A molecular dynamics study of the correlations between solvent-accessible surface, molecular volume, and folding state.
We analyzed the correlations between molecular volume, solvent-accessible surface, and folding state (secondary structure content) for unfolded conformers of alpha (holo- and apomyoglobin) and beta (retinal-binding protein) proteins and a small water-soluble alanine-rich alpha-helical peptide. Conformers with different degrees of folding were obtained using molecular dynamics at constant temperature and pressure with implicit solvent (dielectric constant adjustment) for all four systems and with explicit solvent for the single helix peptide. Our results support the view that unfolded conformations are not necessary extended, that volume variation is not a good indication of folding state and that the simple model of water penetrating the interior of the protein does not explain the increase in volume upon unfolding.
Floriano
Wely B
WB
Biological Sciences Department, California State Polytechnic University Pomona, 3801 W Temple Ave, Pomona, California 91768, USA.
Domont
Gilberto B
GB
Nascimento
Marco A C
MA
D000409:Alanine / Q000031:analogs & derivatives; D000595:Amino Acid Sequence; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009211:Myoglobin / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012177:Retinol-Binding Proteins / Q000737:chemistry; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D009211:Myoglobin; D010455:Peptides; D011506:Proteins; D012177:Retinol-Binding Proteins; D012997:Solvents; D014867:Water; D000409:Alanine