1
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Wilson CJ, de Groot BL, Gapsys V. Resolving coupled pH titrations using alchemical free energy calculations. J Comput Chem 2024; 45:1444-1455. [PMID: 38471815 DOI: 10.1002/jcc.27318] [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: 09/17/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 03/14/2024]
Abstract
In a protein, nearby titratable sites can be coupled: the (de)protonation of one may affect the other. The degree of this interaction depends on several factors and can influence the measured p K a . Here, we derive a formalism based on double free energy differences ( Δ Δ G ) for quantifying the individual site p K a values of coupled residues. As Δ Δ G values can be obtained by means of alchemical free energy calculations, the presented approach allows for a convenient estimation of coupled residue p K a s in practice. We demonstrate that our approach and a previously proposed microscopic p K a formalism, can be combined with alchemical free energy calculations to resolve pH-dependent protein p K a values. Toy models and both, regular and constant-pH molecular dynamics simulations, alongside experimental data, are used to validate this approach. Our results highlight the insights gleaned when coupling and microstate probabilities are analyzed and suggest extensions to more complex enzymatic contexts. Furthermore, we find that naïvely computed p K a values that ignore coupling, can be significantly improved when coupling is accounted for, in some cases reducing the error by half. In short, alchemical free energy methods can resolve the p K a values of both uncoupled and coupled residues.
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Affiliation(s)
- Carter J Wilson
- Department of Mathematics, The University of Western Ontario, London, Ontario, Canada
- Centre for Advanced Materials and Biomaterials Research (CAMBR), The University of Western Ontario, London, Ontario, Canada
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Computational Chemistry, Janssen Research & Development, Beerse, Belgium
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2
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Silva TFD, Vila-Viçosa D, Reis PBPS, Victor BL, Diem M, Oostenbrink C, Machuqueiro M. The Impact of Using Single Atomistic Long-Range Cutoff Schemes with the GROMOS 54A7 Force Field. J Chem Theory Comput 2018; 14:5823-5833. [DOI: 10.1021/acs.jctc.8b00758] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Tomás F. D. Silva
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Pedro B. P. S. Reis
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Bruno L. Victor
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Matthias Diem
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
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3
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Reis PPS, Vila-Viçosa D, Campos SRR, Baptista A, Machuqueiro M. Role of Counterions in Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimers. ACS OMEGA 2018; 3:2001-2009. [PMID: 30023821 PMCID: PMC6045380 DOI: 10.1021/acsomega.7b01708] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/08/2018] [Indexed: 05/25/2023]
Abstract
Electrostatic interactions play a pivotal role in the structure and mechanism of action of most biomolecules. There are several conceptually different methods to deal with electrostatics in molecular dynamics simulations. Ionic strength effects are usually introduced using such methodologies and can have a significant impact on the quality of the final conformation space obtained. We have previously shown that full system neutralization can lead to wrong lipidic phases in the 25% PA/PC bilayer (J. Chem. Theory Comput. 2014,10, 5483-5492). In this work, we investigate how two limit approaches to the ionic strength treatment (implicitly with GRF or using full system neutralization with either GRF or PME) can influence the conformational space of the second-generation PAMAM dendrimer. Constant-pH MD simulations were used to map PAMAM's conformational space at its full pH range (from 2.5 to 12.5). Our simulations clearly captured the coupling between protonation and conformation in PAMAM. Interestingly, the dendrimer conformational distribution was almost independent of the ionic strength treatment methods, which is in contrast to what we have observed in charged lipid bilayers. Overall, our results confirm that both GRF with implicit ionic strength and a fully neutralized system with PME are valid approaches to model charged globular systems, using the GROMOS 54A7 force field.
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Affiliation(s)
- Pedro
B. P. S. Reis
- Centro
de Química e Bioquímica, Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Centro
de Química e Bioquímica, Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Sara R. R. Campos
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - António
M. Baptista
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica, Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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4
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Barroso daSilva FL, Dias LG. Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. Biophys Rev 2017; 9:699-728. [PMID: 28921104 PMCID: PMC5662048 DOI: 10.1007/s12551-017-0311-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/01/2017] [Indexed: 12/20/2022] Open
Abstract
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-of-the-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.
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Affiliation(s)
- Fernando Luís Barroso daSilva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do café, s/no. - Universidade de São Paulo, BR-14040-903, Ribeirão Preto, SP, Brazil.
- UCD School of Physics, UCD Institute for Discovery, University College Dublin, Belfield, Dublin 4, Ireland.
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Luis Gustavo Dias
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Av. Bandeirantes, 3900 - Universidade de São Paulo, BR-14040-901, Ribeirão Preto, SP, Brazil
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5
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Perazzo J, Castanho MARB, Sá Santos S. Pharmacological Potential of the Endogenous Dipeptide Kyotorphin and Selected Derivatives. Front Pharmacol 2017; 7:530. [PMID: 28127286 PMCID: PMC5226936 DOI: 10.3389/fphar.2016.00530] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/20/2016] [Indexed: 12/27/2022] Open
Abstract
The endogenous peptide kyotorphin (KTP) has been extensively studied since it was discovered in 1979. The dipeptide is distributed unevenly over the brain but the majority is concentrated in the cerebral cortex. The putative KTP receptor has not been identified yet. As many other neuropeptides, KTP clearance is mediated by extracellular peptidases and peptide transporters. From the wide spectrum of biological activity of KTP, analgesia was by far the most studied. The mechanism of action is still unclear, but researchers agree that KTP induces Met-enkephalins release. More recently, KTP was proposed as biomarker of Alzheimer disease. Despite all that, KTP limited pharmacological value prompted researchers to develop derivatives more lipophilic and therefore more prone to cross the blood–brain barrier (BBB), and also more resistant to enzymatic degradation. Conjugation of KTP with functional molecules, such as ibuprofen, generated a new class of compounds with additional biological properties. Moreover, the safety profile of these derivatives compared to opioids and their efficacy as neuroprotective agents greatly increases their pharmacological value.
