title: Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants.
abstract: In this study, we examined the unfolding processes of native beta(2)-microglobulin and two related variants, one with an N-terminal hexapeptide deletion DeltaN6 and another with Lys57-Asp58 cleavage, by high-temperature molecular dynamics simulations. Three simulation models were used, molecular dynamics (MD) simulations with explicit water solvation, MD simulations with the CHARMM EEF1 force field and Langevin dynamics with the CHARMM EEF1 force field. Our simulations reproduce many of the experimentally observed structural changes. The most striking agreement is in the beta-strands to alpha-helix transition. In our simulations, strands beta(3), beta(4) and beta(5) consistently change to alpha-helix, whereas beta(8) changes to an alpha-helix only briefly. Through comparisons of the conformational behavior of the native, the DeltaN6 and the Lys-cut beta(2)-m, using the three simulation methods, we identified the consensus conformational changes that differentiate between the native beta(2)-m and its two variants. We found that the main effect of the removal of the N-terminal hexapeptide is to increase the separation between strands beta(2) and beta(6) and to facilitate the beta to alpha transition. On the other hand, the lysine cleavage only increases the flexibility of strand beta(5) and does not affect the interactions between strands beta(2) and beta(6). These conformational changes may relate to polymerization tendencies of these variants.
authors.affiliation: Basic Research Program, SAIC-Frederick, Inc, Laboratory of Experimental and Computational Biology, NCI-FCRDC, Frederick, MD 21702, USA.
authors.forename: Buyong
authors.initials: B
authors.lastname: Ma
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D000686:Amyloidosis / Q000209:etiology; D003198:Computer Simulation; D014644:Genetic Variation; D006801:Humans; D008958:Models, Molecular; D009038:Motion; D018583:Pliability; D011487:Protein Conformation; D011489:Protein Denaturation; D017433:Protein Structure, Secondary; D012995:Solubility; D013696:Temperature; D001613:beta 2-Microglobulin / Q000737:chemistry* / Q000235:genetics
chemical_list: D001613:beta 2-Microglobulin