Paper Citing NAMD - Abstract
Paliwal, A.; Asthagiri, D.; Bossev, D.P.; Paulaitis, M.E.
Pressure denaturation of staphylococcal nuclease studied by neutron small-angle scattering and molecular simulation
BIOPHYSICAL JOURNAL, 87:3479-3492, NOV 2004
We studied the pressure-induced folding/unfolding transition of staphylococcal nuclease (SN) over a pressure range of similar to1-3 kilobars at 25degreesC by small-angle neutron scattering and molecular dynamics simulations. We find that applying pressure leads to a twofold increase in the radius of gyration derived from the small-angle neutron scattering spectra, and P(r), the pair distance distribution function, broadens and shows a transition from a unimodal to a bimodal distribution as the protein unfolds. The results indicate that the globular structure of SN is retained across the folding/unfolding transition although this structure is less compact and elongated relative to the native structure. Pressure-induced unfolding is initiated in the molecular dynamics simulations by inserting water molecules into the protein interior and applying pressure. The P(r) calculated from these simulations likewise broadens and shows a similar unimodal-to-bimodal transition with increasing pressure. The simulations also reveal that the bimodal P(r) for the pressure-unfolded state arises as the protein expands and forms two subdomains that effectively diffuse apart during initial stages of unfolding. Hydrophobic contact maps derived from the simulations show that water insertions into the protein interior and the application of pressure together destabilize hydrophobic contacts between these two subdomains. The findings support a mechanism for the pressure-induced unfolding of SN in which water penetration into the hydrophobic core plays a central role.
