Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies.

ABSTRACT: Protein structure and dynamics in nonaqueous solvents are here investigated using molecular dynamics simulation studies, by considering two model proteins (ubiquitin and cutinase) in hexane, under varying hydration conditions. Ionization of the protein groups is treated assuming "pH memory," i.e., using the ionization states characteristic of aqueous solution. Neutralization of charged groups by counterions is done by considering a counterion for each charged group that cannot be made neutral by establishing a salt bridge with another charged group; this treatment is more physically reasonable for the nonaqueous situation, contrasting with the usual procedures. Our studies show that hydration has a profound effect on protein stability and flexibility in nonaqueous solvents. The structure b

SUBMITTER: Soares CM 

PROVIDER: S-EPMC1302733 | biostudies-literature | 2003 Mar

REPOSITORIES: biostudies-literature