We are excited to share with you our research advances in the computational investigation of metalloenzymes dynamics and reaction mechanisms.
Collagen is the most abundant protein in the human body and the main component of the extracellular matrix (ECM). And collagenolysis- collagen hydrolysis- is a central biochemical process in the ECM precisely regulated in normal physiology. However, abnormal collagen catabolism underlines the development of numerous pathological conditions, including arthritis, fibrosis, tumor growth, and metastasis.
The main type of enzymes performing collagen degradation are members of the zinc-dependent matrix metalloproteinase (MMP) family. Knowledge about the intimate mechanism of collagenolysis can provide novel opportunities for modulating this process.
One of the most important members of the MMP family, is matrix metalloproteinase-1 (MMP-1). MMP-1 is a two-domain protein and MMP-1 catalyzed collagenolysis and its regulation are driven by complex conformational rearrangements involving interdomain flexibility.Our research aims to advance the current understanding of MMP-1 collagenolysis by providing novel insights about the conformational and free energy changes, catalytic mechanisms, and molecular motions involved in key states of the collagenolytic cycle. This research is supported by NIH.
Members of the non-heme iron(II)-and 2-oxoglutarate (2OG)-dependent oxygenase family of enzymes catalyze incredibly diverse reactions with vital biological roles, making them attractive targets for therapeutics development. These include reactions of hydroxylation, demethylation, halogenation, ring-opening, extension and closure, desaturation, C-C and C-N bond creation, and others.
One of the essential roles of 2OG oxygenases is the demethylation of DNA and RNA bases. DNA and RNA get frequently exposed to exogenous and endogenous chemical modifications by alkylating agents, such as environmental agents and drugs, which can lead to cytotoxic and mutagenic damage. Therefore, organisms have developed multiple repair strategies to remove such damage-causing modifications from their bases, involving nucleic acids repair enzymes.
Particular research targets of interest in our group from the 2OG family of oxygenases are the nucleic acid demethylases (NADMs)-enzymes involved in the cellular response to alkylation damage. The NADMs perform hydroxylation of N-methylated DNA and RNA bases. Specifically, we study the bacterial AlkB enzyme, the human homologs- AlkBH2 and AlkBH5, and the human fat-mass and obesity-associated (FTO) protein.
Applying computational chemistry methods, our research reveals substrate-binding processes and catalytic mechanisms. Furthermore, our studies elucidate conformational changes outside the enzyme’s active sites facilitating catalysis.
Applying QM/MM and MD methods, our research reveals conformational changes occurring during the substrate-binding process, catalytic mechanisms, and how the protein environment influences the catalytic events in NADMs. Furthermore, the studies reveal how key residues involved in binding and catalysis participate in correlated motions with the second coordination spheres and beyond. Such an insight longer term will enable the design of enzyme-specific inhibitors.