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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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MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4 Zn. J Comput Aided Mol Des 2023; 37:167-182. [PMID: 36930332 PMCID: PMC10050039 DOI: 10.1007/s10822-023-00499-0] [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: 01/10/2023] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
Carbonic anhydrase is an attractive drug target for the treatment of many diseases. This paper examines the ability of end-state MM/GBSA methods to rank inhibitors of carbonic anhydrase in terms of their binding affinities. The MM/GBSA binding energies were evaluated using different atomic charge schemes (Mulliken, ESP and NPA) at different levels of theories, including Hartree-Fock, B3LYP-D3(BJ), and M06-2X with the 6-31G(d,p) basis set. For a large test set of 32 diverse inhibitors, the use of B3LYP-D3(BJ) ESP atomic charges yielded the strongest correlation with experiment (R2 = 0.77). The use of the recently enhanced Autodock Vina and zinc optimised AD4Zn force field also predicted ligand binding affinities with moderately strong correlation (R2 = 0.64) at significantly lower computational cost. However, the docked poses deviate significantly from crystal structures. Overall, this study demonstrates the applicability of docking to estimate ligand binding affinities for a diverse range of CA inhibitors, and indicates that more theoretically robust MM/GBSA simulations show promise for improving the accuracy of predicted binding affinities, as long as a validated set of parameters is used.
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3
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Kumar S, Deshpande PA. Efficient proton shuttle makes SazCA an excellent CO 2 hydration enzyme. J Biomol Struct Dyn 2022:1-10. [PMID: 35862658 DOI: 10.1080/07391102.2022.2100828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The fastest member of the carbonic anhydrase family catalysing the reversible hydration of carbon dioxide to bicarbonate ions has been recently reported to be SazCA. While thermostable, this enzyme shows exceptional activity at 353 K for the reaction. This study explores the molecular basis for the exceptional activity of SazCA, in contrast to SspCA, probed using molecular dynamics simulations. Our simulations, carried out at different temperatures, indicate the presence of efficient proton shuttle between the active zinc centre and His64 residue in the two enzymes. The proton accepting His64 residue was identified to have in and out conformations with the in conformations being supportive to proton acceptance. Our simulations show a large population of in conformations in SazCA making the enzyme exhibit an exceptional activity. The RMSF and H-bonds analysis confirmed the role of His2 and His207 in supporting the attainment of in conformations in SazCA resulting in exceptional activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shashi Kumar
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Parag A Deshpande
- Quantum and Molecular Engineering Laboratory, Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
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4
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Paul TK, Taraphder S. Molecular modelling of two coordination states of Zn(II) ion at the active site of human carbonic anhydrase II. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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5
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Paul TK, Taraphder S. Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II. Chemphyschem 2020; 21:1455-1473. [DOI: 10.1002/cphc.202000177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/17/2020] [Indexed: 12/12/2022]
Affiliation(s)
- 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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6
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Bharatiy S, Hazra M, Paul M, Mohapatra S, Samantaray D, Dubey R, Sanyal S, Datta S, Hazra S. In Silico Designing of an Industrially Sustainable Carbonic Anhydrase Using Molecular Dynamics Simulation. ACS OMEGA 2016; 1:1081-1103. [PMID: 30023502 PMCID: PMC6044688 DOI: 10.1021/acsomega.6b00041] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/15/2016] [Indexed: 06/08/2023]
Abstract
Carbonic anhydrase (CA) is a family of metalloenzymes that has the potential to sequestrate carbon dioxide (CO2) from the environment and reduce pollution. The goal of this study is to apply protein engineering to develop a modified CA enzyme that has both higher stability and activity and hence could be used for industrial purposes. In the current study, we have developed an in silico method to understand the molecular basis behind the stability of CA. We have performed comparative molecular dynamics simulation of two homologous α-CA, one of thermophilic origin (Sulfurihydrogenibium sp.) and its mesophilic counterpart (Neisseria gonorrhoeae), for 100 ns each at 300, 350, 400, and 500 K. Comparing the trajectories of two proteins using different stability-determining factors, we have designed a highly thermostable version of mesophilic α-CA by introducing three mutations (S44R, S139E, and K168R). The designed mutant α-CA maintains conformational stability at high temperatures. This study shows the potential to develop industrially stable variants of enzymes while maintaining high activity.
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Affiliation(s)
- Sachin
Kumar Bharatiy
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Mousumi Hazra
- Department
of Botany and Microbiology, Gurukula Kangri
University, Haridwar 249404, Uttarakhand, India
| | - Manish Paul
- Department
of Microbiology, Orissa University of Agriculture
and Technology, Bhubaneswar 751003, Odisha, India
| | - Swati Mohapatra
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Deviprasad Samantaray
- Department
of Microbiology, Orissa University of Agriculture
and Technology, Bhubaneswar 751003, Odisha, India
| | - Ramesh
Chandra Dubey
- Department
of Botany and Microbiology, Gurukula Kangri
University, Haridwar 249404, Uttarakhand, India
| | - Shourjya Sanyal
- Complex
and Adaptive System Laboratory, School of Physics, University College Dublin, Dublin 4, Ireland
| | - Saurav Datta
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Saugata Hazra
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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7
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Dutta D, Mishra S. Loss of Catalytic Activity in the E134D, H67A, and H349A Mutants of DapE: Mechanistic Analysis with QM/MM Investigation. J Phys Chem B 2016; 120:11654-11664. [DOI: 10.1021/acs.jpcb.6b07446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Debodyuti Dutta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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Zheng S, Tang Q, He J, Du S, Xu S, Wang C, Xu Y, Lin F. VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems. J Chem Inf Model 2016; 56:811-8. [PMID: 26998926 DOI: 10.1021/acs.jcim.5b00687] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools.
