1
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Robinson Brown DC, Webber TR, Casey TM, Franck J, Shell MS, Han S. Computation of Overhauser dynamic nuclear polarization processes reveals fundamental correlation between water dynamics, structure, and solvent restructuring entropy. Phys Chem Chem Phys 2024; 26:14637-14650. [PMID: 38742831 DOI: 10.1039/d4cp00030g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Hydration water dynamics, structure, and thermodynamics are crucially important to understand and predict water-mediated properties at molecular interfaces. Yet experimentally and directly quantifying water behavior locally near interfaces at the sub-nanometer scale is challenging, especially at interfaces submerged in biological solutions. Overhauser dynamic nuclear polarization (ODNP) experiments measure equilibrium hydration water dynamics within 8-15 angstroms of a nitroxide spin probe on instantaneous timescales (10 picoseconds to nanoseconds), making ODNP a powerful tool for probing local water dynamics in the vicinity of the spin probe. As with other spectroscopic techniques, concurrent computational analysis is necessary to gain access to detailed molecular level information about the dynamic, structural, and thermodynamic properties of water from experimental ODNP data. We chose a model system that can systematically tune the dynamics of water, a water-glycerol mixture with compositions ranging from 0 to 0.3 mole fraction glycerol. We demonstrate the ability of molecular dynamics (MD) simulations to compute ODNP spectroscopic quantities, and show that translational, rotational, and hydrogen bonding dynamics of hydration water align strongly with spectroscopic ODNP parameters. Moreover, MD simulations show tight correlations between the dynamic properties of water that ODNP captures and the structural and thermodynamic behavior of water. Hence, experimental ODNP readouts of varying water dynamics suggest changes in local structural and thermodynamic hydration water properties.
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Affiliation(s)
- Dennis C Robinson Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Thomas R Webber
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Thomas M Casey
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - John Franck
- Department of Chemistry, Syracuse University, Syracuse, NY, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA.
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2
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Mahanta DD, Brown DR, Webber T, Pezzotti S, Schwaab G, Han S, Shell MS, Havenith M. Bridging the Gap in Cryopreservation Mechanism: Unraveling the Interplay between Structure, Dynamics, and Thermodynamics in Cryoprotectant Aqueous Solutions. J Phys Chem B 2024; 128:3720-3731. [PMID: 38584393 DOI: 10.1021/acs.jpcb.4c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cryoprotectants play a crucial role in preserving biological material, ensuring their viability during storage and facilitating crucial applications such as the conservation of medical compounds, tissues, and organs for transplantation. However, the precise mechanism by which cryoprotectants modulate the thermodynamic properties of water to impede the formation and growth of ice crystals, thus preventing long-term damage, remains elusive. This is evident in the use of empirically optimized recipes for mixtures that typically contain DMSO, glycerol, and various sugar constituents. Here, we use terahertz calorimetry, Overhauser nuclear polarization, and molecular dynamics simulations to show that DMSO exhibits a robust structuring effect on water around its methyl groups, reaching a maximum at a DMSO mole fraction of XDMSO = 0.33. In contrast, glycerol exerts a smaller water-structuring effect, even at higher concentrations (Scheme 1). These results potentially suggest that the wrapped water around DMSO's methyl group, which can be evicted upon ligand binding, may render DMSO a more surface-active cryoprotectant than glycerol, while glycerol may participate more as a viscogen that acts on the entire sample. These findings shed light on the molecular intricacies of cryoprotectant solvation behavior and have potentially significant implications for optimizing cryopreservation protocols.
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Affiliation(s)
- Debasish Das Mahanta
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum 44780, Germany
- Department of Physics, Technische Universität (TU) Dortmund, Dortmund 44227, Germany
| | - Dennis Robinson Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Thomas Webber
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Simone Pezzotti
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum 44780, Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum 44780, Germany
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum 44780, Germany
- Department of Physics, Technische Universität (TU) Dortmund, Dortmund 44227, Germany
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3
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Lorenz-Ochoa KA, Baiz CR. Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates. J Am Chem Soc 2023; 145:27800-27809. [PMID: 38061016 DOI: 10.1021/jacs.3c10862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Cells achieve high spatiotemporal control over biochemical processes through compartmentalization to membrane-bound as well as membraneless organelles that assemble by liquid-liquid phase separation. Characterizing the balance of forces within these environments is essential to understanding their stability and function, and water is an integral part of the condensate, playing an important role in mediating electrostatic and hydrogen-bonding interactions. Here, we investigate the ultrafast, picosecond hydrogen-bond dynamics of a model biocondensate consisting of a peptide poly-l-arginine (Poly-R) and the nucleic acid adenosine monophosphate (AMP) using coherent two-dimensional infrared (2D IR) spectroscopy. We investigated three vibrational modes: the arginine side-chain C═N stretches, an AMP ring mode, and the amide backbone carbonyl stretching modes. Dynamics slow considerably between the dilute phase and the condensate phase for each vibrational probe. For example, the arginine side-chain C═N modes slow from 0.38 to 2.26 ps due to strong electrostatic interactions. All-atom molecular dynamics simulations provide an atomistic interpretation of the H-bond network disruption resulting from electrostatic contributions as well as collapse within the condensate. Simulations predict that a fraction of water molecules are highly constrained within the condensate, explaining the observed slowdown in the H-bond dynamics.
