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Mishima K, Kano N. Contribution Factors of the First Kind Calculated for the Marcus Electron-Transfer Rate and Their Applications. J Phys Chem B 2023; 127:8509-8524. [PMID: 37782079 DOI: 10.1021/acs.jpcb.3c03420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
In this study, we applied the concept of the "contribution factor of the first kind (CFFK)" to the original electron-transfer (ET) rate theory proposed by Marcus. Mathematical derivations provided simple and convenient formulas for estimating the relative contributions of ten physical and chemical parameters involved in the Marcus ET rate formula: (1) the maximum strength of the electronic coupling energy between two molecules, (2) the exponential decay rate of the electronic coupling energy versus the distance between both molecules, (3) the distance between both molecules, (4) the equilibrium distance between both molecules, (5) the Gibbs free energy, (6) reorganization free energy in the prefactor of the Marcus ET rate equation, (7) reorganization free energy in the denominator of the exponential term, (8) reorganization free energy in the argument of the exponential term, (9) Boltzmann constant times absolute temperature in the prefactor of the rate equation, and (10) Boltzmann constant times absolute temperature in the denominator of the exponential term. We applied our theories to (i) ET reactions at bacterial photosynthesis reaction centers, PSI and PSII, and soluble ferredoxins (Fd); (ii) intraprotein ET reactions for designed azurin mutants; and (iii) ET reactions in flavodoxin (Fld). The formulas and calculations suggest that the theory behind the CFFK is useful for quantitatively identifying major and minor physical and chemical factors and corresponding trade-offs, all of which affect the magnitude of the Marcus ET rate.
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Affiliation(s)
- Kenji Mishima
- Independent Researcher, Bunkyo-ku, Tokyo 113-0024, Japan
| | - Naoki Kano
- Department of Chemistry and Chemical Engineering, Faculty of Engineering, Niigata University, 8050 Ikarashi 2-Nocho, Nishi-ku, Niigata 950-2181, Japan
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2
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Tumbic GW, Li J, Jiang T, Hossan MY, Feng C, Thielges MC. Interdomain Interactions Modulate the Active Site Dynamics of Human Inducible Nitric Oxide Synthase. J Phys Chem B 2022; 126:6811-6819. [PMID: 36056879 PMCID: PMC10110350 DOI: 10.1021/acs.jpcb.2c04091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide synthase (NOS) is a homodimeric flavohemoprotein responsible for catalyzing the oxidation of l-arginine (l-Arg) to citrulline and nitric oxide. Electrons are supplied for the reaction via interdomain electron transfer between an N-terminal heme-containing oxygenase domain and a FMN-containing (sub)domain of a C-terminal reductase domain. Extensive attention has focused on elucidating how conformational dynamics regulate electron transfer between the domains. Here we investigate the impact of the interdomain FMN-heme interaction on the heme active site dynamics of inducible NOS (iNOS). Steady state linear and time-resolved two-dimensional infrared (2D IR) spectroscopy was applied to probe a CO ligand at the heme within the oxygenase domain for full-length and truncated or mutated constructs of human iNOS. Whereas the linear IR spectra of the CO ligand were identical among the constructs, 2D IR spectroscopy revealed variation in the frequency dynamics. The wild-type constructs that can properly form the FMN/oxygenase docked state due to the presence of both the FMN and oxygenase domains showed slower dynamics than the oxygenase domain alone. Introduction of the mutation (E546N) predicted to perturb electrostatic interactions between the domains resulted in measured dynamics intermediate between those for the full-length and individual oxygenase domain, consistent with perturbation to the docked/undocked equilibrium. These results indicate that docking of the FMN domain to the oxygenase domain not only brings the FMN cofactor within electron transfer distance of the heme domain but also modulates the dynamics sensed by the CO ligand within the active site in a way expected to promote efficient electron transfer.
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Affiliation(s)
- Goran W Tumbic
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jinghui Li
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Ting Jiang
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Md Yeathad Hossan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Changjian Feng
- Department of Pharmaceutical Sciences, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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3
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Reid KM, Singh AK, Bikash CR, Wei J, Tal-Gan Y, Vinh NQ, Leitner DM. The origin and impact of bound water around intrinsically disordered proteins. Biophys J 2022; 121:540-551. [PMID: 35074392 PMCID: PMC8874019 DOI: 10.1016/j.bpj.2022.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/14/2021] [Accepted: 01/13/2022] [Indexed: 12/29/2022] Open
Abstract
Proteins and water couple dynamically over a wide range of time scales. Motivated by their central role in protein function, protein-water dynamics and thermodynamics have been extensively studied for structured proteins, where correspondence to structural features has been made. However, properties controlling intrinsically disordered protein (IDP)-water dynamics are not yet known. We report results of megahertz-to-terahertz dielectric spectroscopy and molecular dynamics simulations of a group of IDPs with varying charge content along with structured proteins of similar size. Hydration water around IDPs is found to exhibit more heterogeneous rotational and translational dynamics compared with water around structured proteins of similar size, yielding on average more restricted dynamics around individual residues of IDPs, charged or neutral, compared with structured proteins. The on-average slower water dynamics is found to arise from excess tightly bound water in the first hydration layer, which is related to greater exposure to charged groups. The more tightly bound water to IDPs correlates with the smaller hydration shell found experimentally, and affects entropy associated with protein-water interactions, the contribution of which we estimate based on the dielectric measurements and simulations. Water-IDP dynamic coupling at terahertz frequencies is characterized by the dielectric measurements and simulations.