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Affiliation(s)
- Suqing Zheng
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Qing Tang
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Jian He
- Center for Translational Medicine, Department of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Shahekou, Dalian, Liaoning 116023, P. R. China
| | - Shiyu Du
- Engineering Laboratory of Specialty Fibers and Nuclear Energy Materials, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences , 519 Zhuangshi Avenue, Zhenhai, Ningbo, Zhejiang 315201, P. R. China
| | - Shaofang Xu
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Chaojie Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
| | - Yong Xu
- Center of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, Guangdong 510530, P. R. China
| | - Fu Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou 325035, P. R. China
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Halder P, Taraphder S. Identification of putative unfolding intermediates of the mutant His-107-tyr of human carbonic anhydrase II in a multidimensional property space. Proteins 2016; 84:726-43. [PMID: 26756542 DOI: 10.1002/prot.24980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 11/25/2015] [Accepted: 12/10/2015] [Indexed: 11/05/2022]
Abstract
In this article, we develop an extensive search procedure of the multi-dimensional folding energy landscape of a protein. Our aim is to identify different classes of structures that have different aggregation propensities and catalytic activity. Following earlier studies by Daggett et al. [Jong, D. D.; Riley, R.: Alonso, D.O.: Dagett, V. J. Mol. Biol. 2002, 319, 229], a series of high temperature all-atom classical molecular simulation studies has been carried out to derive a multi-dimensional property space. Dynamical changes in these properties are then monitored by projecting them along a one-dimensional reaction coordinate, dmean . We have focused on the application of this method to partition a wide array of conformations of wild type human carbonic anhydrase II (HCA II) and its unstable mutant His-107-Tyr along dmean by sampling a 35-dimensional property space. The resultant partitioning not only reveals the distribution of conformations corresponding to stable structures of HCA II and its mutant, but also allows the monitoring of several partially unfolded and less stable conformations of the mutant. We have investigated the population of these conformations at different stages of unfolding and collected separate sets of structures that are widely separated in the property space. The dynamical diversity of these sets are examined in terms of the loading of their respective first principal component. The partially unfolded structures thus collected are qualitatively mapped on to the experimentally postulated light molten globule (MGL) and molten globule (MG) intermediates with distinct aggregation propensities and catalytic activities. Proteins 2016; 84:726-743. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Puspita Halder
- 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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10
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Paul S, Taraphder S. Determination of the Reaction Coordinate for a Key Conformational Fluctuation in Human Carbonic Anhydrase II. J Phys Chem B 2015; 119:11403-15. [DOI: 10.1021/acs.jpcb.5b03655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sanjib 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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12
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Duarte F, Amrein BA, Kamerlin SCL. Modeling catalytic promiscuity in the alkaline phosphatase superfamily. Phys Chem Chem Phys 2013; 15:11160-77. [PMID: 23728154 PMCID: PMC3693508 DOI: 10.1039/c3cp51179k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/02/2013] [Indexed: 12/19/2022]
Abstract
In recent years, it has become increasingly clear that promiscuity plays a key role in the evolution of new enzyme function. This finding has helped to elucidate fundamental aspects of molecular evolution. While there has been extensive experimental work on enzyme promiscuity, computational modeling of the chemical details of such promiscuity has traditionally fallen behind the advances in experimental studies, not least due to the nearly prohibitive computational cost involved in examining multiple substrates with multiple potential mechanisms and binding modes in atomic detail with a reasonable degree of accuracy. However, recent advances in both computational methodologies and power have allowed us to reach a stage in the field where we can start to overcome this problem, and molecular simulations can now provide accurate and efficient descriptions of complex biological systems with substantially less computational cost. This has led to significant advances in our understanding of enzyme function and evolution in a broader sense. Here, we will discuss currently available computational approaches that can allow us to probe the underlying molecular basis for enzyme specificity and selectivity, discussing the inherent strengths and weaknesses of each approach. As a case study, we will discuss recent computational work on different members of the alkaline phosphatase superfamily (AP) using a range of different approaches, showing the complementary insights they have provided. We have selected this particular superfamily, as it poses a number of significant challenges for theory, ranging from the complexity of the actual reaction mechanisms involved to the reliable modeling of the catalytic metal centers, as well as the very large system sizes. We will demonstrate that, through current advances in methodologies, computational tools can provide significant insight into the molecular basis for catalytic promiscuity, and, therefore, in turn, the mechanisms of protein functional evolution.
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Affiliation(s)
- Fernanda Duarte
- Uppsala University, Science for Life Laboratory (SciLifeLab), Cell and Molecular Biology, Uppsala, Sweden. ; ;
| | - Beat Anton Amrein
- Uppsala University, Science for Life Laboratory (SciLifeLab), Cell and Molecular Biology, Uppsala, Sweden. ; ;
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13
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Bernadat G, Supuran CT, Iorga BI. Carbonic anhydrase binding site parameterization in OPLS-AA force field. Bioorg Med Chem 2012. [PMID: 23182217 DOI: 10.1016/j.bmc.2012.10.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The parameterization of carbonic anhydrase binding site in OPLS-AA force field was performed using quantum chemistry calculations. Both OH2 and OH(-) forms of the binding site were considered, showing important differences in terms of atomic partial charges. Three different parameterization protocols were used, and the results obtained highlighted the importance of including an extended binding site in the charge calculation. The force field parameters were subsequently validated using standard molecular dynamics simulations. The results presented in this work should greatly facilitate the use of molecular dynamics simulations for studying the carbonic anhydrase, and more generally, the metallo-enzymes.
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Affiliation(s)
- Guillaume Bernadat
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Labex LERMIT, Centre de Recherche de Gif, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
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14
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Schmid M, Nogueira ES, Monnard FW, Ward TR, Meuwly M. Arylsulfonamides as inhibitors for carbonic anhydrase: prediction & validation. Chem Sci 2012. [DOI: 10.1039/c1sc00628b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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15
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Maupin CM, Castillo N, Taraphder S, Tu C, McKenna R, Silverman DN, Voth GA. Chemical rescue of enzymes: proton transfer in mutants of human carbonic anhydrase II. J Am Chem Soc 2011; 133:6223-34. [PMID: 21452838 PMCID: PMC4120857 DOI: 10.1021/ja1097594] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In human carbonic anhydrase II (HCA II), the mutation of position 64 from histidine to alanine (H64A) disrupts the rate limiting proton transfer (PT) event, resulting in a reduction of the catalytic activity of the enzyme as compared to the wild-type. Potential of mean force (PMF) calculations utilizing the multistate empirical valence bond (MS-EVB) methodology for H64A HCA II yields a PT free energy barrier significantly higher than that found in the wild-type enzyme. This high barrier, determined in the absence of exogenous buffer and assuming no additional ionizable residues in the PT pathway, indicates the likelihood of alternate enzyme pathways that utilize either ionizable enzyme residues (self-rescue) and/or exogenous buffers (chemical rescue). It has been shown experimentally that the catalytic activity of H64A HCA II can be chemically rescued to near wild-type levels by the addition of the exogenous buffer 4-methylimidazole (4MI). Crystallographic studies have identified two 4MI binding sites, yet site-specific mutations intended to disrupt 4MI binding have demonstrated these sites to be nonproductive. In the present work, MS-EVB simulations show that binding of 4MI near Thr199 in the H64A HCA II mutant, a binding site determined by NMR spectroscopy, results in a viable chemical rescue pathway. Additional viable rescue pathways are also identified where 4MI acts as a proton transport intermediary from the active site to ionizable residues on the rim of the active site, revealing a probable mode of action for the chemical rescue pathway.