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Affiliation(s)
- Keegan A Lorenz-Ochoa
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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4
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Yang L, Guo S, Hou C, Jiang S, Shi L, Ma X, Zheng B, Fang Y, Ye L, He X. Low-Entropy Hydration Shells at the Spike RBD's Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants. Biomolecules 2023; 13:1628. [PMID: 38002310 PMCID: PMC10669249 DOI: 10.3390/biom13111628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/29/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023] Open
Abstract
The infectivity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is primarily determined by the binding affinity between the receptor-binding domain (RBD) of the spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor. Here, through screening off pseudo hydrophilic groups on protein surfaces, the distribution of low-entropy regions on hydration shells of the ACE2 receptor and the RBDs of multiple SARS-CoV-2 variants was demonstrated. Shape matching between the low-entropy hydration shells of multiple SARS-CoV-2 variants and the ACE2 receptor has been identified as a mechanism that drives hydrophobic attraction between the RBDs and the ACE2 receptor, which estimates the binding affinity. Low-entropy regions of the hydration shells, which play important roles in determining the binding of other viruses and their receptors, are demonstrated. The RBD-ACE2 binding is thus found to be guided by hydrophobic collapse between the shape-matched low-entropy regions of the hydration shells of the proteins. A measure of the low-entropy status of the hydration shells can be estimated by calculating genuine hydrophilic groups within the binding sites. An important indicator of the contagiousness of SARS-CoV-2 variants is the low-entropy level of its hydration shells at the spike protein binding site.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
| | - Chengyu Hou
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China;
| | - Shenda Jiang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
| | - Bing Zheng
- Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education) and School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China;
| | - Yi Fang
- Department of Mathematics, Nanchang University, Nanchang 330031, China;
| | - Lin Ye
- School of System Design and Intelligent Manufacturing, Southern University of Science and Technology, Shenzhen 518055, China;
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (S.G.); (S.J.); (L.S.); (X.M.)
- Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China
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5
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Hill TD, Basnet S, Lepird HH, Rightnowar BW, Moran SD. Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy. J Chem Phys 2023; 159:165101. [PMID: 37870142 PMCID: PMC10597647 DOI: 10.1063/5.0167991] [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] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.
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Affiliation(s)
| | - Sunil Basnet
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Hannah H. Lepird
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Blaze W. Rightnowar
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Sean D. Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
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6
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Reid KM, Poudel H, Leitner DM. Dynamics of Hydrogen Bonds between Water and Intrinsically Disordered and Structured Regions of Proteins. J Phys Chem B 2023; 127:7839-7847. [PMID: 37672685 DOI: 10.1021/acs.jpcb.3c03102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Recent studies indicate more restricted dynamics of water around intrinsically disordered proteins (IDPs) than structured proteins. We examine here the dynamics of hydrogen bonds between water molecules and two proteins, small ubiquitin-related modifier-1 (SUMO-1) and ubiquitin-conjugating enzyme E2I (UBC9), which we compare around intrinsically disordered regions (IDRs) and structured regions of these proteins. It has been recognized since some time that excluded volume effects, which influence access of water molecules to hydrogen-bonding sites, and the strength of hydrogen bonds between water and protein affect hydrogen bond lifetimes. While we find those two properties to mediate lifetimes of hydrogen bonds between water and protein residues in this study, we also find that the lifetimes are affected by the concentration of charged groups on other nearby residues. These factors are more important in determining the hydrogen bond lifetimes than whether a residue hydrogen bonding with water belongs to an IDR or to a structured region.
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Affiliation(s)
- Korey M Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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7
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Ghosh B, Layek S, Bhattacharyya D, Sengupta N. Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and dynamics. J Chem Phys 2023; 159:095101. [PMID: 37655772 DOI: 10.1063/5.0154977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023] Open
Abstract
DNA deformability and differential hydration are crucial determinants of biological processes ranging from genetic material packaging to gene expression; their associative details, however, remain inadequately understood. Herein, we report investigations of the dynamic and thermodynamic responses of the local hydration of a variety of base pair sequences. Leveraging in silico sampling and our in-house analyses, we first report the local conformational propensity of sequences that are either predisposed toward the canonical A- or B-conformations or are restrained to potential transitory pathways. It is observed that the transition from the unrestrained A-form to the B-form leads to lengthwise structural deformation. The insertion of intermittent -(CG)- base pairs in otherwise homogeneous -(AT)- sequences bears dynamical consequences for the vicinal hydration layer. Calculation of the excess (pair) entropy suggests substantially higher values of hydration water surrounding A conformations over the B- conformations. Applying the Rosenfeld approximation, we project that the diffusivity of water molecules proximal to canonical B conformation is least for the minor groove of the canonical B-conformation. We determine that structure, composition, and conformation specific groove dimension together influence the local hydration characteristics and, therefore, are expected to be important determinants of biological processes.
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Affiliation(s)
- Brataraj Ghosh
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Sarbajit Layek
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics, Bidhannagar, Kolkata, West Bengal 700064, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
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8
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Das Mahanta D, Brown DR, Pezzotti S, Han S, Schwaab G, Shell MS, Havenith M. Local solvation structures govern the mixing thermodynamics of glycerol-water solutions. Chem Sci 2023; 14:7381-7392. [PMID: 37416713 PMCID: PMC10321518 DOI: 10.1039/d3sc00517h] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
Glycerol is a major cryoprotective agent and is widely used to promote protein stabilization. By a combined experimental and theoretical study, we show that global thermodynamic mixing properties of glycerol and water are dictated by local solvation motifs. We identify three hydration water populations, i.e., bulk water, bound water (water hydrogen bonded to the hydrophilic groups of glycerol) and cavity wrap water (water hydrating the hydrophobic moieties). Here, we show that for glycerol experimental observables in the THz regime allow quantification of the abundance of bound water and its partial contribution to the mixing thermodynamics. Specifically, we uncover a 1 : 1 connection between the population of bound waters and the mixing enthalpy, which is further corroborated by the simulation results. Therefore, the changes in global thermodynamic quantity - mixing enthalpy - are rationalized at the molecular level in terms of changes in the local hydrophilic hydration population as a function of glycerol mole fraction in the full miscibility range. This offers opportunities to rationally design polyol water, as well as other aqueous mixtures to optimize technological applications by tuning mixing enthalpy and entropy based on spectroscopic screening.
