Exploration of partially unfolded states of human alpha-lactalbumin by molecular dynamics simulation

Molecular dynamics simulations are used to probe the properties of nonnativ e states of the protein human alpha -lactalbumin (human alpha -LA) with a d etailed atomistic model in an implicit aqueous solvent environment. To samp le the conformational space, a biasing force is introduced that increases t he radius of gyration relative to the native state and generates a large nu mber of low-energy conformers that differ in terms of their root-mean-squar e deviation, for a given radius of gyration. The resulting structures are r elaxed by unbiased simulations and used as models of the molten globule and partly denatured states of human alpha -LA, based on measured radii of gyr ation obtained from nuclear magnetic resonance experiments. The ensembles o f structures agree in their overall properties with experimental data avail able for the human alpha -LA molten globule and its more denatured states. In particular, the simulation results show that the native-like fold of the alpha -domain is preserved in the molten globule. Further, a considerable proportion of the antiparallel beta -strand in the beta -domain are present . This indicates that the lack of hydrogen exchange protection found experi mentally for the beta -domain is due to rearrangement of the beta -sheet in volving transient populations of non-native beta -structures. The simulatio ns also provide details concerning the ensemble of structures that contribu te as the molten globule unfolds and shows, in accord with experimental dat a, that unfolding is not cooperative; i.e. the various structural elements do not unfold simultaneously. (C) 2001 Academic Press.