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Ding Y, Huang J. DP/MM: A Hybrid Model for Zinc-Protein Interactions in Molecular Dynamics. J Phys Chem Lett 2024; 15:616-627. [PMID: 38198685 DOI: 10.1021/acs.jpclett.3c03158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Zinc-containing proteins are vital for many biological processes, yet accurately modeling them using classical force fields is hindered by complicated polarization and charge transfer effects. This study introduces DP/MM, a hybrid force field scheme that utilizes a deep potential model to correct the atomic forces of zinc ions and their coordinated atoms, elevating them from MM to QM levels of accuracy. Trained on the difference between MM and QM atomic forces across diverse zinc coordination groups, the DP/MM model faithfully reproduces structural characteristics of zinc coordination during simulations, such as the tetrahedral coordination of Cys4 and Cys3His1 groups. Furthermore, DP/MM allows water exchange in the zinc coordination environment. With its unique blend of accuracy, efficiency, flexibility, and transferability, DP/MM serves as a valuable tool for studying structures and dynamics of zinc-containing proteins and also represents a pioneering approach in the evolving landscape of machine learning potentials for molecular modeling.
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Affiliation(s)
- Ye Ding
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Jing Huang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
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2
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Paul TK, Taraphder S. Nonlinear Reaction Coordinate of an Enzyme Catalyzed Proton Transfer Reaction. J Phys Chem B 2022; 126:1413-1425. [PMID: 35138854 DOI: 10.1021/acs.jpcb.1c08760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present an in-depth study on the theoretical calculation of an optimum reaction coordinate as a linear or nonlinear combination of important collective variables (CVs) sampled from an ensemble of reactive transition paths for an intramolecular proton transfer reaction catalyzed by the enzyme human carbonic anhydrase (HCA) II. The linear models are optimized by likelihood maximization for a given number of CVs. The nonlinear models are based on an artificial neural network with the same number of CVs and optimized by minimizing the root-mean-square error in comparison to a training set of committor estimators generated for the given transition. The nonlinear reaction coordinate thus obtained yields the free energy of activation and rate constant as 9.46 kcal mol-1 and 1.25 × 106 s-1, respectively. These estimates are found to be in quantitative agreement with the known experimental results. We have also used an extended autoencoder model to show that a similar analysis can be carried out using a single CV only. The resultant free energies and kinetics of the reaction slightly overestimate the experimental data. The implications of these results are discussed using a detailed microkinetic scheme of the proton transfer reaction catalyzed by HCA II.
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Affiliation(s)
- Tanmoy Kumar Paul
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Srabani Taraphder
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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3
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Kim JK, Lee C, Lim SW, Adhikari A, Andring JT, McKenna R, Ghim CM, Kim CU. Elucidating the role of metal ions in carbonic anhydrase catalysis. Nat Commun 2020; 11:4557. [PMID: 32917908 PMCID: PMC7486293 DOI: 10.1038/s41467-020-18425-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/20/2020] [Indexed: 01/07/2023] Open
Abstract
Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the catalytic roles of metal ions in a model metalloenzyme system, human carbonic anhydrase II (CA II). Through a comparative study on the intermediate states of the zinc-bound native CA II and non-native metal-substituted CA IIs, we demonstrate that the characteristic metal ion coordination geometries (tetrahedral for Zn2+, tetrahedral to octahedral conversion for Co2+, octahedral for Ni2+, and trigonal bipyramidal for Cu2+) directly modulate the catalytic efficacy. In addition, we reveal that the metal ions have a long-range (~10 Å) electrostatic effect on restructuring water network in the active site. Our study provides evidence that the metal ions in metalloenzymes have a crucial impact on the catalytic mechanism beyond their primary chemical properties.
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Affiliation(s)
- Jin Kyun Kim
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Cheol Lee
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Seon Woo Lim
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Aniruddha Adhikari
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Jacob T. Andring
- grid.15276.370000 0004 1936 8091Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610 USA
| | - Robert McKenna
- grid.15276.370000 0004 1936 8091Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610 USA
| | - Cheol-Min Ghim
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
| | - Chae Un Kim
- grid.42687.3f0000 0004 0381 814XDepartment of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Republic of Korea
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4
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Tolbert AE, Ervin CS, Ruckthong L, Paul TJ, Jayasinghe-Arachchige VM, Neupane KP, Stuckey JA, Prabhakar R, Pecoraro VL. Heteromeric three-stranded coiled coils designed using a Pb(II)(Cys) 3 template mediated strategy. Nat Chem 2020; 12:405-411. [PMID: 32123337 DOI: 10.1038/s41557-020-0423-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 01/19/2020] [Indexed: 11/09/2022]
Abstract
Three-stranded coiled coils are peptide structures constructed from amphipathic heptad repeats. Here we show that it is possible to form pure heterotrimeric three-stranded coiled coils by combining three distinct characteristics: (1) a cysteine sulfur layer for metal coordination, (2) a thiophilic, trigonal pyramidal metalloid (Pb(II)) that binds to these sulfurs and (3) an adjacent layer of reduced steric bulk generating a cavity where water can hydrogen bond to the cysteine sulfur atoms. Cysteine substitution in an a site yields Pb(II)A2B heterotrimers, while d sites provide pure Pb(II)C2D or Pb(II)CD2 scaffolds. Altering the metal from Pb(II) to Hg(II) or shifting the relative position of the sterically less demanding layer removes heterotrimer specificity. Because only two of the eight or ten hydrophobic layers are perturbed, catalytic sites can be introduced at other regions of the scaffold. A Zn(II)(histidine)3(H2O) centre can be incorporated at a remote location without perturbing the heterotrimer selectivity, suggesting a unique strategy to prepare dissymmetric catalytic sites within self-assembling de novo-designed proteins.