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Affiliation(s)
- Debasish Das Mahanta
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum 44780 Bochum Germany
- Department of Physics, Technische Universität Dortmund 44227 Dortmund Germany
| | - Dennis Robinson Brown
- Department of Chemical Engineering, University of California Santa Barbara California 93106-5080 USA
| | - Simone Pezzotti
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum 44780 Bochum Germany
| | - Songi Han
- Department of Chemical Engineering, University of California Santa Barbara California 93106-5080 USA
- Department of Chemistry and Biochemistry, University of California Santa Barbara California 93106-9510 USA
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum 44780 Bochum Germany
| | - M Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara California 93106-5080 USA
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum 44780 Bochum Germany
- Department of Physics, Technische Universität Dortmund 44227 Dortmund Germany
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9
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Yang L, Guo S, Liao C, Hou C, Jiang S, Li J, Ma X, Shi L, Ye L, He X. Spatial Layouts of Low-Entropy Hydration Shells Guide Protein Binding. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2300022. [PMID: 37483413 PMCID: PMC10362119 DOI: 10.1002/gch2.202300022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/29/2023] [Indexed: 07/25/2023]
Abstract
Protein-protein binding enables orderly biological self-organization and is therefore considered a miracle of nature. Protein‒protein binding is driven by electrostatic forces, hydrogen bonding, van der Waals force, and hydrophobic interactions. Among these physical forces, only hydrophobic interactions can be considered long-range intermolecular attractions between proteins due to the electrostatic shielding of surrounding water molecules. Low-entropy hydration shells around proteins drive hydrophobic attraction among them that essentially coordinate protein‒protein binding. Here, an innovative method is developed for identifying low-entropy regions of hydration shells of proteins by screening off pseudohydrophilic groups on protein surfaces and revealing that large low-entropy regions of the hydration shells typically cover the binding sites of individual proteins. According to an analysis of determined protein complex structures, shape matching between a large low-entropy hydration shell region of a protein and that of its partner at the binding sites is revealed as a universal law. Protein‒protein binding is thus found to be mainly guided by hydrophobic collapse between the shape-matched low-entropy hydration shells that is verified by bioinformatics analyses of hundreds of structures of protein complexes, which cover four test systems. A simple algorithm is proposed to accurately predict protein binding sites.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
- School of AerospaceMechanical and Mechatronic EngineeringThe University of SydneyNSW2006Australia
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Chenchen Liao
- School of Electronics and Information EngineeringHarbin Institute of TechnologyHarbin150080P. R. China
| | - Chengyu Hou
- School of Electronics and Information EngineeringHarbin Institute of TechnologyHarbin150080P. R. China
| | - Shenda Jiang
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
| | - Lin Ye
- School of System Design and Intelligent ManufacturingSouthern University of Science and TechnologyShenzhen518055P. R. China
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special EnvironmentsCenter for Composite Materials and StructuresHarbin Institute of TechnologyHarbin150080P. R. China
- Shenzhen STRONG Advanced Materials Research Institute Co., LtdShenzhen518035P. R. China
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10
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Fleming PJ, Correia JJ, Fleming KG. Revisiting macromolecular hydration with HullRadSAS. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:215-224. [PMID: 36602579 DOI: 10.1007/s00249-022-01627-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023]
Abstract
Hydration of biological macromolecules is important for their stability and function. Historically, attempts have been made to describe the degree of macromolecular hydration using a single parameter over a narrow range of values. Here, we describe a method to calculate two types of hydration: surface shell water and entrained water. A consideration of these two types of hydration helps to explain the "hydration problem" in hydrodynamics. The combination of these two types of hydration allows accurate calculation of hydrodynamic volume and related macromolecular properties such as sedimentation and diffusion coefficients, intrinsic viscosities, and the concentration-dependent non-ideality identified with sedimentation velocity experiments.
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Affiliation(s)
- Patrick J Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - John J Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Karen G Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
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11
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Robinson Brown DC, Webber TR, Jiao S, Rivera Mirabal DM, Han S, Shell MS. Relationships between Molecular Structural Order Parameters and Equilibrium Water Dynamics in Aqueous Mixtures. J Phys Chem B 2023; 127:4577-4594. [PMID: 37171393 DOI: 10.1021/acs.jpcb.3c00826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Water's unique thermophysical properties and how it mediates aqueous interactions between solutes have long been interpreted in terms of its collective molecular structure. The seminal work of Errington and Debenedetti [Nature 2001, 409, 318-321] revealed a striking hierarchy of relationships among the thermodynamic, dynamic, and structural properties of water, motivating many efforts to understand (1) what measures of water structure are connected to different experimentally accessible macroscopic responses and (2) how many such structural metrics are adequate to describe the collective structural behavior of water. Diffusivity constitutes a particularly interesting experimentally accessible equilibrium property to investigate such relationships because advanced NMR techniques allow the measurement of bulk and local water dynamics in nanometer proximity to molecules and interfaces, suggesting the enticing possibility of measuring local diffusivities that report on water structure. Here, we apply statistical learning methods to discover persistent structure-dynamic correlations across a variety of simulated aqueous mixtures, from alcohol-water to polypeptoid-water systems. We investigate a variety of molecular water structure metrics and find that an unsupervised statistical learning algorithm (namely, sequential feature selection) identifies only two or three independent structural metrics that are sufficient to predict water self-diffusivity accurately. Surprisingly, the translational diffusivity of water across all mixed systems studied here is strongly correlated with a measure of tetrahedral order given by water's triplet angle distribution. We also identify a separate small number of structural metrics that well predict an important thermodynamic property, the excess chemical potential of an idealized methane-sized hydrophobe in water. Ultimately, we offer a Bayesian method of inferring water structure by using only structure-dynamics linear regression models with experimental Overhauser dynamic nuclear polarization (ODNP) measurements of water self-diffusivity. This study thus quantifies the relationships among several distinct structural order parameters in water and, through statistical learning, reveals the potential to leverage molecular structure to predict fundamental thermophysical properties. In turn, these findings suggest a framework for solving the inverse problem of inferring water's molecular structure using experimental measurements such as ODNP studies that probe local water properties.