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Affiliation(s)
- Juliana Perazzo
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa Lisboa, Portugal
| | - Miguel A R B Castanho
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa Lisboa, Portugal
| | - Sónia Sá Santos
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa Lisboa, Portugal
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6
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Wu X, Lee J, Brooks BR. Origin of pK a Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water. J Phys Chem B 2016; 121:3318-3330. [PMID: 27700118 DOI: 10.1021/acs.jpcb.6b08249] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein internal ionizable groups can exhibit large shifts in pKa values. Although the environment and interaction changes have been extensively studied both experimentally and computationally, direct calculation of pKa values of these internal ionizable groups in explicit water is challenging due to energy barriers in solvent interaction and in conformational transition. The virtual mixture of multiple states (VMMS) method is a new approach designed to study chemical state equilibrium. This method constructs a virtual mixture of multiple chemical states in order to sample the conformational space of all states simultaneously and to avoid crossing energy barriers related to state transition. By applying VMMS to 25 variants of staphylococcal nuclease with lysine residues at internal positions, we obtained the pKa values of these lysine residues and investigated the physics underlining the pKa shifts. Our calculation results agree reasonably well with experimental measurements, validating the VMMS method for pKa calculation and providing molecular details of the protonation equilibrium for protein internal ionizable groups. Based on our analyses of protein conformation relaxation, lysine side chain flexibility, water penetration, and the microenvironment, we conclude that the hydrophobicity of the microenvironment around the lysine side chain (which affects water penetration differently for different protonation states) plays an important role in the pKa shifts.
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Affiliation(s)
- Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Juyong Lee
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
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7
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Khan FI, Bisetty K, Gu KR, Singh S, Permaul K, Hassan MI, Wei DQ. Molecular dynamics simulation of chitinase I from Thermomyces lanuginosus SSBP to ensure optimal activity. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1237024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Faez Iqbal Khan
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, South Africa
| | - Ke-Ren Gu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
| | - Suren Singh
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Kugen Permaul
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, New Delhi, India
| | - Dong-Qing Wei
- School of Chemistry and Chemical Engineering, Henan University of Technology, Henan, China
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8
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Khan FI, Wei DQ, Gu KR, Hassan MI, Tabrez S. Current updates on computer aided protein modeling and designing. Int J Biol Macromol 2016; 85:48-62. [DOI: 10.1016/j.ijbiomac.2015.12.072] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022]
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9
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Magalhães PR, Machuqueiro M, Baptista AM. Constant-pH Molecular Dynamics Study of Kyotorphin in an Explicit Bilayer. Biophys J 2016; 108:2282-90. [PMID: 25954885 DOI: 10.1016/j.bpj.2015.03.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 03/05/2015] [Accepted: 03/26/2015] [Indexed: 10/23/2022] Open
Abstract
To our knowledge, we present the first constant-pH molecular dynamics study of the neuropeptide kyotorphin in the presence of an explicit lipid bilayer. The overall conformation freedom of the peptide was found to be affected by the interaction with the membrane, in accordance with previous results using different methodologies. Analysis of the interactions between the N-terminus amine group of the peptide and several lipid atoms shows that the membrane is able to stabilize both ionized and neutral forms of kyotorphin, resulting in a pKa value that is similar to the one obtained in water. This illustrates how a detailed molecular model of the membrane leads to rather different results than would be expected from simply regarding it as a low-dielectric slab.
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Affiliation(s)
- Pedro R Magalhães
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - António M Baptista
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
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10
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Santos HAF, Vila-Viçosa D, Teixeira VH, Baptista AM, Machuqueiro M. Constant-pH MD Simulations of DMPA/DMPC Lipid Bilayers. J Chem Theory Comput 2015; 11:5973-9. [DOI: 10.1021/acs.jctc.5b00956] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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11
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Carvalheda CA, Campos SRR, Baptista AM. The Effect of Membrane Environment on Surfactant Protein C Stability Studied by Constant-pH Molecular Dynamics. J Chem Inf Model 2015; 55:2206-17. [PMID: 26397014 DOI: 10.1021/acs.jcim.5b00076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pulmonary surfactant protein C (SP-C) is a small peptide with two covalently linked fatty acyl chains that plays a crucial role in the formation and stabilization of the pulmonary surfactant reservoirs during the compression and expansion steps of the respiratory cycle. Although its function is known to be tightly related to its highly hydrophobic character and key interactions maintained with specific lipid components, much is left to understand about its molecular mechanism of action. Also, although it adopts a mainly helical structure while associated with the membrane, factors as pH variation and deacylation have been shown to affect its stability and function. In this work, the conformational behavior of both the acylated and deacylated SP-C isoforms was studied in a DPPC bilayer under different pH conditions using constant-pH molecular dynamics simulations. Our findings show that both protein isoforms are remarkably stable over the studied pH range, even though the acylated isoform exhibits a labile helix-turn-helix motif rarely observed in the other isoform. We estimate similar tilt angles for the two isoforms over the studied pH range, with a generally higher degree of internalization of the basic N-terminal residues in the deacylated case, and observe and discuss some protonation-conformation coupling effects. Both isoforms establish contacts with the surrounding lipid molecules (preferentially with the sn-2 ester bonds) and have a local effect on the conformational behavior of the surrounding lipid molecules, the latter being more pronounced for acylated SP-C.