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Affiliation(s)
- C. Mark Maupin
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112
| | - Norberto Castillo
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112
| | - Srabani Taraphder
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Chingkuang Tu
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610
| | - David N. Silverman
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610
| | - Gregory A. Voth
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112
- Department of Chemistry, James Frank Institute, and Computation Institute, University of Chicago, 5735 S. Ellis Ave., Chicago, IL 60637
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Zhang JL, Zheng QC, Zhang HX. Theoretical improvement of the specific inhibitor of human carbonic anhydrase VII. Comput Biol Chem 2011; 35:50-6. [PMID: 21320803 DOI: 10.1016/j.compbiolchem.2011.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 01/12/2011] [Accepted: 01/13/2011] [Indexed: 10/18/2022]
Abstract
The selectivity of a known arylsulfonamides inhibitor for two isozymes II and VII of human carbonic anhydrases (hCAs) was studied by homology modeling, molecular docking and molecular dynamics methods. The results show that the selectivity of the inhibitor for two isozymes is due to the different side chain lengths between N67 of hCA II and Q64 of hCA VII. One more methene group in the side chain of Q64 of hCA VII makes it possible to form the hydrogen bond with the bromide atom of the known inhibitor. From the point of view, the modification to the known inhibitor was performed to obtain an inhibitor with higher selectivity. The complex conformations of the new designed inhibitor and two isozymes designate the formation of the hydrogen bond between the newly added group (hydroxypropyl group) and Q64 of hCA VII but N67 of hCA II. The results of the binding free energy from the MM/PBSA approach also prove the selectivity improvement of the new inhibitor in comparison with the known inhibitor. The work will help the design of the isozyme-specific inhibitors of hCA VII.
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Affiliation(s)
- Ji-Long Zhang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People's Republic of China
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17
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Lin F, Wang R. Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems. J Chem Theory Comput 2010; 6:1852-70. [PMID: 26615845 DOI: 10.1021/ct900454q] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Metal ions are indispensable for maintaining the structural stability and catalytic activity of metalloproteins. Molecular modeling studies of such proteins with force fields, however, are often hampered by the "missing parameter" problem. In this study, we have derived bond-stretching and angle-bending parameters applicable to zinc-containing systems which are compatible with the AMBER force field. A total of 18 model systems were used to mimic the common coordination configurations observed in the complexes formed by zinc-containing metalloproteins. The Hessian matrix of each model system computed at the B3LYP/6-311++G(2d,2p) level was then analyzed by Seminario's method to derive the desired force constants. These parameters were validated extensively in structural optimizations and molecular dynamics simulations of four selected model systems as well as one protein-ligand complex formed by carbonic anhydrase II. The best performance was achieved by a bonded model in combination with the atomic partial charges derived by the restrained electrostatic potential method. After some minor optimizations, this model was also able to reproduce the vibrational frequencies computed by quantum mechanics. This study provides a comprehensive set of force field parameters applicable to a variety of zinc-containing molecular systems. In principle, our approach can be applied to other molecular systems with missing force field parameters.
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Affiliation(s)
- Fu Lin
- State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, People's Republic of China
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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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Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-90-481-3034-4_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Proton transport in carbonic anhydrase: Insights from molecular simulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:332-41. [PMID: 19765680 DOI: 10.1016/j.bbapap.2009.09.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 09/03/2009] [Accepted: 09/05/2009] [Indexed: 12/14/2022]
Abstract
This article reviews the insights gained from molecular simulations of human carbonic anhydrase II (HCA II) utilizing non-reactive and reactive force fields. The simulations with a reactive force field explore protein transfer and transport via Grotthuss shuttling, while the non-reactive simulations probe the larger conformational dynamics that underpin the various contributions to the rate-limiting proton transfer event. Specific attention is given to the orientational stability of the His64 group and the characteristics of the active site water cluster, in an effort to determine both of their impact on the maximal catalytic rate. The explicit proton transfer and transport events are described by the multistate empirical valence bond (MS-EVB) method, as are alternative pathways for the excess proton charge defect to enter/leave the active site. The simulation results are interpreted in light of experimental results on the wild-type enzyme and various site-specific mutations of HCA II in order to better elucidate the key factors that contribute to its exceptional efficiency.
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21
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Maupin CM, McKenna R, Silverman DN, Voth GA. Elucidation of the proton transport mechanism in human carbonic anhydrase II. J Am Chem Soc 2009; 131:7598-608. [PMID: 19438233 PMCID: PMC2774804 DOI: 10.1021/ja8091938] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human carbonic anhydrase II (HCA II) is one of the fastest known enzymes, which utilizes a rate-limiting proton transport (PT) step in its enzymatic reaction. To evaluate the PT event at an atomistic level, the multistate empirical valence bond (MS-EVB) method has been utilized in this work. It is observed that the PT event in HCA II exploits a transient active site water cluster to transport the excess proton between the catalytic zinc-bound water/hydroxide and the proton shuttling residue, His64. This PT event is found to be dependent on the enzyme's ability to form and stabilize the active site water cluster in addition to its ability to orient His64 in a favorable conformation. Evaluation of the PT free energy barrier for different orientations of His64 reveals this residue's vital role as a proton transporter and elucidates its direct effect on the barrier to PT through the active site water. It is suggested that the rate-limiting step oscillates between the active site water PT event to His64 and the de/protonation of His64 depending on the exogenous buffer concentration and the orientation of His64. In the absence of a PT acceptor/donor at position 64, it is found that the excess proton will utilize one of three distinct paths to enter/leave the active site. This latter result not only allows for an increased understanding of how enzymes capitalize on the protein/solvent interface to guide excess protons to/from areas of interest, it also provides valuable insight into the chemical rescue experiments on HCA II mutants.