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Affiliation(s)
| | - Thomas R Webber
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Daniela M Rivera Mirabal
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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12
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Zhang H, Sundaresan S, Webb MA. Molecular Dynamics Investigation of Nanoscale Hydrophobicity of Polymer Surfaces: What Makes Water Wet? J Phys Chem B 2023. [PMID: 37043668 DOI: 10.1021/acs.jpcb.3c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
The wettability of a polymer surface─related to its hydrophobicity or tendency to repel water─can be crucial for determining its utility, such as for a coating or a purification membrane. While wettability is commonly associated with the macroscopic measurement of a contact angle between surface, water, and air, the molecular physics that underlie these macroscopic observations are not fully known, and anticipating the relative behavior of different polymers is challenging. To address this gap in molecular-level understanding, we use molecular dynamics simulations to investigate and contrast interactions of water with six chemically distinct polymers: polytetrafluoroethylene, polyethylene, polyvinyl chloride, poly(methyl methacrylate), Nylon-66, and poly(vinyl alcohol). We show that several prospective quantitative metrics for hydrophobicity agree well with experimental contact angles. Moreover, the behavior of water in proximity to these polymer surfaces can be distinguished with analysis of interfacial water dynamics, extent of hydrogen bonding, and molecular orientation─even when macroscopic measures of hydrophobicity are similar. The predominant factor dictating wettability is found to be the extent of hydrogen bonding between polymer and water, but the precise manifestation of hydrogen bonding and its impact on surface water structure varies. In the absence of hydrogen bonding, other molecular interactions and polymer mechanics control hydrophobic ordering. These results provide new insights into how polymer chemistry specifically impacts water-polymer interactions and translates to surface hydrophobicity. Such factors may facilitate the design or processing of polymer surfaces to achieve targeted wetting behavior, and presented analyses can be useful in studying the interfacial physics of other systems.
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Affiliation(s)
- Hang Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sankaran Sundaresan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Michael A Webb
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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13
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de Bruyn E, Dorn AE, Zimmermann O, Rossetti G. SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories. BIOLOGY 2023; 12:biology12040581. [PMID: 37106781 PMCID: PMC10135740 DOI: 10.3390/biology12040581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023]
Abstract
The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion-residue interactions play an important role in the structures and behaviors of IDPs.
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Affiliation(s)
- Emile de Bruyn
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Anton Emil Dorn
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Olav Zimmermann
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Giulia Rossetti
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Neurology, RWTH Aachen University, 52062 Aachen, Germany
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14
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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15
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Dehlouz A, Jaubert JN, Galliero G, Bonnissel M, Privat R. Entropy Scaling-Based Correlation for Estimating the Self-Diffusion Coefficients of Pure Fluids. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c01086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aghilas Dehlouz
- Université de Lorraine, École Nationale Supérieure des Industries Chimiques, Laboratoire Réactions et Génie des Procédés (UMR CNRS 7274), 1 rue Grandville, 54000 Nancy, France
- Gaztransport & Technigaz (GTT), 1 route de Versailles, 78470 Saint-Rémy-lès-Chevreuse, France
| | - Jean-Noël Jaubert
- Université de Lorraine, École Nationale Supérieure des Industries Chimiques, Laboratoire Réactions et Génie des Procédés (UMR CNRS 7274), 1 rue Grandville, 54000 Nancy, France
| | - Guillaume Galliero
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS TotalEnergies, LFCR UMR 5150, 64013 Pau, France
| | - Marc Bonnissel
- Gaztransport & Technigaz (GTT), 1 route de Versailles, 78470 Saint-Rémy-lès-Chevreuse, France
| | - Romain Privat
- Université de Lorraine, École Nationale Supérieure des Industries Chimiques, Laboratoire Réactions et Génie des Procédés (UMR CNRS 7274), 1 rue Grandville, 54000 Nancy, France
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16
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Doan LC, Dahanayake JN, Mitchell-Koch KR, Singh AK, Vinh NQ. Probing Adaptation of Hydration and Protein Dynamics to Temperature. ACS OMEGA 2022; 7:22020-22031. [PMID: 35785325 PMCID: PMC9245114 DOI: 10.1021/acsomega.2c02843] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Protein dynamics is strongly influenced by the surrounding environment and physiological conditions. Here we employ broadband megahertz-to-terahertz spectroscopy to explore the dynamics of water and myoglobin protein on an extended time scale from femto- to nanosecond. The dielectric spectra reveal several relaxations corresponding to the orientational polarization mechanism, including the dynamics of loosely bound, tightly bound, and bulk water, as well as collective vibrational modes of protein in an aqueous environment. The dynamics of loosely bound and bulk water follow non-Arrhenius behavior; however, the dynamics of water molecules in the tightly bound layer obeys the Arrhenius-type relation. Combining molecular simulations and effective-medium approximation, we have determined the number of water molecules in the tightly bound hydration layer and studied the dynamics of protein as a function of temperature. The results provide the important impact of water on the biochemical functions of proteins.