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Affiliation(s)
- Audrey E Tolbert
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Leela Ruckthong
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok, Thailand
| | - Thomas J Paul
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | | | - Kosh P Neupane
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA. .,Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
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5
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Park D, Lee MS. Kinetic Study of CO 2 Hydration by Small-Molecule Catalysts with A Second Coordination Sphere that Mimic the Effect of the Thr-199 Residue of Carbonic Anhydrase. Biomimetics (Basel) 2019; 4:E66. [PMID: 31581538 PMCID: PMC6963681 DOI: 10.3390/biomimetics4040066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/11/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023] Open
Abstract
Zinc complexes were synthesized as catalysts that mimic the ability of carbonic anhydrase (CA) for the CO2 hydration reaction (H2O + CO2 → H+ + HCO3-). For these complexes, a tris(2-pyridylmethyl)amine (TPA) ligand mimicking only the active site, and a 6-((bis(pyridin-2-ylmethyl)amino)methyl)pyridin-2-ol (TPA-OH) ligand mimicking the hydrogen-bonding network of the secondary coordination sphere of CA were used. Potentiometric pH titration was used to determine the deprotonation ability of the Zn complexes, and their pKa values were found to be 8.0 and 6.8, respectively. Stopped-flow spectrophotometry was used to confirm the CO2 hydration rate. The rate constants were measured to be 648.4 and 730.6 M-1s-1, respectively. The low pKa value was attributed to the hydrogen-bonding network of the secondary coordination sphere of the catalyst that mimics the behavior of CA, and this was found to increase the CO2 hydration rate of the catalyst.
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Affiliation(s)
- DongKook Park
- Green Materials & Processes Group, Korea Institute of Industrial Technology (KITECH), 55, Jongga-ro, Jung-gu, Ulsan 44413, Korea.
| | - Man Sig Lee
- Green Materials & Processes Group, Korea Institute of Industrial Technology (KITECH), 55, Jongga-ro, Jung-gu, Ulsan 44413, Korea.
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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Kim S, Sung J, Yeon J, Choi SH, Jin MS. Crystal Structure of a Highly Thermostable α-Carbonic Anhydrase from Persephonella marina EX-H1. Mol Cells 2019; 42:460-469. [PMID: 31250619 PMCID: PMC6602146 DOI: 10.14348/molcells.2019.0029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/23/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022] Open
Abstract
Bacterial α-type carbonic anhydrase (α-CA) is a zinc metalloenzyme that catalyzes the reversible and extremely rapid interconversion of carbon dioxide to bicarbonate. In this study, we report the first crystal structure of a hyperthermostable α-CA from Persephonella marina EXH1 (pm CA) in the absence and presence of competitive inhibitor, acetazolamide. The structure reveals a compactly folded pm CA homodimer in which each monomer consists of a 10-stranded β-sheet in the center. The catalytic zinc ion is coordinated by three highly conserved histidine residues with an exchangeable fourth ligand (a water molecule, a bicarbonate anion, or the sulfonamide group of acetazolamide). Together with an intramolecular disulfide bond, extensive interfacial networks of hydrogen bonds, ionic and hydrophobic interactions stabilize the dimeric structure and are likely responsible for the high thermal stability. We also identified novel binding sites for calcium ions at the crystallographic interface, which serve as molecular glue linking negatively charged and otherwise repulsive surfaces. Furthermore, this large negatively charged patch appears to further increase the thermostability at alkaline pH range via favorable charge-charge interactions between pm CA and solvent molecules. These findings may assist development of novel α-CAs with improved thermal and/or alkaline stability for applications such as CO2 capture and sequestration.
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Affiliation(s)
- Subin Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005,
Korea
| | - Jongmin Sung
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005,
Korea
| | - Jungyoon Yeon
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005,
Korea
| | - Seung Hun Choi
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005,
Korea
| | - Mi Sun Jin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005,
Korea
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8
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Paul S, Paul TK, Taraphder S. Orthogonal order parameters to model the reaction coordinate of an enzyme catalyzed reaction. J Mol Graph Model 2019; 90:18-32. [PMID: 30959266 DOI: 10.1016/j.jmgm.2019.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/01/2019] [Accepted: 03/26/2019] [Indexed: 01/03/2023]
Abstract
The choice of suitable collective variables in formulating an optimal reaction coordinate is a challenging task for activated transitions between a pair of stable states especially when dealing with biochemical changes such as enzyme catalyzed reactions. A detailed benchmarking study is carried out on the choice of collective variables that can distinguish between the stable states unambiguously. We specifically address the issue if these variables may be directly used to model the optimal reaction coordinate, or if it would be better to use their orthogonalized counterparts. The proposed computational scheme is applied to the rate determining intramolecular proton transfer step in the enzyme human carbonic anhydrase II. The optimum reaction coordinate is determined with and without orthogonalization of the collective variables pertinent to a key conformational fluctuation and the actual proton transfer step at the active site of the enzyme. Suitability of the predicted reaction coordinates in different processes is examined in terms of the free energy profile projected along the reaction coordinate, the rate constant of transition and the underlying molecular mechanism of barrier crossing. Our results indicate that a better agreement with earlier simulation and experimental data is obtained when the orthogonalized collective variables are used to model the reaction coordinate.
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Affiliation(s)
- Sanjib Paul
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, India
| | - Tanmoy Kumar Paul
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, India
| | - Srabani Taraphder
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, India.
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9
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Singh S, Lomelino CL, Mboge MY, Frost SC, McKenna R. Cancer Drug Development of Carbonic Anhydrase Inhibitors beyond the Active Site. Molecules 2018; 23:E1045. [PMID: 29710858 PMCID: PMC6099549 DOI: 10.3390/molecules23051045] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 01/29/2023] Open
Abstract
Carbonic anhydrases (CAs) catalyze the reversible hydration of carbon dioxide to produce bicarbonate and a proton. Multiple CA isoforms are implicated in a range of diseases, including cancer. In solid tumors, continuously dividing cells create hypoxic conditions that eventually lead to an acidic microenvironment. Hypoxic tumor cells have different mechanisms in place to regulate and adjust the surrounding microenvironment for survival. These mechanisms include expression of CA isoform IX (CA IX) and XII (CA XII). These enzymes help maintain a physiological intracellular pH while simultaneously contributing to an acidic extracellular pH, leading to tumor cell survival. Expression of CA IX and CA XII has also been shown to promote tumor cell invasion and metastasis. This review discusses the characteristics of CA IX and CA XII, their mechanism of action, and validates their prospective use as anticancer targets. We discuss the current status of small inhibitors that target these isoforms, both classical and non-classical, and their future design in order to obtain isoform-specificity for CA IX and CA XII. Biologics, such as monoclonal antibodies, monoclonal-radionuclide conjugated chimeric antibodies, and antibody-small molecule conjugates are also discussed.
