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Khan T, Halder B, Das N, Sen P. Role of Associated Water Dynamics on Protein Stability and Activity in Crowded Milieu. J Phys Chem B 2024. [PMID: 39224956 DOI: 10.1021/acs.jpcb.4c04337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Macromolecular crowding bridges in vivo and in vitro studies by simulating cellular complexities such as high viscosity and limited space while maintaining the experimental feasibility. Over the last two decades, the impact of macromolecular crowding on protein stability and activity has been a significant topic of study and discussion, though still lacking a thorough mechanistic understanding. This article investigates the role of associated water dynamics on protein stability and activity within crowded environments, using bromelain and Ficoll-70 as the model systems. Traditional crowding theory primarily attributes protein stability to entropic effects (excluded volume) and enthalpic interactions. However, our recent findings suggest that water structure modulation plays a crucial role in a crowded environment. In this report, we strengthen the conclusion of our previous study, i.e., rigid-associated water stabilizes proteins via entropy and destabilizes them via enthalpy, while flexible water has the opposite effect. In the process, we addressed previous shortcomings with a systematic concentration-dependent study using a single-domain protein and component analysis of solvation dynamics. More importantly, we analyze bromelain's hydrolytic activity using the Michaelis-Menten model to understand kinetic parameters like maximum velocity (Vmax) achieved by the system and the Michaelis-Menten coefficient (KM). Results indicate that microviscosity (not the bulk viscosity) controls the enzyme-substrate (ES) complex formation, where an increase in the microviscosity makes the ES complex formation less favorable. On the other hand, flexible associated water dynamics were found to favor the rate of product formation significantly from the ES complex, while rigid associated water hinders it. This study improves our understanding of protein stability and activity in crowded environments, highlighting the critical role of associated water dynamics.
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Affiliation(s)
- Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, UP 208 016, India
| | - Bisal Halder
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, UP 208 016, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, UP 208 016, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, UP 208 016, India
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2
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Mukherjee S, Mondal S, Acharya S, Bagchi B. Tug-of-War between Internal and External Frictions and Viscosity Dependence of Rate in Biological Reactions. PHYSICAL REVIEW LETTERS 2022; 128:108101. [PMID: 35333093 DOI: 10.1103/physrevlett.128.108101] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/13/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
The role of water in biological processes is studied in three reactions, namely, the Fe-CO bond rupture in myoglobin, GB1 unfolding, and insulin dimer dissociation. We compute both internal and external components of friction on relevant reaction coordinates. In all of the three cases, the cross-correlation between forces from protein and water is found to be large and negative that serves to reduce the total friction significantly, increase the calculated reaction rate, and weaken solvent viscosity dependence. The computed force spectrum reveals bimodal 1/f noise, suggesting the use of a non-Markovian rate theory.
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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3
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Mukherjee S, Acharya S, Mondal S, Banerjee P, Bagchi B. Structural Stability of Insulin Oligomers and Protein Association-Dissociation Processes: Free Energy Landscape and Universal Role of Water. J Phys Chem B 2021; 125:11793-11811. [PMID: 34674526 DOI: 10.1021/acs.jpcb.1c05811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Association and dissociation of proteins are important biochemical events. In this Feature Article, we analyze the available studies of these processes for insulin oligomers in aqueous solution. We focus on the solvation of the insulin monomer in water, stability and dissociation of its dimer, and structural integrity of the hexamer. The intricate role of water in solvation of the dimer- and hexamer-forming surfaces, in long-range interactions between the monomers and the stability of the oligomers, is discussed. Ten water molecules inside the central cavity stabilize the structure of the insulin hexamer. We discuss how different order parameters can be used to understand the dissociation of the insulin dimer. The calculation of the rate using a recently computed multidimensional free energy provides considerable insight into the interplay between protein and water dynamics.
