title: How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics.
abstract: The tunnel region at triosephosphate isomerase (TIM)'s dimer interface, distant from its catalytic site, is a target site for certain benzothiazole derivatives that inhibit TIM's catalytic activity in Trypanosoma cruzi, the parasite that causes Chagas disease. We performed multiple 100-ns molecular-dynamics (MD) simulations and elastic network modeling (ENM) on both apo and complex structures to shed light on the still unclear inhibitory mechanism of one such inhibitor, named bt10. Within the time frame of our MD simulations, we observed stabilization of aromatic clusters at the dimer interface and enhancement of intersubunit hydrogen bonds in the presence of bt10, which point to an allosteric effect rather than destabilization of the dimeric structure. The collective dynamics dictated by the topology of TIM is known to facilitate the closure of its catalytic loop over the active site that is critical for substrate entrance and product release. We incorporated the ligand's effect on vibrational dynamics by applying mixed coarse-grained ENM to each one of 54,000 MD snapshots. Using this computationally efficient technique, we observed altered collective modes and positive shifts in eigenvalues due to the constraining effect of bt10 binding. Accordingly, we observed allosteric changes in the catalytic loop's dynamics, flexibility, and correlations, as well as the solvent exposure of catalytic residues. A newly (to our knowledge) introduced technique that performs residue-based ENM scanning of TIM revealed the tunnel region as a key binding site that can alter global dynamics of the enzyme.
authors.affiliation: Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey.
authors.forename: Zeynep
authors.initials: Z
authors.lastname: Kurkcuoglu
authors.affiliation: Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey.
authors.forename: Doga
authors.initials: D
authors.lastname: Findik
authors.affiliation: Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali, Istanbul, Turkey.
authors.forename: Ebru Demet
authors.initials: ED
authors.lastname: Akten
authors.affiliation: Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey. Electronic address: doruker@boun.edu.tr.
authors.forename: Pemra
authors.initials: P
authors.lastname: Doruker
mesh_terms: D000494:Allosteric Regulation; D055162:Biocatalysis; D020134:Catalytic Domain; D019281:Dimerization; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D025341:Principal Component Analysis; D015800:Protozoan Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D012997:Solvents / Q000737:chemistry; D014305:Triose-Phosphate Isomerase / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D014349:Trypanosoma cruzi
chemical_list: D015800:Protozoan Proteins; D012997:Solvents; D014305:Triose-Phosphate Isomerase