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Affiliation(s)
- Luan C. Doan
- Department
of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Jayangika N. Dahanayake
- Department
of Chemistry, Faculty of Science, University
of Kelaniya, Kelaniya 11600, Sri Lanka
| | | | - Abhishek K. Singh
- Department
of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Nguyen Q. Vinh
- Department
of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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17
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Abstract
![]()
Water is essential
for the structure, dynamics, energetics, and
thus the function of biomolecules. It is a formidable challenge to
elicit, in microscopic detail, the role of the solvation-related driving
forces of biomolecular processes, such as the enthalpy and entropy
contributions to the underlying free-energy landscape. In this Perspective,
we discuss recent developments and applications of computational methods
that provide a spatially resolved map of hydration thermodynamics
in biomolecular systems and thus yield atomic-level insights to guide
the interpretation of experimental observations. An emphasis is on
the challenge of quantifying the hydration entropy, which requires
characterization of both the motions of the biomolecules and of the
water molecules in their surrounding.
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Affiliation(s)
- Saumyak Mukherjee
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
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18
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Jiao S, Rivera Mirabal DM, DeStefano AJ, Segalman RA, Han S, Shell MS. Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics. Biomacromolecules 2022; 23:1745-1756. [PMID: 35274944 DOI: 10.1021/acs.biomac.1c01687] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We use molecular dynamics simulations to investigate the effect of polypeptoid sequence on the structure and dynamics of its hydration waters. Polypeptoids provide an excellent platform to study small-molecule hydration in disordered polymers, as they can be precisely synthesized with a variety of sidechain chemistries. We examine water behavior near a set of peptoid oligomers in which the number and placement of nonpolar versus polar sidechains are systematically varied. To do this, we leverage a new computational workflow enabling accurate sampling of polypeptoid conformations. We find that the hydration waters are less dense, are more tetrahedral, and have slower dynamics compared to bulk water. The magnitude of these shifts increases with the number of nonpolar groups. We also find that shifts in the water structure and dynamics are strongly correlated, suggesting that experimental insight into the dynamics of hydration water obtained by Overhauser dynamic nuclear polarization (ODNP) also contains information about water structural properties. We then demonstrate the ability of ODNP to probe site-specific dynamics of hydration water near these model peptoid systems.
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Affiliation(s)
- Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Daniela M Rivera Mirabal
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Chemical Engineering, University of Puerto Rico, Mayagüez, Puerto Rico 00681, United States
| | - Audra J DeStefano
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Rachel A Segalman
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Materials, University of California, Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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19
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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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20
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Jin T, Long F, Zhang Q, Zhuang W. Site-Specific Water Dynamics in the First Hydration Layer of an Anti-Freeze Glyco-Protein: A Simulation Study. Phys Chem Chem Phys 2022; 24:21165-21177. [DOI: 10.1039/d2cp00883a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antifreeze glycoproteins (AFGPs) inhibit ice recrystallization by a mechanism remaining largely elusive. Dynamics of AFGPs’ hydration water and its involvement in the antifreeze activity, for instance, have not been identified...
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21
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Bin M, Yousif R, Berkowicz S, Das S, Schlesinger D, Perakis F. Wide-angle X-ray scattering and molecular dynamics simulations of supercooled protein hydration water. Phys Chem Chem Phys 2021; 23:18308-18313. [PMID: 34269785 DOI: 10.1039/d1cp02126e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the mechanism responsible for the protein low-temperature crossover observed at T≈ 220 K can help us improve current cryopreservation technologies. This crossover is associated with changes in the dynamics of the system, such as in the mean-squared displacement, whereas experimental evidence of structural changes is sparse. Here we investigate hydrated lysozyme proteins by using a combination of wide-angle X-ray scattering and molecular dynamics (MD) simulations. Experimentally we suppress crystallization by accurate control of the protein hydration level, which allows access to temperatures down to T = 175 K. The experimental data indicate that the scattering intensity peak at Q = 1.54 Å-1, attributed to interatomic distances, exhibits temperature-dependent changes upon cooling. In the MD simulations it is possible to decompose the water and protein contributions and we observe that, while the protein component is nearly temperature independent, the hydration water peak shifts in a fashion similar to that of bulk water. The observed trends are analysed by using the water-water and water-protein radial distribution functions, which indicate changes in the local probability density of hydration water.
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Affiliation(s)
- Maddalena Bin
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden.
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22
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Li K, Qi Y, Zhou Y, Sun X, Zhang Z. Microstructure and Properties of Poly(ethylene glycol)-Segmented Polyurethane Antifouling Coatings after Immersion in Seawater. Polymers (Basel) 2021; 13:polym13040573. [PMID: 33672921 PMCID: PMC7918847 DOI: 10.3390/polym13040573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 12/12/2022] Open
Abstract
Polyurethane has a microphase separation structure, while polyethylene glycol (PEG) can form a hydrated layer to resist protein adsorption. In this paper, PEG was introduced to polyurethane to improve the antifouling properties of the polyurethane, providing a new method and idea for the preparation of new antifouling polyurethane materials. The mechanical properties, hydrophilicity, swelling degree, microphase separation and antifouling performance of the coatings were evaluated. The response characteristics of the polyurethane coatings in a seawater environment were studied, and the performance changes of coatings in seawater were tested. The results showed that the crystallized PEG soft segments increased, promoting microphase separation. The stress at 100% and the elasticity modulus of the polyurethane material also markedly increased, in addition to increases in the swelling degree in seawater, the water contact angle decreased. A total of 25% of PEG incorporated into a soft segment can markedly improve the antibacterial properties of the coatings, but adding more PEG has little significant effect. After immersion in seawater, the coatings became softer and more elastic. This is because water molecules formed hydrogen bonding with the amino NH, which resulted in a weakening effect being exerted on the carbonyl C=O hydrogen bonding and ether oxygen group crystallization.