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Puja Banerjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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4
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Magdziarz T, Mitusińska K, Bzówka M, Raczyńska A, Stańczak A, Banas M, Bagrowska W, Góra A. AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective. Bioinformatics 2020; 36:2599-2601. [PMID: 31860077 PMCID: PMC7178393 DOI: 10.1093/bioinformatics/btz946] [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: 10/14/2019] [Revised: 12/11/2019] [Accepted: 12/17/2019] [Indexed: 11/15/2022] Open
Abstract
Motivation Tunnels, pores, channels, pockets and cavities contribute to proteins architecture and performance. However, analysis and characteristics of transportation pathways and internal binding cavities are performed separately. We aimed to provide universal tool for analysis of proteins integral interior with access to detailed information on the ligands transportation phenomena and binding preferences. Results AQUA-DUCT version 1.0 is a comprehensive method for macromolecules analysis from the intramolecular voids perspective using small ligands as molecular probes. This version gives insight into several properties of macromolecules and facilitates protein engineering and drug design by the combination of the tracking and local mapping approach to small ligands. Availability and implementation http://www.aquaduct.pl. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tomasz Magdziarz
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Maria Bzówka
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Agata Raczyńska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Agnieszka Stańczak
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Michał Banas
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Weronika Bagrowska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
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5
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Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
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Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
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6
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Mukherjee S, Mondal S, Bagchi B. Mechanism of Solvent Control of Protein Dynamics. PHYSICAL REVIEW LETTERS 2019; 122:058101. [PMID: 30822020 DOI: 10.1103/physrevlett.122.058101] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Indexed: 06/09/2023]
Abstract
We find that the coupled interactions between protein and water polarization fluctuations play a dominant role in driving the configuration space random walk of solvated proteins. We perform atomistic molecular dynamics simulations on five proteins. Owing to a very low dielectric constant of protein, its dipolar groups experience forces from water along with local forces due to protein atoms. Energy fluctuations reveal a pronounced anticorrelation between protein and water contributions. The protein energy spectrum shows bimodal 1/f noise, which can be attributed to the influence of water on the dynamics of protein.
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
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7
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Heid E, Braun D. Fundamental limitations of the time-dependent Stokes shift for investigating protein hydration dynamics. Phys Chem Chem Phys 2019; 21:4435-4443. [DOI: 10.1039/c8cp07623e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the TDSS measured in protein systems, large protein contributions fully obscure hydration dynamics.
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Affiliation(s)
- Esther Heid
- Department of Computational Biological Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
| | - Daniel Braun
- Department of Computational Biological Chemistry
- Faculty of Chemistry
- University of Vienna
- 1090 Vienna
- Austria
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8
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Honegger P, Heid E, Schmode S, Schröder C, Steinhauser O. Changes in protein hydration dynamics by encapsulation or crowding of ubiquitin: strong correlation between time-dependent Stokes shift and intermolecular nuclear Overhauser effect. RSC Adv 2019; 9:36982-36993. [PMID: 35539058 PMCID: PMC9075347 DOI: 10.1039/c9ra08008b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022] Open
Abstract
The local changes in protein hydration dynamics upon encapsulation of the protein or macromolecular crowding are essential to understand protein function in cellular environments. We were able to obtain a spatially-resolved picture of the influence of confinement and crowding on the hydration dynamics of the protein ubiquitin by analyzing the time-dependent Stokes shift (TDSS), as well as the intermolecular Nuclear Overhauser Effect (NOE) at different sites of the protein by large-scale computer simulation of single and multiple proteins in water and confined in reverse micelles. Besides high advanced space resolved information on hydration dynamics we found a strong correlation of the change in NOE upon crowding or encapsulation and the change in the integral TDSS relaxation times in all investigated systems relative to the signals in a diluted protein solution. Changes in local protein hydration dynamics caused by encapsulation or crowding are reflected in the TDSS and the intermolecular NOE alike.![]()
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Esther Heid
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Stella Schmode
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Christian Schröder
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
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9
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Capdevila DA, Edmonds KA, Campanello GC, Wu H, Gonzalez-Gutierrez G, Giedroc DP. Functional Role of Solvent Entropy and Conformational Entropy of Metal Binding in a Dynamically Driven Allosteric System. J Am Chem Soc 2018; 140:9108-9119. [PMID: 29953213 PMCID: PMC6425489 DOI: 10.1021/jacs.8b02129] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Allostery is a regulatory phenomenon whereby ligand binding to one site influences the binding of the same or a different ligand to another site on a macromolecule. The physical origins of allosteric regulation remain under intense investigation. In general terms, ligand-induced structural changes, perturbations of residue-specific dynamics, and surrounding solvent molecules all potentially contribute to the global energetics of allostery. While the role of solvent is generally well understood in regulatory events associated with major protein structural rearrangements, the degree to which protein dynamics impact solvent degrees of freedom is unclear, particularly in cases of dynamically driven allostery. With the aid of new crystal structures, extensive calorimetric and residue-specific dynamics studies over a range of time scales and temperatures, we dissect for the first time the relative degree to which changes in solvent entropy and residue-specific dynamics impact dynamically driven, allosteric inhibition of DNA binding by Zn in the zinc efflux repressor, CzrA (chromosomal zinc-regulated repressor). We show that non-native residue-specific dynamics in allosterically impaired CzrA mutants are accompanied by significant perturbations in solvent entropy that cannot be predicted from crystal structures. We conclude that functional dynamics are not necessarily restricted to protein residues but involve surface water molecules that may be responding to ligand (Zn)-mediated perturbations in protein internal motions that define the conformational ensemble, rather than major structural rearrangements.