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Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Abhishek K. Singh
- Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia
| | | | - Jessica Wei
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, Nevada
| | - Nguyen Q. Vinh
- Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia,Corresponding author
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada,Corresponding author
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4
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Wu H, Ghaani MR, Nandi PK, English NJ. Investigation of Dipolar Response of the Hydrated Hen-Egg White Lysozyme Complex under Externally Applied Electric Fields: Insights from Non-equilibrium Molecular Dynamics. J Phys Chem B 2022; 126:858-868. [PMID: 35060735 PMCID: PMC8819654 DOI: 10.1021/acs.jpcb.1c07096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- HaoLun Wu
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mohammad Reza Ghaani
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Prithwish K. Nandi
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- Irish Centre for High-End Computing, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland
| | - Niall J. English
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
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5
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Hruska E, Gale A, Liu F. Bridging the Experiment-Calculation Divide: Machine Learning Corrections to Redox Potential Calculations in Implicit and Explicit Solvent Models. J Chem Theory Comput 2022; 18:1096-1108. [PMID: 34991320 DOI: 10.1021/acs.jctc.1c01040] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Prediction of redox potentials is essential for catalysis and energy storage. Although density functional theory (DFT) calculations have enabled rapid redox potential predictions for numerous compounds, prominent errors persist compared to experimental measurements. In this work, we develop machine learning (ML) models to reduce the errors of redox potential calculations in both implicit and explicit solvent models. Training and testing of the ML correction models are based on the diverse ROP313 data set with experimental redox potentials measured for organic and organometallic compounds in a variety of solvents. For the implicit solvent approach, our ML models can reduce both the systematic bias and the number of outliers. ML corrected redox potentials also demonstrate less sensitivity to DFT functional choice. For the explicit solvent approach, we significantly reduce the computational costs by embedding the microsolvated cluster in implicit bulk solvent, obtaining converged redox potential results with a smaller solvation shell. This combined implicit-explicit solvent model, together with GPU-accelerated quantum chemistry methods, enabled rapid generation of a large data set of explicit-solvent-calculated redox potentials for 165 organic compounds, allowing detailed investigation of the error sources in explicit solvent redox potential calculations.
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Affiliation(s)
- Eugen Hruska
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ariel Gale
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Fang Liu
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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6
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Belyanchikov MA, Savinov M, Bedran ZV, Bednyakov P, Proschek P, Prokleska J, Abalmasov VA, Petzelt J, Zhukova ES, Thomas VG, Dudka A, Zhugayevych A, Prokhorov AS, Anzin VB, Kremer RK, Fischer JKH, Lunkenheimer P, Loidl A, Uykur E, Dressel M, Gorshunov B. Dielectric ordering of water molecules arranged in a dipolar lattice. Nat Commun 2020; 11:3927. [PMID: 32764722 PMCID: PMC7411056 DOI: 10.1038/s41467-020-17832-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 07/17/2020] [Indexed: 11/09/2022] Open
Abstract
Intermolecular hydrogen bonds impede long-range (anti-)ferroelectric order of water. We confine H2O molecules in nanosized cages formed by ions of a dielectric crystal. Arranging them in channels at a distance of ~5 Å with an interchannel separation of ~10 Å prevents the formation of hydrogen networks while electric dipole-dipole interactions remain effective. Here, we present measurements of the temperature-dependent dielectric permittivity, pyrocurrent, electric polarization and specific heat that indicate an order-disorder ferroelectric phase transition at T0 ≈ 3 K in the water dipolar lattice. Ab initio molecular dynamics and classical Monte Carlo simulations reveal that at low temperatures the water molecules form ferroelectric domains in the ab-plane that order antiferroelectrically along the channel direction. This way we achieve the long-standing goal of arranging water molecules in polar order. This is not only of high relevance in various natural systems but might open an avenue towards future applications in biocompatible nanoelectronics. Despite the apparent simplicity of a H2O molecule, the mutual ferroelectric ordering of the molecules is unresolved. Here, the authors realize a macroscopic ferroelectric phase transition in a network of dipole-dipole coupled water molecules located in nanopores of gemstone.
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Affiliation(s)
- M A Belyanchikov
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia.