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Affiliation(s)
- Catarina A Carvalheda
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, 2780-157 Oeiras, Portugal
| | - Sara R R Campos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, 2780-157 Oeiras, Portugal
| | - António M Baptista
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, 2780-157 Oeiras, Portugal
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12
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Flannelly DF, Aoki TG, Aristilde L. Short-time dynamics of pH-dependent conformation and substrate binding in the active site of beta-glucosidases: A computational study. J Struct Biol 2015; 191:352-64. [PMID: 26160737 DOI: 10.1016/j.jsb.2015.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 06/17/2015] [Accepted: 07/03/2015] [Indexed: 12/25/2022]
Abstract
The complete degradation of cellulose to glucose is essential to carbon turnover in terrestrial ecosystems and to engineered biofuel production. A rate-limiting step in this pathway is catalyzed by beta-glucosidase (BG) enzymes, which convert cellulobiose into two glucose molecules. The activity of these enzymes has been shown to vary with solution pH. However, it is not well understood how pH influences the enzyme conformation required for catalytic action on the substrate. A structural understanding of this pH effect is important for predicting shifts in BG activity in bioreactors and environmental matrices, in addition to informing targeted protein engineering. Here we applied molecular dynamics simulations to explore conformational and substrate binding dynamics in two well-characterized BGs of bacterial (Clostridium cellulovorans) and fungal (Trichoderma reesei) origins as a function of pH. The enzymes were simulated in an explicit solvated environment, with NaCl as electrolytes, at their prominent ionization states obtained at pH 5, 6, 7, and 7.5. Our findings indicated that pH-dependent changes in the ionization states of non-catalytic residues localized outside of the immediate active site led to pH-dependent disruption of the active site conformation. This disruption interferes with favorable H-bonding interactions with catalytic residues required to initiate catalysis on the substrate. We also identified specific non-catalytic residues that are involved in stabilizing the substrate at the optimal pH for enzyme activity. The simulations further revealed the dynamics of water-bridging interactions both outside and inside the substrate binding cleft during structural changes in the enzyme-substrate complex. These findings provide new structural insights into the pH-dependent substrate binding specificity in BGs.
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Affiliation(s)
- David F Flannelly
- The Institute for Comparative and Environmental Toxicology, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Thalia G Aoki
- Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Ludmilla Aristilde
- The Institute for Comparative and Environmental Toxicology, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA; Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA.
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13
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Vila-Viçosa D, Teixeira VH, Baptista AM, Machuqueiro M. Constant-pH MD Simulations of an Oleic Acid Bilayer. J Chem Theory Comput 2015; 11:2367-76. [DOI: 10.1021/acs.jctc.5b00095] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diogo Vila-Viçosa
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Edifı́cio C8 Campo Grande, 1749-016 Lisboa, Portugal
| | - Vitor H. Teixeira
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Edifı́cio C8 Campo Grande, 1749-016 Lisboa, Portugal
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Edifı́cio C8 Campo Grande, 1749-016 Lisboa, Portugal
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14
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Vila-Viçosa D, Teixeira VH, Santos HAF, Baptista AM, Machuqueiro M. Treatment of Ionic Strength in Biomolecular Simulations of Charged Lipid Bilayers. J Chem Theory Comput 2014; 10:5483-92. [DOI: 10.1021/ct500680q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Diogo Vila-Viçosa
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Vitor H. Teixeira
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Hugo A. F. Santos
- Faculty
of Sciences, BioFIG−Centre for Biodiversity, Functional and
Integrative Genomics, University of Lisboa, 1649-004 Lisboa, Portugal
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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15
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Dzimbova T, Bocheva A, Pajpanova T. Kyotorphin analogues containing unnatural amino acids: synthesis, analgesic activity and computer modeling of their interactions with μ-receptor. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0953-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Vila-Viçosa D, Francesconi O, Machuqueiro M. Why a diaminopyrrolic tripodal receptor binds mannosides in acetonitrile but not in water? Beilstein J Org Chem 2014; 10:1513-23. [PMID: 25161708 PMCID: PMC4142876 DOI: 10.3762/bjoc.10.156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/28/2014] [Indexed: 12/16/2022] Open
Abstract
Intermolecular interactions involving carbohydrates and their natural receptors play important roles in several biological processes. The development of synthetic receptors is very useful to study these recognition processes. Recently, it was synthetized a diaminopyrrolic tripodal receptor that is selective for mannosides, which are obtained from mannose, a sugar with significant relevance in living systems. However, this receptor is significantly more active in acetonitrile than in water. In this work, we performed several molecular dynamics and constant-pH molecular dynamics simulations in acetonitrile and water to evaluate the conformational space of the receptor and to understand the molecular detail of the receptor–mannoside interaction. The protonation states sampled by the receptor show that the positive charges are always as distant as possible in order to avoid large intramolecular repulsions. Moreover, the conformational space of the receptor is very similar in water above pH 4.0 and in acetonitrile. From the simulations with the mannoside, we observe that the interactions are more specific in acetonitrile (mainly hydrogen bonds) than in water (mainly hydrophobic). Our results suggest that the readiness of the receptor to bind mannoside is not significantly affected in water (above pH 4.0). Probably, the hydrogen bond network that is formed in acetonitrile (which is weaker in water) is the main reason for the higher activity in this solvent. This work also presents a new implementation of the stochastic titration constant-pH molecular dynamics method to a synthetic receptor of sugars and attests its ability to describe the protonation/conformation coupling in these molecules.
