Explicit and implicit water simulations of a β-hairpin peptide

Buyong Ma, Ruth Nussinov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


The conformational properties of a β-hairpin peptide (YITNSDGTWT) were studied by using both explicit and implicit water simulations. The conformational space of the peptide was scanned by using a restricted hydrogen-bonding search method. The search method used generated the conformational space with enough diversity and good representation of β- hairpin structures. By using a total surface area-based treatment of hydrophobic interactions, implicit water simulations failed to discriminate between experimental β-hairpin structures from the rest of the conformers present in the authors' conformation library. However, with inclusion of vibrational free energy and accounting separately for polar and nonpolar surface areas, the nuclear magnetic resonance structure was ranked successfully as the most stable conformation. There is a loose correlation between the conformational energies by the continuum model and the conformational energies by explicit water simulation for conformers with similar structures. However, in terms of solvation energy, both approaches have a much better correlation. By using proper treatment of surface effect (partition of the surface area into polar and nonpolar areas) and including vibrational free-energy contribution, the continuum models should be reliable. Furthermore, the authors found that, for this peptide, β-hairpin structures have large vibrational entropy that contributes decisively to the stability of folded β-hairpin structures.

Original languageEnglish
Pages (from-to)73-87
Number of pages15
JournalProteins: Structure, Function and Genetics
Issue number1
StatePublished - 1 Oct 1999


  • Conformational energy
  • Continuum solvation model
  • Explicit water model
  • Free-energy simulation
  • Hydrophobic interaction
  • Peptide conformation
  • Vibrational entropy
  • β-hairpin peptide


Dive into the research topics of 'Explicit and implicit water simulations of a β-hairpin peptide'. Together they form a unique fingerprint.

Cite this