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Affiliation(s)
- Srishti Singh
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Carrie L Lomelino
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Mam Y Mboge
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Susan C Frost
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
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Ye L, Song Q, Lo BTW, Zheng J, Kong D, Murray CA, Tang CC, Tsang SCE. Decarboxylation of Lactones over Zn/ZSM-5: Elucidation of the Structure of the Active Site and Molecular Interactions. Angew Chem Int Ed Engl 2017; 56:10711-10716. [PMID: 28618178 DOI: 10.1002/anie.201704347] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/05/2017] [Indexed: 11/08/2022]
Abstract
Herein, we report the catalytic decarboxylation of γ-valerolactone (GVL) over Zn/ZSM-5 to butene, followed by aromatization at high yield with co-feeding of water. An evaluation of the catalytic performance after prolonged periods of time showed that a water molecule is essential to maintain the decarboxylation and aromatization activities and avoid rapid catalyst deactivation. Synchrotron X-ray powder diffraction and Rietveld refinement were then used to elucidate the structures of adsorbed GVL and immobilized Zn species in combination with EXAFS and NMR spectroscopy. A new route for the cooperative hydrolysis of GVL by framework Zn-OH and Brønsted acidic sites to butene and then to aromatic compounds has thus been demonstrated. The structures and fundamental pathways for the nucleophilic attack of terminal Zn-OH sites are comparable to those of Zn-containing enzymes in biological systems.
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Affiliation(s)
- Lin Ye
- Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
| | - Qi Song
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC, Shanghai, 201208, China
| | - Benedict T W Lo
- Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
| | - Junlin Zheng
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC, Shanghai, 201208, China
| | - Dejing Kong
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC, Shanghai, 201208, China
| | - Claire A Murray
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Chiu C Tang
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - S C Edman Tsang
- Department of Chemistry, University of Oxford, Oxford, OX1 3QR, UK
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11
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Ye L, Song Q, Lo BTW, Zheng J, Kong D, Murray CA, Tang CC, Tsang SCE. Decarboxylation of Lactones over Zn/ZSM-5: Elucidation of the Structure of the Active Site and Molecular Interactions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lin Ye
- Department of Chemistry; University of Oxford; Oxford OX1 3QR UK
| | - Qi Song
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC; Shanghai 201208 China
| | | | - Junlin Zheng
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC; Shanghai 201208 China
| | - Dejing Kong
- Shanghai Research Institute of Petrochemical Technology SRIPT, SINOPEC; Shanghai 201208 China
| | - Claire A. Murray
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Didcot Oxfordshire OX11 0DE UK
| | - Chiu C. Tang
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Didcot Oxfordshire OX11 0DE UK
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12
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Lugo-Martinez J, Pejaver V, Pagel KA, Jain S, Mort M, Cooper DN, Mooney SD, Radivojac P. The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease. PLoS Comput Biol 2016; 12:e1005091. [PMID: 27564311 PMCID: PMC5001644 DOI: 10.1371/journal.pcbi.1005091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/02/2016] [Indexed: 01/12/2023] Open
Abstract
Elucidating the precise molecular events altered by disease-causing genetic variants represents a major challenge in translational bioinformatics. To this end, many studies have investigated the structural and functional impact of amino acid substitutions. Most of these studies were however limited in scope to either individual molecular functions or were concerned with functional effects (e.g. deleterious vs. neutral) without specifically considering possible molecular alterations. The recent growth of structural, molecular and genetic data presents an opportunity for more comprehensive studies to consider the structural environment of a residue of interest, to hypothesize specific molecular effects of sequence variants and to statistically associate these effects with genetic disease. In this study, we analyzed data sets of disease-causing and putatively neutral human variants mapped to protein 3D structures as part of a systematic study of the loss and gain of various types of functional attribute potentially underlying pathogenic molecular alterations. We first propose a formal model to assess probabilistically function-impacting variants. We then develop an array of structure-based functional residue predictors, evaluate their performance, and use them to quantify the impact of disease-causing amino acid substitutions on catalytic activity, metal binding, macromolecular binding, ligand binding, allosteric regulation and post-translational modifications. We show that our methodology generates actionable biological hypotheses for up to 41% of disease-causing genetic variants mapped to protein structures suggesting that it can be reliably used to guide experimental validation. Our results suggest that a significant fraction of disease-causing human variants mapping to protein structures are function-altering both in the presence and absence of stability disruption. Identifying the molecular changes caused by mutations is a major challenge in understanding and treating human genetic disease. To address this problem, we have developed a wide range of profiling tools designed to predict specific types of functional site from protein 3D structures. We then apply these tools to data sets of inherited disease-associated and putatively neutral amino acid substitutions and estimate the relative contribution of the loss and gain of functional residues in disease. Our results suggest that alterations of molecular function are involved in a significant number of cases of human genetic disease and are over-represented as compared to putatively neutral variants. Additionally, we use experimental data to show that it is possible to computationally identify the loss of specific functional events in disease pathogenesis. Finally, our methodology can be used to reliably identify the potential molecular consequences of disease-causing genetic variants and hence prioritize experimental validation.
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Affiliation(s)
- Jose Lugo-Martinez
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America
| | - Vikas Pejaver
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America
| | - Kymberleigh A. Pagel
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America
| | - Shantanu Jain
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Sean D. Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States of America
- * E-mail: (SDM); (PR)
| | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, Indiana, United States of America
- * E-mail: (SDM); (PR)
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13
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Comparison and analysis of zinc and cobalt-based systems as catalytic entities for the hydration of carbon dioxide. PLoS One 2013; 8:e66187. [PMID: 23840420 PMCID: PMC3688778 DOI: 10.1371/journal.pone.0066187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 05/05/2013] [Indexed: 11/19/2022] Open
Abstract
In nature, the zinc metalloenzyme carbonic anhydrase II (CAII) efficiently catalyzes the conversion of carbon dioxide (CO2) to bicarbonate under physiological conditions. Many research efforts have been directed towards the development of small molecule mimetics that can facilitate this process and thus have a beneficial environmental impact, but these efforts have met very limited success. Herein, we undertook quantum mechanical calculations of four mimetics, 1,5,9-triazacyclododedacane, 1,4,7,10-tetraazacyclododedacane, tris(4,5-dimethyl-2-imidazolyl)phosphine, and tris(2-benzimidazolylmethyl)amine, in their complexed form either with the Zn2+ or the Co2+ ion and studied their reaction coordinate for CO2 hydration. These calculations demonstrated that the ability of the complex to maintain a tetrahedral geometry and bind bicarbonate in a unidentate manner were vital for the hydration reaction to proceed favorably. Furthermore, these calculations show that the catalytic activity of the examined zinc complexes was insensitive to coordination states for zinc, while coordination states above four were found to have an unfavorable effect on product release for the cobalt counterparts.