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Affiliation(s)
- Diogo Vila-Viçosa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Oscar Francesconi
- Dipartimento di Chimica, Università di Firenze, Polo Scientifico e Tecnológico, 50019 Sesto Fiorentino, Firenze, Italy
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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17
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Teixeira VH, Vila-Viçosa D, Baptista AM, Machuqueiro M. Protonation of DMPC in a Bilayer Environment Using a Linear Response Approximation. J Chem Theory Comput 2014; 10:2176-84. [DOI: 10.1021/ct5000082] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vitor H. Teixeira
- Centro
de Química e Bioquímica, Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Centro
de Química e Bioquímica, Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica, Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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18
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Goh GB, Hulbert BS, Zhou H, Brooks CL. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism. Proteins 2014; 82:1319-31. [PMID: 24375620 DOI: 10.1002/prot.24499] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 11/13/2013] [Accepted: 12/12/2013] [Indexed: 12/14/2022]
Abstract
pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible.
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Affiliation(s)
- Garrett B Goh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
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19
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Kurut A, Henriques J, Forsman J, Skepö M, Lund M. Role of histidine for charge regulation of unstructured peptides at interfaces and in bulk. Proteins 2013; 82:657-67. [DOI: 10.1002/prot.24445] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/12/2013] [Accepted: 09/26/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Anıl Kurut
- Division of Theoretical Chemistry; Lund University; P.O. Box 124 SE-22100 Lund Sweden
| | - João Henriques
- Division of Theoretical Chemistry; Lund University; P.O. Box 124 SE-22100 Lund Sweden
| | - Jan Forsman
- Division of Theoretical Chemistry; Lund University; P.O. Box 124 SE-22100 Lund Sweden
| | - Marie Skepö
- Division of Theoretical Chemistry; Lund University; P.O. Box 124 SE-22100 Lund Sweden
| | - Mikael Lund
- Division of Theoretical Chemistry; Lund University; P.O. Box 124 SE-22100 Lund Sweden
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20
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Bhattacharjee N, Rani P, Biswas P. Capturing molten globule state of α-lactalbumin through constant pH molecular dynamics simulations. J Chem Phys 2013; 138:095101. [PMID: 23485328 DOI: 10.1063/1.4793470] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The recently developed methods of constant pH molecular dynamics directly captures the correlation between protonation and conformation to probe protein structure, function, and dynamics. In this work, we investigate the effect of pH on the conformational properties of the protein human α-lactalbumin. Constant pH simulations at both acidic and alkaline medium indicate the formation of the molten globule state, which is in accordance with the previous experimental observations (especially, in acidic medium). The size of the protein measured by its radius of gyration (RG) exhibits a marked increase in both acidic and alkaline medium, which matches with the corresponding experimentally observed value of RG found in the molten globule. The probability of native contacts is also considerably reduced at acidic and basic pH as compared to that of native structure crystallized at neutral pH. The mean fractal dimension D2 of the protein records a sharp increase in basic medium as compared to those in neutral and acidic solutions implying a significant pH induced conformational change. The mean square fluctuations of all residues of the entire protein are found to increase by several folds in both acidic and basic medium, which may be correlated with the normalized solvent accessibility of the residues indicating role of solvent accessible surface area on protein internal dynamics. The helices comprising the α-domain of the protein are moderately preserved in the acidic and alkaline pH. However, the β-sheet structures present in the β-domain are completely disrupted in both acidic as well as basic pH.
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21
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Fuzo CA, Degrève L. The pH dependence of flavivirus envelope protein structure: insights from molecular dynamics simulations. J Biomol Struct Dyn 2013; 32:1563-74. [DOI: 10.1080/07391102.2013.827132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Vila-Viçosa D, Teixeira VH, Santos HAF, Machuqueiro M. Conformational Study of GSH and GSSG Using Constant-pH Molecular Dynamics Simulations. J Phys Chem B 2013; 117:7507-17. [DOI: 10.1021/jp401066v] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Diogo Vila-Viçosa
- Centro de Química
e Bioquímica and Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Vitor H. Teixeira
- Centro de Química
e Bioquímica and Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Hugo A. F. Santos
- Centro de Química
e Bioquímica and Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- Centro de Química
e Bioquímica and Departamento
de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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23
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Goh GB, Knight JL, Brooks CL. Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids. J Phys Chem Lett 2013; 4:760-766. [PMID: 23526474 PMCID: PMC3601767 DOI: 10.1021/jz400078d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one of the emerging frontiers in the field of nucleic acid biology. The recent development of a constant pH molecular dynamics simulation (CPHMDMSλD) framework for simulating nucleic acids has provided a tool for realistic simulations of pH-dependent dynamics. We enhanced the CPHMDMSλD framework with pH-based replica exchange (pH-REX), which significantly improves the sampling of both titration and spatial coordinates. The results from our pKa calculations for the GAAA tetraloop, which was predicted with lower accuracy previously due to sampling challenges, demonstrates that pH-REX reduces the average unsigned error (AUE) to 0.7 pKa units, and the error of the most poorly predicted residue A17 was drastically reduced from 2.9 to 1.2 pKa unit. Lastly, we show that pH-REX CPHMDMSλD simulations can be used to identify the dominant conformation of nucleic acid structures in alternate pH environments. This work suggests that pH-REX CPHMDMSλD simulations provide a practical tool for predicting nucleic acid protonation equilibrium from first-principles, and offering structural and mechanistic insight into the study of pH-dependent properties of nucleic acids.
