1
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Lu LN, Liu C, Yang ZZ, Zhao DX. Refined models of coordination between Al3+/Mg2+ and enzyme in molecular dynamics simulation in terms of ABEEM polarizable force field. J Mol Graph Model 2022; 114:108190. [DOI: 10.1016/j.jmgm.2022.108190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
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2
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Shi Y, Michael MA, Zhang Y. HNO to NO Conversion Mechanism with Copper Zinc Superoxide Dismutase, Comparison with Heme Protein Mediated Conversions, and the Origin of Questionable Reversibility. Chemistry 2021; 27:5019-5027. [PMID: 33398888 DOI: 10.1002/chem.202100015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Indexed: 11/08/2022]
Abstract
The interconversion of NO and HNO, via copper zinc superoxide dismutase (CuZnSOD), is important in biomedicine and for HNO detection. Many mechanistic questions, including the decades-long debate on reversibility, were resolved in this work. Calculations of various active-site and full-protein models show that the basic mechanism is proton-coupled electron transfer with a computed barrier of 10.98 kcal mol-1 , which is in excellent agreement with experimental results (10.62 kcal mol-1 ), and this nonheme protein-mediated reaction has many significant mechanistic differences compared with the conversions mediated by heme proteins due to geometric and electronic factors. The reasons for the irreversible nature of this conversion and models with the first thermodynamically favorable and kinetically feasible mechanism for the experimental reverse reaction were discovered. Such results are the first for nonheme enzyme mediated HNO to NO conversions, which shall facilitate other related studies and HNO probe development.
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Affiliation(s)
- Yelu Shi
- Department of Chemistry and Chemical Biology, Stevens Institute, of Technology, 1 Castle Point on Hudson, Hoboken, NJ, 07030, USA.,College of Science and Technology, Wenzhou-Kean University, 88 Daxue Rd, Wenzhou, Zhejiang, 325060, P.R. China
| | - Matthew A Michael
- Department of Chemistry and Chemical Biology, Stevens Institute, of Technology, 1 Castle Point on Hudson, Hoboken, NJ, 07030, USA
| | - Yong Zhang
- Department of Chemistry and Chemical Biology, Stevens Institute, of Technology, 1 Castle Point on Hudson, Hoboken, NJ, 07030, USA
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3
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Lu LN, Liu C, Yang ZZ. Systematic Parameterization and Simulation of Boronic Acid-β-Lactamase Aqueous Solution in Developing the ABEEMσπ Polarizable Force Field. J Phys Chem A 2020; 124:8614-8632. [PMID: 32910648 DOI: 10.1021/acs.jpca.0c06806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Boronic acid, an inhibitor of β-lactamase, has begun to be applied to the treatment of biological infections and tumors. Scientists are working to develop new and more effective boronic acid. Molecular dynamics (MD) simulation provides a powerful auxiliary tool for drug design. However, the current force fields have no boron-related parameters. In this work, an atom-bond electronegativity equalization method at the σπ level (ABEEMσπ) polarizable force field (ABEEMσπ PFF) of boronic acid and β-lactamase has been developed to determine the potential functions and parameters. The interaction between boron and serine in β-lactamase is regarded as a bonded mode. The interaction between them is simulated by the Morse potential energy function, which is close to the experimental change of the stretching potential energy in a large range. The potential energy surfaces of the bond length, bond angle, and dihedral angle of boronic acid-β-lactamase have the same stability point and change trend as M06-2X/6-311G**. For 47 boronic acid-β-lactamase training molecules, the linear correlation coefficient (R) of the charge distribution between the ABEEMσπ PFF and HF/STO-3G is greater than 0.96. Attributed to the fact that the charge distribution of the ABEEMσπ PFF can fluctuate with the change of geometry and environment, the polarization effect and charge-transfer effect are well reflected. The binding ability of different boronic acids with the same β-lactamase is different. A total of 10 boronic acid-β-lactamase model molecules and 10 boronic acid-β-lactamase and water complexes are simulated. The order of binding energy of five large model molecules calculated by the ABEEMσπ PFF is consistent with that of the MP2 method. The binding energies of boronic acid-β-lactamase and water complexes are close to those of the MP2 method. The results of MD simulation of five aqueous boronic acid-β-lactamase complexes in the NVT ensemble verify the rationality of boron-related parameters of the ABEEMσπ PFF, which have a good application prospect. This study lays a solid theoretical foundation for further study of the inhibition of boronic acid on β-lactamase.
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Affiliation(s)
- Li-Nan Lu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
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4
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Boopathi S, Dinh Quoc Huy P, Gonzalez W, Theodorakis PE, Li MS. Zinc binding promotes greater hydrophobicity inAlzheimer's Aβ42peptide than copper binding: Molecular dynamics and solvation thermodynamics studies. Proteins 2020; 88:1285-1302. [DOI: 10.1002/prot.25901] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/04/2020] [Accepted: 05/13/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Subramanian Boopathi
- Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de IngenieríaUniversidad de Talca Talca Chile
| | | | - Wendy Gonzalez
- Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de IngenieríaUniversidad de Talca Talca Chile
- Millennium Nucleus of Ion Channels‐Associated Diseases (MiNICAD)Universidad de Talca Talca Chile
| | | | - Mai Suan Li
- Institute of PhysicsPolish Academy of Sciences Warsaw Poland
- Institute for Computational Science and Technology, Quang Trung Software City Tan Chanh Hiep Ward Ho Chi Minh City Vietnam
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5
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Huy Pham DQ, Krupa P, Nguyen HL, La Penna G, Li MS. Computational Model to Unravel the Function of Amyloid-β Peptides in Contact with a Phospholipid Membrane. J Phys Chem B 2020; 124:3300-3314. [DOI: 10.1021/acs.jpcb.0c00771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dinh Quoc Huy Pham
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Hoang Linh Nguyen
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu
Duc District, 00133 Ho Chi Minh City, Vietnam
| | - Giovanni La Penna
- National Research Council of Italy (CNR), Institute for Chemistry of Organometallic Compounds (ICCOM), 50019 Florence, Italy
- National Institute for Nuclear Physics (INFN), Section of Roma-Tor Vergata, 00186 Roma, Italy
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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6
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Kwiatos N, Jędrzejczak-Krzepkowska M, Krzemińska A, Delavari A, Paneth P, Bielecki S. Evolved Fusarium oxysporum laccase expressed in Saccharomyces cerevisiae. Sci Rep 2020; 10:3244. [PMID: 32094483 PMCID: PMC7039978 DOI: 10.1038/s41598-020-60204-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/14/2020] [Indexed: 02/06/2023] Open
Abstract
Fusarium oxysporum laccase was functionally expressed in Saccharomyces cerevisiae and engineered towards higher expression levels and higher reactivity towards 2,6-dimethoxyphenol, that could be used as a mediator for lignin modification. A combination of classical culture optimization and protein engineering led to around 30 times higher activity in the culture supernatant. The winner mutant exhibited three times lower Km, four times higher kcat and ten times higher catalytic efficiency than the parental enzyme. The strategy for laccase engineering was composed of a combination of random methods with a rational approach based on QM/MM MD studies of the enzyme complex with 2,6-dimethoxyphenol. Laccase mediator system with 2,6-dimethoxyphenol caused fulvic acids release from biosolubilized coal.
