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Free energy calculations of enzymatic reactions for biotechnological applications

Project FEP_CLD
Research Area Bio Sciences
Principal Investigator(s) Pietro Vidossich
Institution(s)
  • Universitat Autònoma de Barcelona, Unitat de Química Física, Barcelona, Spain
  • University of Amsterdam, Van Hoff Institute for Molecular Sciences, Amsterdam, The Netherlands

Abstract

Understanding structure-function relationships in heme proteins is a key step towards the development of biotechnological applications. Molecular modeling may contribute valuable insight in this respect providing the atomic and electronic rearrangements that take place during catalysis and the forces that guide them. Our project targets the enzyme chlorite dismutase (Cld), the catalyst of the last step of the bacterial perchlorate respiratory pathway i.e. the conversion of chlorite to chloride and dioxygen (ClO2- → Cl- + O2, reaction 1). Perchlorate-reducing bacteria have recently become important subjects of research because of their potential use in remediation of contaminated water. Our objective is to pinpoint the structural determinants that make Cld an efficient and selective catalyst for reaction 1 (as opposed to other heme proteins). To the scope we will use ab initio molecular dynamics simulations, based on DFT/MM interacting potentials, and a new free energy method based on metadynamics aimed at reducing the computational cost of these type of calculations.

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