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Affiliation(s)
- C. Mark Maupin
- Center for Biophysical Modeling and Simulation and Department of Chemistry, UniVersity of Utah, Salt Lake City, Utah 84112
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, UniVersity of Florida, GainesVille, Florida 32610
| | - David N. Silverman
- Department of Biochemistry and Molecular Biology, College of Medicine, UniVersity of Florida, GainesVille, Florida 32610
- Department of Pharmacology and Therapeutics, College of Medicine, UniVersity of Florida, GainesVille, Florida 32610
| | - Gregory A. Voth
- Center for Biophysical Modeling and Simulation and Department of Chemistry, UniVersity of Utah, Salt Lake City, Utah 84112
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22
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Lin Y, Cao Z, Mo Y. Functional role of Asp160 and the deprotonation mechanism of ammonium in the Escherichia coli ammonia channel protein AmtB. J Phys Chem B 2009; 113:4922-9. [PMID: 19278252 PMCID: PMC2676109 DOI: 10.1021/jp810651m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecular dynamics simulations on the wild-type AmtB protein and its D160A homology model have been performed. Although no significant structural changes due to the mutation of Asp160 were observed, calculations confirmed the critical role of Asp160 for the recognition and binding of NH(4)(+) in AmtB. The carboxyl group of Asp160 is approximately 8 A from NH(4)(+), but their favorable through-space electrostatic interaction is further enhanced by a hydrogen bond chain involving Ala162 (the backbone carbonyl group) and Gly163 (the backbone amide group). This explains the occurrence of the second binding site in AmtB which does not exist in the D160A mutant, as shown in the computed energy profiles. As the initially buried carboxyl group of Asp160 links to the ammonium ion in the periplasmic binding vestibule through a chain of water molecules, a likely deprotonation venue thus is from ammonium to Asp160. Combined QM(PM3)/MM molecular dynamics simulations showed that indeed Asp160 can serve as the proton acceptor and the overall proton transfer process needs to overcome a barrier of merely 7.7 kcal/mol, which is in good agreement with our previous QM(DFT)/MM optimizations. Significantly, the proton transfer adopts an unconventional mechanism by migrating the negative charge from the carboxyl group of Asp160 to NH(4)(+) via two water molecules, which can be illustrated as -CO(2)(-)...H(2)O...H(2)O...NH(4)(+) --> -COOH...H(2)O...OH(-)...NH(4)(+) --> -COOH...H(2)O...H(2)O...NH(3). Apparently, this is also a charge recombination process and thus is exothermic.
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Affiliation(s)
- Yuchun Lin
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Zexing Cao
- Department of Chemistry, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
- Department of Chemistry, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
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23
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La Motta C, Sartini S, Mugnaini L, Salerno S, Simorini F, Taliani S, Marini AM, Da Settimo F, Lavecchia A, Novellino E, Antonioli L, Fornai M, Blandizzi C, Del Tacca M. Exploiting the Pyrazolo[3,4-d]pyrimidin-4-one Ring System as a Useful Template To Obtain Potent Adenosine Deaminase Inhibitors. J Med Chem 2009; 52:1681-92. [DOI: 10.1021/jm801427r] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Concettina La Motta
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Stefania Sartini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Laura Mugnaini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Silvia Salerno
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Francesca Simorini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Sabrina Taliani
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Anna Maria Marini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Federico Da Settimo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Antonio Lavecchia
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Ettore Novellino
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Luca Antonioli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Matteo Fornai
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Corrado Blandizzi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Mario Del Tacca
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
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24
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Frison G, Ohanessian G. Metal-histidine-glutamate as a regulator of enzymatic cycles: a case study of carbonic anhydrase. Phys Chem Chem Phys 2009; 11:374-83. [DOI: 10.1039/b812916a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Maupin CM, Saunders MG, Thorpe IF, McKenna R, Silverman DN, Voth GA. Origins of enhanced proton transport in the Y7F mutant of human carbonic anhydrase II. J Am Chem Soc 2008; 130:11399-408. [PMID: 18671353 PMCID: PMC2562593 DOI: 10.1021/ja802264j] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human carbonic anhydrase II (HCA II), among the fastest enzymes known, catalyzes the reversible hydration of CO 2 to HCO 3 (-). The rate-limiting step of this reaction is believed to be the formation of an intramolecular water wire and transfer of a proton across the active site cavity from a zinc-bound solvent to a proton shuttling residue (His64). X-ray crystallographic studies have shown this intramolecular water wire to be directly stabilized through hydrogen bonds via a small well-defined set of amino acids, namely, Tyr7, Asn62, Asn67, Thr199, and Thr200. Furthermore, X-ray crystallographic and kinetic studies have shown that the mutation of tyrosine 7 to phenylalanine, Y7F HCA II, has the effect of increasing the proton transfer rate by 7-fold in the dehydration direction of the enzyme reaction compared to wild-type (WT). This increase in the proton transfer rate is postulated to be linked to the formation of a more directional, less branched, water wire. To evaluate this proposal, molecular dynamics simulations have been employed to study water wire formation in both the WT and Y7F HCA II mutant. These studies reveal that the Y7F mutant enhances the probability of forming small water wires and significantly extends the water wire lifetime, which may account for the elevated proton transfer seen in the Y7F mutant. Correlation analysis of the enzyme and intramolecular water wire indicates that the Y7F mutant significantly alters the interaction of the active site waters with the enzyme while occupancy data of the water oxygens reveals that the Y7F mutant stabilizes the intramolecular water wire in a manner that maximizes smaller water wire formation. This increase in the number of smaller water wires is likely to elevate the catalytic turnover of an already very efficient enzyme.
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26
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Roy A, Taraphder S. Effect of electrostatic interactions on the formation of proton transfer pathways in human carbonic anhydrase II. J CHEM SCI 2008. [DOI: 10.1007/s12039-007-0068-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Abstract
We have studied room-temperature structural and dynamic properties of the p53 DNA-binding domain in both DNA-bound and DNA-free states. A cumulative 55 ns of explicit solvent molecular dynamics simulations with the particle mesh Ewald treatment of electrostatics was performed. It was found that the mean structures in the production portions of the trajectories agree well with the crystal structure: backbone root-mean-square deviations are in the range of 1.6 and 2.0 A. In both simulations, noticeable backbone deviations from the crystal structure are observed only in loop L6, due to the lack of crystal packing in the simulations. More deviations are observed in the DNA-free simulation, apparently due to the absence of DNA. Computed backbone B-factor is also in qualitative agreement with the crystal structure. Interestingly, little backbone structural change is observed between the mean simulated DNA-bound and DNA-free structures. A notable difference is observed only at the DNA-binding interface. The correlation between native contacts and inactivation mechanisms of tumor mutations is also discussed. In the H2 region, tumor mutations at sites D281, R282, E285, and E286 may weaken five key interactions that stabilize H2, indicating that their inactivation mechanisms may be related to the loss of local structure around H2, which in turn may reduce the overall stability to a measurable amount. In the L2 region, tumor mutations at sites Y163, K164, E171, V173, L194, R249, I251, and E271 are likely to be responsible for the loss of stability in the protein. In addition to apparent DNA contacts that are related to DNA binding, interactions R175/S183, S183/R196, and E198/N235 are highly occupied only in the DNA-bound form, indicating that they are more likely to be responsible for DNA binding.