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Affiliation(s)
- Natalia Kwiatos
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Marzena Jędrzejczak-Krzepkowska
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Agnieszka Krzemińska
- Institute of Physics, Lodz University of Technology, Wólczańska 219, 90-924, Lodz, Poland
| | | | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wróblewskiego 15, 93-590, Lodz, Poland
| | - Stanisław Bielecki
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland.
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7
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Haghshenas H, Tavakol H, Kaviani B, Mohammadnezhad G. AMBER Force Field Parameters for Cobalt-Containing Biological Systems: A Systematic Derivation Study. J Phys Chem B 2020; 124:777-787. [PMID: 31912730 DOI: 10.1021/acs.jpcb.9b10739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present work, the parameterization of a set of cobalt-containing systems has been performed to create a comprehensive library for bonding parameters of biological Co-containing systems. A standard process for the extraction and validation of parameters was employed, which could be used to create force field parameters for the other metal-containing systems. All protein data banks were searched to extract common chemical groups in bonding with cobalt, and finally, 16 structures were designed to represent the binding model of the chemical moieties with cobalt. The Hessian matrix of each structure was computed at the B3LYP/6-311++G(2d,2p) level of theory and the Seminario method was employed to compute cobalt bond stretching and angle bending parameters. Validation of the derived parameters was performed using structural minimization and molecular dynamics (MD) simulations of four models. Further validation was performed using an extensive MD simulation on carbonic anhydrase II as a common cobalt-containing metalloprotein. The results demonstrated that among models, the bonded model in combination with the RESP charges can produce the most reliable and accurate structural conformations for the metal site of cobalt-containing systems.
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Affiliation(s)
- Hamed Haghshenas
- Division of Biochemistry, Department of Biology, Faculty of Sciences , Shahrekord University , Shahrekord 038 , Iran
| | - Hossein Tavakol
- Department of Chemistry , Isfahan University of Technology , Isfahan 84156-83111 , Iran
| | - Bita Kaviani
- Division of Genetics, Department of Biology, Faculty of Sciences , Islamic Azad University , Shahrekord Branch , Shahrekord 65234-98712 , Iran
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8
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Strodel B, Coskuner-Weber O. Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer's Disease: Insights from Computational Chemistry Studies. J Chem Inf Model 2019; 59:1782-1805. [PMID: 30933519 DOI: 10.1021/acs.jcim.8b00983] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Monomers and oligomers of the amyloid-β peptide aggregate to form the fibrils found in the brains of Alzheimer's disease patients. These monomers and oligomers are largely disordered and can interact with transition metal ions, affecting the mechanism and kinetics of amyloid-β aggregation. Due to the disordered nature of amyloid-β, its rapid aggregation, as well as solvent and paramagnetic effects, experimental studies face challenges in the characterization of transition metal ions bound to amyloid-β monomers and oligomers. The details of the coordination chemistry between transition metals and amyloid-β obtained from experiments remain debated. Furthermore, the impact of transition metal ion binding on the monomeric or oligomeric amyloid-β structures and dynamics are still poorly understood. Computational chemistry studies can serve as an important complement to experimental studies and can provide additional knowledge on the binding between amyloid-β and transition metal ions. Many research groups conducted first-principles calculations, ab initio molecular dynamics simulations, quantum mechanics/classical mechanics simulations, and classical molecular dynamics simulations for studying the interplay between transition metal ions and amyloid-β monomers and oligomers. This review summarizes the current understanding of transition metal interactions with amyloid-β obtained from computational chemistry studies. We also emphasize the current view of the coordination chemistry between transition metal ions and amyloid-β. This information represents an important foundation for future metal ion chelator and drug design studies aiming to combat Alzheimer's disease.
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Affiliation(s)
- Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , Jülich 52425 , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätstrasse 1 , Düsseldorf 40225 , Germany
| | - Orkid Coskuner-Weber
- Molecular Biotechnology , Turkish-German University , Sahinkaya Caddesi, No. 86, Beykoz , Istanbul 34820 , Turkey
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9
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Olloqui-Sariego JL, Márquez I, Frutos-Beltrán E, Díaz-Moreno I, De la Rosa MA, Calvente JJ, Andreu R, Díaz-Quintana A. Key Role of the Local Hydrophobicity in the East Patch of Plastocyanins on Their Thermal Stability and Redox Properties. ACS OMEGA 2018; 3:11447-11454. [PMID: 31459248 PMCID: PMC6645426 DOI: 10.1021/acsomega.8b01612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/06/2018] [Indexed: 06/10/2023]
Abstract
Understanding the molecular basis of the thermal stability and functionality of redox proteins has important practical applications. Here, we show a distinct thermal dependence of the spectroscopic and electrochemical properties of two plastocyanins from the thermophilic cyanobacterium Phormidium laminosum and their mesophilic counterpart from Synechocystis sp. PCC 6803, despite the similarity of their molecular structures. To explore the origin of these differences, we have mimicked the local hydrophobicity in the east patch of the thermophilic protein by replacing a valine of the mesophilic plastocyanin by isoleucine. Interestingly, the resulting mutant approaches the thermal stability, redox thermodynamics, and dynamic coupling of the flexible site motions of the thermophilic protein, indicating the existence of a close connection between the hydrophobic packing of the east patch region of plastocyanin and the functional control and stability of the oxidized and reduced forms of the protein.
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Affiliation(s)
- José Luis Olloqui-Sariego
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Inmaculada Márquez
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Estrella Frutos-Beltrán
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Miguel A. De la Rosa
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Juan José Calvente
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Rafael Andreu
- Departamento
de Química Física, Universidad
de Sevilla, c/ Profesor García González, 1, 41012 Sevilla, Spain
| | - Antonio Díaz-Quintana
- Instituto
de Investigaciones Químicas, cicCartuja, Universidad de Sevilla y CSIC, Avd. Américo Vespucio 49, 41092 Sevilla, Spain
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10
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Pham DQH, Li MS, La Penna G. Copper Binding Induces Polymorphism in Amyloid-β Peptide: Results of Computational Models. J Phys Chem B 2018; 122:7243-7252. [PMID: 29957993 DOI: 10.1021/acs.jpcb.8b03983] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Amyloid-β (Aβ) peptides are intrinsically disordered peptides, and their aggregation is the hallmark of Alzheimer's disease development. The propensity of the Aβ peptide to intermolecular interactions, the latter favoring different types of oligomers and aggregated forms, has been the object of a huge number of studies. Several facts are now established: the presence of large amount of d-block (M) ions (Zn, Cu, and Fe) in the aggregated forms; the 1:1 M/Aβ ratio favors the formation of amorphous aggregates, with an aggregation rate lower than that in the absence of such ions. In particular, statistical models describing the interactions between copper and amyloid peptides are mandatory to explain the relationship between neurodegeneration, copper dyshomeostasis, and overproduction of reactive oxygen species, the latter event occurring with aging. In this work, we show, by replica-exchange molecular dynamics simulations, that a copper ion (Cu2+) bound as in the experimentally observed prevailing coordination enhances the probability of closed structures that hinder the formation of extended intermolecular hydrogen bonds that stabilize fibrillar ordered aggregated forms. On the other hand, this effect enhances the catalytic role of the complex during the lifetime of soluble forms.
