Helix versus sheet formation in a small peptide.
Segments with the amino acid sequence EKAYLRT (glutamine-lysine-alanine-tyrosine-leucine-arginine-threonine) appear in naturally occurring proteins both in alpha-helices and beta-sheets. For this reason, we have used this peptide to study how secondary structure formation in proteins depends on the local environment. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. Results in gas phase are compared with that in an implicit solvent. We find that both the solvated molecule and EKAYLRT in gas phase form an alpha-helix when not interacting with other molecules. However, in the vicinity of a beta-strand, the peptide forms a beta-strand. Because of this change in secondary structure our peptide may provide a simple model for the alpha-->beta transition that is supposedly related to the outbreak of prion diseases and similar illnesses.
Peng
Yong
Y
Department of Physics, Michigan Technological University, Houghton, Michigan 49931-1291, USA.
Hansmann
Ulrich H E
UH
D000595:Amino Acid Sequence; D003198:Computer Simulation; D019281:Dimerization; D004735:Energy Transfer; D005740:Gases; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D044367:Phase Transition; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012996:Solutions; D012997:Solvents / Q000737:chemistry; D013696:Temperature
D005740:Gases; D010455:Peptides; D012996:Solutions; D012997:Solvents