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Affiliation(s)
- Garrett B Goh
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
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24
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Abstract
The role of pH-dependent protonation equilibrium in modulating RNA dynamics and function is one of the key unanswered questions in RNA biology. Molecular dynamics (MD) simulations can provide insight into the mechanistic roles of protonated nucleotides, but it is only capable of modeling fixed protonation states and requires prior knowledge of the key residue's protonation state. Recently, we developed a framework for constant pH molecular dynamics simulations (CPHMDMSλD) of nucleic acids, where the nucleotides' protonation states are modeled as dynamic variables that are coupled to the structural dynamics of the RNA. In the present study, we demonstrate the application of CPHMDMSλD to the lead-dependent ribozyme; establishing the validity of this approach for modeling complex RNA structures. We show that CPHMDMSλD accurately predicts the direction of the pKa shifts and reproduces experimentally-measured microscopic pKa values with an average unsigned error of 1.3 pKa units. The effects of coupled titration states in RNA structures are modeled, and the importance of conformation sampling is highlighted. The general accuracy of CPHMDMSλD simulations in reproducing pH-dependent observables reported in this work demonstrates that constant pH simulations provides a powerful tool to investigate pH-dependent processes in nucleic acids.
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Affiliation(s)
- Garrett B Goh
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
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25
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Enkavi G, Li J, Mahinthichaichan P, Wen PC, Huang Z, Shaikh SA, Tajkhorshid E. Simulation studies of the mechanism of membrane transporters. Methods Mol Biol 2013; 924:361-405. [PMID: 23034756 DOI: 10.1007/978-1-62703-017-5_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Membrane transporters facilitate active transport of their specific substrates, often against their electrochemical gradients across the membrane, through coupling the process to various sources of cellular energy, for example, ATP binding and hydrolysis in primary transporters, and pre-established electrochemical gradient of molecular species other than the substrate in the case of secondary transporters. In order to provide efficient energy-coupling mechanisms, membrane transporters have evolved into molecular machines in which stepwise binding, translocation, and transformation of various molecular species are closely coupled to protein conformational changes that take the transporter from one functional state to another during the transport cycle. Furthermore, in order to prevent the formation of leaky states and to be able to pump the substrate against its electrochemical gradient, all membrane transporters use the widely-accepted "alternating access mechanism," which ensures that the substrate is only accessible from one side of the membrane at a given time, but relies on complex and usually global protein conformational changes that differ for each family of membrane transporters. Describing the protein conformational changes of different natures and magnitudes is therefore at the heart of mechanistic studies of membrane transporters. Here, using a number of membrane transporters from diverse families, we present common protocols used in setting up and performing molecular dynamics simulations of membrane transporters and in analyzing the results, in order to characterize relevant motions of the system. The emphasis will be on highlighting how optimal design of molecular dynamics simulations combined with mechanistically oriented analysis can shed light onto key functionally relevant protein conformational changes in this family of membrane proteins.
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Affiliation(s)
- Giray Enkavi
- Department of Biochemistry, Center for Biophysics and Computational Biology, College of Medicine, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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26
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Henriques J, Costa PJ, Calhorda MJ, Machuqueiro M. Charge parametrization of the DvH-c3 heme group: validation using constant-(pH,E) molecular dynamics simulations. J Phys Chem B 2012. [PMID: 23199023 DOI: 10.1021/jp3082134] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We studied the effect of using different heme group charge parametrization methods and schemes (Merz-Kollman, CHELPG, and single- and multiconformational RESP) on the quality of the results produced by the constant-(pH,E) MD method, applied to the redox titration of Desulfovibrio vulgaris Hildenborough cytochrome c(3). These new and more accurate charge sets enabled us to overcome the previously reported dependence of the method's performance on the dielectric constant, ε, assigned to the protein region. In particular, we found a systematic, clear shift of the E(mod) toward more negative values than those previously reported, in agreement with an electrostatics based reasoning. The simulations showed strong coupling between protonating/redox sites. We were also able to capture significant direct and, especially, indirect interactions between hemes, such as those mediated by histidine 67. Our results highlight the importance of having a good quantum description of the system before deriving atomic partial charges for classic force fields.