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Affiliation(s)
- Daiana A. Capdevila
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102 United States
| | - Katherine A. Edmonds
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102 United States
| | - Gregory C. Campanello
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102 United States
| | - Hongwei Wu
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102 United States
| | - Giovanni Gonzalez-Gutierrez
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405 United States
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102 United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405 United States
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10
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Mukherjee S, Mondal S, Bagchi B. Distinguishing dynamical features of water inside protein hydration layer: Distribution reveals what is hidden behind the average. J Chem Phys 2018; 147:024901. [PMID: 28711050 DOI: 10.1063/1.4990693] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Since the pioneering works of Pethig, Grant, and Wüthrich on a protein hydration layer, many studies have been devoted to find out if there are any "general and universal" characteristic features that can distinguish water molecules inside the protein hydration layer from bulk. Given that the surface itself varies from protein to protein, and that each surface facing the water is heterogeneous, search for universal features has been elusive. Here, we perform an atomistic molecular dynamics simulation in order to propose and demonstrate that such defining characteristics can emerge if we look not at average properties but the distribution of relaxation times. We present results of calculations of distributions of residence times and rotational relaxation times for four different protein-water systems and compare them with the same quantities in the bulk. The distributions in the hydration layer are unusually broad and log-normal in nature due to the simultaneous presence of peptide backbones that form weak hydrogen bonds, hydrophobic amino acid side chains that form no hydrogen bond, and charged polar groups that form a strong hydrogen bond with the surrounding water molecules. The broad distribution is responsible for the non-exponential dielectric response and also agrees with large specific heat of the hydration water. Our calculations reveal that while the average time constant is just about 2-3 times larger than that of bulk water, it provides a poor representation of the real behaviour. In particular, the average leads to the erroneous conclusion that water in the hydration layer is bulk-like. However, the observed and calculated lower value of static dielectric constant of hydration layer remained difficult to reconcile with the broad distribution observed in dynamical properties. We offer a plausible explanation of these unique properties.
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, India
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11
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Mondal S, Mukherjee S, Bagchi B. Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study. J Chem Phys 2018; 147:154901. [PMID: 29055291 DOI: 10.1063/1.4995420] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self- and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slow component approximately in the 20-80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component has multiple origins, namely, adjacent charges in amino acid side chains, hydrogen bonded water molecules and a dynamically coupled motion between side chain and water. In addition, the charges enforce a structural ordering of nearby water molecules and helps to form a local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component, whereas the initial ultrafast decay arises predominantly (approximately 80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi-quantitative manner.