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23
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Pounot K, Grime GW, Longo A, Zamponi M, Noferini D, Cristiglio V, Seydel T, Garman EF, Weik M, Foderà V, Schirò G. Zinc determines dynamical properties and aggregation kinetics of human insulin. Biophys J 2021; 120:886-898. [PMID: 33545104 DOI: 10.1016/j.bpj.2020.11.2280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/08/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022] Open
Abstract
Protein aggregation is a widespread process leading to deleterious consequences in the organism, with amyloid aggregates being important not only in biology but also for drug design and biomaterial production. Insulin is a protein largely used in diabetes treatment, and its amyloid aggregation is at the basis of the so-called insulin-derived amyloidosis. Here, we uncover the major role of zinc in both insulin dynamics and aggregation kinetics at low pH, in which the formation of different amyloid superstructures (fibrils and spherulites) can be thermally induced. Amyloid aggregation is accompanied by zinc release and the suppression of water-sustained insulin dynamics, as shown by particle-induced x-ray emission and x-ray absorption spectroscopy and by neutron spectroscopy, respectively. Our study shows that zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein and suggests that introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity.
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Affiliation(s)
- Kevin Pounot
- Applied Physics, University of Tübingen, Tübingen, Baden-Würtemberg, Germany.
| | | | - Alessandro Longo
- Istituto per lo Studio dei Materiali Nanostrutturati, CNR, Palermo, Italy
| | - Michaela Zamponi
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH Outstation at MLZ, Garching, Germany
| | - Daria Noferini
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH Outstation at MLZ, Garching, Germany
| | | | - Tilo Seydel
- Science Division, Institut Max von Laue-Paul Langevin, Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Vito Foderà
- Pharmacy, University of Copenhagen, Copenhagen, Denmark.
| | - Giorgio Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France.
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24
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Zhao H. What do we learn from enzyme behaviors in organic solvents? - Structural functionalization of ionic liquids for enzyme activation and stabilization. Biotechnol Adv 2020; 45:107638. [PMID: 33002582 DOI: 10.1016/j.biotechadv.2020.107638] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/05/2020] [Accepted: 09/25/2020] [Indexed: 12/16/2022]
Abstract
Enzyme activity in nonaqueous media (e.g. conventional organic solvents) is typically lower than in water by several orders of magnitude. There is a rising interest of developing new nonaqueous solvent systems that are more "water-like" and more biocompatible. Therefore, we need to learn from the current state of nonaqueous biocatalysis to overcome its bottleneck and provide guidance for new solvent design. This review firstly focuses on the discussion of how organic solvent properties (such as polarity and hydrophobicity) influence the enzyme activity and stability, and how these properties impact the enzyme's conformation and dynamics. While hydrophobic organic solvents usually lead to the maintenance of enzyme activity, solvents carrying functional groups like hydroxys and ethers (including crown ethers and cyclodextrins) can lead to enzyme activation. Ionic liquids (ILs) are designable solvents that can conveniently incorporate these functional groups. Therefore, we systematically survey these ether- and/or hydroxy-functionalized ILs, and find most of them are highly compatible with enzymes leading to high activity and stability. In particular, ILs carrying both ether and tert-alcohol groups are among the most enzyme-activating solvents. Future direction is to learn from enzyme behaviors in both water and nonaqueous media to design biocompatible "water-like" solvents.
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Affiliation(s)
- Hua Zhao
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO 80639, United States.
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25
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Monroe J, Barry M, DeStefano A, Aydogan Gokturk P, Jiao S, Robinson-Brown D, Webber T, Crumlin EJ, Han S, Shell MS. Water Structure and Properties at Hydrophilic and Hydrophobic Surfaces. Annu Rev Chem Biomol Eng 2020; 11:523-557. [PMID: 32169001 DOI: 10.1146/annurev-chembioeng-120919-114657] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The properties of water on both molecular and macroscopic surfaces critically influence a wide range of physical behaviors, with applications spanning from membrane science to catalysis to protein engineering. Yet, our current understanding of water interfacing molecular and material surfaces is incomplete, in part because measurement of water structure and molecular-scale properties challenges even the most advanced experimental characterization techniques and computational approaches. This review highlights progress in the ongoing development of tools working to answer fundamental questions on the principles that govern the interactions between water and surfaces. One outstanding and critical question is what universal molecular signatures capture the hydrophobicity of different surfaces in an operationally meaningful way, since traditional macroscopic hydrophobicity measures like contact angles fail to capture even basic properties of molecular or extended surfaces with any heterogeneity at the nanometer length scale. Resolving this grand challenge will require close interactions between state-of-the-art experiments, simulations, and theory, spanning research groups and using agreed-upon model systems, to synthesize an integrated knowledge of solvation water structure, dynamics, and thermodynamics.