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Affiliation(s)
- Dinh Quoc Huy Pham
- Institute of Physics , Polish Academy of Sciences , Al. Lotnikow 32/46 , 02-668 Warsaw , Poland.,Institute for Computational Science and Technology , 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City 700000 , Vietnam
| | - Mai Suan Li
- Institute of Physics , Polish Academy of Sciences , Al. Lotnikow 32/46 , 02-668 Warsaw , Poland
| | - Giovanni La Penna
- National Research Council Italy (CNR), Institute for Chemistry of Organometallic Compounds (ICCOM) , 50019 Florence , Italy.,Italian Institute for Nuclear Physics (INFN), Section of Roma-Tor Vergata , Rome 00133 , Italy
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11
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Mutter ST, Deeth RJ, Turner M, Platts JA. Benchmarking of copper(II) LFMM parameters for studying amyloid-β peptides. J Biomol Struct Dyn 2017; 36:1145-1153. [DOI: 10.1080/07391102.2017.1313780] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Shaun T. Mutter
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - Robert J. Deeth
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, UK
| | - Matthew Turner
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - James A. Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
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12
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Comba P, Eisenschmidt A, Gahan LR, Hanson GR, Mehrkens N, Westphal M. Dinuclear Zn II and mixed Cu II-Zn II complexes of artificial patellamides as phosphatase models. Dalton Trans 2016; 45:18931-18945. [PMID: 27841434 DOI: 10.1039/c6dt03787a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The patellamides (cyclic pseudo-octapeptides) are produced by Prochloron, a symbiont of the ascidians, marine invertebrate filter feeders. These pseudo-octapeptides are present in the cytoplasm and a possible natural function of putative metal complexes of these compounds is hydrolase activity, however the true biological role is still unknown. The dinuclear CuII complexes of synthetic patellamide derivatives have been shown in in vitro experiments to be efficient hydrolase model catalysts. Many hydrolase enzymes, specifically phosphatases and carboanhydrases, are ZnII-based enzymes and therefore, we have studied the ZnII and mixed ZnII/CuII solution chemistry of a series of synthetic patellamide derivatives, including solution structural and computational work, with the special focus on model phosphatase chemistry with bis-(2,4-dinitrophenyl)phosphate (BDNPP) as the substrate. The ZnII complexes of a series of ligands are shown to form complexes of similar structure and stability compared to the well-studied CuII analogues and the phosphatase reactivities are also similar. Since the complex stabilities and phosphatase activities are generally a little lower compared to those of CuII and since the concentration of ZnII in Prochloron cells is slightly smaller, we conclude that the CuII complexes of the patellamides are more likely to be of biological importance.
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Affiliation(s)
- Peter Comba
- Universität Heidelberg, Anorganisch-Chemisches Institut und Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR), INF 270, D-69120 Heidelberg, Germany.
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13
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Huy PDQ, Vuong QV, La Penna G, Faller P, Li MS. Impact of Cu(II) Binding on Structures and Dynamics of Aβ 42 Monomer and Dimer: Molecular Dynamics Study. ACS Chem Neurosci 2016; 7:1348-1363. [PMID: 27454036 DOI: 10.1021/acschemneuro.6b00109] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The classical force field, which is compatible with the Amber force field 99SB, has been obtained for the interaction of Cu(II) with monomer and dimers of amyloid-β peptides using the coordination where Cu(II) is bound to His6, His13 (or His14), and Asp1 with distorted planar geometry. The newly developed force field and molecular dynamics simulation were employed to study the impact of Cu(II) binding on structures and dynamics of Aβ42 monomer and dimers. It was shown that in the presence of Cu(II) the β content of monomer is reduced substantially compared with the wild-type Aβ42 suggesting that, in accord with experiments, metal ions facilitate formation of amorphous aggregates rather than amyloid fibrils with cross-β structures. In addition, one possible mechanism for amorphous assembly is that the Asp23-Lys28 salt bridge, which plays a crucial role in β sheet formation, becomes more flexible upon copper ion binding to the Aβ N-terminus. The simulation of dimers was conducted with the Cu(II)/Aβ stoichiometric ratios of 1:1 and 1:2. For the 1:1 ratio Cu(II) delays the Aβ dimerization process as observed in a number of experiments. The mechanism underlying this phenomenon is associated with slow formation of interchain salt bridges in dimer as well as with decreased hydrophobicity of monomer upon Cu-binding.
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Affiliation(s)
- Pham Dinh Quoc Huy
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Institute
for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi
Minh City, Vietnam
| | - Quan Van Vuong
- Institute
for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi
Minh City, Vietnam
- Department
of Chemistry, Nagoya University, Nagoya 464-8602, Japan
| | - Giovanni La Penna
- National Research Council of Italy CNR, Institute
for Chemistry of Organometallic Compounds ICCOM, 50019 Florence, Italy
- Italian Institute for Nuclear Physics INFN, Section
of Roma-Tor Vergata, 50019 Florence, Italy
| | - Peter Faller
- Biometals
and Biological Chemistry, Institute of Chemistry, University of Strasbourg, 4 rue B. Pascal, 67081 Strasbourg, France
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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14
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Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases. Struct Chem 2016. [DOI: 10.1007/s11224-016-0764-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, Götz AW. Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1857:1594-1606. [PMID: 27317965 PMCID: PMC4995112 DOI: 10.1016/j.bbabio.2016.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/21/2016] [Accepted: 06/14/2016] [Indexed: 01/22/2023]
Abstract
Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126(II), with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151(II) and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.
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Affiliation(s)
- Longhua Yang
- Department of Chemistry, Nanchang University, 999 Xuefudadao, Nanchang, Jiangxi 330031, China; San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA
| | - Åge A Skjevik
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA; Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA.
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16
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Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, Götz AW. Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field. Data Brief 2016; 8:1209-14. [PMID: 27547799 PMCID: PMC4979044 DOI: 10.1016/j.dib.2016.07.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/01/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. This article presents parameters for the cofactors of ba3-type CcO that are compatible with the all-atom Amber ff12SB and ff14SB force fields. Specifically, parameters were developed for the CuA pair, heme b, and the dinuclear center that consists of heme a3 and CuB bridged by a hydroperoxo group. The data includes geometries in XYZ coordinate format for cluster models that were employed to compute proton transfer energies and derive bond parameters and point charges for the force field using density functional theory. Also included are the final parameter files that can be employed with the Amber leap program to generate input files for molecular dynamics simulations with the Amber software package. Based on the high resolution (1.8 Å) X-ray crystal structure of the ba3-type CcO from Thermus thermophilus (Protein Data Bank ID number PDB: 3S8F), we built a model that is embedded in a POPC lipid bilayer membrane and solvated with TIP3P water molecules and counterions. We provide PDB data files of the initial model and the equilibrated model that can be used for further studies.
