Interactions of S-peptide analogue in aqueous urea and trimethylamine-N- oxide solutions

A molecular dynamics simulation study

Rahul Sarma, Sandip Paul

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

The ability of the osmolyte, trimethylamine-N-oxide (TMAO), to protect proteins from deleterious effect of urea, another commonly available osmolyte, is well-established. However, the molecular mechanism of this counteraction is not understood yet. To provide a molecular level understanding of how TMAO protects proteins in highly concentrated urea solution, we report here molecular dynamics simulation results of a 15-residue model peptide in two different conformations: helix and extended. For both conformations, simulations are carried out in pure water as well as in binary and ternary aqueous solutions of urea and TMAO. Analysis of solvation characteristics reveals direct interactions of urea and TMAO with peptide residues. However, the number of TMAO molecules that enter in the first solvation shell of the peptide is significantly lower than that of urea, and, unlike water and urea, TMAO shows its inability to form hydrogen bond with backbone oxygen and negatively charged sidechains. Preferential accumulation of urea near the peptide surface and preferential exclusion of TMAO from the peptide surface are observed. Inclusion of osmolytes in the peptide solvation shell leads to dehydration of the peptide in binary and ternary solutions of urea and TMAO. Solvation of peptide residues are investigated more closely by calculating the number of hydrogen bonds between the peptide and solution species. It is found that number of hydrogen bonds formed by the peptide with solution species increases in binary urea solution (relative to pure water) and this relative enhancement in hydrogen bond number reduces upon addition of TMAO. Our simulation results also suggest that, in the ternary solution, the peptide solvation layer is better mixed in terms of water and urea as compared to binary urea solution. Implications of the results for counteraction mechanism of TMAO are discussed.

Original languageEnglish (US)
Article number034504
JournalJournal of Chemical Physics
Volume139
Issue number3
DOIs
StatePublished - 2013
Externally publishedYes

Fingerprint

Molecular Dynamics Simulation
ureas
peptides
Urea
Molecular dynamics
analogs
molecular dynamics
Peptides
oxides
Computer simulation
Solvation
solvation
simulation
interactions
Hydrogen
Hydrogen bonds
hydrogen bonds
Water
water
Conformations

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry
  • Medicine(all)

Cite this

Interactions of S-peptide analogue in aqueous urea and trimethylamine-N- oxide solutions : A molecular dynamics simulation study. / Sarma, Rahul; Paul, Sandip.

In: Journal of Chemical Physics, Vol. 139, No. 3, 034504, 2013.

Research output: Contribution to journalArticle

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