title: Molecular dynamics simulations of isolated helices of myoglobin.
abstract: The apo form of myoglobin has two non-native stable states that have been experimentally characterized. Investigation of these states has suggested possible folding pathways for myoglobin. We have performed molecular dynamics simulations on solvated isolated helices of myoglobin to investigate the relationship between the intrinsic stabilities of the isolated helices and the structure and folding pathway of apomyoglobin. Analyses of hydrogen bonding and fluctuations from simulations at 298 and 368 K are used to explore the relative stabilities of the helices of myoglobin. The ordering observed is A approximately G approximately H > B > E > F, which mirrors both the experimental equilibrium and kinetic data available for apomyoglobin. The experimental observation that a subdomain comprising helices A, G, and H is an important early intermediate and our result that these helices are the most stable suggest that the intrinsically more stable helices form early in the folding process and that this significantly influences the folding pathway.
authors.affiliation: Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: J D
authors.initials: JD
authors.lastname: Hirst
authors.forename: C L
authors.initials: CL
authors.lastname: Brooks
mesh_terms: D000595:Amino Acid Sequence; D001059:Apoproteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009038:Motion; D009211:Myoglobin / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary
chemical_list: D001059:Apoproteins; D009211:Myoglobin; D010446:Peptide Fragments; C010857:apomyoglobin