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Gorantla K, Krishnan A, Waheed SO, Varghese A, DiCastri I, LaRouche C, Paik M, Fields GB, Karabencheva-Christova TG. Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1. Biochemistry 2024; 63:1925-1940. [PMID: 38963231 PMCID: PMC11309001 DOI: 10.1021/acs.biochem.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
Collagen hydrolysis, catalyzed by Zn(II)-dependent matrix metalloproteinases (MMPs), is a critical physiological process. Despite previous computational investigations into the catalytic mechanisms of MMP-mediated collagenolysis, a significant knowledge gap in understanding remains regarding the influence of conformational sampling and entropic contributions at physiological temperature on enzymatic collagenolysis. In our comprehensive multilevel computational study, employing quantum mechanics/molecular mechanics (QM/MM) metadynamics (MetD) simulations, we aimed to bridge this gap and provide valuable insights into the catalytic mechanism of MMP-1. Specifically, we compared the full enzyme-substrate complex in solution, clusters in solution, and gas-phase to elucidate insights into MMP-1-catalyzed collagenolysis. Our findings reveal significant differences in the catalytic mechanism when considering thermal effects and the dynamic evolution of the system, contrasting with conventional static potential energy surface QM/MM reaction path studies. Notably, we observed a significant stabilization of the critical tetrahedral intermediate, attributed to contributions from conformational flexibility and entropy. Moreover, we found that protonation of the scissile bond nitrogen occurs via proton transfer from a Zn(II)-coordinated hydroxide rather than from a solvent water molecule. Following C-N bond cleavage, the C-terminus remains coordinated to the catalytic Zn(II), while the N-terminus forms a hydrogen bond with a solvent water molecule. Subsequently, the release of the C-terminus is facilitated by the coordination of a water molecule. Our study underscores the pivotal role of protein conformational dynamics at physiological temperature in stabilizing the transition state of the rate-limiting step and key intermediates, compared to the corresponding reaction in solution. These fundamental insights into the mechanism of collagen degradation provide valuable guidance for the development of MMP-1-specific inhibitors.
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Affiliation(s)
- Koteswara
Rao Gorantla
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Anandhu Krishnan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Sodiq O. Waheed
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ann Varghese
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Isabella DiCastri
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
| | - Ciara LaRouche
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
| | - Meredith Paik
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Gregg B. Fields
- Department
of Chemistry and Biochemistry and I-HEALTH, Florida Atlantic University, Jupiter, Florida 33458, United States
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Rao D, Zhu L, Liu W, Guo Z. Molecular Mechanism of Double-Displacement Retaining β-Kdo Glycosyltransferase WbbB. J Phys Chem B 2024. [PMID: 39051443 DOI: 10.1021/acs.jpcb.4c02073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Glycosyltransferases (GTs) are pivotal enzymes involved in glycosidic bond synthesis, which can lead to either retention or inversion of the glycosyl moiety's anomeric configuration. However, the catalytic mechanism for retaining GTs remains a subject of controversy. In this study, we employ MD and QM/MM metadynamics to investigate the double-displacement catalytic mechanism of the retaining β-Kdo transferase WbbB. Our findings demonstrate that the nucleophile Asp232 initiates the reaction by attacking the sugar ring containing a carboxylate at the anomeric position, forming a covalent adduct. Subsequently, the adduct undergoes a rotational rearrangement, ensuring proper orientation of the anomeric carbon for the acceptor substrate. In the second step, Glu158 acts as the catalytic base to abstract the proton of the acceptor substrate to complete the transglycosylation reaction. Notably, His265 does not function as the anticipated catalytic acid; instead, it stabilizes the phosphate group through H-bonding interactions. Our simulations support the double-displacement mechanism implicated from the crystallographic studies of WbbB. This mechanism deviates from the common SNi-type and retaining glycoside hydrolase mechanisms, thereby expanding our understanding of GT catalytic mechanisms.