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Affiliation(s)
- João Henriques
- Centro de Química e Bioquímica and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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27
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Vila-Viçosa D, Campos SRR, Baptista AM, Machuqueiro M. Reversibility of prion misfolding: insights from constant-pH molecular dynamics simulations. J Phys Chem B 2012; 116:8812-21. [PMID: 22803931 DOI: 10.1021/jp3034837] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The prion protein (PrP) is the cause of a group of diseases known as transmissible spongiform encephalopathies (TSEs). Creutzfeldt-Jakob disease and bovine spongiform encephalopathy are examples of TSEs. Although the normal form of PrP (PrP(C)) is monomeric and soluble, it can misfold into a pathogenic form (PrP(Sc)) that has a high content of β-structure and can aggregate forming amyloid fibrils. The mechanism of conversion of PrP(C) into PrP(Sc) is not known but different triggers have been proposed. It can be catalyzed by a PrP(Sc) sample, or it can be induced by an external factor, such as low pH. The pH effect on the structure of PrP was recently studied by computational methods [Campos et al. J. Phys. Chem. B 2010, 114, 12692-12700], and an evident trend of loss of helical structure was observed with pH decrease, together with a gain of β-structures. In particular, one simulation at pH 2 showed an evident misfolding transition. The main goal of the present work was to study the effects of a change in pH to 7 in several transient conformations of this simulation, in order to draw some conclusions about the reversibility of PrP misfolding. Although the most significant effect caused by the change of pH to 7 was a global stabilization of the protein structure, we could also observe that some conformational transitions induced by pH 2 were reversible in many of our simulations, namely those started from the early moments of the misfolding transition. This observation is in good agreement with experiments showing that, even at pH as low as 1.7, it is possible to revert the misfolding process [Bjorndahl et al. Biochemistry 2011, 50, 1162-1173].
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Affiliation(s)
- Diogo Vila-Viçosa
- Centro de Química e Bioquímica e Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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28
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Sabri Dashti D, Meng Y, Roitberg AE. pH-replica exchange molecular dynamics in proteins using a discrete protonation method. J Phys Chem B 2012; 116:8805-11. [PMID: 22694266 DOI: 10.1021/jp303385x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protonation equilibria in biological molecules modulates structure, dynamics, and function. A pH-replica exchange molecular dynamics (pH-REMD) method is described here to improve the coupling between conformational and protonation sampling. Under a Hamiltonian replica exchange setup, conformations are swapped between two neighboring replicas, which themselves are at different pHs. The method has been validated on a series of biological systems. We applied pH-REMD to a series of model compounds, to an terminally charged ADFDA pentapeptide, and to a heptapeptide derived from the ovomucoid third domain (OMTKY3). In all of those systems, the predicted pK(a) by pH-REMD is very close to the experimental value and almost identical to the ones obtained by constant pH molecular dynamics (CpH MD). The method presented here, pH-REMD, has the advantage of faster convergence properties due to enhanced sampling of both conformation and protonation spaces.
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Affiliation(s)
- Danial Sabri Dashti
- Department of Physics and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-8435, USA
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29
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Goh GB, Knight JL, Brooks CL. Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent. J Chem Theory Comput 2011; 8:36-46. [PMID: 22337595 DOI: 10.1021/ct2006314] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nucleosides of adenine and cytosine have pKa values of 3.50 and 4.08, respectively, and are assumed to be unprotonated under physiological conditions. However, evidence from recent NMR and X-Ray crystallography studies has revealed the prevalence of protonated adenine and cytosine in RNA macromolecules. Such nucleotides with elevated pKa values may play a role in stabilizing RNA structure and participate in the mechanism of ribozyme catalysis. With the work presented here, we establish the framework and demonstrate the first constant pH MD simulations (CPHMD) for nucleic acids in explicit solvent in which the protonation state is coupled to the dynamical evolution of the RNA system via λ-dynamics. We adopt the new functional form λ(Nexp) for λ that was recently developed for Multi-Site λ-Dynamics (MSλD) and demonstrate good sampling characteristics in which rapid and frequent transitions between the protonated and unprotonated states at pH = pKa are achieved. Our calculated pKa values of simple nucleotides are in a good agreement with experimentally measured values, with a mean absolute error of 0.24 pKa units. This work demonstrates that CPHMD can be used as a powerful tool to investigate pH-dependent biological properties of RNA macromolecules.
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Affiliation(s)
- Garrett B Goh
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
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30
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Simulation of multihaem cytochromes. FEBS Lett 2011; 586:510-8. [DOI: 10.1016/j.febslet.2011.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 11/19/2022]
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31
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Machuqueiro M, Baptista AM. Is the prediction of pK
a
values by constant-pH molecular dynamics being hindered by inherited problems? Proteins 2011; 79:3437-47. [DOI: 10.1002/prot.23115] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 05/27/2011] [Accepted: 06/09/2011] [Indexed: 01/20/2023]
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32
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Ribeiro MMB, Pinto A, Pinto M, Heras M, Martins I, Correia A, Bardaji E, Tavares I, Castanho M. Inhibition of nociceptive responses after systemic administration of amidated kyotorphin. Br J Pharmacol 2011; 163:964-73. [PMID: 21366550 PMCID: PMC3130928 DOI: 10.1111/j.1476-5381.2011.01290.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 12/22/2010] [Accepted: 01/20/2011] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND PURPOSE Kyotorphin (KTP; L-Tyr-L-Arg), an endogenous neuropeptide, is potently analgesic when delivered directly to the central nervous system. Its weak analgesic effects after systemic administration have been explained by inability to cross the blood-brain barrier (BBB) and detract from the possible clinical use of KTP as an analgesic. In this study, we aimed to increase the lipophilicity of KTP by amidation and to evaluate the analgesic efficacy of a new KTP derivative (KTP-amide - KTP-NH(2) ). EXPERIMENTAL APPROACH We synthesized KTP-NH(2) . This peptide was given systemically to assess its ability to cross the BBB. A wide range of pain models, including acute, sustained and chronic inflammatory and neuropathic pain, were used to characterize analgesic efficacies of KTP-NH(2) . Binding to opioid receptors and toxicity were also measured. KEY RESULTS KTP-NH(2) , unlike its precursor KTP, was lipophilic and highly analgesic following systemic administration in several acute and chronic pain models, without inducing toxic effects or affecting motor responses and blood pressure. Binding to opioid receptors was minimal. KTP-NH(2) inhibited nociceptive responses of spinal neurons. Its analgesic effects were prevented by intrathecal or i.p. administration of naloxone. CONCLUSIONS AND IMPLICATIONS Amidation allowed KTP to show good analgesic ability after systemic delivery in acute and chronic pain models. The indirect opioid-mediated actions of KTP-NH(2) may explain why this compound retained its analgesic effects although the usual side effects of opioids were absent, which is a desired feature in next-generation pain medications.
