Can we predict the structure, dynamics, and function of a protein merely from its polypeptide sequence? Theoretically yes, but it has been proven challenging in practice. Although we can’t solve the big question as a whole yet, we can break it down into smaller puzzles. We endeavor to understand the atomic basis of the thermostability and long-range communication of a two-domain protein, human Pin1.
We found that a peripheral mutation (Q33E) unexpectedly destabilized the WW domain of Pin1, an all β-sheet domain, despite the existing experimental and computational evidence suggesting it is a benign mutation. NMR studies attributed the thermostability loss to reorganizations of electrostatic and hydrophobic interactions, resulting in propagated conformational perturbations. Microsecond MD simulations suggested the wild type fold relied on couplings between a surface electrostatic network and a highly conserved hydrophobic core; Q33E directly perturbed the former, thereby disrupting the latter.
The cooperative conformational changes of Pin1 WW in response to Q33E coincided with its allosteric role. Previous studies suggest Pin1 WW regulates the activity of the catalytic domain by strengthening or weakening the interdomain contact upon various substrate binding. However, the atomic basis of such interdomain communication remains unclear. We used NMR to map out the broad interdomain surface and used MD simulations to identify atomic passages in correlation with four sets of interdomain distances. We then dissected the sub-conformations in the WW domain that correlated with the interdomain distances and used that as the reference to rationalize the interdomain conformation of S16E-Pin1, a mimic of the only phosphorylation modification at the substrate binding site. Finally, we speculated that the broad interdomain surface and the ability of Pin1 to adopt versatile interdomain conformations allowed Pin1 to accommodate various substrates and post-translational modifications.