| | - M Savinov
- Institute of Physics, Czech Academy of Sciences, 18221, Praha 8, Czech Republic
| | - Z V Bedran
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia
| | - P Bednyakov
- Institute of Physics, Czech Academy of Sciences, 18221, Praha 8, Czech Republic
| | - P Proschek
- Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, 12116, Prague 2, Czech Republic
| | - J Prokleska
- Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, 12116, Prague 2, Czech Republic
| | - V A Abalmasov
- Institute of Automation and Electrometry SB RAS, 630090, Novosibirsk, Russia
| | - J Petzelt
- Institute of Physics, Czech Academy of Sciences, 18221, Praha 8, Czech Republic
| | - E S Zhukova
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia
| | - V G Thomas
- Sobolev Institute of Geology and Mineralogy, RAS, 630090, Novosibirsk, Russia.,Novosibirsk State University, 630090, Novosibirsk, Russia
| | - A Dudka
- Shubnikov Institute of Crystallography, "Crystallography and Photonics", Russian Academy of Sciences, 119333, Moscow, Russia
| | - A Zhugayevych
- Skolkovo Institute of Science and Technology, 143026, Moscow, Russia
| | - A S Prokhorov
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia.,Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow, Russia
| | - V B Anzin
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia.,Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow, Russia
| | - R K Kremer
- Max-Planck-Institut für Festkörperforschung, 70569, Stuttgart, Germany
| | - J K H Fischer
- Experimental Physics V, University of Augsburg, 86135, Augsburg, Germany.,T. Kimura Lab, Department of Advanced Materials Science, University of Tokyo, Tokyo, Japan
| | - P Lunkenheimer
- Experimental Physics V, University of Augsburg, 86135, Augsburg, Germany
| | - A Loidl
- Experimental Physics V, University of Augsburg, 86135, Augsburg, Germany
| | - E Uykur
- 1.Physikalisches Institut, Universität Stuttgart, 70569, Stuttgart, Germany
| | - M Dressel
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia.,1.Physikalisches Institut, Universität Stuttgart, 70569, Stuttgart, Germany
| | - B Gorshunov
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia.
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7
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Li S, Schmidt B. Replica exchange MD simulations of two-dimensional water in graphene nanocapillaries: rhombic versus square structures, proton ordering, and phase transitions. Phys Chem Chem Phys 2019; 21:17640-17654. [PMID: 31364628 DOI: 10.1039/c9cp00849g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen bond patterns, proton ordering, and phase transitions of monolayer ice in two-dimensional hydrophobic confinement are fundamentally different from those found for bulk ice. To investigate the behavior of quasi-2D ice, we perform molecular dynamics simulations of water confined between fixed graphene plates at a distance of 0.65 nm. While experimental results are still limited and theoretical investigations are often based on a single, often empirically based force field model, this work presents a systematic study modeling the water-graphene interaction by effective Lennard-Jones potentials previously derived from high-level ab initio CCSD(T) calculations of water adsorbed on graphene [Phys. Chem. Chem. Phys., 2013, 15, 4995]. For the water-water interaction different water force fields, i.e. SPCE, TIP3P, TIP4P, TIP4P/ICE, and TIP5P, are used. The water occupancy of the graphene capillary at a pressure of 1000 MPa is determined to be between 13.5 and 13.9 water molecules per square nanometer, depending on the choice of the water force field. Based on these densities, we explore the structure and dynamics of quasi-2D water for temperatures ranging from 200 K to about 600 K for each of the five force fields. To ensure complete sampling of the configurational space and to overcome the barriers separating metastable structures, these simulations are based on the replica exchange molecular dynamics technique. We report different tetragonal hydrogen bond patterns, which are classified as nearly square or as rhombic. While many of these arrangements are essentially flat, in some cases puckered arrangements are found, too. Also the proton ordering of the quasi-2D water structures is considered, allowing us to identify them as ferroelectric, ferrielectric or antiferroelectric. For temperatures between 200 K and 400 K we find several second-order phase transitions from one ice structure to another, changing in many cases both the arrangements of the oxygen atoms and the proton ordering. For temperatures between 400 K and 600 K there are melting-like transitions from a monolayer of ice to a monolayer of liquid water. These first-order phase transitions have a latent heat between 3.4 and 4.0 kJ mol-1. Both the values of the transition temperatures and of the latent heats display considerable model dependence for the five different water models investigated here.
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Affiliation(s)
- Shujuan Li
- Institute for Mathematics, Freie Universität Berlin, Arnimallee 6, D-14195 Berlin, Germany.
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8
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Jiang X, Futera Z, Blumberger J. Ergodicity-Breaking in Thermal Biological Electron Transfer? Cytochrome C Revisited. J Phys Chem B 2019; 123:7588-7598. [PMID: 31405279 DOI: 10.1021/acs.jpcb.9b05253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It was recently suggested that certain redox proteins operate in an ergodicity-breaking regime to facilitate biological electron transfer (ET). A signature for this is a large variance reorganization free energy (several electronvolts) but a significantly smaller Stokes reorganization free energy due to incomplete protein relaxation on the time scale of the ET event. Here we investigate whether this picture holds for oxidation of cytochrome c in aqueous solution, at various levels of theory including classical molecular dynamics with two additive and one electronically polarizable force field, and QM/MM calculations with the QM region treated by full electrostatic DFT embedding and by the perturbed matrix method. Sampling the protein and energy gap dynamics over more than 250 ns, we find no evidence for ergodicity-breaking effects. In particular, the inclusion of electronic polarizability of the heme group at QM/MM levels did not induce nonergodic effects, contrary to previous reports by Matyushov et al. The well-known problem of overestimation of reorganization free energies with additive force fields is cured when the protein and solvent are treated as electronically polarizable. Ergodicity-breaking effects may occur in other redox proteins, and our results suggest that long simulations, ideally on the ET time scale, with electronically polarizable force fields are required to obtain strong numerical evidence for them.