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Affiliation(s)
| | | | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900
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28
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Roy A, Taraphder S. Identification of Proton-Transfer Pathways in Human Carbonic Anhydrase II. J Phys Chem B 2007; 111:10563-76. [PMID: 17691838 DOI: 10.1021/jp073499t] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the probable proton-transfer pathways from the surface of human carbonic anhydrase II into the active site cavity through His-64 that has been widely implicated as a key residue along the proton-transfer path. A recursive analysis of hydrogen-bonded clusters in the static crystallographic structure shows that there is no complete path through His-64 in either of its experimentally detected conformations. Side chain conformational fluctuation of His-64 from its outward conformation toward the active site is found to provide a crucial dynamic connectivity needed to complete the path coupled to local reorganization of the protein structure and hydration. The energy and free energy barriers along the detected pathway have been estimated to derive the mechanism of His-64 rotation toward the active site. We also investigate a dynamical connectivity map that highlights networks of disordered water molecules that may promote a direct (and probably transient) access of the solvent to the active site. Our studies reveal how such solvent access channels may be related to the putative proton shuttle mediated by His-64. The paths thus identified can be potentially used as reaction coordinates for further studies on the molecular mechanism of enzyme action.
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Affiliation(s)
- Arijit Roy
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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29
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Riccardi D, Schaefer P, Yang Y, Yu H, Ghosh N, Prat-Resina X, König P, Li G, Xu D, Guo H, Elstner M, Cui Q. Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B 2007; 110:6458-69. [PMID: 16570942 DOI: 10.1021/jp056361o] [Citation(s) in RCA: 250] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Motivated by the long-term goal of understanding vectorial biological processes such as proton transport (PT) in biomolecular ion pumps, a number of developments were made to establish combined quantum mechanical/molecular mechanical (QM/MM) methods suitable for studying chemical reactions involving significant charge separation in the condensed phase. These developments were summarized and discussed with representative problems. Specifically, free energy perturbation and boundary potential methods for treating long-range electrostatics were implemented to test the robustness of QM/MM results for protein systems. It was shown that consistent models with sufficient sampling were able to produce quantitatively satisfactory results, such as pKa for titritable groups in the interior of T4-lysozyme, while an inconsistent treatment of electrostatics or lack of sufficient sampling may produce incorrect results. Modifications were made to an approximate density functional theory (SCC-DFTB) to improve the description of proton affinity and hydrogen-bonding, which are crucial for the treatment of PT in polar systems. Test calculations on water autoionization showed clearly that both improvements are necessary for quantitatively reliable results. Finally, the newly established SCC-DFTB/MM-GSBP protocol was used to explore mechanistic issues in carbonic anhydrase (CA). Preliminary results suggest that PT in CA occurs mainly through short water wires containing two water molecules in a thermally activated fashion. Although longer water wires occur with similar frequencies, PT along those pathways, on average, has substantially higher barriers, a result not expected based on previous studies. The fluctuations of water molecules peripheral to the water wire were found to make a larger impact on the PT energetics compared to polar protein residues in the active site, which are largely pre-organized and therefore have less tendency to reorganize during the reaction.
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Affiliation(s)
- Demian Riccardi
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, Wisconsin 53706, USA
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30
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Swanson JMJ, Maupin CM, Chen H, Petersen MK, Xu J, Wu Y, Voth GA. Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. J Phys Chem B 2007; 111:4300-14. [PMID: 17429993 PMCID: PMC2548316 DOI: 10.1021/jp070104x] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The excess proton in aqueous media plays a pivotal role in many fundamental chemical (e.g., acid-base chemistry) and biological (e.g., bioenergetics and enzyme catalysis) processes. Understanding the hydrated proton is, therefore, crucial for chemistry, biology, and materials sciences. Although well studied for over 200 years, excess proton solvation and transport remains to this day mysterious, surprising, and perhaps even misunderstood. In this feature article, various efforts to address this problem through computer modeling and simulation will be described. Applications of computer simulations to a number of important and interesting systems will be presented, highlighting the roles of charge delocalization and Grotthuss shuttling, a phenomenon unique in many ways to the excess proton in water.
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Affiliation(s)
- Jessica M J Swanson
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112-0850, USA
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31
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Shimahara H, Yoshida T, Shibata Y, Shimizu M, Kyogoku Y, Sakiyama F, Nakazawa T, Tate SI, Ohki SY, Kato T, Moriyama H, Kishida KI, Tano Y, Ohkubo T, Kobayashi Y. Tautomerism of Histidine 64 Associated with Proton Transfer in Catalysis of Carbonic Anhydrase. J Biol Chem 2007; 282:9646-9656. [PMID: 17202139 DOI: 10.1074/jbc.m609679200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The imidazole (15)N signals of histidine 64 (His(64)), involved in the catalytic function of human carbonic anhydrase II (hCAII), were assigned unambiguously. This was accomplished by incorporating the labeled histidine as probes for solution NMR analysis, with (15)N at ring-N(delta1) and N(epsilon2), (13)Cat ring-Cepsilon1, (13)C and (15)N at all carbon and nitrogen, or (15)N at the amide nitrogen and the labeled glycine with (13)C at the carbonyl carbon. Using the pH dependence of ring-(15)N signals and a comparison between experimental and simulated curves, we determined that the tautomeric equilibrium constant (K(T)) of His(64) is 1.0, which differs from that of other histidine residues. This unique value characterizes the imidazole nitrogen atoms of His(64) as both a general acid (a) and base (b): its epsilon2-nitrogen as (a) releases one proton into the bulk, whereas its delta1-nitrogen as (b) extracts another proton from a water molecule within the water bridge coupling to the zinc-bound water inside the cave. This accelerates the generation of zinc-bound hydroxide to react with the carbon dioxide. Releasing the productive bicarbonate ion from the inside separates the water bridge pathway, in which the next water molecules move into beside zinc ion. A new water molecule is supplied from the bulk to near the delta1-nitrogen of His(64). These reconstitute the water bridge. Based on these features, we suggest here a catalytic mechanism for hCAII: the tautomerization of His(64) can mediate the transfers of both protons and water molecules at a neutral pH with high efficiency, requiring no time- or energy-consuming processes.