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Affiliation(s)
- M M B Ribeiro
- Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Lisboa, Portugal
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33
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Yang L, Zhang J, Ho B, Ding JL. Histidine-mediated pH-sensitive regulation of M-ficolin:GlcNAc binding activity in innate immunity examined by molecular dynamics simulations. PLoS One 2011; 6:e19647. [PMID: 21573188 PMCID: PMC3088710 DOI: 10.1371/journal.pone.0019647] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 04/04/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND M-ficolin, a pathogen recognition molecule in the innate immune system, binds sugar residues including N-acetyl-D-glucosamine (GlcNAc), which is displayed on invading microbes and on apoptotic cells. The cis and trans Asp282-Cys283 peptide bond in the M-ficolin, which was found to occur at neutral and acidic pH in crystal structures, has been suggested to represent binding and non-binding activity, respectively. A detailed understanding of the pH-dependent conformational changes in M-ficolin and pH-mediated discrimination mechanism of GlcNAc-binding activity are crucial to both immune-surveillance and clearance of apoptotic cells. METHODOLOGY/PRINCIPAL FINDINGS By immunodetection analysis, we found that the pH-sensitive binding of GlcNAc is regulated by a conformational equilibrium between the active and inactive states of M-ficolin. We performed constant pH molecular dynamics (MD) simulation at a series of pH values to explore the pH effect on the cis-trans isomerization of the Asp282-Cys283 peptide bond in the M-ficolin fibrinogen-like domain (FBG). Analysis of the hydrogen bond occupancy of wild type FBG compared with three His mutants (H251A, H284A and H297A) corroborates that His284 is indispensible for pH-dependent binding. H251A formed new but weaker hydrogen bonds with GlcNAc. His297, unlike the other two His mutants, is more dependent on the solution pH and also contributes to cis-trans isomerization of the Asp282-Cys283 peptide bond in weak basic solution. CONCLUSIONS/SIGNIFICANCE Constant pH MD simulation indicated that the cis active isomer of Asp282-Cys283 peptide bond was predominant around neutral pH while the trans bond gradually prevailed towards acidic environment. The protonation of His284 was found to be associated with the trans-to-cis isomerization of Asp282-Cys283 peptide bond which dominantly regulates the GlcNAc binding. Our MD simulation approach provides an insight into the pH-sensitive proteins and hence, ligand binding activity.
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Affiliation(s)
- Lifeng Yang
- Computational and Systems Biology, Singapore-MIT Alliance (SMA),
Singapore, Singapore
- Department of Biological Sciences, National University of Singapore,
Singapore, Singapore
| | - Jing Zhang
- Department of Biological Sciences, National University of Singapore,
Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering (NGS),
National University of Singapore, Singapore
| | - Bow Ho
- Department of Microbiology, Yong Loo Lin School of Medicine, Singapore,
Singapore
| | - Jeak Ling Ding
- Computational and Systems Biology, Singapore-MIT Alliance (SMA),
Singapore, Singapore
- Department of Biological Sciences, National University of Singapore,
Singapore, Singapore
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Antosiewicz JM, Shugar D. Poisson–Boltzmann continuum-solvation models: applications to pH-dependent properties of biomolecules. MOLECULAR BIOSYSTEMS 2011; 7:2923-49. [DOI: 10.1039/c1mb05170a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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35
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Campos SRR, Machuqueiro M, Baptista AM. Constant-pH Molecular Dynamics Simulations Reveal a β-Rich Form of the Human Prion Protein. J Phys Chem B 2010; 114:12692-700. [DOI: 10.1021/jp104753t] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sara R. R. Campos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - António M. Baptista
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
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36
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Machuqueiro M, Campos SRR, Soares CM, Baptista AM. Membrane-Induced Conformational Changes of Kyotorphin Revealed by Molecular Dynamics Simulations. J Phys Chem B 2010; 114:11659-67. [DOI: 10.1021/jp104418g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Miguel Machuqueiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal, and Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, C5, 1749-016 Lisboa, Portugal
| | - Sara R. R. Campos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal, and Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, C5, 1749-016 Lisboa, Portugal
| | - Cláudio M. Soares
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal, and Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, C5, 1749-016 Lisboa, Portugal
| | - António M. Baptista
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal, and Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, C5, 1749-016 Lisboa, Portugal
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Aleksandrov A, Thompson D, Simonson T. Alchemical free energy simulations for biological complexes: powerful but temperamental.... J Mol Recognit 2010; 23:117-27. [PMID: 19693787 DOI: 10.1002/jmr.980] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Free energy simulations compare multiple ligand:receptor complexes by "alchemically" transforming one into another, yielding binding free energy differences. Since their introduction in the 1980s, many technical and theoretical obstacles were surmounted, and the method ("MDFE," since molecular dynamics are often used) has matured into a powerful tool. We describe its current status, its effectiveness, and the challenges it faces. MDFE has provided chemical accuracy for many systems but remains expensive, with significant human overhead costs. The bottlenecks have shifted, partly due to increased computer power. To