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Affiliation(s)
- Xiuyun Jiang
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - Zdenek Futera
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
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9
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Matveev VV. Cell theory, intrinsically disordered proteins, and the physics of the origin of life. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 149:114-130. [PMID: 30965040 DOI: 10.1016/j.pbiomolbio.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/01/2019] [Accepted: 04/05/2019] [Indexed: 12/30/2022]
Abstract
Cell theory, as formulated by Theodor Schwann in 1839, introduced the idea that the cell is the main structural unit of living nature. Later, in solving the problem of cell multiplication, Rudolf Virchow expanded the cell theory with a postulate: all cells only arise from pre-existing cells. But what did the very first cell arise from? This paper proposes extending the Virchow's law by the assumption that between the nonliving protocell and the first living cell the continuity of fundamental physical properties (the principle of invariance of physical properties) is preserved. The protocell is understood here as a cell-shaped physical system on the basis of the self-organized biologically significant prebiotic macromolecules, primarily peptides, having a potential to transform into the living cell. Biophase is considered as the physical basis of the membraneless protocell, the internal environment of which is separated from the external environment due to the phase of adsorbed water. The evidence is given that the first protocells may have been formed on the basis of intrinsically disordered peptides. Data on the similarity of the physical properties of living cells and the following model systems are given: protein and artificial polymer solutions, coacervate droplets, and ion-exchange resin granules. Available data on the similarity of the physical properties of cell models and living cells allow us to rephrase the Virchow's postulate as follows: the physical properties of a living cell could only arise from pre-existing physical properties of the protocell.
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Affiliation(s)
- Vladimir V Matveev
- Laboratory of Cell Physiology, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave 4, St. Petersburg, 194064, Russia.
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10
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Leitner DM, Yamato T. MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Abstract
Proteins interact with their aqueous surroundings, thereby modifying the physical properties of the solvent. The extent of this perturbation has been investigated by numerous methods in the past half-century, but a consensus has still not emerged regarding the spatial range of the perturbation. To a large extent, the disparate views found in the current literature can be traced to the lack of a rigorous definition of the perturbation range. Stating that a particular solvent property differs from its bulk value at a certain distance from the protein is not particularly helpful since such findings depend on the sensitivity and precision of the technique used to probe the system. What is needed is a well-defined decay length, an intrinsic property of the protein in a dilute aqueous solution, that specifies the length scale on which a given physical property approaches its bulk-water value. Based on molecular dynamics simulations of four small globular proteins, we present such an analysis of the structural and dynamic properties of the hydrogen-bonded solvent network. The results demonstrate unequivocally that the solvent perturbation is short-ranged, with all investigated properties having exponential decay lengths of less than one hydration shell. The short range of the perturbation is a consequence of the high energy density of bulk water, rendering this solvent highly resistant to structural perturbations. The electric field from the protein, which under certain conditions can be long-ranged, induces a weak alignment of water dipoles, which, however, is merely the linear dielectric response of bulk water and, therefore, should not be thought of as a structural perturbation. By decomposing the first hydration shell into polarity-based subsets, we find that the hydration structure of the nonpolar parts of the protein surface is similar to that of small nonpolar solutes. For all four examined proteins, the mean number of water-water hydrogen bonds in the nonpolar subset is within 1% of the value in bulk water, suggesting that the fragmentation and topography of the nonpolar protein-water interface has evolved to minimize the propensity for protein aggregation by reducing the unfavorable free energy of hydrophobic hydration.
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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12
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Pandey HD, Leitner DM. Thermodynamics of Hydration Water around an Antifreeze Protein: A Molecular Simulation Study. J Phys Chem B 2017; 121:9498-9507. [DOI: 10.1021/acs.jpcb.7b05892] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
| | - David M. Leitner
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
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13
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Malferrari M, Savitsky A, Mamedov MD, Milanovsky GE, Lubitz W, Möbius K, Semenov AY, Venturoli G. Trehalose matrix effects on charge-recombination kinetics in Photosystem I of oxygenic photosynthesis at different dehydration levels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1440-1454. [DOI: 10.1016/j.bbabio.2016.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 05/03/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
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14
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 PMCID: PMC6407618 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
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15
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16
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Matyushov DV. Protein electron transfer: is biology (thermo)dynamic? JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:473001. [PMID: 26558324 DOI: 10.1088/0953-8984/27/47/473001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life's ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein's elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic activated kinetics, which extends the transition-state theory to dynamically dispersive media. Releasing the grip of thermodynamics in kinetic calculations through nonergodicity provides the mechanism for an efficient optimization between reaction rates and the spectrum of relaxation times of the protein-water thermal bath. Bath dynamics, it appears, play as important role as the free energy in optimizing biology's performance.
