Molecular dynamics simulations of β-hairpin folding

• Published in: Proteins, structure, function, and bioinformatics Vol. 37; no. 3; pp. 325 - 333
• Main Authors: Wang, Hongwu, Varady, Judith, Ng, Lily, Sung, Shen-Shu
• Format: Journal Article
• Language: English
• Published: New York John Wiley & Sons, Inc 15.11.1999
• Subjects: Algorithms; Computer Simulation; helix; Models, Chemical; molecular dynamics; Monte Carlo Method; Peptides - chemistry; Protein Folding; Protein Structure, Secondary; Proteins - chemistry; secondary structure; β-hairpin
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/(SICI)1097-0134(19991115)37:3<325::AID-PROT2>3.0.CO;2-E

Molecular dynamics simulations of β‐hairpin folding have been carried out with a solvent‐referenced potential at 274 K. The model peptide V4DPGV4 formed stable β‐hairpin conformations and the β‐hairpin ratio calculated by the DSSP algorithm was about 56% in the 50‐ns simulation. Folding into β‐hairpin conformations is independent of the initial conformations. The simulations provided insights into the folding mechanism. The hydrogen bond often formed in a β‐turn first, and then propagated by forming more hydrogen bonds along the strands. Unfolding and refolding occurred repeatedly during the simulations. Both the hydrogen bonding and the hydrophobic interaction played important roles in forming the ordered structure. Without the hydrophobic effect, stable β‐hairpin conformations did not form in the simulations. With the same energy functions, the alanine‐based peptide (AAQAA)3Y folded into helical conformations, in agreement with experiments. Folding into an α‐helix or a β‐hairpin is amino acid sequence‐dependent. Proteins 1999;37:325–333. ©1999 Wiley‐Liss, Inc.