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14
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Akıncıoğlu A, Akbaba Y, Göçer H, Göksu S, Gülçin İ, Supuran CT. Novel sulfamides as potential carbonic anhydrase isoenzymes inhibitors. Bioorg Med Chem 2013; 21:1379-85. [PMID: 23394864 DOI: 10.1016/j.bmc.2013.01.019] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/03/2013] [Accepted: 01/10/2013] [Indexed: 01/05/2023]
Abstract
Sulfamides represent an important class of biologically active compounds. A series of novel sulfamides were synthesized from 1-aminoindanes, 1-aminotetralin, 2-aminoindanes and 2-aminotetralin via the reactions of free amines, benzyl alcohol and chlorosulfonyl isocyanate (CSI) followed by hydrogenolysis of the obtained sulfamoylcarbamates. Carbonic anhydrase (CA, EC 4.2.1.1) inhibitory effects of the new sulfamides have been investigated. The human (h) isozymes hCA I and hCA II have been investigated in this study by using an esterase assay with 4-nitrophenyl acetate as substrate. The new sulfamides showed inhibition constants in the micro-submicromolar range, with one compound (N-(indane-1-yl)sulfamide) showing a Ki of 0.45μM against hCA I and of 1.07μM against hCA II.
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Affiliation(s)
- Akın Akıncıoğlu
- Faculty of Science, Department of Chemistry, Atatürk University, 25240 Erzurum, Turkey
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15
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Akbaba Y, Akıncıoğlu A, Göçer H, Göksu S, Gülçin İ, Supuran CT. Carbonic anhydrase inhibitory properties of novel sulfonamide derivatives of aminoindanes and aminotetralins. J Enzyme Inhib Med Chem 2013; 29:35-42. [DOI: 10.3109/14756366.2012.750311] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yusuf Akbaba
- Faculty of Science, Department of Chemistry, Atatürk University
ErzurumTurkey
| | - Akın Akıncıoğlu
- Faculty of Science, Department of Chemistry, Atatürk University
ErzurumTurkey
| | - Hülya Göçer
- Faculty of Science, Department of Chemistry, Atatürk University
ErzurumTurkey
- Agri Ibrahim Cecen University, Central Researching Laboratory
AgriTurkey
| | - Süleyman Göksu
- Faculty of Science, Department of Chemistry, Atatürk University
ErzurumTurkey
| | - İlhami Gülçin
- Faculty of Science, Department of Chemistry, Atatürk University
ErzurumTurkey
| | - Claudiu T. Supuran
- Universita degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Via della Lastruccia, Sesto Fiorentino (Florence)Italy
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16
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Sattler W, Parkin G. Structural characterization of zinc bicarbonate compounds relevant to the mechanism of action of carbonic anhydrase. Chem Sci 2012. [DOI: 10.1039/c2sc20167d] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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17
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Cuesta-Seijo JA, Borchert MS, Navarro-Poulsen JC, Schnorr KM, Mortensen SB, Lo Leggio L. Structure of a dimeric fungal α-type carbonic anhydrase. FEBS Lett 2011; 585:1042-8. [PMID: 21377464 DOI: 10.1016/j.febslet.2011.03.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 02/16/2011] [Accepted: 03/01/2011] [Indexed: 10/18/2022]
Abstract
The crystal structure of Aspergillus oryzae carbonic anhydrase (AoCA) was determined at 2.7Å resolution and it revealed a dimer, which only has precedents in the α class in two membrane and cancer-associated enzymes. α carbonic anhydrases are underrepresented in fungi compared to the β class, this being the first structural representative. The overall fold and zinc binding site resemble other well studied carbonic anhydrases. A major difference is that the histidine, thought to be the major proton shuttle residue in most mammalian enzymes, is replaced by a phenylalanine in AoCA. This finding poses intriguing questions as to the biological functions of fungal α carbonic anhydrases, which are promising candidates for biotechnological applications.
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18
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Riccardi D, Yang S, Cui Q. Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations. BIOCHIMICA ET BIOPHYSICA ACTA 2010; 1804:342-51. [PMID: 19679196 PMCID: PMC6787916 DOI: 10.1016/j.bbapap.2009.07.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 07/24/2009] [Accepted: 07/29/2009] [Indexed: 10/20/2022]
Abstract
Recent QM/MM analyses of proton transfer function of human carbonic anhydrase II (CAII) are briefly reviewed. The topics include a preliminary analysis of nuclear quadrupole coupling constant calculations for the zinc ion and more detailed analyses of microscopic pK(a) of the zinc-bound water and free energy profile for the proton transfer. From a methodological perspective, our results emphasize that performing sufficient sampling is essential to the calculation of all these quantities, which reflects the well solvated nature of CAII active site. From a mechanistic perspective, our analyses highlight the importance of electrostatics in shaping the energetics and kinetics of proton transfer in CAII for its function. We argue that once the pK(a) for the zinc-bound water is modulated to be in the proper range (approximately 7.0), proton transfer through a relatively well solvated cavity towards/from the protein surface (His64) does not require any major acceleration. Therefore, although structural details like the length of the water wire between the donor and acceptor groups still may make a non-negligible contribution, our computational results and the framework of analysis suggest that the significance of such "fine-tuning" is likely secondary to the modulation of pK(a) of the zinc-bound water. We encourage further experimental analysis with mutation of (charged) residues not in the immediate neighborhood of the zinc ion to quantitatively test this electrostatics based framework; in particular, Phi analysis based on these mutations may shed further light into the relative importance of the classical Grotthus mechanism and the "proton hole" pathway that we have proposed recently for CAII.
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Affiliation(s)
- Demian Riccardi
- Department of Biochemistry, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
| | - Shuo Yang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
- BACTER Institute, University of Wisconsin, Madison, 433 Babcock Drive, Madison, WI 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
- BACTER Institute, University of Wisconsin, Madison, 433 Babcock Drive, Madison, WI 53706
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19
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Avvaru BS, Kim CU, Sippel KH, Gruner SM, Agbandje-McKenna M, Silverman DN, McKenna R. A short, strong hydrogen bond in the active site of human carbonic anhydrase II. Biochemistry 2010; 49:249-51. [PMID: 20000378 PMCID: PMC2810610 DOI: 10.1021/bi902007b] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The crystal structure of human carbonic anhydrase II (HCA II) obtained at 0.9 A resolution reveals that a water molecule, termed deep water, Dw, and bound in a hydrophobic pocket of the active site forms a short, strong hydrogen bond with the zinc-bound solvent molecule, a conclusion based on the observed oxygen-oxygen distance of 2.45 A. This water structure has similarities with hydrated hydroxide found in crystals of certain inorganic complexes. The energy required to displace Dw contributes in significant part to the weak binding of CO(2) in the enzyme-substrate complex, a weak binding that enhances k(cat) for the conversion of CO(2) into bicarbonate. In addition, this short, strong hydrogen bond is expected to contribute to the low pK(a) of the zinc-bound water and to promote proton transfer in catalysis.