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Affiliation(s)
- Dmitry V Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
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17
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Tayi AS, Kaeser A, Matsumoto M, Aida T, Stupp SI. Supramolecular ferroelectrics. Nat Chem 2015; 7:281-94. [PMID: 25803466 DOI: 10.1038/nchem.2206] [Citation(s) in RCA: 257] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/12/2015] [Indexed: 12/25/2022]
Abstract
Supramolecular chemistry uses non-covalent interactions to coax molecules into forming ordered assemblies. The construction of ordered materials with these reversible bonds has led to dramatic innovations in organic electronics, polymer science and biomaterials. Here, we review how supramolecular strategies can advance the burgeoning field of organic ferroelectricity. Ferroelectrics - materials with a spontaneous and electrically reversible polarization - are touted for use in non-volatile computer memories, sensors and optics. Historically, this physical phenomenon has been studied in inorganic materials, although some organic examples are known and strong interest exists to extend the search for ferroelectric molecular systems. Other undiscovered applications outside this regime could also emerge. We describe the key features necessary for molecular and supramolecular dipoles in organic ferroelectrics and their incorporation into ordered systems, such as porous frameworks and liquid crystals. The goal of this Review is to motivate the development of innovative supramolecular ferroelectrics that exceed the performance and usefulness of known systems.
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Affiliation(s)
- Alok S Tayi
- 1] Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02143, USA [2] Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Adrien Kaeser
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Michio Matsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takuzo Aida
- 1] Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan [2] RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Samuel I Stupp
- 1] Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, USA [2] Department of Chemistry, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, USA [3] Department of Medicine, Northwestern University, 251 East Huron Street, Chicago, Illinois 60611, USA [4] Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, Illinois 60611, USA
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Chandramouli B, Zazza C, Mancini G, Brancato G. Boundary condition effects on the dynamic and electric properties of hydration layers. J Phys Chem A 2015; 119:5465-75. [PMID: 25752804 DOI: 10.1021/jp511824t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water solvation has a central role in several biochemical processes ranging from protein folding to biomolecular recognition and enzyme catalysis. Because of its importance, the structure and dynamics of hydration layers around biological macromolecules have been the targets of a great number of experimental and computational studies. In the present contribution, we have investigated the effects of periodic boundary conditions (PBCs), as used in conjunction with molecular dynamics (MD) simulations, on the dynamic and electric properties of water layers. In particular, we have systematically performed MD simulations of neat water and biomolecules in aqueous solutions by imposing a different external dielectric constant, a generally overlooked parameter in PBC simulations. The effect of the system size has also been addressed. Overall, our results consistently indicate that the dipole moment properties of water layers, and specifically the dipole moment fluctuations and the reorientational correlation functions, can be sensitive to the choice of the external boundary conditions, whereas other molecular properties, such as the self-diffusion coefficient and the reorientational relaxation times, are not affected. We think that our investigation may help to assess appropriate simulation conditions for modeling the aqueous environment of relevant biochemical systems and processes.
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Affiliation(s)
| | - Costantino Zazza
- †Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Giordano Mancini
- †Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,‡Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Giuseppe Brancato
- †Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,‡Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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19
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Abstract
The network of hydrogen bonds characteristic of bulk water is significantly disturbed at the protein-water interface, where local fields induce mutually frustrated dipolar domains with potentially novel structure and dynamics. Here the dipolar susceptibility of hydration shells of lysozyme is studied by molecular dynamics simulations in a broad range of temperatures, 140-300 K. The real part of the susceptibility passes through a broad maximum as a function of temperature. The maximum shifts to higher temperatures with increasing frequency of the dielectric experiment. This phenomenology is consistent with that reported for bulk relaxor ferroelectrics, where it is related to the formation of dipolar nanodomains. Nanodomains in the hydration shell extend 12-15 Å from the protein surface into the bulk. Their dynamics are significantly slower than the dynamics of bulk water. The domains dynamically freeze into a ferroelectric glass below 160 K, at which point the Arrhenius plot of the dipolar relaxation time becomes significantly steeper.
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20
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Li S, Schmidt B. Molecular dynamics simulations of proton-ordered water confined in low-diameter carbon nanotubes. Phys Chem Chem Phys 2015; 17:7303-16. [DOI: 10.1039/c5cp00236b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metastable ferroelectric, ferrielectric, and antiferroelectric structures of water confined in carbon nanotubes and their abrupt or continuous transitions are identified.