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Affiliation(s)
- Hideto Shimahara
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1211; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871; Institute for Protein Research, Osaka University, Suita, Osaka 565-0871; Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan
| | - Takuya Yoshida
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871
| | - Yasutaka Shibata
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871
| | - Masato Shimizu
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871
| | - Yoshimasa Kyogoku
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871
| | - Fumio Sakiyama
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871
| | | | - Shin-Ichi Tate
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1211
| | - Shin-Ya Ohki
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1211
| | - Takeshi Kato
- Medical School Osaka University, Suita, Osaka 565-0871
| | | | | | - Yasuo Tano
- Medical School Osaka University, Suita, Osaka 565-0871
| | - Tadayasu Ohkubo
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871
| | - Yuji Kobayashi
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871; Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka 569-1094, Japan.
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32
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Riccardi D, König P, Prat-Resina X, Yu H, Elstner M, Frauenheim T, Cui Q. "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. J Am Chem Soc 2007; 128:16302-11. [PMID: 17165785 PMCID: PMC2561195 DOI: 10.1021/ja065451j] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Proton transfers are fundamental to chemical processes in solution and biological systems. Often, the well-known Grotthuss mechanism is assumed where a series of sequential "proton hops" initiates from the donor and combines to produce the net transfer of a positive charge over a long distance. Although direct experimental evidence for the sequential proton hopping has been obtained recently, alternative mechanisms may be possible in complex molecular systems. To understand these events, all accessible protonation states of the mediating groups should be considered. This is exemplified by transfers through water where the individual water molecules can exist in three protonation states (water, hydronium, and hydroxide); as a result, an alternative to the Grotthuss mechanism for a proton transfer through water is to generate a hydroxide by first protonating the acceptor and then transfer the hydroxide toward the donor through water. The latter mechanism can be most generally described as the transfer of a "proton hole" from the acceptor to the donor where the "hole" characterizes the deprotonated state of any mediating molecule. This pathway is distinct and is rarely considered in the discussion of proton-transfer processes. Using a calibrated quantum mechanical/molecular mechanical (QM/MM) model and an effective sampling technique, we study proton transfers in two solution systems and in Carbonic Anhydrase II. Although the relative weight of the "proton hole" and Grotthuss mechanisms in a specific system is difficult to determine precisely using any computational approach, the current study establishes an energetics motivated framework that hinges on the donor/acceptor pKa values and electrostatics due to the environment to argue that the "proton hole" transfer is likely as important as the classical Grotthuss mechanism for proton transport in many complex molecular systems.
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Affiliation(s)
- Demian Riccardi
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, Wisconsin 53706, USA
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33
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Schaefer P, Riccardi D, Cui Q. Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys 2007; 123:014905. [PMID: 16035867 DOI: 10.1063/1.1940047] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A robust approach for dealing with electrostatic interactions for spherical boundary conditions has been implemented in the QM/MM framework. The development was based on the generalized solvent boundary potential (GSBP) method proposed by Im et al. [J. Chem. Phys. 114, 2924 (2001)], and the specific implementation was applied to the self-consistent-charge density-functional tight-binding approach as the quantum mechanics (QM) level, although extension to other QM methods is straightforward. Compared to the popular stochastic boundary-condition scheme, the new protocol offers a balanced treatment between quantum mechanics/molecular mechanics (QM/MM) and MM/MM interactions; it also includes the effect of the bulk solvent and macromolecule atoms outside of the microscopic region at the Poisson-Boltzmann level. The new method was illustrated with application to the enzyme human carbonic anhydrase II and compared to stochastic boundary-condition simulations using different electrostatic treatments. The GSBP-based QM/MM simulations were most consistent with available experimental data, while conventional stochastic boundary simulations yielded various artifacts depending on different electrostatic models. The results highlight the importance of carefully treating electrostatics in QM/MM simulations of biomolecules and suggest that the commonly used truncation schemes should be avoided in QM/MM simulations, especially in simulations that involve extensive conformational samplings. The development of the GSBP-based QM/MM protocol has opened up the exciting possibility of studying chemical events in very complex biomolecular systems in a multiscale framework.
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Affiliation(s)
- Patricia Schaefer
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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Bhatt D, Fisher SZ, Tu C, McKenna R, Silverman DN. Location of binding sites in small molecule rescue of human carbonic anhydrase II. Biophys J 2006; 92:562-70. [PMID: 17071654 PMCID: PMC1751391 DOI: 10.1529/biophysj.106.093203] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small molecule rescue of mutant forms of human carbonic anhydrase II (HCA II) occurs by participation of exogenous donors/acceptors in the proton transfer pathway between the zinc-bound water and solution. To examine more thoroughly the energetics of this activation, we have constructed a mutant, H64W HCA II, which we have shown is activated by 4-methylimidazole (4-MI) by a mechanism involving the binding of 4-MI to the side chain of Trp-64 approximately 8 A from the zinc. A series of experiments are consistent with the activation of H64W HCA II by the interaction of imidazole and pyridine derivatives as exogenous proton donors with the indole ring of Trp-64; these experiments include pH profiles and H/D solvent isotope effects consistent with proton transfer, observation of approximately fourfold greater activation with the mutant containing Trp-64 compared with Gly-64, and the observation by x-ray crystallography of the binding of 4-MI associated with the indole side chain of Trp-64 in W5A-H64W HCA II. Proton donors bound at the less flexible side chain of Trp-64 in W5A-H64W HCA II do not show activation, but such donors bound at the more flexible Trp-64 of H64W HCA II do show activation, supporting suggestions that conformational mobility of the binding site is associated with more efficient proton transfer. Evaluation using Marcus theory showed that the activation of H64W HCA II by these proton donors was reflected in the work functions w(r) and w(p) rather than in the intrinsic Marcus barrier itself, consistent with the role of solvent reorganization in catalysis.