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Affiliation(s)
- Longhua Yang
- Department of Chemistry, Nanchang University, 999 Xuefudadao, Nanchang, Jiangxi 330031, China; San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Åge A Skjevik
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Wen-Ge Han Du
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Louis Noodleman
- Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, USA
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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17
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Zanetti-Polzi L, Corni S, Daidone I, Amadei A. Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteins. Phys Chem Chem Phys 2016; 18:18450-9. [PMID: 27339768 DOI: 10.1039/c6cp03394f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here, a methodology is proposed to investigate the collective fluctuation modes of an arbitrary set of observables, maximally contributing to the fluctuation of another functionally relevant observable. The methodology, based on the analysis of fully classical molecular dynamics (MD) simulations, exploits the essential dynamics (ED) method, originally developed to analyse the collective motions in proteins. We apply this methodology to identify the residues that are more relevant for determining the reduction potential (E(0)) of a redox-active protein. To this aim, the fluctuation modes of the single-residue electrostatic potentials mostly contributing to the fluctuations of the total electrostatic potential (the main determinant of E(0)) are investigated for wild-type azurin and two of its mutants with a higher E(0). By comparing the results here obtained with a previous study on the same systems [Zanetti-Polzi et al., Org. Biomol. Chem., 2015, 13, 11003] we show that the proposed methodology is able to identify the key sites that determine E(0). This information can be used for a general deeper understanding of the molecular mechanisms on the basis of the redox properties of the proteins under investigation, as well as for the rational design of mutants with a higher or lower E(0). From the results of the present analysis we propose a new azurin mutant that, according to our calculations, shows a further increase of E(0).
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Affiliation(s)
- Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010, L'Aquila, Italy.
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18
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Zanetti-Polzi L, Bortolotti CA, Daidone I, Aschi M, Amadei A, Corni S. A few key residues determine the high redox potential shift in azurin mutants. Org Biomol Chem 2015; 13:11003-13. [PMID: 26381463 DOI: 10.1039/c5ob01819f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The wide range of variability of the reduction potential (E(0)) of blue-copper proteins has been the subject of a large number of studies in the past several years. In particular, a series of azurin mutants have been recently rationally designed tuning E(0) over a very broad range (700 mV) without significantly altering the redox-active site [Marshall et al., Nature, 2009, 462, 113]. This clearly suggests that interactions outside the primary coordination sphere are relevant to determine E(0) in cupredoxins. However, the molecular determinants of the redox potential variability are still undisclosed. Here, by means of atomistic molecular dynamics simulations and hybrid quantum/classical calculations, the mechanisms that determine the E(0) shift of two azurin mutants with high potential shifts are unravelled. The reduction potentials of native azurin and of the mutants are calculated obtaining results in good agreement with the experiments. The analysis of the simulations reveals that only a small number of residues (including non-mutated ones) are relevant in determining the experimentally observed E(0) variation via site-specific, but diverse, mechanisms. These findings open the path to the rational design of new azurin mutants with different E(0).
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Affiliation(s)
- Laura Zanetti-Polzi
- Center S3, CNR-Institute of Nanoscience, Via Campi 213/A, 41125, Modena, Italy.
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19
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An integrating strategy of AMBER force field parameters for the photoinduced copper nucleases. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1603-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Favre E, Daina A, Carrupt PA, Nurisso A. Modeling the met form of human tyrosinase: a refined and hydrated pocket for antagonist design. Chem Biol Drug Des 2014; 84:206-15. [PMID: 24612747 DOI: 10.1111/cbdd.12306] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/31/2014] [Indexed: 11/30/2022]
Abstract
Tyrosinases are type 3 copper proteins involved in melanin biosynthesis, responsible for skin and hair color in mammals. To steer tyrosinase inhibitor discovery for therapeutic and cosmetic purposes, structural information about human tyrosinase is necessary. As this protein has never been crystallized so far, we derived a robust homology model built using structural information from Streptomyces castaneoglobisporus and Ipomea batata catecholoxidase enzymes. The active site containing two copper atoms in co-ordination with six histidine residues was refined through an optimization protocol based on molecular mechanics parameters for copper co-ordination and charges calculated by quantum mechanics methods. Five structural water molecules and a hydroxyl ion were found to be essential for optimization. The superimposition of the human homology model on crystallographic structures of tyrosinases from other species revealed similar overall backbone topologies, active site conformations, and conserved water molecules. Phenylthiourea (PTU), the tyrosinase inhibitor of reference, was then docked into the solvated human active pocket. A binding mode consistent with crystallographic information was obtained. Taken together, these findings demonstrated that the human tyrosinase model, deposited in the Protein Model Database, is a reliable structure for future rational inhibitor design projects.
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Affiliation(s)
- Elisabeth Favre
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, 30, Quai Ernest-Ansermet, CH-1211, Geneva, Switzerland
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21
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Wei C, Lazim R, Zhang D. Importance of polarization effect in the study of metalloproteins: application of polarized protein specific charge scheme in predicting the reduction potential of azurin. Proteins 2014; 82:2209-19. [PMID: 24753270 DOI: 10.1002/prot.24584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/07/2014] [Accepted: 04/12/2014] [Indexed: 11/08/2022]
Abstract
Molecular dynamics (MD) simulation is commonly used in the study of protein dynamics, and in recent years, the extension of MD simulation to the study of metalloproteins is gaining much interest. Choice of force field is crucial in MD studies, and the inclusion of metal centers complicates the process of accurately describing the electrostatic environment that surrounds the redox centre. Herein, we would like to explore the importance of including electrostatic contribution from both protein and solvent in the study of metalloproteins. MD simulations with the implementation of thermodynamic integration will be conducted to model the reduction process of azurin from Pseudomonas aeruginosa. Three charge schemes will be used to derive the partial charges of azurin. These charge schemes differ in terms of the amount of immediate environment, respective to copper, considered during charge fitting, which ranges from the inclusion of copper and residues in the first coordination sphere during density functional theory charge fitting to the comprehensive inclusion of protein and solvent effect surrounding the metal centre using polarized protein-specific charge scheme. From the simulations conducted, the relative reduction potential of the mutated azurins respective to that of wild-type azurin (ΔEcal) were calculated and compared with experimental values. The ΔEcal approached experimental value with increasing consideration of environmental effect hence substantiating the importance of polarization effect in the study of metalloproteins. This study also attests the practicality of polarized protein-specific charge as a computational tool capable of incorporating both protein environment and solvent effect into MD simulations.