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Affiliation(s)
- Shujuan Li
- Institute for Mathematics
- Freie Universität Berlin
- D-14195 Berlin
- Germany
| | - Burkhard Schmidt
- Institute for Mathematics
- Freie Universität Berlin
- D-14195 Berlin
- Germany
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21
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Alicki R, Leitner DM. Size-Dependent Accuracy of Nanoscale Thermometers. J Phys Chem B 2014; 119:9000-5. [DOI: 10.1021/jp508047q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Robert Alicki
- Institute
of Theoretical Physics and Astrophysics, University of Gdansk, Gdansk, Poland
- Freiburg
Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - David M. Leitner
- Department
of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
- Freiburg
Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
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22
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Callis PR. Simulating electrostatic effects on electronic transitions in proteins. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923571] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Elton DC, Fernández-Serra MV. Polar nanoregions in water: A study of the dielectric properties of TIP4P/2005, TIP4P/2005f and TTM3F. J Chem Phys 2014; 140:124504. [DOI: 10.1063/1.4869110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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24
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Xu Y, Leitner DM. Vibrational Energy Flow through the Green Fluorescent Protein–Water Interface: Communication Maps and Thermal Boundary Conductance. J Phys Chem B 2014; 118:7818-26. [DOI: 10.1021/jp412141z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yao Xu
- Department
of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
- Physikalische
Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - David M. Leitner
- Department
of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
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25
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Abstract
Electron transfer between redox proteins participating in energy chains of biology is required to proceed with high energetic efficiency, minimizing losses of redox energy to heat. Within the standard models of electron transfer, this requirement, combined with the need for unidirectional (preferably activationless) transitions, is translated into the need to minimize the reorganization energy of electron transfer. This design program is, however, unrealistic for proteins whose active sites are typically positioned close to the polar and flexible protein-water interface to allow inter-protein electron tunneling. The high flexibility of the interfacial region makes both the hydration water and the surface protein layer act as highly polar solvents. The reorganization energy, as measured by fluctuations, is not minimized, but rather maximized in this region. Natural systems in fact utilize the broad breadth of interfacial electrostatic fluctuations, but in the ways not anticipated by the standard models based on equilibrium thermodynamics. The combination of the broad spectrum of static fluctuations with their dispersive dynamics offers the mechanism of dynamical freezing (ergodicity breaking) of subsets of nuclear modes on the time of reaction/residence of the electron at a redox cofactor. The separation of time-scales of nuclear modes coupled to electron transfer allows dynamical freezing. In particular, the separation between the relaxation time of electro-elastic fluctuations of the interface and the time of conformational transitions of the protein caused by changing redox state results in dynamical freezing of the latter for sufficiently fast electron transfer. The observable consequence of this dynamical freezing is significantly different reorganization energies describing the curvature at the bottom of electron-transfer free energy surfaces (large) and the distance between their minima (Stokes shift, small). The ratio of the two reorganization energies establishes the parameter by which the energetic efficiency of protein electron transfer is increased relative to the standard expectations, thus minimizing losses of energy to heat. Energetically efficient electron transfer occurs in a chain of conformationally quenched cofactors and is characterized by flattened free energy surfaces, reminiscent of the flat and rugged landscape at the stability basin of a folded protein.
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Affiliation(s)
- Dmitry V Matyushov
- Center for Biological Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287-1504, USA.
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26
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Fenimore PW, Frauenfelder H, Magazù S, McMahon BH, Mezei F, Migliardo F, Young RD, Stroe I. Concepts and problems in protein dynamics. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.06.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Comez L, Lupi L, Morresi A, Paolantoni M, Sassi P, Fioretto D. More Is Different: Experimental Results on the Effect of Biomolecules on the Dynamics of Hydration Water. J Phys Chem Lett 2013; 4:1188-1192. [PMID: 26282040 DOI: 10.1021/jz400360v] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biological interfaces characterized by a complex mixture of hydrophobic, hydrophilic, or charged moieties interfere with the cooperative rearrangement of the hydrogen-bond network of water. In the present study, this solute-induced dynamical perturbation is investigated by extended frequency range depolarized light scattering experiments on an aqueous solution of a variety of systems of different nature and complexity such as small hydrophobic and hydrophilic molecules, amino acids, dipeptides, and proteins. Our results suggest that a reductionist approach is not adequate to describe the rearrangement of hydration water because a significant increase of the dynamical retardation and extension of the perturbation occurs when increasing the chemical complexity of the solute.
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Affiliation(s)
- Lucia Comez
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Laura Lupi
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Assunta Morresi
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Marco Paolantoni
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Paola Sassi
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
| | - Daniele Fioretto
- †Dipartimento di Fisica and ‡IOM-CNR c/o Dipartimento di Fisica, Università di Perugia, Via Pascoli, I-06123 Perugia, Italy
- §Dipartimento di Chimica and ⊥Centro di Eccellenza sui Materiali Innovativi Nanostrutturati (CEMIN), Università di Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy
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28
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Xu Y, Gnanasekaran R, Leitner DM. The dielectric response to photoexcitation of GFP: A molecular dynamics study. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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29
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LeBard DN, Martin DR, Lin S, Woodbury NW, Matyushov DV. Protein dynamics to optimize and control bacterial photosynthesis. Chem Sci 2013. [DOI: 10.1039/c3sc51327k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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30
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Analysis of Water and Hydrogen Bond Dynamics at the Surface of an Antifreeze Protein. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/125071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We examine dynamics of water molecules and hydrogen bonds at the water-protein interface of the wild-type antifreeze protein from spruce budworm Choristoneura fumiferana and a mutant that is not antifreeze active by all-atom molecular dynamics simulations. Water dynamics in the hydration layer around the protein is analyzed by calculation of velocity autocorrelation functions and their power spectra, and hydrogen bond time correlation functions are calculated for hydrogen bonds between water molecules and the protein. Both water and hydrogen bond dynamics from subpicosecond to hundred picosecond time scales are sensitive to location on the protein surface and appear correlated with protein function. In particular, hydrogen bond lifetimes are longest for water molecules hydrogen bonded to the ice-binding plane of the wild type, whereas hydrogen bond lifetimes between water and protein atoms on all three planes are similar for the mutant.