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Affiliation(s)
- Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
| | - Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, India
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12
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Miyazaki M, Naito A, Ikeda T, Klyne J, Sakota K, Sekiya H, Dopfer O, Fujii M. Real-time observation of the photoionization-induced water rearrangement dynamics in the 5-hydroxyindole-water cluster by time-resolved IR spectroscopy. Phys Chem Chem Phys 2018; 20:3079-3091. [PMID: 29143839 DOI: 10.1039/c7cp06127g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvation plays an essential role in controlling the mechanism and dynamics of chemical reactions in solution. The present study reveals that changes in the local solute-solvent interaction have a great impact on the timescale of solvent rearrangement dynamics. Time-resolved IR spectroscopy has been applied to a hydration rearrangement reaction in the monohydrated 5-hydroxyindole-water cluster induced by photoionization of the solute molecule. The water molecule changes the stable hydration site from the indolic NH site to the substituent OH site, both of which provide a strongly attractive potential for hydration. The rearrangement time constant amounts to 8 ± 2 ns, and is further slowed down by a factor of more than five at lower excess energy. These rearrangement times are slower by about three orders of magnitude than those reported for related systems where the water molecule is repelled from a repulsive part of the interaction potential toward an attractive well. The excess energy dependence of the time constant is well reproduced by RRKM theory. Differences in the reaction mechanism are discussed on the basis of energy relaxation dynamics.
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Affiliation(s)
- Mitsuhiko Miyazaki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 R1-15, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
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13
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Biswas R, Bagchi B. Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:013001. [PMID: 29205175 DOI: 10.1088/1361-648x/aa9b1d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.
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14
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Martin DR, Forsmo JE, Matyushov DV. Complex Dynamics of Water in Protein Confinement. J Phys Chem B 2017; 122:3418-3425. [PMID: 29206460 DOI: 10.1021/acs.jpcb.7b10448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper studies single-molecule and collective dynamics of water confined in protein powders by means of molecular dynamics simulations. The single-particle dynamics show a modest retardation compared to the bulk but become highly stretched in the powder, with the stretching exponent of ≃0.2. The collective dynamics of the total water dipole are affected by intermolecular correlations inside water and by cross-correlations between the water and the protein. The dielectric spectrum of water in the powder has two nearly equal-amplitude peaks: a Debye peak with ≃16 ps relaxation time and a highly stretched peak with the relaxation time of ≃13 ns and a stretching exponent of ≃0.12. The slower relaxation component is not seen in the single-molecule correlation functions and can be assigned to elastic protein motions displacing water in the powder. The loss spectrum of the intermediate scattering function reported by neutron-scattering experiments is also highly stretched, with the high-frequency wing scaling according to a power law. Translational dynamics can become much slower in the powder than in the bulk but are overshadowed by the rotational loss in the overall loss spectrum of neutron scattering.
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Affiliation(s)
| | - James E Forsmo
- College of Engineering , Georgia Institute of Technology , 225 North Avenue , Atlanta , Georgia 30332 , United States
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15
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Matyushov DV, Newton MD. Electrode reactions in slowly relaxing media. J Chem Phys 2017; 147:194506. [DOI: 10.1063/1.5003022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Dmitry V. Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, USA
| | - Marshall D. Newton
- Chemistry Department, Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973-5000, USA
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16
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Seyedi S, Matyushov DV. Ergodicity breaking of iron displacement in heme proteins. SOFT MATTER 2017; 13:8188-8201. [PMID: 29082406 DOI: 10.1039/c7sm01561e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by the softening of the force constant for atomic/molecular displacements by electrostatic and van der Waals forces from the protein-water thermal bath. Displacement softening passes through a nonergodic dynamical transition when the relaxation time of the force-force correlation function enters, with increasing temperature, the instrumental observation window. Two crossover temperatures are identified. The lower crossover, presently connected to the glass transition, is related to the dynamical unfreezing of rotations of water molecules within nanodomains polarized by charged surface residues of the protein. The higher crossover temperature, usually assigned to the dynamical transition, marks the onset of water translations. All crossovers are ergodicity breaking transitions depending on the corresponding observation windows. Allowing stretched exponential relaxation of the protein-water thermal bath significantly improves the theory-experiment agreement when applied to solid protein samples studied by Mössbauer spectroscopy.
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Affiliation(s)
- Salman Seyedi
- Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287, USA
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17
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Mondal S, Mukherjee S, Bagchi B. Protein Hydration Dynamics: Much Ado about Nothing? J Phys Chem Lett 2017; 8:4878-4882. [PMID: 28978201 DOI: 10.1021/acs.jpclett.7b02324] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science , Bengaluru, Karnataka 560 012, India
| | - Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science , Bengaluru, Karnataka 560 012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science , Bengaluru, Karnataka 560 012, India
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