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Affiliation(s)
- Caiyi Wei
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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22
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Wise O, Coskuner O. New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue. J Comput Chem 2014; 35:1278-89. [DOI: 10.1002/jcc.23622] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 02/06/2014] [Accepted: 03/23/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Olivia Wise
- Department of Chemistry; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
- Neurosciences Institute; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
| | - Orkid Coskuner
- Department of Chemistry; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
- Neurosciences Institute; The University of Texas at San Antonio, One UTSA Circle; San Antonio Texas 78249
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23
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Xiang JY, Ponder JW. An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field. J Chem Theory Comput 2014; 10:298-311. [PMID: 25045338 PMCID: PMC4102146 DOI: 10.1021/ct400778h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An extensible polarizable force field for transition metal ion was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parameterization were presented for copper (II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins. Molecular dynamics (MD) simulations were performed on aqueous copper (II) ion at various temperatures, as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn-Teller distortion for hexa-aqua copper (II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a 6-coordination first solvation shell for aqueous copper (II) ion and a 1.8ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies.
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Affiliation(s)
- Jin Yu Xiang
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - Jay W Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
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24
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Characterization of the polymorphic states of copper(II)-bound Aβ(1-16) peptides by computational simulations. J Comput Chem 2013; 34:2524-36. [DOI: 10.1002/jcc.23416] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/23/2013] [Accepted: 08/01/2013] [Indexed: 01/07/2023]
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25
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Neves RPP, Sousa SF, Fernandes PA, Ramos MJ. Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins. J Chem Theory Comput 2013; 9:2718-32. [DOI: 10.1021/ct400055v] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Rui P. P. Neves
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE,
Departamento de Química e Bioquímica,
Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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26
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Comba P, Martin B, Sanyal A. An efficient fluctuating charge model for transition metal complexes. J Comput Chem 2013; 34:1598-608. [DOI: 10.1002/jcc.23297] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/18/2013] [Accepted: 03/22/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Peter Comba
- Anorganisch-Chemisches Institut; Universität Heidelberg; INF 270; D-69120; Heidelberg; Germany
| | - Bodo Martin
- Anorganisch-Chemisches Institut; Universität Heidelberg; INF 270; D-69120; Heidelberg; Germany
| | - Avik Sanyal
- Anorganisch-Chemisches Institut; Universität Heidelberg; INF 270; D-69120; Heidelberg; Germany
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27
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Bochot C, Favre E, Dubois C, Baptiste B, Bubacco L, Carrupt PA, Gellon G, Hardré R, Luneau D, Moreau Y, Nurisso A, Réglier M, Serratrice G, Belle C, Jamet H. Unsymmetrical binding modes of the HOPNO inhibitor of tyrosinase: from model complexes to the enzyme. Chemistry 2013; 19:3655-64. [PMID: 23362183 DOI: 10.1002/chem.201202643] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 11/15/2012] [Indexed: 11/10/2022]
Abstract
The deciphering of the binding mode of tyrosinase (Ty) inhibitors is essential to understand how to regulate the tyrosinase activity. In this paper, by combining experimental and theoretical methods, we studied an unsymmetrical tyrosinase functional model and its interaction with 2-hydroxypyridine-N-oxide (HOPNO), a new and efficient competitive inhibitor for bacterial Ty. The tyrosinase model was a dinuclear copper complex bridged by a chelated ring with two different complexing arms (namely (bis(2-ethylpyridyl)amino)methyl and (bis(2-methylpyridyl)amino)methyl). The geometrical asymmetry of the complex induces an unsymmetrical binding of HOPNO. Comparisons have been made with the binding modes obtained on similar symmetrical complexes. Finally, by using quantum mechanics/molecular mechanics (QM/MM) calculations, we studied the binding mode in tyrosinase from a bacterial source. A new unsymmetrical binding mode was obtained, which was linked to the second coordination sphere of the enzyme.
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Affiliation(s)
- Constance Bochot
- Département de Chimie Moléculaire, Equipes CIRe et Chimie Théorique, Université J. Fourier, UMR-CNRS 5250, ICMG FR-2607, BP 53, 38041, Grenoble, Cedex 09, France
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28
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Mondal S, Ghosh S, De S. A molecular simulation based assessment of binding of metal ions on micelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:11329-11336. [PMID: 22775454 DOI: 10.1021/la301928a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
An assessment of the ability of a micellar surface to bind different metal ions using molecular simulation is presented in this study. Sodium dodecyl sulfate (SDS) is considered as the anionic surfactant. Various relevant characteristics of SDS-metal ion systems are estimated to quantify preferential binding of metal ions. These are electrostatic energy, total potential energy of the system, radial distribution function, and entropy and free energy change of the system. By examining these parameters, the relative extents of binding of different metal ions to the micellar surface are assessed.
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Affiliation(s)
- Sourav Mondal
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India
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29
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Peters MB, Yang Y, Wang B, Füsti-Molnár L, Weaver MN, Merz KM. Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF). J Chem Theory Comput 2010; 6:2935-2947. [PMID: 20856692 PMCID: PMC2941202 DOI: 10.1021/ct1002626] [Citation(s) in RCA: 333] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Currently the Protein Data Bank (PDB) contains over 18,000 structures that contain a metal ion including Na, Mg, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Cd, Ir, Pt, Au, and Hg. In general, carrying out classical molecular dynamics (MD) simulations of metalloproteins is a convoluted and time consuming process. Herein, we describe MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model (Hoops et al., J. Am. Chem. Soc. 1991, 113, 8262-8270) into the AMBER Force Field (FF). MCPB was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs. The PDB was mined for all Zn containing structures with most being tetrahedrally bound. The most abundant primary shell ligand combinations were extracted and FFs were created. These include Zn bound to CCCC, CCCH, CCHH, CHHH, HHHH, HHHO, HHOO, HOOO, HHHD, and HHDD (O = water and the remaining are 1 letter amino acid codes). Bond and angle force constants and RESP charges were obtained from B3LYP/6-31G* calculations of model structures from the various primary shell combinations. MCPB and ZAFF can be used to create FFs for MD simulations of metalloproteins to study enzyme catalysis, drug design and metalloprotein crystal refinement.
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Affiliation(s)
- Martin B. Peters
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - Yue Yang
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - Bing Wang
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - László Füsti-Molnár
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - Michael N. Weaver
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435
| | - Kenneth M. Merz
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, Florida 32611-8435
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30
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Surface residues dynamically organize water bridges to enhance electron transfer between proteins. Proc Natl Acad Sci U S A 2010; 107:11799-804. [PMID: 20547871 DOI: 10.1073/pnas.0914457107] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cellular energy production depends on electron transfer (ET) between proteins. In this theoretical study, we investigate the impact of structural and conformational variations on the electronic coupling between the redox proteins methylamine dehydrogenase and amicyanin from Paracoccus denitrificans. We used molecular dynamics simulations to generate configurations over a duration of 40 ns (sampled at 100-fs intervals) in conjunction with an ET pathway analysis to estimate the ET coupling strength of each configuration. In the wild-type complex, we find that the most frequently occurring molecular configurations afford superior electronic coupling due to the consistent presence of a water molecule hydrogen-bonded between the donor and acceptor sites. We attribute the persistence of this water bridge to a "molecular breakwater" composed of several hydrophobic residues surrounding the acceptor site. The breakwater supports the function of nearby solvent-organizing residues by limiting the exchange of water molecules between the sterically constrained ET region and the more turbulent surrounding bulk. When the breakwater is affected by a mutation, bulk solvent molecules disrupt the water bridge, resulting in reduced electronic coupling that is consistent with recent experimental findings. Our analysis suggests that, in addition to enabling the association and docking of the proteins, surface residues stabilize and control interprotein solvent dynamics in a concerted way.