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Affiliation(s)
- Jacob Monroe
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Mikayla Barry
- Department of Materials, University of California, Santa Barbara, California 93106, USA
| | - Audra DeStefano
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Pinar Aydogan Gokturk
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Sally Jiao
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Dennis Robinson-Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Thomas Webber
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Ethan J Crumlin
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; .,Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
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26
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Roy VP, Kubarych KJ. A simple lattice Monte Carlo simulation to model interfacial and crowded water rearrangements. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Srivastava A, Malik S, Karmakar S, Debnath A. Dynamic coupling of a hydration layer to a fluid phospholipid membrane: intermittency and multiple time-scale relaxations. Phys Chem Chem Phys 2020; 22:21158-21168. [DOI: 10.1039/d0cp02803g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the coupling of a hydration layer and a lipid membrane is crucial to gaining access to membrane dynamics and understanding its functionality towards various biological processes.
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Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
| | - Sheeba Malik
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences
- Tata Institute of Fundamental Research
- Hyderabad 500107
- India
| | - Ananya Debnath
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
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28
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Lin W, Klein J. Control of surface forces through hydrated boundary layers. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2019.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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29
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Stephens AD, Kaminski Schierle GS. The role of water in amyloid aggregation kinetics. Curr Opin Struct Biol 2019; 58:115-123. [PMID: 31299481 DOI: 10.1016/j.sbi.2019.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/30/2019] [Accepted: 06/06/2019] [Indexed: 12/16/2022]
Abstract
The role of water in protein function and aggregation is highly important and may hold some answers to understanding initiation of misfolding diseases such as Parkinson's, Alzheimer's and Huntington's where soluble intrinsically disordered proteins (IDPs) aggregate into fibrillar structures. IDPs are highly dynamic and have larger solvent exposed areas compared to globular proteins, meaning they make and break hydrogen bonds with the surrounding water more frequently. The mobility of water can be altered by presence of ions, sugars, osmolytes, proteins and membranes which differ in different cell types, cell compartments and also as cells age. A reduction in water mobility and thus protein mobility enhances the probability that IDPs can associate to form intermolecular bonds and propagate into aggregates. This poses an interesting question as to whether localised water mobility inside cells can influence the propensity of an IDP to aggregate and furthermore whether it can influence fibril polymorphism and disease outcome.
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Affiliation(s)
- Amberley D Stephens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Gabriele S Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
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30
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Thompson MC, Barad BA, Wolff AM, Sun Cho H, Schotte F, Schwarz DMC, Anfinrud P, Fraser JS. Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme. Nat Chem 2019; 11:1058-1066. [PMID: 31527847 PMCID: PMC6815256 DOI: 10.1038/s41557-019-0329-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 08/09/2019] [Indexed: 12/21/2022]
Abstract
Correlated motions of proteins are critical to function, but these features are difficult to resolve using traditional structure determination techniques. Time-resolved X-ray methods hold promise for addressing this challenge, but have relied on the exploitation of exotic protein photoactivity, and are therefore not generalizable. Temperature jumps, through thermal excitation of the solvent, have been utilized to study protein dynamics using spectroscopic techniques, but their implementation in X-ray scattering experiments has been limited. Here, we perform temperature-jump small- and wide-angle X-ray scattering measurements on a dynamic enzyme, cyclophilin A, demonstrating that these experiments are able to capture functional intramolecular protein dynamics on the microsecond timescale. We show that cyclophilin A displays rich dynamics following a temperature jump, and use the resulting time-resolved signal to assess the kinetics of conformational changes. Two relaxation processes are resolved: a fast process is related to surface loop motions, and a slower process is related to motions in the core of the protein that are critical for catalytic turnover.
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Affiliation(s)
- Michael C Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin A Barad
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander M Wolff
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Hyun Sun Cho
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Friedrich Schotte
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M C Schwarz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Philip Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
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31
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Fuglestad B, Kerstetter NE, Wand AJ. Site-Resolved and Quantitative Characterization of Very Weak Protein-Ligand Interactions. ACS Chem Biol 2019; 14:1398-1402. [PMID: 31246002 DOI: 10.1021/acschembio.9b00353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Very weak interactions between small organic molecules and proteins have long been predicted and are expected to have dissociation constants of hundreds of millimolar and above. Unfortunately, quantitative evaluation of binding in a high-resolution structural context for this affinity regime is particularly difficult and often impossible using existing experimental approaches. Here, we show that nanoscale encapsulation of single protein molecules within the water core of reverse micelles enables the detection and evaluation of weak binding interactions at atomic resolution using solution NMR spectroscopy. This strategy is used to survey the interactions of a set of small molecules with the cytokine interleukin-1β (IL-1β). The interaction of IL-1β with these molecules is found to vary from more diffuse and weak binding modes to more specific and with a relatively higher affinity. The interactions detected here cover a large portion of the protein surface and have dissociation constants mostly in the low molar range. These results illustrate the ability of a protein to interact productively with a variety of small molecule functional groups and point to a broader potential to target even relatively featureless protein surfaces for applications in chemical biology and drug discovery.
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Affiliation(s)
- Brian Fuglestad
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Nicole E. Kerstetter
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - A. Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States
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32
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Pradhan MR, Nguyen MN, Kannan S, Fox SJ, Kwoh CK, Lane DP, Verma CS. Characterization of Hydration Properties in Structural Ensembles of Biomolecules. J Chem Inf Model 2019; 59:3316-3329. [DOI: 10.1021/acs.jcim.8b00453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mohan R. Pradhan
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - Minh N. Nguyen
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Stephen J. Fox
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Chee Keong Kwoh
- School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798
| | - David P. Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Chandra S. Verma
- Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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33
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Schindl A, Hagen ML, Muzammal S, Gunasekera HAD, Croft AK. Proteins in Ionic Liquids: Reactions, Applications, and Futures. Front Chem 2019; 7:347. [PMID: 31179267 PMCID: PMC6543490 DOI: 10.3389/fchem.2019.00347] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/26/2019] [Indexed: 01/01/2023] Open
Abstract
Biopolymer processing and handling is greatly facilitated by the use of ionic liquids, given the increased solubility, and in some cases, structural stability imparted to these molecules. Focussing on proteins, we highlight here not just the key drivers behind protein-ionic liquid interactions that facilitate these functionalities, but address relevant current and potential applications of protein-ionic liquid interactions, including areas of future interest.