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Affiliation(s)
- Deepa Bhatt
- Department of Pharmacology and Therapeutics, College of Medicine, University of Florida, Gainesville, Florida, USA
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35
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Small YA, Guallar V, Soudackov AV, Hammes-Schiffer S. Hydrogen Bonding Pathways in Human Dihydroorotate Dehydrogenase. J Phys Chem B 2006; 110:19704-10. [PMID: 17004840 DOI: 10.1021/jp065034t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydroorotate dehydrogenase (DHOD) catalyzes the only redox reaction in the pathway for pyrimidine biosynthesis. In this reaction, a proton is transferred from a carbon atom of the substrate to a serine residue, and a hydride is transferred from another carbon atom of the substrate to a cofactor. The deprotonation of the substrate is postulated to involve a proton relay mechanism along a hydrogen bonding pathway in the active site. In this paper, molecular dynamics simulations are used to identify and characterize potential hydrogen bonding pathways that could facilitate the redox reaction catalyzed by human DHOD. The observed pathways involve hydrogen bonding of the active base serine to a water molecule, which is hydrogen bonded to the substrate carboxylate group or a threonine residue. The threonine residue is positioned to enable proton transfer to another water molecule leading to the bulk solvent. The impact of mutating the active base serine to cysteine is also investigated. This mutation is found to increase the average donor-acceptor distances for proton and hydride transfer and to disrupt the hydrogen bonding pathways observed for the wild-type enzyme. These effects could lead to a significant decrease in enzyme activity, as observed experimentally for the analogous mutant in Escherichia coli DHOD.
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Affiliation(s)
- Yolanda A Small
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, 16802, USA
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36
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König PH, Ghosh N, Hoffmann M, Elstner M, Tajkhorshid E, Frauenheim T, Cui Q. Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps. J Phys Chem A 2006; 110:548-63. [PMID: 16405327 PMCID: PMC2728601 DOI: 10.1021/jp052328q] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of quantum mechanics-molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.
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Affiliation(s)
- P H König
- Theoretische Physik, Universität Paderborn, Warburger Strasse 100, 33098 Paderborn, Germany
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37
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Park JG, Sill PC, Makiyi EF, Garcia-Sosa AT, Millard CB, Schmidt JJ, Pang YP. Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A. Bioorg Med Chem 2005; 14:395-408. [PMID: 16203152 DOI: 10.1016/j.bmc.2005.08.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 08/08/2005] [Accepted: 08/09/2005] [Indexed: 10/25/2022]
Abstract
Botulinum neurotoxin serotype A (BoNTA) is one of the most toxic substances known. Currently, there is no antidote to BoNTA. Small molecules identified from high-throughput screening reportedly inhibit the endopeptidase--the zinc-bound, catalytic domain of BoNTA--at a drug concentration of 20 microM. However, optimization of these inhibitors is hampered by challenges including the computational evaluation of the ability of a zinc ligand to compete for coordination with nearby residues in the active site of BoNTA. No improved inhibitor of the endopeptidase has been reported. This article reports the development of a serotype-selective, small-molecule inhibitor of BoNTA with a K(i) of 12 microM. This inhibitor was designed to coordinate the zinc ion embedded in the active site of the enzyme for affinity and to interact with a species-specific residue in the active site for selectivity. It is the most potent small-molecule inhibitor of BoNTA reported to date. The results suggest that multiple molecular dynamics simulations using the cationic dummy atom approach are useful to structure-based design of zinc protease inhibitors.
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Affiliation(s)
- Jewn Giew Park
- Computer-Aided Molecular Design Laboratory, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
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38
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Sakharov DV, Lim C. Zn protein simulations including charge transfer and local polarization effects. J Am Chem Soc 2005; 127:4921-9. [PMID: 15796557 DOI: 10.1021/ja0429115] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nearly half of all proteins contain metal ions, which perform a wide variety of specific functions associated with life processes. However, insights into the local/global, structural and dynamical fluctuations in metalloproteins from molecular dynamics simulations have been hampered by the "conventional" potential energy function (PEF) used in nonmetalloprotein simulations, which does not take into the nonnegligible charge transfer and polarization effects in many metal complexes. Here, we have carried out molecular dynamics simulations of Zn(2+) bound to Cys(-) and/or His(0) in proteins using both the conventional PEF and a novel PEF that accounts for the significant charge transfer and polarization effects in these Zn complexes. Simulations with the conventional PEF yield a nontetrahedral Cys(2)His(2) Zn-binding site and significantly overestimate the experimental Zn-S(Cys(-)) distance. In contrast, simulations with the new PEF accurately reproduce the experimentally observed tetrahedral structures of Cys(2)His(2) and Cys(4) Zn-binding sites in proteins, even when the simulation started from a nontetrahedral Zn(2+) configuration. This suggests that simulations with the new PEF could account for coordinational changes at Zn, which occurs during the folding/unfolding of Zn-finger proteins and certain enzymatic reactions The strategy introduced here can easily be applied to investigate Zn(2+) interacting with protein ligands other than Cys(-) and His(0). It can also be extended to study the interaction of other metals that have significant charge transfer and polarization effects.
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Affiliation(s)
- Dmitri V Sakharov
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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39
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Garcia-Viloca M, Nam K, Alhambra C, Gao J. Solvent and Protein Effects on the Vibrational Frequency Shift and Energy Relaxation of the Azide Ligand in Carbonic Anhydrase. J Phys Chem B 2004. [DOI: 10.1021/jp047526g] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mireia Garcia-Viloca
- Department of Chemistry, Supercomputing Institute, and Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Kwangho Nam
- Department of Chemistry, Supercomputing Institute, and Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Cristóbal Alhambra
- Department of Chemistry, Supercomputing Institute, and Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jiali Gao
- Department of Chemistry, Supercomputing Institute, and Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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40
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Abstract
The seminal hypotheses proposed over the years for enzymatic catalysis are scrutinized. The historical record is explored from both biochemical and theoretical perspectives. Particular attention is given to the impact of molecular motions within the protein on the enzyme's catalytic properties. A case study for the enzyme dihydrofolate reductase provides evidence for coupled networks of predominantly conserved residues that influence the protein structure and motion. Such coupled networks have important implications for the origin and evolution of enzymes, as well as for protein engineering.
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Affiliation(s)
- Stephen J Benkovic
- Department of Chemistry, 152 Davey Laboratory, Pennsylvania State University, University Park, PA 16802, USA.