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Affiliation(s)
- Deming Rao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Lin Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Weiqiong Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Zhiyong Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
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3
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Messias A, Capece L, De Simone G, Coletta M, Ascenzi P, Estrin DA. Mechanism of Peroxynitrite Interaction with Ferric M. tuberculosis Nitrobindin: A Computational Study. Inorg Chem 2024; 63:9907-9918. [PMID: 38754069 DOI: 10.1021/acs.inorgchem.4c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Nitrobindins (Nbs) are all-β-barrel heme proteins present along the evolutionary ladder. They display a highly solvent-exposed ferric heme group with the iron atom being coordinated by the proximal His residue and a water molecule at the distal position. Ferric nitrobindins (Nb(III)) play a role in the conversion of toxic peroxynitrite (ONOO-) to harmless nitrate, with the value of the second-order rate constant being similar to those of most heme proteins. The value of the second-order rate constant of Nbs increases as the pH decreases; this suggests that Nb(III) preferentially reacts with peroxynitrous acid (ONOOH), although ONOO- is more nucleophilic. In this work, we shed light on the molecular basis of the ONOO- and ONOOH reactivity of ferric Mycobacterium tuberculosis Nb (Mt-Nb(III)) by dissecting the ligand migration toward the active site, the water molecule release, and the ligand binding process by computer simulations. Classical molecular dynamics simulations were performed by employing a steered molecular dynamics approach and the Jarzynski equality to obtain ligand migration free energy profiles for both ONOO- and ONOOH. Our results indicate that ONOO- and ONOOH migration is almost unhindered, consistent with the exposed metal center of Mt-Nb(III). To further analyze the ligand binding process, we computed potential energy profiles for the displacement of the Fe(III)-coordinated water molecule using a hybrid QM/MM scheme at the DFT level and a nudged elastic band approach. These results indicate that ONOO- exhibits a much larger barrier for ligand displacement than ONOOH, suggesting that water displacement is assisted by protonation of the leaving group by the incoming ONOOH.
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Affiliation(s)
- Andresa Messias
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Luciana Capece
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Giovanna De Simone
- Department of Sciences, Roma Tre University, Viale G. Marconi, 446, I-00146 Roma, Italy
| | - Massimo Coletta
- IRCCS Fondazione Bietti, Via Santo Stefano Rotondo, 6, 00184 Roma, Italy
| | - Paolo Ascenzi
- Department of Sciences, Roma Tre University, Viale G. Marconi, 446, I-00146 Roma, Italy
- Accademia Nazionale dei Lincei, Via della Lungara, 10, 00165 Roma, Italy
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes 2160, C1428EHA Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
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Ion BF, Aboelnga MM, Gauld JW. QM/MM investigation of the discriminatory pre-transfer editing mechanism operated by Lysyl-tRNA synthetase. J Biomol Struct Dyn 2024:1-9. [PMID: 38197420 DOI: 10.1080/07391102.2023.2301054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/26/2023] [Indexed: 01/11/2024]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that remarkable facilitate the aminoacylation process during translation. With a high fidelity, the mischarged tRNA is prevented through implementing pre- and post-transfer proofreading mechanisms. For instance, Lysine-tRNA synthetase charges the native substrate, lysine, to its cognate tRNA. In spite of the great structural similarity between lysine to the noncognate and toxic ornithine, with the side chain of lysine being only one methylene group longer, LysRS is able to achieve this discrimination with a high efficiency. In this work, the hybrid quantum mechanics/molecular mechanics (QM/MM) investigation was applied to probe the pre-transfer editing mechanism catalyzed by lysyl-tRNA synthetase to reject the noncognte aminoacyl, L-ornityl (Orn), compared to the cognate substrate, L-lysyl. Particularly, the self-cyclization pre-transfer editing mechanism was explored for the two substrates. The substrate-assisted self-cyclization editing of Orn-AMP, where its phosphate moiety acts as the catalytic base, is found to be the rate-determining step with an energy barrier of 101.2 kJ mol-1. Meanwhile, the corresponding rate-limiting pathway for the native Lys-AMP lies at 140.2 kJ mol-1. This observation clearly indicated the infeasibility of this catalytic scenario in the presence of the native substrate. Interestingly, a thermodynamically favorable cyclic product of -92.9 kJ mol-1 with respect to the aminoacyl reactant complex demonstrated evidence of a successful pre-transfer editing. This reaction resulted in the discharge of the on-cognate -ornithine derivative from LysU's active site. These valuable mechanistic insights are valuable to enrich our knowledge of this extremely efficient and specific catalytic machinery of LysRS.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bogdan F Ion
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Mohamed M Aboelnga
- Chemistry Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - James W Gauld
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
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