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Varghese A, Waheed SO, Gorantla K, DiCastri I, LaRouche C, Kaski B, Fields GB, Karabencheva-Christova TG. Catalytic Mechanism of Collagen Hydrolysis by Zinc(II)-Dependent Matrix Metalloproteinase-1. J Phys Chem B 2023; 127:9697-9709. [PMID: 37931179 PMCID: PMC10659029 DOI: 10.1021/acs.jpcb.3c04293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
Human matrix metalloproteinase-1 (MMP-1) is a zinc(II)-dependent enzyme that catalyzes collagenolysis. Despite the availability of extensive experimental data, the mechanism of MMP-1-catalyzed collagenolysis remains poorly understood due to the lack of experimental structure of a catalytically productive enzyme-substrate complex of MMP-1. In this study, we apply molecular dynamics and combined quantum mechanics/molecular mechanics to reveal the reaction mechanism of MMP-1 based on a computationally modeled structure of the catalytically competent complex of MMP-1 that contains a large triple-helical peptide substrate. Our proposed mechanism involves the participation of an auxiliary (second) water molecule (wat2) in addition to the zinc(II)-coordinated water (wat1). The reaction initiates through a proton transfer to Glu219, followed by a nucleophilic attack by a zinc(II)-coordinated hydroxide anion nucleophile at the carbonyl carbon of the scissile bond, leading to the formation of a tetrahedral intermediate (IM2). The process continues with a hydrogen-bond rearrangement to facilitate proton transfer from wat2 to the amide nitrogen of the scissile bond and, finally, C-N bond cleavage. The calculations indicate that the rate-determining step is the water-mediated nucleophilic attack with an activation energy barrier of 22.3 kcal/mol. Furthermore, the calculations show that the hydrogen-bond rearrangement/proton-transfer step can proceed in a consecutive or concerted manner, depending on the conformation of the tetrahedral intermediate, with the consecutive mechanism being energetically preferable. Overall, the study reveals the crucial role of a second water molecule and the dynamics for effective MMP-1-catalyzed collagenolysis.
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Affiliation(s)
- Ann Varghese
- 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
| | - Koteswararao Gorantla
- 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
| | - Brendan Kaski
- Department
of Kinesiology and Integrative Physiology, 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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Xia YL, Li YP, Fu YX, Liu SQ. The Energetic Origin of Different Catalytic Activities in Temperature-Adapted Trypsins. ACS OMEGA 2020; 5:25077-25086. [PMID: 33043186 PMCID: PMC7542600 DOI: 10.1021/acsomega.0c02401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/09/2020] [Indexed: 05/08/2023]
Abstract
Psychrophilic enzymes were always observed to have higher catalytic activity (k cat) than their mesophilic homologs at room temperature, while the origin of this phenomenon remains obscure. Here, we used two different temperature-adapted trypsins, the psychrophilic Atlantic cod trypsin (ACT) and the mesophilic bovine trypsin (BT), as a model system to explore the energetic origin of their different catalytic activities using computational methods. The results reproduce the characteristic changing trends in the activation free energy, activation enthalpy, and activation entropy between the psychrophilic and mesophilic enzymes, where, in particular, the slightly decreased activation free energy of ACT is determined by its considerably reduced activation enthalpy rather than by its more negative activation entropy compared to BT. The calculated electrostatic contributions to the solvation free energies in the reactant state/ground sate (RS/GS) and transition state (TS) show that, going from BT to ACT, the TS stabilization has a predominant effect over the RS stabilization on lowering the activation enthalpy of ACT. Comparison between the solvation energy components reveals a more optimized electrostatic preorganization to the TS in ACT, which provides a larger stabilization to the TS through reducing the reorganization energy, thus resulting in the lower activation enthalpy and hence lower activation free energy of ACT. Thus, it can be concluded that it is the difference in the protein electrostatic environment, and hence its different stabilizing effects on the TS, that brings about the different catalytic activities of different temperature-adapted trypsins.