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31
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Rajapandian V, Hakkim V, Subramanian V. Molecular Dynamics Studies on Native, Loop-Contracted, and Metal Ion-Substituted Azurins. J Phys Chem B 2010; 114:8474-86. [DOI: 10.1021/jp911301v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- V. Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Hakkim
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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32
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Changes in non-core regions stabilise plastocyanin from the thermophilic cyanobacterium Phormidium laminosum. J Biol Inorg Chem 2010; 15:329-38. [PMID: 19915878 DOI: 10.1007/s00775-009-0605-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 10/19/2009] [Indexed: 10/20/2022]
Abstract
We report a theoretical investigation on the different stabilities of two plastocyanins. The first one belongs to the thermophilic cyanobacterium Phormidium laminosum and the second one belongs to its mesophilic relative Synechocystis sp. These proteins share the same topology and secondary-structure elements; however, the melting temperatures of their oxidised species differ by approximately 15 K. Long-time-scale molecular dynamics simulations, performed at different temperatures, show that the thermophilic protein optimises a set of intramolecular interactions (interstrand hydrogen bonding, salt bridging and hydrophobic clustering) within the region that comprises the strands beta 5 and beta 6, loop L5 and the helix. This region exhibits most of the differences in the primary sequence between the two proteins and, in addition, it is involved in the interaction with known physiological partners. Further work is in progress to unveil the specific structural features responsible for the different thermal stability of the two proteins.
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33
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Structural investigation of zymogenic and activated forms of human blood coagulation factor VIII: a computational molecular dynamics study. BMC STRUCTURAL BIOLOGY 2010; 10:7. [PMID: 20184747 PMCID: PMC2837666 DOI: 10.1186/1472-6807-10-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 02/25/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND Human blood coagulation factor VIII (fVIII) is a large plasma glycoprotein with sequential domain arrangement in the order A1-a1-A2-a2-B-a3-A3-C1-C2. The A1, A2 and A3 domains are interconnected by long linker peptides (a1, a2 and a3) that possess the activation sites. Proteolysis of fVIII zymogen by thrombin or factor Xa results in the generation of the activated form (fVIIIa) which serves as a critical co-factor for factor IXa (fIXa) enzyme in the intrinsic coagulation pathway. RESULTS In our efforts to elucidate the structural differences between fVIII and fVIIIa, we developed the solution structural models of both forms, starting from an incomplete 3.7 A X-ray crystal structure of fVIII zymogen, using explicit solvent MD simulations. The full assembly of B-domainless single-chain fVIII was built between the A1-A2 (Ala1-Arg740) and A3-C1-C2 (Ser1669-Tyr2332) domains. The structural dynamics of fVIII and fVIIIa, simulated for over 70 ns of time scale, enabled us to evaluate the integral motions of the multi-domain assembly of the co-factor and the possible coordination pattern of the functionally important calcium and copper ion binding in the protein. CONCLUSIONS MD simulations predicted that the acidic linker peptide (a1) between the A1 and A2 domains is largely flexible and appears to mask the exposure of putative fIXa enzyme binding loop (Tyr555-Asp569) region in the A2 domain. The simulation of fVIIIa, generated from the zymogen structure, predicted that the linker peptide (a1) undergoes significant conformational reorganization upon activation by relocating completely to the A1-domain. The conformational transition led to the exposure of the Tyr555-Asp569 loop and the surrounding region in the A2 domain. While the proposed linker peptide conformation is predictive in nature and warrants further experimental validation, the observed conformational differences between the zymogen and activated forms may explain and support the large body of experimental data that implicated the critical importance of the cleavage of the peptide bond between the Arg372 and Ser373 residues for the full co-factor activity of fVIII.
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34
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Deeth RJ, Diedrich C. Structural and mechanistic insights into the oxy form of tyrosinase from molecular dynamics simulations. J Biol Inorg Chem 2010; 15:117-29. [PMID: 19690900 DOI: 10.1007/s00775-009-0577-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 08/07/2009] [Indexed: 10/20/2022]
Abstract
The first, long time scale (16-ns) ligand field molecular dynamics (LFMD) simulations of the oxy form of tyrosinase are reported. The calculations use our existing type 3 copper force field for the peroxido-bridged [Cu(2)O(2)](2+) unit which is here translated from MMFF into the AMBER format together with a new charge scheme. The protein secondary and tertiary structures are not significantly altered by removing the 'caddie' protein, ORF378, which must be bound to tyrosinase before crystals will grow. A comprehensive principal component analysis of the Cartesian coordinates from the final 8 ns shows that the protein backbone is relatively rigid. However, the significant butterfly fold of the [Cu(2)O(2)](2+) moiety observed in the X-ray structure, presumably due to the caddie protein tyrosine at the active site, is absent in the simulations. LFMD gives a clear and persistent distinction between equatorial and axial Cu-N distances, with the latter about 0.2 A longer and remaining syn to each other. However, the two coordination spheres display important differences. LFMD simulations of the symmetric model complex [mu-eta(2):mu(2)-O(2){Cu(Meim)(3)}(2)](2+) (Meim is 5-methyl-1H-imidazole) provide a mechanism for syn-anti interchange of axial ligands which suggests, in combination with the old experimental X-ray data, the new LFMD simulations and traditional coordination chemistry arguments, that His(54) on Cu(A) is 'insipiently axial' and that a combination of a butterfly distortion of the [Cu(2)O(2)](2+) group and a rotation of the Cu(A)(His)(3) moiety converts the vacant, initially axial, binding site on Cu(A) into a much more favourable equatorial site.
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Affiliation(s)
- Robert J Deeth
- Inorganic Computational Chemistry Group, Department of Chemistry, University of Warwick, Coventry, UK.
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35
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Rajapandian V, Raman SS, Hakkim V, Parthasarathi R, Subramanian V. Molecular mechanics and molecular dynamics study on azurin using extensible and systematic force field (ESFF). ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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Díaz-Moreno I, Muñoz-López FJ, Frutos-Beltrán E, De la Rosa MA, Díaz-Quintana A. Electrostatic strain and concerted motions in the transient complex between plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum. Bioelectrochemistry 2009; 77:43-52. [PMID: 19616485 DOI: 10.1016/j.bioelechem.2009.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 06/04/2009] [Accepted: 06/04/2009] [Indexed: 11/15/2022]
Abstract
Many fleeting macromolecular interactions, like those being involved in electron transport, are essential in biology. However, little is known about the behaviour of the partners and their dynamics within their short-lived complex. To tackle such issue, we have performed molecular dynamics simulations on an electron transfer complex formed by plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum. Besides simulations of the isolated partners, two independent trajectories of the complex were calculated, starting from the two different conformations in the NMR ensemble. The first one leads to a more stable ensemble with a shorter distance between the metal sites of the two partners. The second experiences a significant drift of the complex conformation. Analyses of the distinct calculations show that the conformation of cytochrome f is strained upon binding of its partner, and relaxes upon its release. Interestingly, the principal component analysis of the trajectories indicates that plastocyanin displays a concerted motion with the small domain of cytochrome f that can be attributed to electrostatic interactions between the two proteins.