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31
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Nazmutdinov RR, Bronshtein MD, Zinkicheva TT, Chi Q, Zhang J, Ulstrup J. Modeling and computations of the intramolecular electron transfer process in the two-heme protein cytochrome c(4). Phys Chem Chem Phys 2012; 14:5953-65. [PMID: 22430606 DOI: 10.1039/c2cp24084j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The di-heme protein Pseudomonas stutzeri cytochrome c(4) (cyt c(4)) has emerged as a useful model for studying long-range protein electron transfer (ET). Recent experimental observations have shown a dramatically different pattern of intramolecular ET between the two heme groups in different local environments. Intramolecular ET in homogeneous solution is too slow (>10 s) to be detected but fast (ms-μs) intramolecular ET in an electrochemical environment has recently been achieved by controlling the molecular orientation of the protein assembled on a gold electrode surface. In this work we have performed computational modeling of the intramolecular ET process by a combination of density functional theory (DFT) and quantum mechanical charge transfer theory to disclose reasons for this difference. We first address the electronic structures of the model heme core with histidine and methionine axial ligands in both low- and high-spin states by structure-optimized DFT. The computations enable estimating the intramolecular reorganization energy of the ET process for different combinations of low- and high-spin heme couples. Environmental reorganization free energies, work terms ("gating") and driving force were determined using dielectric continuum models. We then calculated the electronic transmission coefficient of the intramolecular ET rate using perturbation theory combined with the electronic wave functions determined by the DFT calculations for different heme group orientations and Fe-Fe separations. The reactivity of low- and high-spin heme groups was notably different. The ET rate is exceedingly low for the crystallographic equilibrium orientation but increases by several orders of magnitude for thermally accessible non-equilibrium configurations. Deprotonation of the propionate carboxyl group was also found to enhance the ET rate significantly. The results are discussed in relation to the observed surface immobilization effect and support the notion of conformationally gated ET.
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Affiliation(s)
- Renat R Nazmutdinov
- Kazan National Research Technological University, 420015 Kazan, Republic Tatarstan, Russian Federation
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32
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Martin DR, Ozkan SB, Matyushov DV. Dissipative electro-elastic network model of protein electrostatics. Phys Biol 2012; 9:036004. [PMID: 22555305 DOI: 10.1088/1478-3975/9/3/036004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We propose a dissipative electro-elastic network model to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped dynamics of the normal modes of the network characterized by two friction coefficients. The electrostatic component is introduced to the model through atomic charges of the protein force field. The overall effect of the electrostatic fluctuations of the network is recorded through the frequency-dependent response functions of the electrostatic potential and electric field at the protein active site. We also consider the dynamics of displacements of individual residues in the network and the dynamics of distances between pairs of residues. The model is tested against loss spectra of residue displacements and the electrostatic potential and electric field at the heme's iron from all-atom molecular dynamics simulations of three hydrated globular proteins.
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Affiliation(s)
- Daniel R Martin
- Center for Biological Physics, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504, USA
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33
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Alijabbari N, Chen Y, Sizov I, Globus T, Gelmont B. Molecular dynamics modeling of the sub-THz vibrational absorption of thioredoxin from E. coli. J Mol Model 2011; 18:2209-18. [PMID: 21947449 DOI: 10.1007/s00894-011-1238-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 09/08/2011] [Indexed: 11/25/2022]
Abstract
Sub-terahertz (THz) vibrational modes of the protein thioredoxin in a water environment were simulated using molecular dynamics (MD) in order to find the conditions needed for simulation convergence, improve the correlation between experimental and simulated absorption frequencies, and ultimately enhance the predictive capabilities of computational modeling. Thioredoxin from E. coli was used as a model molecule for protocol development and to optimize the simulation parameters. The empirically parameterized software packages Amber 8 and 10 were used in this work. Using atomic trajectories from the constant energy and volume MD simulations, thioredoxin's sub-THz vibrational spectra and absorption coefficients were calculated in a quasi-harmonic approximation. An optimal production run length ~100 ps was found, in agreement with experimental data on thioredoxin relaxation dynamics. At the same time, a new procedure was developed for averaging correlation matrices of atomic coordinates in MD simulations. In particular, the open source package ptraj was edited to improve a matrix-analyzing function. Averaging only six matrices gave much more consistent results, with absorption peak intensities exceeding those from the individual spectra and a rather good correlation between simulated vibrational frequencies and experimental data.
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Affiliation(s)
- Naser Alijabbari
- Department of Electrical & Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA
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34
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Matyushov DV. Nanosecond Stokes Shift Dynamics, Dynamical Transition, and Gigantic Reorganization Energy of Hydrated Heme Proteins. J Phys Chem B 2011; 115:10715-24. [DOI: 10.1021/jp200409z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Dmitry V. Matyushov
- Center for Biological Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
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35
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Gnanasekaran R, Agbo JK, Leitner DM. Communication maps computed for homodimeric hemoglobin: Computational study of water-mediated energy transport in proteins. J Chem Phys 2011; 135:065103. [DOI: 10.1063/1.3623423] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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36
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Perticaroli S, Comez L, Paolantoni M, Sassi P, Morresi A, Fioretto D. Extended Frequency Range Depolarized Light Scattering Study of N-Acetyl-leucine-methylamide–Water Solutions. J Am Chem Soc 2011; 133:12063-8. [DOI: 10.1021/ja202272k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefania Perticaroli
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Lucia Comez
- Dipartimento di Fisica, Universitá degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- IOM-CNR c/o Dipartimento di Fisica, Universitá di Perugia, Via Pascoli, I-06123, Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Paola Sassi
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Assunta Morresi
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Daniele Fioretto
- Dipartimento di Fisica, Universitá degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
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37
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Matyushov DV, Morozov AY. Electrostatics of the protein-water interface and the dynamical transition in proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:011908. [PMID: 21867214 DOI: 10.1103/physreve.84.011908] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Indexed: 05/31/2023]
Abstract
Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the local motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean-square displacements of iron of metmyoglobin reported by Mössbauer spectroscopy. We show that high displacement of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean-square displacements when the corresponding relaxation times enter the instrumental resolution window.