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Affiliation(s)
- Yuan-Ling Xia
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan, Yunnan University, Kunming 650091, Yunnan, China
- Editorial
Office of Journal of Yunnan University (Natural Sciences Edition), Yunnan University, Kunming 650091, Yunnan, China
| | - Yong-Ping Li
- School
of Agriculture, Yunnan University, Kunming 650091, Yunnan, China
| | - Yun-Xin Fu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan, Yunnan University, Kunming 650091, Yunnan, China
- Human
Genetics Center and Division of Biostatistics, School of Public Health, The University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Shu-Qun Liu
- State
Key Laboratory for Conservation and Utilization of Bio-Resources in
Yunnan, Yunnan University, Kunming 650091, Yunnan, China
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3
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Abstract
Quantum mechanics (QM) methods provide a fine description of receptor-ligand interactions and of chemical reactions. Their use in drug design and drug discovery is increasing, especially for complex systems including metal ions in the binding sites, for the design of highly selective inhibitors, for the optimization of bi-specific compounds, to understand enzymatic reactions, and for the study of covalent ligands and prodrugs. They are also used for generating molecular descriptors for predictive QSAR/QSPR models and for the parameterization of force fields. Thanks to the continuous increase of computational power offered by GPUs and to the development of sophisticated algorithms, QM methods are becoming part of the standard tools used in computer-aided drug design (CADD). We present the most used QM methods and software packages, and we discuss recent representative applications in drug design and drug discovery.
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Affiliation(s)
- Martin Kotev
- Global Research Informatics/Cheminformatics and Drug Design, Evotec (France) SAS, Toulouse, France
| | - Laurie Sarrat
- Global Research Informatics/Cheminformatics and Drug Design, Evotec (France) SAS, Toulouse, France
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Batha S, Arman H, Larionov OV, Musie GT. Zinc(II) complexes of a versatile heptadentate ligand as phosphohydrolase structural and functional mimics. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.119077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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5
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Świderek K, Tuñón I, Moliner V, Bertran J. Computational strategies for the design of new enzymatic functions. Arch Biochem Biophys 2015; 582:68-79. [PMID: 25797438 PMCID: PMC4554825 DOI: 10.1016/j.abb.2015.03.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 11/28/2022]
Abstract
In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels-Alder and Retro-Aldolase, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful design strategies.
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Affiliation(s)
- K Świderek
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain; Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - I Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain
| | - V Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - J Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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Abstract
An appreciable part of enzymes operating in vivo is associated with lipid membranes. The function of such enzymes can be influenced by the presence of domains containing proteins and/or composed of different lipids. The corresponding experimental model-system studies can be performed under well controlled conditions, e.g., on a planar supported lipid bilayer or surface-immobilized vesicles. To clarify what may happen in such systems, we propose general kinetic equations describing the enzyme-catalyzed substrate conversion occurring via the Michaelis-Menten (MM) mechanism on a membrane with domains which do not directly participate in reaction. For two generic situations when a relatively slow reaction takes place primarily in or outside domains, we take substrate saturation and lateral substrate-substrate interactions at domains into account and scrutinize the dependence of the reaction rate on the average substrate coverage. With increasing coverage, depending on the details, the reaction rate reaches saturation via an inflection point or monotonously as in the conventional MM case. In addition, we show analytically the types of reaction kinetics occurring primarily at domain boundaries. In the physically interesting situation when the domain growth is fast on the reaction time scale, the latter kinetics are far from conventional. The opposite situation when the reaction is fast and controlled by diffusion has been studied by using the Monte Carlo technique. The corresponding results indicate that the dependence of the reaction kinetics on the domain size may be weak.
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Affiliation(s)
- Vladimir P Zhdanov
- Division of Biological Physics, Department of Applied Physics, Chalmers University of Technology, SE-41296 Göteborg, Sweden. Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk 630090, Russia
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