Energetic Coupling and Structural Deactivation of Respiratory Complex I

• Grant number: 24/08682-8
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: March 01, 2025
• End date: February 29, 2028
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Guilherme Menegon Arantes
• Grantee: Edwine Tendong
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 23/00934-5 - Computational methodologies for simulation of proton-coupled electron transfer in biomolecules, AP.R

Abstract

Respiratory complex I is the largest known asymmetric membrane protein and is responsible for transducing approximately half of the chemical energy used in a cell. It catalyzes the transfer of electrons from the metabolite NADH to coenzyme-Q, coupled to proton pumping and the generation of an electrochemical transmembrane gradient. Despite decades of research, fundamental questions still persist particularly regarding the mechanisms of coupling and regulation of the enzyme. Here, we propose to apply advanced molecular simulation methodologies in combination with experimental results obtained by collaborators to elucidate these mechanistic aspects of complex I.In particular, we will investigate the protonation states of residues in the coenzyme-Q binding sites and the central transmembrane region, under different substrate occupancy and composition conditions, using a new and robust implementation of constant pH simulations molecular dynamics (CpHMD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) potentials for proton transfer processes. We will also determine the detailed molecular mechanism for structural transition between active and de-active (A-D, or closed-open) forms of the mammalian complex I, including changes in its internal hydration and exposure of the coenzyme-Q binding sites, which regulates enzyme function and prevents reverse electron transfer. For this second part, a combination of methods in artificial intelligence, molecular dynamics simulations, Markov state models and experimental cryo-EM densities will be used to map transition pathways and estimate the thermodynamics and kinetics for the (A-D) structural conversion. These pathways may also reveal putative binding sites for targeting small-molecule modulators of the regulatory transition with biomedical relevance to treatment of ischemia-reperfusion injury and metabolic diseases.The research proposed here is ambitious but entirely achievable given the candidate's expertise and our research group's pioneering work in molecular simulations of the electron transport chain. This proposal will continue our current collaboration with the University of Cambridge (UK) where structural and kinetic studies will be directly compared, refined, and validated against our simulations. (AU)