Protein topology determines cysteine oxidation fate: the case of sulfenyl amide formation among protein families

PLoS Comput Biol. 2015 Mar 5;11(3):e1004051. doi: 10.1371/journal.pcbi.1004051. eCollection 2015 Mar.

Abstract

Cysteine residues have a rich chemistry and play a critical role in the catalytic activity of a plethora of enzymes. However, cysteines are susceptible to oxidation by Reactive Oxygen and Nitrogen Species, leading to a loss of their catalytic function. Therefore, cysteine oxidation is emerging as a relevant physiological regulatory mechanism. Formation of a cyclic sulfenyl amide residue at the active site of redox-regulated proteins has been proposed as a protection mechanism against irreversible oxidation as the sulfenyl amide intermediate has been identified in several proteins. However, how and why only some specific cysteine residues in particular proteins react to form this intermediate is still unknown. In the present work using in-silico based tools, we have identified a constrained conformation that accelerates sulfenyl amide formation. By means of combined MD and QM/MM calculation we show that this conformation positions the NH backbone towards the sulfenic acid and promotes the reaction to yield the sulfenyl amide intermediate, in one step with the concomitant release of a water molecule. Moreover, in a large subset of the proteins we found a conserved beta sheet-loop-helix motif, which is present across different protein folds, that is key for sulfenyl amide production as it promotes the previous formation of sulfenic acid. For catalytic activity, in several cases, proteins need the Cysteine to be in the cysteinate form, i.e. a low pKa Cys. We found that the conserved motif stabilizes the cysteinate by hydrogen bonding to several NH backbone moieties. As cysteinate is also more reactive toward ROS we propose that the sheet-loop-helix motif and the constraint conformation have been selected by evolution for proteins that need a reactive Cys protected from irreversible oxidation. Our results also highlight how fold conservation can be correlated to redox chemistry regulation of protein function.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amides / chemistry*
  • Amides / metabolism
  • Computational Biology
  • Cysteine / chemistry*
  • Cysteine / metabolism
  • Models, Molecular
  • Oxidation-Reduction
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism*
  • Sulfenic Acids / chemistry*
  • Sulfenic Acids / metabolism

Substances

  • Amides
  • Proteins
  • Sulfenic Acids
  • Cysteine

Grant support

LAD is CONICET doctoral fellow, EL is a UBA doctoral fellow. AGT and MAM are members of the CONICET. This work was supported by PICT-No. 2010-2805, PICTO-GSK 2012, Subsidio Bunge yBorn para enfermedades Infecciosas 2010, and Universidad de Buenos Aires CyT No. 20020110100061 awarded to AGT and MAM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.