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42
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Chen H, Li S, Jiang Y. A Density Functional Theory Study on the Intramolecular Proton Transfer in the Enzyme Carbonic Anhydrase. J Phys Chem A 2003. [DOI: 10.1021/jp026788k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui Chen
- Department of Chemistry, Institute of Theoretical and Computational Chemistry, Lab of Mesoscopic Materials Science, Nanjing University, Nanjing 210093, PRC
| | - Shuhua Li
- Department of Chemistry, Institute of Theoretical and Computational Chemistry, Lab of Mesoscopic Materials Science, Nanjing University, Nanjing 210093, PRC
| | - Yuansheng Jiang
- Department of Chemistry, Institute of Theoretical and Computational Chemistry, Lab of Mesoscopic Materials Science, Nanjing University, Nanjing 210093, PRC
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43
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Taraphder S, Hummer G. Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam. J Am Chem Soc 2003; 125:3931-40. [PMID: 12656628 DOI: 10.1021/ja016860c] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton-transfer reactions form an integral part of bioenergetics and enzymatic catalysis. The identification of proton-conducting pathways inside a protein is a key to understanding the mechanisms of biomolecular proton transfer. Proton pathways are modeled here as hydrogen bonded networks of proton-conducting groups, including proton-exchanging groups of amino acid side chains and bound water molecules. We focus on the identification of potential proton-conducting pathways inside a protein of known structure. However, consideration of the static structure alone is often not sufficient to detect suitable proton-transfer paths, leading, for example, from the protein surface to the active site buried inside the protein. We include dynamic fluctuations of amino acid side chains and water molecules into our analysis. To illustrate the method, proton transfer into the active site of cytochrome P450cam is studied. The cooperative rotation of amino acids and motion of water molecules are found to connect the protein surface to the molecular oxygen. Our observations emphasize the intrinsic dynamical nature of proton pathways where critical connections in the network may be transiently provided by mobile groups.
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Affiliation(s)
- Srabani Taraphder
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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44
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Smedarchina Z, Siebrand W, Fernández-Ramos A, Cui Q. Kinetic isotope effects for concerted multiple proton transfer: a direct dynamics study of an active-site model of carbonic anhydrase II. J Am Chem Soc 2003; 125:243-51. [PMID: 12515527 DOI: 10.1021/ja0210594] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rate constant of the reaction catalyzed by the enzyme carbonic anhydrase II, which removes carbon dioxide from body fluids, is calculated for a model of the active site. The rate-determining step is proton transfer from a zinc-bound water molecule to a histidine residue via a bridge of two or more water molecules. The structure of the active site is known from X-ray studies except for the number and location of the water molecules. Model calculations are reported for a system of 58 atoms including a four-coordinated zinc ion connected to a methylimidazole molecule by a chain of two waters, constrained to reproduce the size of the active site. The structure and vibrational force field are calculated by an approximate density functional treatment of the proton-transfer step at the Self-Consistent-Charge Density Functional Tight Binding (SCC-DFTB) level. A single transition state is found indicating concerted triple proton transfer. Direct-dynamics calculations for proton and deuteron transfer and combinations thereof, based on the Approximate Instanton Method and on Variational Transition State Theory with Tunneling Corrections, are in fair agreement and yield rates that are considerably higher and kinetic isotope effects (KIEs) that are somewhat higher than experiment. Classical rate constants obtained from Transition State Theory are smaller than the quantum values but the corresponding KIEs are five times larger. For multiple proton transfer along water bridges classical KIEs are shown to be generally larger than quantum KIEs, which invalidates the standard method to distinguish tunneling and over-barrier transfer. In the present case, a three-way comparison of classical and quantum results with the observed data is necessary to conclude that proton transfer along the bridge proceeds by tunneling. The results suggest that the two-water bridge is present in low concentrations but makes a substantial contribution to proton transport because of its high efficiency. Bridging structures containing more water molecules may have lower energies but are expected to be less efficient. The observed exponential dependence of the KIEs on the deuterium concentration in H(2)O/D(2)O mixtures implies concerted transfer and thus rules out substantial contributions from structures that lead to stepwise transfer via solvated hydronium ions, which presumably dominate proton transfer in less efficient carbonic anhydrase isozymes.
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Affiliation(s)
- Zorka Smedarchina
- Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A 0R6.
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45
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Cui Q, Karplus M. Is a “Proton Wire” Concerted or Stepwise? A Model Study of Proton Transfer in Carbonic Anhydrase. J Phys Chem B 2003. [DOI: 10.1021/jp021931v] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qiang Cui
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, and Laboratoire de Chimie Biophysique, ISIS, Universitè Louis Pasteur, 67000 Strasbourg, France
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Avenue, Madison, Wisconsin 53706, and Laboratoire de Chimie Biophysique, ISIS, Universitè Louis Pasteur, 67000 Strasbourg, France
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46
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Pang YP. Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method. Proteins 2001; 45:183-9. [PMID: 11599021 DOI: 10.1002/prot.1138] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
I report herein two 2.0 ns (1.0 fs time step) MD simulations of two zinc complexes bridged by a hydroxide in phosphotriesterase (PTE) employing the nonbonded method and the cationic dummy atom method that uses virtual atoms to impose orientational requirement for zinc ligands. The cationic dummy atom method was able to simulate the four-ligand coordination of the two zinc complexes in PTE. The distance (3.39 +/- 0.07A) between two nearby zinc ions in the time-average structure of PTE derived from the MD simulation using the cationic dummy atoms matched that in the X-ray structure (3.31 +/- 0.001A). Unequivocally, the time-average structure of PTE was able to fit into the experimentally determined difference electron density map of the corresponding X-ray structure. The results demonstrate the practicality of the cationic dummy atom method for MD simulations of zinc proteins bound with multiple zinc ions. In contrast, a 2.0 ns (1.0 fs time step) MD simulation using the nonbonded method revealed a striking difference in the active site between the X-ray structure and the time-average structure that was unable to fit into the density map of PTE. The results suggest that caution should be used in the MD simulations using the nonbonded method.
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Affiliation(s)
- Y P Pang
- Mayo Clinic Cancer Center, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA.
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47
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Comparison of DFT, Møller–Plesset, and coupled cluster calculations of the proton dissociation energies of imidazole and N -methylacetamide in the presence of zinc(II). ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(01)00405-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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48
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Čuma M, Schmitt UW, Voth GA. A Multi-State Empirical Valence Bond Model for Weak Acid Dissociation in Aqueous Solution. J Phys Chem A 2001. [DOI: 10.1021/jp0038207] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Čuma
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, 315 S. 1400 E. Rm 2020, University of Utah, Salt Lake City, Utah 84112-0850
| | - Udo W. Schmitt
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, 315 S. 1400 E. Rm 2020, University of Utah, Salt Lake City, Utah 84112-0850
| | - Gregory A. Voth
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, 315 S. 1400 E. Rm 2020, University of Utah, Salt Lake City, Utah 84112-0850
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49
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50
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Čuma M, Schmitt UW, Voth GA. A multi-state empirical valence bond model for acid–base chemistry in aqueous solution. Chem Phys 2000. [DOI: 10.1016/s0301-0104(00)00071-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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