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Theoretical Chemistry Accounts

, Volume 106, Issue 1–2, pp 55–61 | Cite as

Assessment of conformation and energetics of the N-terminal part of elafin via computer simulations

  • Roman G. Efremov
  • Pavel E. Volynsky
  • Manuel A. M. Dauchez
  • Dmitry E. Nolde
  • Alexander S. Arseniev
  • Alain J. P. Alix
Regular article

Abstract.

Elafin, a specific inhibitor of elastase, is thought to play a regulatory role in inflammation. An NMR-derived solution structure of recombinant elafin has been reported [Francart et al. (1997) J Mol Biol 268:666 ], although the conformation of its flexible N-terminal part is not established. There is experimental evidence that the N terminus (residues 1–15) of elafin interacts with the cell membrane. To explore the conformational preferences of residues in this region, we have performed Monte Carlo simulations of the peptide in water, in cyclohexane, and in a model membrane. Additionally, 3.7-ns molecular dynamics with explicit water was carried out. The main results were that the hydrophobic environment stabilizes an α helix in the region 6–11, the peptide is unordered in water, and it is attached to the membrane via the amphiphilic α-helix 6–11, which inserts with its N terminus forming an angle of about 60° to the membrane plane. We therefore assume that in nonpolar media the N-terminal part of elafin forms a short α helix which might act as a membrane anchor.

Key words: Peptide-membrane interactions Secondary structure Protein conformation Solvation potential Molecular modeling 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • Roman G. Efremov
    • 1
  • Pavel E. Volynsky
    • 1
  • Manuel A. M. Dauchez
    • 2
  • Dmitry E. Nolde
    • 1
  • Alexander S. Arseniev
    • 1
  • Alain J. P. Alix
    • 2
  1. 1. M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, Moscow V-437, 117871 GSP, Russia, e-mail: efremov@nmr.ruRU
  2. 2. Laboratoire de Spectroscopies et Structures Biomoléculaires, Faculté des Sciences, Université de Reims Champagne-Ardenne, IFR53 Biomolécules, B.P. 1039, 51687 Reims Cédex 2, France, e-mail: alain.alix@univ-reims.frFR

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