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Affiliation(s)
- Balendu Sankara Avvaru
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
| | - Chae Un Kim
- Department of Cornell High Energy Synchrotron Source (CHESS)Cornell University, Ithaca, NY 14853, USA
| | - Katherine H. Sippel
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
| | - Sol M. Gruner
- Department of Cornell High Energy Synchrotron Source (CHESS)Cornell University, Ithaca, NY 14853, USA
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
| | - David N. Silverman
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
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20
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Abstract
Carbonic anhydrase, a zinc metalloenzyme, catalyzes the reversible hydration of carbon dioxide to bicarbonate. It is involved in processes connected with acid-base homeostasis, respiration, and photosynthesis. More than 100 distinct human carbonic anhydrase II (HCAII) 3D structures have been generated in last 3 decades [Liljas A, et al. (1972) Nat New Biol 235:131-137], but a structure of an HCAII in complex with CO(2) or HCO(3)(-) has remained elusive. Here, we report previously undescribed structures of HCAII:CO(2) and HCAII:HCO(3)(-) complexes, together with a 3D molecular film of the enzymatic reaction observed successively in the same crystal after extended exposure to X-ray. We demonstrate that the unexpected enzyme activation was caused in an X-ray dose-dependent manner. Although X-ray damage to macromolecular samples has long been recognized [Ravelli RB, Garman EF (2006) Curr Opin Struct Biol 16:624-629], the detailed structural analysis reports on X-ray-driven reactions have been very rare in literature to date. Here, we report on enzyme activation and the associated chemical reaction in a crystal at 100 K. We propose mechanisms based on water photoradiolysis and/or electron radiolysis as the main cause of enzyme activation.
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21
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“Multi-Scale” QM/MM Methods with Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB). ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-1-4020-9956-4_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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22
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Krishnamurthy VM, Kaufman GK, Urbach AR, Gitlin I, Gudiksen KL, Weibel DB, Whitesides GM. Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem Rev 2008; 108:946-1051. [PMID: 18335973 PMCID: PMC2740730 DOI: 10.1021/cr050262p] [Citation(s) in RCA: 561] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Vijay M. Krishnamurthy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George K. Kaufman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Adam R. Urbach
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Irina Gitlin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Katherine L. Gudiksen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Douglas B. Weibel
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
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23
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Riccardi D, Cui Q. pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications. J Phys Chem A 2007; 111:5703-11. [PMID: 17506534 DOI: 10.1021/jp070699w] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To quantitatively explore the applicability of the generalized solvent boundary potential (GSBP) based QM/MM approach as a "multiscale" framework for studying chemical reactions in biomolecules, the structural and energetic properties of the Human Carbonic Anhydrase II (CAII) are analyzed and compared to those from periodic boundary condition (PBC) simulations and available experimental data. Although the atomic fluctuations from GSBP based simulations are consistently lower compared to those from PBC simulations or crystallographic data, the fluctuations and internal coordinate distributions for residues in the proximity of the active site as well as diffusion constants of active-site water molecules are fairly well described by GSBP simulations. The pKa of the zinc-bound water, calculated with a SCC-DFTB/MM-GSBP based thermodynamic integration approach, agrees well with experiments for the wild type CAII. For the E106Q mutant, however, a 9 pKa unit downward shift relative to the wild type is found in contrast with previous experiments that found little change. This dramatic discrepancy signals a possible change in the mechanism for the interconversion between CO2/HCO3- in the E106Q mutant, which may be similar to the bicarbonate mediated mechanism proposed for the Co2+ substituted CAII (J. Am. Chem. Soc. 2001, 123, 5861).1 The study highlights pKa analyses as a valuable approach for quantitatively validating the computational model for complex biomolecules as well as for revealing energetic properties intimately related to the chemical process of interest.
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Affiliation(s)
- Demian Riccardi
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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24
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Kinetic and mechanistic studies of the reactivity of Zn–OHn (n=1 or 2) species in small molecule analogs of zinc-containing metalloenzymes. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2006. [DOI: 10.1016/s0065-3160(06)41002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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25
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Suzuki A, Ando T, Yamato I, Miyazaki S. FCANAL: Structure based protein function prediction method. Application to enzymes and binding proteins. CHEM-BIO INFORMATICS JOURNAL 2005. [DOI: 10.1273/cbij.5.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ayumi Suzuki
- Department of Biological Science and Technology, Tokyo University of Science
| | - Tadashi Ando
- Department of Biological Science and Technology, Tokyo University of Science
| | - Ichiro Yamato
- Department of Biological Science and Technology, Tokyo University of Science
| | - Satoru Miyazaki
- Department of Pharmaceutical Sciences, Tokyo University of Science
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26
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Whittington DA, Grubb JH, Waheed A, Shah GN, Sly WS, Christianson DW. Expression, Assay, and Structure of the Extracellular Domain of Murine Carbonic Anhydrase XIV. J Biol Chem 2004; 279:7223-8. [PMID: 14660577 DOI: 10.1074/jbc.m310809200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carbonic anhydrase (CA) XIV is the most recently identified mammalian carbonic anhydrase isozyme, and its presence has been demonstrated in a number of tissues. Full-length CA XIV is a transmembrane protein composed of an extracellular catalytic domain, a single transmembrane helix, and a short intracellular polypeptide segment. The amino acid sequence identity of human CA XIV relative to the other membrane-associated isozymes (CA IV, CA IX, and CA XII) is 34-46%. We report here the expression and purification of both the full-length enzyme and a truncated, secretory form of murine CA XIV. Both forms of this isozyme are highly active, and both show an abrogation of activity in the presence of 0.2% SDS, in contrast to the behavior of murine CA IV. We also report the crystal structure of the extracellular domain of murine CA XIV at 2.8 A resolution and of an enzyme-acetazolamide complex at 2.9 A resolution. The structure shows a monomeric glycoprotein with a topology similar to that of other mammalian CA isozymes. Based on the x-ray crystallographic results, we compare and contrast known structures of membrane-associated CA isozymes to rationalize the structural elements responsible for the SDS resistance of CA IV and to discuss prospects for the design of selective inhibitors of membrane-associated CA isozymes.
