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Keywords:

  • MD simulation;
  • S[BOND]S bridge;
  • OPLS-AA;
  • AMBER ff03;
  • helicity;
  • native contacts

Abstract

The role of the 17 disulfide (S[BOND]S) bridges in preserving the native conformation of human serum albumin (HSA) is investigated by performing classical molecular dynamics (MD) simulations on protein structures with intact and, respectively, reduced S[BOND]S bridges. The thermal unfolding simulations predict a clear destabilization of the protein secondary structure upon reduction of the S[BOND]S bridges as well as a significant distortion of the tertiary structure that is revealed by the changes in the protein native contacts fraction. The effect of the S[BOND]S bridges reduction on the protein compactness was tested by calculating Gibbs free energy profiles with respect to the protein gyration radius. The theoretical results obtained using the OPLS-AA and the AMBER ff03 force fields are in agreement with the available experimental data. Beyond the validation of the simulation method, the results here reported provide new insights into the mechanism of the protein reductive/oxidative unfolding/folding processes. It is predicted that in the native conformation of the protein, the thiol ([BOND]SH) groups belonging to the same reduced S[BOND]S bridge are located in potential wells that maintain them in contact. The [BOND]SH pairs can be dispatched by specific conformational transitions of the peptide chain located in the neighborhood of the cysteine residues. © 2012 Wiley Periodicals, Inc. Biopolymers 97:889–898, 2012.