The evolution of catalytic function in the HIV-1 protease

M. K. Singh, K. Streu, A. J. McCrone, B. N. Dominy

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The evolution of species is a complex phenomenon based on the optimization of a multidimensional function referred to as fitness. At the level of biomolecular evolution, the fitness function can be reduced to include physiochemical properties relevant to the biological function of a particular molecule. In this work, questions involving the physical-chemical mechanisms underlying the evolution of HIV-1 protease are addressed through molecular simulation and subsequent analysis of thermodynamic properties related to the activity of the enzyme. Specifically, the impact of 40 single amino acid mutations on the binding affinity toward the matrix/capsid (MA/CA) substrate and corresponding transition state intermediate has been characterized using a molecular mechanics Poisson-Boltzmann surface area approach. We demonstrate that this approach is capable of extracting statistically significant information relevant to experimentally determined catalytic activity. Further, no correlation was observed between the effect of mutations on substrate and transition state binding, suggesting independent evolutionary pathways toward optimizing substrate specificity and catalytic activity. In addition, a detailed analysis of calculated binding affinity data suggests that ground-state destabilization (reduced binding affinity for the substrate) could be a contributing factor in the evolutionary optimization of HIV-1 protease. A numerical model is developed to demonstrate that ground-state destabilization is a valid mechanism for activity optimization given the high concentrations of substrate experienced by the functional enzyme in vivo.
Original languageEnglish
Pages (from-to)792-805
Number of pages14
JournalJournal of Molecular Biology
Volume408
Issue number4
DOIs
Publication statusPublished - 13 May 2011

Fingerprint

Mutation
Capsid
Enzymes
Substrate Specificity
Mechanics
Thermodynamics
Amino Acids
Human immunodeficiency virus 1 p16 protease

Keywords

  • computer-simulations
  • human-immunodeficiency-virus
  • drug-resistant-mutations
  • free-energy calculations
  • binding free-energies
  • HIV-1 protease
  • MM-PBSA
  • molecular dynamics
  • enzymatic evolution
  • molecular-dynamics
  • resolution crystal-structures
  • activity
  • evolution
  • catalytic function

Cite this

Singh, M. K., Streu, K., McCrone, A. J., & Dominy, B. N. (2011). The evolution of catalytic function in the HIV-1 protease. Journal of Molecular Biology , 408(4), 792-805. https://doi.org/10.1016/j.jmb.2011.02.031
Singh, M. K. ; Streu, K. ; McCrone, A. J. ; Dominy, B. N. / The evolution of catalytic function in the HIV-1 protease. In: Journal of Molecular Biology . 2011 ; Vol. 408, No. 4. pp. 792-805.
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Singh, MK, Streu, K, McCrone, AJ & Dominy, BN 2011, 'The evolution of catalytic function in the HIV-1 protease', Journal of Molecular Biology , vol. 408, no. 4, pp. 792-805. https://doi.org/10.1016/j.jmb.2011.02.031

The evolution of catalytic function in the HIV-1 protease. / Singh, M. K.; Streu, K.; McCrone, A. J.; Dominy, B. N.

In: Journal of Molecular Biology , Vol. 408, No. 4, 13.05.2011, p. 792-805.

Research output: Contribution to journalArticle

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