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Affiliation(s)
- Douglas A Whittington
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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27
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Abstract
John Edsall's investigations of human erythrocyte carbonic anhydrase, a zinc metalloenzyme that powerfully catalyzes the reversible hydration of carbon dioxide, highlighted a conundrum regarding the correct hydration product. The measured kinetic parameters could not be reconciled with the choice of carbonic acid, since its bimolecular recombination rate with enzyme would exceed the diffusion limit. The alternate choice of bicarbonate obviated the recombination rate problem but required that the active site deprotonation exceed the diffusion-limited maximum rate by an even greater extent. This paradox was resolved in favor of bicarbonate when the unsuspected role of buffer species indirectly deprotonating the enzyme was finally proposed, spurring numerous investigations to verify the hypothesis. Edsall's laboratory also reported the accidental discovery of the first competitive inhibitor, imidazole. This opened new avenues to understanding the binding of the CO(2) substrate and stimulated many investigations on this inhibitor. Paramagnetic NMR and crystallographic studies demonstrated that the only other known competitive inhibitor, phenol, apparently shared this unusual binding site. Despite enormous progress since Edsall's retirement, particularly the use of site-directed mutagenesis approaches, the precise interactions of carbon dioxide and bicarbonate with specific active site moieties remain as elusive today as when Edsall first considered these questions.
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Affiliation(s)
- Raja G Khalifah
- BioStratum Incorporated, 4620 Creekstone Drive, Suite 200, Durham, North Carolina 27703, USA.
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28
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Smith KS, Ingram-Smith C, Ferry JG. Roles of the conserved aspartate and arginine in the catalytic mechanism of an archaeal beta-class carbonic anhydrase. J Bacteriol 2002; 184:4240-5. [PMID: 12107142 PMCID: PMC135220 DOI: 10.1128/jb.184.15.4240-4245.2002] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The roles of an aspartate and an arginine, which are completely conserved in the active sites of beta-class carbonic anhydrases, were investigated by steady-state kinetic analyses of replacement variants of the beta-class enzyme (Cab) from the archaeon Methanobacterium thermoautotrophicum. Previous kinetic analyses of wild-type Cab indicated a two-step zinc-hydroxide mechanism of catalysis in which the k(cat)/K(m) value depends only on the rate constants for the CO(2) hydration step, whereas k(cat) also depends on rate constants from the proton transfer step (K. S. Smith, N. J. Cosper, C. Stalhandske, R. A. Scott, and J. G. Ferry, J. Bacteriol. 182:6605-6613, 2000). The recently solved crystal structure of Cab shows the presence of a buffer molecule within hydrogen bonding distance of Asp-34, implying a role for this residue in the proton transport step (P. Strop, K. S. Smith, T. M. Iverson, J. G. Ferry, and D. C. Rees, J. Biol. Chem. 276:10299-10305, 2001). The k(cat)/K(m) values of Asp-34 variants were decreased relative to those of the wild type, although not to an extent which supports an essential role for this residue in the CO(2) hydration step. Parallel decreases in k(cat) and k(cat)/K(m) values for the variants precluded any conclusions regarding a role for Asp-34 in the proton transfer step; however, the k(cat) of the D34A variant was chemically rescued by replacement of 2-(N-morpholino)propanesulfonic acid buffer with imidazole at pH 7.2, supporting a role for the conserved aspartate in the proton transfer step. The crystal structure of Cab also shows Arg-36 with two hydrogen bonds to Asp-34. Arg-36 variants had both k(cat) and k(cat)/K(m) values that were decreased at least 250-fold relative to those of the wild type, establishing an essential function for this residue. Imidazole was unable to rescue the k(cat) of the R36A variant; however, partial rescue of the kinetic parameter was obtained with guanidine-HCl indicating that the guanido group of this residue is important.
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Affiliation(s)
- Kerry S Smith
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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29
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Whittington DA, Waheed A, Ulmasov B, Shah GN, Grubb JH, Sly WS, Christianson DW. Crystal structure of the dimeric extracellular domain of human carbonic anhydrase XII, a bitopic membrane protein overexpressed in certain cancer tumor cells. Proc Natl Acad Sci U S A 2001; 98:9545-50. [PMID: 11493685 PMCID: PMC55489 DOI: 10.1073/pnas.161301298] [Citation(s) in RCA: 234] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2001] [Indexed: 01/06/2023] Open
Abstract
Overexpression of the zinc enzyme carbonic anhydrase (CA; EC ) XII is observed in certain human cancers. This bitopic membrane protein contains an N-terminal extracellular catalytic domain, a membrane-spanning alpha-helix, and a small intracellular C-terminal domain. We have determined the three-dimensional structure of the extracellular catalytic domain of human CA XII by x-ray crystallographic methods at 1.55-A resolution. The structure reveals a prototypical CA fold; however, two CA XII domains associate to form an isologous dimer, an observation that is confirmed by studies of the enzyme in solution. The identification of signature GXXXG and GXXXS motifs in the transmembrane sequence that facilitate helix-helix association is additionally consistent with dimeric architecture. The dimer interface is situated so that the active site clefts of each monomer are clearly exposed on one face of the dimer, and the C termini are located together on the opposite face of the dimer to facilitate membrane interaction. The amino acid composition of the active-site cleft closely resembles that of the other CA isozymes in the immediate vicinity of the catalytic zinc ion, but differs in the region of the nearby alpha-helical "130's segment." The structure of the CA XII-acetazolamide complex is also reported at 1.50-A resolution, and prospects for the design of CA XII-specific inhibitors of possible chemotherapeutic value are discussed.