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Affiliation(s)
- Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla and C.S.I.C.), Spain
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37
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Sabolović J, Gomzi V. Structure Prediction of Bis(amino acidato)copper(II) Complexes with a New Force Field for Molecular Modeling. J Chem Theory Comput 2009; 5:1940-54. [DOI: 10.1021/ct9000203] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jasmina Sabolović
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, P.O. Box 291, HR-10001 Zagreb, Croatia, and Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Vjeran Gomzi
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, P.O. Box 291, HR-10001 Zagreb, Croatia, and Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
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38
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Zhu Y, Wang Y, Chen G, Zhan CG. A three-point method for evaluations of AMBER force field parameters: an application to copper-based artificial nucleases. Theor Chem Acc 2009. [DOI: 10.1007/s00214-008-0496-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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39
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Born K, Comba P, Kerscher M, Linti G, Pritzkow H, Rohwer H. Distortional isomerism with copper(i) complexes of 3,7-diazabicyclo[3.3.1]nonane derivatives. Dalton Trans 2009:362-7. [DOI: 10.1039/b810833a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Pavelka M, Burda JV. Computational study of redox active centres of blue copper proteins: a computational DFT study. Mol Phys 2008. [DOI: 10.1080/00268970802672684] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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41
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LeBard DN, Matyushov DV. Redox entropy of plastocyanin: Developing a microscopic view of mesoscopic polar solvation. J Chem Phys 2008; 128:155106. [DOI: 10.1063/1.2904879] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Zhu Y, Su Y, Li X, Wang Y, Chen G. Evaluation of Amber force field parameters for copper(II) with pyridylmethyl-amine and benzimidazolylmethyl-amine ligands: A quantum chemical study. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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de la Lande A, Martí S, Parisel O, Moliner V. Long Distance Electron-Transfer Mechanism in Peptidylglycine α-Hydroxylating Monooxygenase: A Perfect Fitting for a Water Bridge. J Am Chem Soc 2007; 129:11700-7. [PMID: 17764178 DOI: 10.1021/ja070329l] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The active sites of copper enzymes have been the subject of many theoretical and experimental investigations from a number of years. Such studies have embraced topics devoted to the modeling of the first coordination sphere at the metallic cations up to the development of biomimetic, or bioinspired, catalytic systems. At least from the theoretical viewpoint, fewer efforts have been dedicated to elucidate how the two copper cations act concertedly in noncoupled dicopper enzymes such as peptidylglycine alpha-hydroxylating monooxygenase (PHM) and dopamine beta-monooxygenase (DbetaM). In these metalloenzymes, an electronic transfer is assumed between the two distant copper cations (11 A). Recent experimental results suggest that this transfer occurs through water molecules, a phenomenon which has been theoretically evidenced to be of high efficiency in the case of cytochrome b5 (Science, 2005, 310, 1311). In the present contribution dedicated to PHM, we overpass the common theoretical approaches dedicated to the electronic and geometrical structures of sites CuM or CuH restricted to their first coordination spheres and aim at directly comparing theoretical results to the experimentally measured activity of the PHM enzyme. To achieve this goal, molecular dynamics simulations were performed on wild-type and various mutants of PHM. More precisely, we provide an estimate of the electron-transfer efficiency between the CuM and CuH sites by means of such molecular dynamics simulations coupled to Marcus theory joined to the Beratan model to approximate the required coupling matrix elements. The theoretical results are compared to the kinetics measurements performed on wild and mutated PHM. The present work, the dynamic aspects of which are essential, accounts for the experimental results issued from mutagenesis. It supports the conclusion that an electronic transfer can occur between two copper(I) sites along a bridge involving a set of hydrogen and chemical bonds. Residue Gln170 is evidenced to be the keystone of this water-mediated pathway.
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Affiliation(s)
- Aurélien de la Lande
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
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44
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Branco RJF, Fernandes PA, Ramos MJ. Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase. J Phys Chem B 2007; 110:16754-62. [PMID: 16913815 DOI: 10.1021/jp056855l] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzyme Cu, Zn superoxide dismutase (Cu,Zn-SOD) is a ubiquitous oxireductase, which is responsible for the cellular defense against oxidative stress caused by the high toxicity of the superoxide radical, and has been also linked to some cases of familiar amyotrophic lateral sclerosis. In the present study a set of molecular mechanics parameters for the active site of Cu,Zn-SOD has been derived. Afterward, an extensive molecular dynamics simulation has been carried out in an aqueous environment. The obtained results shed a further light on the structural flexibility of the backbone, where the active site is nested, and the solvation shell occupancy. The relatively small backbone deviation, shown by a root-mean-square deviation below 1.0 A, confirms the accuracy of the parameters. The solvent shell analysis has shown that the first solvation shell is located at about 5 A from the copper ion, generating an empty cavity with enough space to accommodate the superoxide radical. The low residence time means that a high permutation rate of water molecules in both solvation shells is consistent with the efficiency of this catalytic mechanism. Hybrid studies using ONIOM methodologies can now be done to evaluate the mechanistic implications of the explicit inclusion of the whole system.
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Affiliation(s)
- Ricardo J F Branco
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
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45
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Op’t Holt BT, Merz KM. Insights into Cu(I) exchange in HAH1 using quantum mechanical and molecular simulations. Biochemistry 2007; 46:8816-26. [PMID: 17616150 PMCID: PMC2527583 DOI: 10.1021/bi7007195] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human antioxidant protein, HAH1, is an important participant in a Cu(I) transport chain, delivering one Cu(I) ion to the Wilson's (WND) or Menkes disease protein (MNK). Full geometry optimizations and second-derivative calculations were performed on several binding site models using the B3LYP functional to derive parameters for the construction of a novel molecular mechanical (MM) force field for Cu(I) and its ligating residues in HAH1. MM minimization and molecular dynamics (MD) calculations were then performed using the AMBER suite to validate the newly generated force field. The X-ray crystal structure of the protein and the geometry of the Cu(I) binding site within the protein were reproduced by the MD simulations on the protein based on rmsd and visual inspection, validating the new force field parameters. The results from the quantum mechanical (QM) and MD simulations suggest that either a two- or three-coordinate exchange reaction is preferred and that it is unlikely that a four-coordinate Cu(I) species plays a role in copper exchange.
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Affiliation(s)
| | - Kenneth M. Merz
- To whom correspondence should be addressed: Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, PO Box 118435, University of Florida, Gainesville, FL 32611-8435. Tel: (352) 392-6973. Fax: (352) 392-8722.
