures of PCI from X-ray and from MD simulation are essentially equal. Thereafter, data from the PCI-CPA and average MD structures together with available biochemical information are used to identify possible structural factors that may determine the inhibitory power of PCI. These structural determinants are used to analyze the mutant structure. The fold of the mutant protein shows a large degree of stability. The N-terminal tail in PCIm differs from the X-ray structure as it does in PCIw, while the mutant's C-terminal tail (which is the primary binding site with CPA) and residues 13–17 present deviations. Differences in fluctuation patterns exist between PCIm and PCIw in residues 2–4 (the N-terminal tail), 13–17, 22–23, 28–81 (the secondary contact site with CPA), and 37–38 (the C-terminal tail); the latter region is rigidified in PCIm. Results show that the MD method is able to sense long-range as well as local perturbative effects produced by amino-acid substitutions in flexible regions of this protein. The simulations suggest that the conformation of the C-terminal tail is less favorable for interaction with the target protein in the mutant than it is in the wild type protein. The Pro-36-Gly mutant is predicted to be a less potent inhibitor.Abbreviations CPA carboxypeptidase A - MD molecular dynamics - NIS non-inertial solvent - PCI potato carboxypeptidase A inhibitor - PCIm mutated inhibitor - PCIw wild inhibitor