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Affiliation(s)
- D A Whittington
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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30
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DiTusa CA, McCall KA, Christensen T, Mahapatro M, Fierke CA, Toone EJ. Thermodynamics of metal ion binding. 2. Metal ion binding by carbonic anhydrase variants. Biochemistry 2001; 40:5345-51. [PMID: 11330997 DOI: 10.1021/bi0017327] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to construct molecular motifs with predictable properties in aqueous solution requires an extensive knowledge of the relationships between structure and energetics. The design of metal binding motifs is currently an area of intense interest in the bioorganic community. To date synthetic motifs designed to bind metal ions lack the remarkable affinities observed in biological systems. To better understand the structural basis of metal ion affinity, we report here the thermodynamics of binding of divalent zinc ions to wild-type and mutant carbonic anhydrases and the interpretation of these parameters in terms of structure. Mutations were made both to the direct His ligand at position 94 and to indirect, or second-shell, ligands Gln-92, Glu-117, and Thr-199. The thermodynamics of ligand binding by several mutant proteins is complicated by the development of a second zinc binding site on mutation; such effects must be considered carefully in the interpretation of thermodynamic data. In all instances modification of the protein produces a complex series of changes in both the enthalpy and entropy of ligand binding. In most cases these effects are most readily rationalized in terms of ligand and protein desolvation, rather than in terms of changes in the direct interactions of ligand and protein. Alteration of second-shell ligands, thought to function primarily by orienting the direct ligands, produces profoundly different effects on the enthalpy of binding, depending on the nature of the residue. These results suggest a range of activities for these ligands, contributing both enthalpic and entropic effects to the overall thermodynamics of binding. Together, our results demonstrate the importance of understanding relationships between structure and hydration in the construction of novel ligands and biological polymers.
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Affiliation(s)
- C A DiTusa
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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31
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Affiliation(s)
- S Lindskog
- Department of Biochemistry, Umeå University, S-90187 Umeå, Sweden
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32
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Simulations of Enzymatic Systems: Perspectives from Car-Parrinello Molecular Dynamics Simulations. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1380-7323(01)80007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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33
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Abstract
Carbonic anhydrases catalyze the reversible hydration of CO(2) [CO(2)+H(2)Oright harpoon over left harpoon HCO(3)(-)+H(+)]. Since the discovery of this zinc (Zn) metalloenzyme in erythrocytes over 65 years ago, carbonic anhydrase has not only been found in virtually all mammalian tissues but is also abundant in plants and green unicellular algae. The enzyme is important to many eukaryotic physiological processes such as respiration, CO(2) transport and photosynthesis. Although ubiquitous in highly evolved organisms from the Eukarya domain, the enzyme has received scant attention in prokaryotes from the Bacteria and Archaea domains and has been purified from only five species since it was first identified in Neisseria sicca in 1963. Recent work has shown that carbonic anhydrase is widespread in metabolically diverse species from both the Archaea and Bacteria domains indicating that the enzyme has a more extensive and fundamental role in prokaryotic biology than previously recognized. A remarkable feature of carbonic anhydrase is the existence of three distinct classes (designated alpha, beta and gamma) that have no significant sequence identity and were invented independently. Thus, the carbonic anhydrase classes are excellent examples of convergent evolution of catalytic function. Genes encoding enzymes from all three classes have been identified in the prokaryotes with the beta and gamma classes predominating. All of the mammalian isozymes (including the 10 human isozymes) belong to the alpha class; however, only nine alpha class carbonic anhydrase genes have thus far been found in the Bacteria domain and none in the Archaea domain. The beta class is comprised of enzymes from the chloroplasts of both monocotyledonous and dicotyledonous plants as well as enzymes from phylogenetically diverse species from the Archaea and Bacteria domains. The only gamma class carbonic anhydrase that has thus far been isolated and characterized is from the methanoarchaeon Methanosarcina thermophila. Interestingly, many prokaryotes contain carbonic anhydrase genes from more than one class; some even contain genes from all three known classes. In addition, some prokaryotes contain multiple genes encoding carbonic anhydrases from the same class. The presence of multiple carbonic anhydrase genes within a species underscores the importance of this enzyme in prokaryotic physiology; however, the role(s) of this enzyme is still largely unknown. Even though most of the information known about the function(s) of carbonic anhydrase primarily relates to its role in cyanobacterial CO(2) fixation, the prokaryotic enzyme has also been shown to function in cyanate degradation and the survival of intracellular pathogens within their host. Investigations into prokaryotic carbonic anhydrase have already led to the identification of a new class (gamma) and future research will undoubtedly reveal novel functions for carbonic anhydrase in prokaryotes.
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Affiliation(s)
- K S Smith
- Department of Biochemistry and Molecular Biology, 204 South Frear Laboratory, The Pennsylvania State University, University Park, PA 16802, USA.
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Mao ZW, Liehr G, van Eldik R. Isolation and Characterization of the First Stable Bicarbonato Complexes of Bis(1,10-phenanthroline)copper(II). Identification of Lipscomb- and Lindskog-like Intermediates. J Am Chem Soc 2000. [DOI: 10.1021/ja994071d] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Abstract
Zinc is required for the activity of > 300 enzymes, covering all six classes of enzymes. Zinc binding sites in proteins are often distorted tetrahedral or trigonal bipyramidal geometry, made up of the sulfur of cysteine, the nitrogen of histidine or the oxygen of aspartate and glutamate, or a combination. Zinc in proteins can either participate directly in chemical catalysis or be important for maintaining protein structure and stability. In all catalytic sites, the zinc ion functions as a Lewis acid. Researchers in our laboratory are dissecting the determinants of molecular recognition and catalysis in the zinc-binding site of carbonic anhydrase. These studies demonstrate that the chemical nature of the direct ligands and the structure of the surrounding hydrogen bond network are crucial for both the activity of carbonic anhydrase and the metal ion affinity of the zinc-binding site. An understanding of naturally occurring zinc-binding sites will aid in creating de novo zinc-binding proteins and in designing new metal sites in existing proteins for novel purposes such as to serve as metal ion biosensors.