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Affiliation(s)
- Dmitry V Matyushov
- Center for Biological Physics, Arizona State University, PO Box 871604, Tempe, AZ 85287-1604, USA.
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38
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Bhattacharjee N, Biswas P. Structure of hydration water in proteins: a comparison of molecular dynamics simulations and database analysis. Biophys Chem 2011; 158:73-80. [PMID: 21665349 DOI: 10.1016/j.bpc.2011.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 05/07/2011] [Accepted: 05/08/2011] [Indexed: 11/15/2022]
Abstract
Hydration layer water molecules play important structural and functional roles in proteins. Despite being a critical component in biomolecular systems, characterizing the properties of hydration water poses a challenge for both experiments and simulations. In this context we investigate the local structure of hydration water molecules as a function of the distance from the protein and water molecules respectively in 188 high resolution protein structures and compare it with those obtained from molecular dynamics simulations. Tetrahedral order parameter of water in proteins calculated from previous and present simulation studies show that the potential of bulk water overestimates the average tetrahedral order parameter compared to those calculated from crystal structures. Hydration waters are found to be more ordered at a distance between the first and second solvation shell from the protein surface. The values of the order parameter decrease sharply when the water molecules are located very near or far away from the protein surface. At small water-water distance, the values of order parameter of water are very low. The average order parameter records a maximum value at a distance equivalent to the first solvation layer with respect to the water-water radial distribution and asymptotically approaches a constant value at large distances. Results from present analysis will help to get a better insight into structure of hydration water around proteins. The analysis will also help to improve the accuracy of water models on the protein surface.
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Sinha SK, Bandyopadhyay S. Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules. J Chem Phys 2011; 134:115101. [DOI: 10.1063/1.3560442] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Zhao HX, Kong XJ, Li H, Jin YC, Long LS, Zeng XC, Huang RB, Zheng LS. Transition from one-dimensional water to ferroelectric ice within a supramolecular architecture. Proc Natl Acad Sci U S A 2011; 108:3481-6. [PMID: 21321232 PMCID: PMC3048133 DOI: 10.1073/pnas.1010310108] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ferroelectric materials are characterized by spontaneous electric polarization that can be reversed by inverting an external electric field. Owing to their unique properties, ferroelectric materials have found broad applications in microelectronics, computers, and transducers. Water molecules are dipolar and thus ferroelectric alignment of water molecules is conceivable when water freezes into special forms of ice. Although the ferroelectric ice XI has been proposed to exist on Uranus, Neptune, or Pluto, evidence of a fully proton-ordered ferroelectric ice is still elusive. To date, existence of ferroelectric ice with partial ferroelectric alignment has been demonstrated only in thin films of ice grown on platinum surfaces or within microdomains of alkali-hydroxide doped ice I. Here we report a unique structure of quasi-one-dimensional (H(2)O)(12n) wire confined to a 3D supramolecular architecture of H(4)CDTA, trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid; 4,4'-bpy, 4,4'-bipyridine). In stark contrast to the bulk, this 1D water wire not only exhibits enormous dielectric anomalies at approximately 175 and 277 K, respectively, but also undergoes a spontaneous transition between "1D liquid" and "1D ferroelectric ice" at approximately 277 K. Hitherto unrevealed properties of the 1D water wire will be valuable to the understanding of anomalous properties of water and synthesis of novel ferroelectric materials.
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Affiliation(s)
- Hai-Xia Zhao
- State Key Laboratory of Physical Chemistry of Solid Surface and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; and
| | - Xiang-Jian Kong
- State Key Laboratory of Physical Chemistry of Solid Surface and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; and
| | - Hui Li
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588
| | - Yi-Chang Jin
- State Key Laboratory of Physical Chemistry of Solid Surface and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; and
| | - La-Sheng Long
- State Key Laboratory of Physical Chemistry of Solid Surface and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; and
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588
| | - Rong-Bin Huang
- State Key Laboratory of Physical Chemistry of Solid Surface and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; and
| | - Lan-Sun Zheng
- State Key Laboratory of Physical Chemistry of Solid Surface and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; and
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Gnanasekaran R, Xu Y, Leitner DM. Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin. J Phys Chem B 2010; 114:16989-96. [PMID: 21126033 DOI: 10.1021/jp109173t] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.
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LeBard DN, Matyushov DV. Protein–water electrostatics and principles of bioenergetics. Phys Chem Chem Phys 2010; 12:15335-48. [DOI: 10.1039/c0cp01004a] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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