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46
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Deeth RJ. Comprehensive Molecular Mechanics Model for Oxidized Type I Copper Proteins: Active Site Structures, Strain Energies, and Entatic Bulging. Inorg Chem 2007; 46:4492-503. [PMID: 17461575 DOI: 10.1021/ic062399j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ligand field molecular mechanics (LFMM) model has been applied to the oxidized Type 1 copper center. In conjunction with the AMBER94 force field implemented in DommiMOE, the ligand field extension of the molecular operating environment (MOE), LFMM parameters for Cu-N(imidazole), Cu-S(thiolate), Cu-S(thioether), and Cu-O(carbonyl) interactions were developed on the basis of experimental and theoretical data for homoleptic model systems. Subsequent LFMM optimizations of the active site model complex [Cu(imidazole)2(SMe)(SMe2]+ agree with high level quantum results both structurally and energetically. Stable trigonal and tetragonal structures are located with the latter about 1.5 kcal mol-1 lower in energy. Fully optimized unconstrained structures were computed for 24 complete proteins containing T1 centers spanning four-coordinate, plastocyanin-like CuN2SS' and stellacyanin-like CuN2SO sites, plus the five-coordinate CuN2SS'O sites of the azurins. The initial structures were based on PDB coordinates augmented by a 10 A layer of water molecules. Agreement between theory and experiment is well within the experimental uncertainties. Moreover, the LFMM results for plastocyanin (Pc), cucumber basic protein (CBP) and azurin (Az) are at least as good as previously reported QM/MM structures and are achieved several orders of magnitude faster. The LFMM calculations suggest the protein provides an entatic strain of about 10 kcal mol-1. However, when combined with the intrinsic 'plasticity' of d9 Cu(II), different starting protein/solvent configurations can have a significant effect on the final optimized structure. This 'entatic bulging' results in relatively large fluctuations in the calculated metal-ligand bond lengths. For example, simply on the basis of 25 different starting configurations of the solvent molecules, the optimized Cu-S(thiolate) bond lengths in Pc vary by 0.04 A while the Cu-S(thioether) distance spans over 0.3 A. These variations are the same order of magnitude as the differences often quoted to correlate the spectroscopic properties from a set of proteins. Isolated optimizations starting from PDB coordinates (or indeed, the PDB structures themselves) may only accidentally correlate with spectroscopic measurements. The present calculations support the work of Warshel who contends that adequate configurational averaging is necessary to make proper contact with experimental properties measured in solution. The LFMM is both sufficiently accurate and fast to make this practical.
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Affiliation(s)
- Robert J Deeth
- Inorganic Computational Chemistry Group, Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK.
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47
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Sundararajan M, Hillier IH, Burton NA. Mechanism of Nitrite Reduction at T2Cu Centers: Electronic Structure Calculations of Catalysis by Copper Nitrite Reductase and by Synthetic Model Compounds. J Phys Chem B 2007; 111:5511-7. [PMID: 17455972 DOI: 10.1021/jp066852o] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism of nitrite reduction at the Cu(II) center of both copper nitrite reductase and a number of corresponding synthetic models has been investigated by using both QM/MM and cluster calculations employing density functional theory methods. The mechanism in both cases is found to be very similar. Initially nitrite is bound in a bidentate fashion to the Cu(II) center via the two oxygen atoms. Upon reduction of the copper center, the two possible coordination modes of the protonated nitrite, by either nitrogen or a single oxygen atom, are close in energy, with nitrogen coordination probably preferred. Further protonation of this species leads to N-O bond cleavage, and an electron transfer from the Cu(I) center to the N-O+ ligand, resulting in loss of NO and regeneration of the resting state of the enzyme having a bound water molecule.
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Affiliation(s)
- Mahesh Sundararajan
- School of Chemistry, University of Manchester, Manchester, M13 9PL, United Kingdom
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48
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Dalosto SD. Computer Simulation of the Interaction of Cu(I) with Cys Residues at the Binding Site of the Yeast Metallochaperone Cu(I)−Atx1. J Phys Chem B 2007; 111:2932-40. [PMID: 17388422 DOI: 10.1021/jp066689x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The copper binding site and electronic structure of the metallochaperone protein Atx1 were investigated using the combination of quantum mechanics methods and molecular mechanics methods in the ONIOM(QM:MM) scheme at the density functional theory (DFT) B3LYP/ 6-31G(d):AMBER level. The residues in the binding site, -Met13-Thr14-Cys15-Cu(I)-Cys18-Gly17-Ser16-, were modeled with QM and the rest of the residues with MM. Our results indicate that the structure for Cu(I)-Atx1 has the copper atom coordinated to two sulfur atoms from Cys15 (2.110 A) and Cys18 (2.141 A) with an angle S-Cu(I) -S of 166 degrees . The potential energy surface of the copper atom is used to estimate its binding energy and the force field for the copper ligands. The potential surface is shallow for the bending mode S-Cu-S, which explains the origin of the disorder observed in crystallographic and nuclear magnetic resonance studies. Using molecular dynamics for Cu(I)-Atx1 in a box of water molecules and in vacuum, with the force field derived in this work, we observed a correlated motion between the side chains of Thr14 and of Lys65 which enhances distortions in the S-Cu-S geometry. The results are compared with recent experiments and the previous models. The vibrational spectra for the copper ligands and for the residues in the binding site were computed. The localized modes for the copper ligands and the amide bands were assigned. The presence of the copper atom affects the amide bands' frequencies of the residues Cys15 and Cys18, giving resolved bands that can be used to sense changes in the binding site upon translocation of copper atom or interaction with target proteins. Furthermore, the EXAFS (extended X-ray absorption fine structure) spectrum of the proposed structure for Cu(I)-Atx1 was calculated and reproduced the experiments fairly well.
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Affiliation(s)
- Sergio D Dalosto
- Department of Physics, University of Washington, Seattle, Washington 98195-1560, USA.
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49
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Bizzarri AR. Topological and dynamical properties of Azurin anchored to a gold substrate as investigated by molecular dynamics simulation. Biophys Chem 2006; 122:206-14. [PMID: 16631301 DOI: 10.1016/j.bpc.2006.03.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Revised: 03/16/2006] [Accepted: 03/19/2006] [Indexed: 11/20/2022]
Abstract
A classical molecular dynamics study of the electron transfer protein azurin, covalently bound to a gold substrate through its native disulphide group, is carried out at full hydration. With the aim of investigating the effects on the protein structure and dynamics as induced by the presence of an electric field, simulations are performed on neutral, positively and negatively charged substrates. A number of parameters, such as the average structure, the root mean square deviations and fluctuations, the intraprotein hydrogen bonds and solvent accessible surface of the protein, are monitored during 10 ns of run. The orientation, the height and the lateral size of the protein, with respect to the substrate are evaluated and compared with the experimental data obtained by scanning probe nanoscopies. The electron transfer properties between the copper redox center and the disulphide bridge bound to the substrate are investigated and briefly discussed.
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Affiliation(s)
- Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, CNISM, Dipartimento di Scienze Ambientali, Università della Tuscia, I-01100 Viterbo, Italy.
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50
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Comba P, Daubinet A, Martin B, Pietzsch HJ, Stephan H. A new molecular mechanics force field for the design of oxotechnetium(V) and oxorhenium(V) radiopharmaceuticals. J Organomet Chem 2006. [DOI: 10.1016/j.jorganchem.2006.01.068] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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