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Affiliation(s)
- K A McCall
- Duke University Medical Center, Durham, NC 27710, USA
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36
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Cini R. Molecular orbital study of complexes of zinc(II) with sulphide, thiomethanolate, thiomethanol, dimethylthioether, thiophenolate, formiate, acetate, carbonate, hydrogen carbonate, iminomethane and imidazole. Relationships with structural and catalytic zinc in some metallo-enzymes. J Biomol Struct Dyn 1999; 16:1225-37. [PMID: 10447206 DOI: 10.1080/07391102.1999.10508330] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Geometry optimization and energy calculations have been performed at the density functional B3LYP/LANL2DZ level on hydrogen sulfide (HS-), dihydrogensulfide (H2S), thiomethanolate (CH3S-), thiomethanol (CH3SH), thiophenolate (C6H5S-), methoxyde (CH3O-), methanol (CH3OH), formiate (HCOO-), acetate (CH3COO-), carbonate (CO3(2-)), hydrogen carbonate (HCO3-), iminomethane (NH=CH2), [ZnS], [ZnS2]2-, [Zn(HS)]+, [Zn(H2S)]2+, [Zn(HS)4]2-, [Zn(CH3S)]+, [Zn(CH3S)2], [Zn(CH3S)3]-, [Zn(CH3S)4]2-, [Zn(CH3SH)]2+, [Zn(CH3SCH3)]2+, [Zn(C6H5S)]+, [Zn(C6H5S)2], [Zn(C6H5S)3]-, [Zn(HS)(NH=CH2)2]+, [Zn(HS)2(NH=CH2)2], [Zn(HS)(H2O)]+, [Zn(HS)(HCOO)], [Zn(HS)2(HCOO)]-, [Zn(CH3O)]+, [Zn(CH3O)2], [Zn(CH3O)3]-, [Zn(CH3O)4]2, [Zn(CH3OH)]2+, [Zn(HCOO)]+, [Zn(CH3COO)]+, [Zn(CH3COO)2], [Zn(CH3COO)3]-, [Zn(CO3)], [Zn(HCO3)]+, and [Zn(HCO3)(Imz)]+ (Imz, 1,3-imidazole). The computed Zn-S bond distances are 2.174A for [ZnS], 2.274 for [Zn(HS)]+, 2.283 for [Zn(CH3S)]+, and 2.271 for [Zn(C6H5S)]+, showing that sulfide anion forms stronger bonds than substituted sulfides. The nature of the substituents on sulfur influences only slightly the Zn-S distance. The optimized tetra-coordinate [Zn(HS)2(NH=CH2)2] molecules has computed Zn-S and Zn-N bond distances of 2.392 and 2.154A which compare well with the experimental values at the solid state obtained via X-ray diffraction for a number of complex molecules. The computed Zn-O bond distances for chelating carboxylate derivatives like [Zn(HOCOO)]+ (1.998A), [Zn(HCOO)]+ (2.021), and [Zn(CH3COO)]+ (2.001) shows that the strength of the bond is not much influenced by the substituent on carboxylic carbon atom and that CH3- and HO- groups have very similar effects. The DFT analysis shows also that the carboxylate Ligand has a preference for the bidentate mode instead of the monodentate one, at least when the coordination number is small.
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Affiliation(s)
- R Cini
- Department of Chemical and Biosystem Sciences and Technologies, University of Siena, Italy.
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Abstract
The structures and reactions of metal ions in proteins are of tremendous interest in bioinorganic chemistry, as is the potential for metals in creating novel medicines. New results combine these aspects in describing an unexpected mode for metal-mediated drug efficacy that relies on well-established principles of metalloprotein structure.
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Affiliation(s)
- H H Thorp
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290, USA
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Abstract
Carbonic anhydrase (CA; carbonate hydro-lyase, EC 4.2.1.1) is a zinc-containing enzyme that catalyzes the reversible hydration of carbon dioxide: CO2+ H2O<-->HCO3(-)+H+. The enzyme is the target for drugs, such as acetazolamide, methazolamide, and dichlorphenamide, for the treatment of glaucoma. There are three evolutionarily unrelated CA families, designated alpha, beta, and gamma. All known CAs from the animal kingdom are of the alpha type. There are seven mammalian CA isozymes with different tissue distributions and intracellular locations, CA I-VII. Crystal structures of human CA I and II, bovine CA III, and murine CA V have been determined. All of them have the same tertiary fold, with a central 10-stranded beta-sheet as the dominating secondary structure element. The zinc ion is located in a cone-shaped cavity and coordinated to three histidyl residues and a solvent molecule. Inhibitors bind at or near the metal center guided by a hydrogen-bonded system comprising Glu-106 and Thr-199. The catalytic mechanism of CA II has been studied in particular detail. It involves an attack of zinc-bound OH- on a CO2 molecule loosely bound in a hydrophobic pocket. The resulting zinc-coordinated HCO3- ion is displaced from the metal ion by H2O. The rate-limiting step is an intramolecular proton transfer from the zinc-bound water molecule to His-64, which serves as a proton shuttle between the metal center and buffer molecules in the reaction medium.
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Affiliation(s)
- S Lindskog
- Department of Biochemistry, Umeå University, Sweden
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39
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Cini R, Musaev DG, Marzilli LG, Morokuma K. Molecular orbital study of complexes of zinc(II) with imidazole and water molecules. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0166-1280(97)90373-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Kiechle FL. Diagnostic Molecular Pathology in the Twenty-first Century. Clin Lab Med 1996. [DOI: 10.1016/s0272-2712(18)30296-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Stote RH, Karplus M. Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Proteins 1995; 23:12-31. [PMID: 8539245 DOI: 10.1002/prot.340230104] [Citation(s) in RCA: 296] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Force field parameters that use a combination of Lennard-Jones and electrostatic interactions are developed for divalent zinc and tested in solution and protein simulations. It is shown that the parameter set gives free energies of solution in good agreement with experiment. Molecular dynamics simulations of carboxypeptidase A and carbonic anhydrase are performed with these zinc parameters and the CHARMM 22 beta all-atom parameter set. The structural results are as accurate as those obtained in published simulations that use specifically bonded models for the zinc ion and the AMBER force field. The inclusion of longer-range electrostatic interactions by use of the Extended Electrostatics model is found to improve the equilibrium conformation of the active site It is concluded that the present parameter set, which permits different coordination geometries and ligand exchange for the zinc ion, can be employed effectively for both solution and protein simulations of zinc-containing systems.
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Affiliation(s)
- R H Stote
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA
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Bertini I, Luchinat C, Mangani S, Pierattelli R. Carbonic Anhydrase: An Example of How the Cavity Governs the Reactivity at the Zinc Ion. COMMENT INORG CHEM 1995. [DOI: 10.1080/02603599508035779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Affiliation(s)
- B V Plapp
- Department of Biochemistry, University of Iowa, Iowa City 52242, USA
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Liljas A, Håkansson K, Jonsson BH, Xue Y. Inhibition and catalysis of carbonic anhydrase. Recent crystallographic analyses. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 219:1-10. [PMID: 8306976 DOI: 10.1007/978-3-642-79502-2_1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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LILJAS A, HAKANSSON K, JONSSON BH, XUE Y. Inhibition and catalysis of carbonic anhydrase. Recent crystallographic analyses. ACTA ACUST UNITED AC 1994. [DOI: 10.1111/j.1432-1033.1994.tb19909.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Krebs JF, Ippolito JA, Christianson DW, Fierke CA. Structural and functional importance of a conserved hydrogen bond network in human carbonic anhydrase II. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)74269-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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