study diverse sets of ligands, force field availability and accuracy can be a major difficulty. Another difficulty is the frequent need to consider multiple states, related to sidechain protonation or buried waters, for example. Sophisticated, automated methods to sample these states are maturing, such as constant pH simulations. Meanwhile, combinations of MDFE and simpler approaches, like continuum dielectric models, can be very effective. As illustrations, we show how, with careful force field parameterization, MDFE accurately predicts binding specificities between complex tetracycline ligands and their targets. We describe substrate binding to the aspartyl-tRNA synthetase enzyme, where many distinct electrostatic states play a role, and a histidine and a Mg(2+) ion act as coupled switches that help enforce a strict preference for the aspartate substrate, relative to several analogs. Overall, MDFE has achieved a predictive status, where novel ligands can be studied and molecular recognition elucidated in depth. It should play an increasing role in the analysis of complex cellular processes and biomolecular engineering.
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Affiliation(s)
- Alexey Aleksandrov
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
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Meng Y, Roitberg AE. Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model. J Chem Theory Comput 2010; 6:1401-1412. [PMID: 20514364 DOI: 10.1021/ct900676b] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A constant pH replica exchange molecular dynamics (REMD) method is proposed and implemented to improve coupled protonation and conformational state sampling. By mixing conformational sampling at constant pH (with discrete protonation states) with a temperature ladder, this method avoids conformational trapping. Our method was tested and applied to seven different biological systems. The constant pH REMD not only predicted pKa correctly for small, model compounds but also converged faster than constant pH molecular dynamics (MD). We further tested our constant pH REMD on a heptapeptide from ovomucoid third domain (OMTKY3). Although constant pH REMD and MD produced very close pKa values, the constant pH REMD showed its advantage in the efficiency of conformational and protonation state samplings.
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Affiliation(s)
- Yilin Meng
- Department of Chemistry and Quantum Theory Project. University of Florida Gainesville, FL 32611-8435
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Machuqueiro M, Baptista AM. Molecular Dynamics at Constant pH and Reduction Potential: Application to Cytochrome c3. J Am Chem Soc 2009; 131:12586-94. [DOI: 10.1021/ja808463e] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Miguel Machuqueiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - António M. Baptista
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
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Abstract
This paper is the thirtieth consecutive installment of the annual review of research concerning the endogenous opioid system. It summarizes papers published during 2007 that studied the behavioral effects of molecular, pharmacological and genetic manipulation of opioid peptides, opioid receptors, opioid agonists and opioid antagonists. The particular topics that continue to be covered include the molecular-biochemical effects and neurochemical localization studies of endogenous opioids and their receptors related to behavior, and the roles of these opioid peptides and receptors in pain and analgesia; stress and social status; tolerance and dependence; learning and memory; eating and drinking; alcohol and drugs of abuse; sexual activity and hormones, pregnancy, development and endocrinology; mental illness and mood; seizures and neurologic disorders; electrical-related activity and neurophysiology; general activity and locomotion; gastrointestinal, renal and hepatic functions; cardiovascular responses; respiration and thermoregulation; and immunological responses.
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Affiliation(s)
- Richard J Bodnar
- Department of Psychology and Neuropsychology Doctoral Sub-Program, Queens College, City University of New York, 65-30 Kissena Blvd.,Flushing, NY 11367, United States.
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Simonson T. Dielectric relaxation in proteins: the computational perspective. PHOTOSYNTHESIS RESEARCH 2008; 97:21-32. [PMID: 18443919 DOI: 10.1007/s11120-008-9293-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 02/18/2008] [Indexed: 05/26/2023]
Abstract
In photoexcitation and electron transfer, a new dipole or charge is introduced, and the structure is adjusted. This adjustment represents dielectric relaxation, which is the focus of this review. We concentrate on a few selected topics. We discuss linear response theory, as a unifying framework and a tool to describe non-equilibrium states. We review recent, molecular dynamics simulation studies that illustrate the calculation of dynamic and thermodynamic properties, such as Stokes shifts or reorganization free energies. We then turn to the macroscopic, continuum electrostatic view. We recall the physical definition of a dielectric constant and revisit the decomposition of the free energy into a reorganization and a static term. We review some illustrative continuum studies and discuss some difficulties that can arise with the continuum approach. In conclusion, we consider recent developments that will increase the accuracy and broaden the scope of all these methods.
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Affiliation(s)
- Thomas Simonson
- Laboratoire de Biochimie (UMR CNRS 7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France.
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Machuqueiro M, Baptista AM. Acidic range titration of HEWL using a constant-pH molecular dynamics method. Proteins 2008; 72:289-98. [DOI: 10.1002/prot.21923] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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