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Affiliation(s)
- Alexandra Schindl
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
- Faculty of Medicine & Health Sciences, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Faculty of Science, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Matthew L. Hagen
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
- Centre for Additive Manufacturing, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Shafaq Muzammal
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Henadira A. D. Gunasekera
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
- Centre for Additive Manufacturing, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Anna K. Croft
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
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34
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Dahanayake JN, Shahryari E, Roberts KM, Heikes ME, Kasireddy C, Mitchell-Koch KR. Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics. J Chem Inf Model 2019; 59:2407-2422. [PMID: 30865440 DOI: 10.1021/acs.jcim.9b00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate the pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer. The finding thus hinted at a handle for rapid evaluation of hydration dynamics at different regions on the protein surface in molecular dynamics simulations. Such an approach may move the analysis of hydration dynamics from a specialized venture to routine analysis, enabling an informatics approach to evaluate the role of hydration dynamics in biomolecular function. This paper first confirms that the correlation between regional diffusive dynamics and hydration layer structure (via water center of mass around protein side-chain atom RDF) is observed as a general relationship across a set of proteins. Second, it seeks to devise an approach for rapid analysis of hydration dynamics, determining the minimum amount of information and computational effort required to get a reliable value of hydration dynamics from structural data in MD simulations based on the protein-water RDF. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically equivalent apparent diffusion coefficients at the 95% confidence level for a set of 92 regions within five different proteins. In summary, RDF analysis of 10 ns of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is anticipated that a quick look at protein-water RDFs, comparing peak heights, will be useful to provide a qualitative ranking of regions of faster and slower hydration dynamics at the protein surface for rapid analysis when investigating the role of solvent dynamics in protein function.
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Affiliation(s)
- Jayangika N Dahanayake
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Elaheh Shahryari
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Kirsten M Roberts
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Micah E Heikes
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Chandana Kasireddy
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Katie R Mitchell-Koch
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
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35
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Panuszko A, Nowak M, Bruździak P, Stasiulewicz M, Stangret J. Amides as models to study the hydration of proteins and peptides — spectroscopic and theoretical approach on hydration in various temperatures. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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36
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Abstract
This article gives an overview of excess-entropy scaling, the 1977 discovery by Rosenfeld that entropy determines properties of liquids like viscosity, diffusion constant, and heat conductivity. We give examples from computer simulations confirming this intriguing connection between dynamics and thermodynamics, counterexamples, and experimental validations. Recent uses in application-related contexts are reviewed, and theories proposed for the origin of excess-entropy scaling are briefly summarized. It is shown that if two thermodynamic state points of a liquid have the same microscopic dynamics, they must have the same excess entropy. In this case, the potential-energy function exhibits a symmetry termed hidden scale invariance, stating that the ordering of the potential energies of configurations is maintained if these are scaled uniformly to a different density. This property leads to the isomorph theory, which provides a general framework for excess-entropy scaling and illuminates, in particular, why this does not apply rigorously and universally. It remains an open question whether all aspects of excess-entropy scaling and related regularities reflect hidden scale invariance in one form or other.
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Affiliation(s)
- Jeppe C Dyre
- Glass and Time, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark
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37
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Dahanayake JN, Mitchell-Koch KR. How Does Solvation Layer Mobility Affect Protein Structural Dynamics? Front Mol Biosci 2018; 5:65. [PMID: 30057902 PMCID: PMC6053501 DOI: 10.3389/fmolb.2018.00065] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme Candida antarctica lipase B, which functions in aqueous and organic solvents, was modeled using molecular dynamics simulations. Data was obtained for the enzyme in acetonitrile, cyclohexane, n-butanol, and tert-butanol, in addition to water. Protein dynamics and solvation shell dynamics are characterized regionally: for each α-helix, β-sheet, and loop or connector region. Correlations are seen between solvent mobility and protein flexibility. So, does local viscosity explain the relationship between protein structural dynamics and solvation layer dynamics? Halle and Davidovic presented a cogent analysis of data describing the global hydrodynamics of a protein (tumbling in solution) that fits a model in which the protein's interfacial viscosity is higher than that of bulk water's, due to retarded water dynamics in the hydration layer (measured in NMR τ2 reorientation times). Numerous experiments have shown coupling between protein and solvation layer dynamics in site-specific measurements. Our data provides spatially-resolved characterization of solvent shell dynamics, showing correlations between regional solvation layer dynamics and protein dynamics in both aqueous and organic solvents. Correlations between protein flexibility and inverse solvent viscosity (1/η) are considered across several protein regions and for a rather disparate collection of solvents. It is seen that the correlation is consistently higher when local solvent shell dynamics are considered, rather than bulk viscosity. Protein flexibility is seen to correlate best with either the local interfacial viscosity or the ratio of the mobility of an organic solvent in a regional solvation layer relative to hydration dynamics around the same region. Results provide insight into the function of aqueous proteins, while also suggesting a framework for interpreting and predicting enzyme structural dynamics in non-aqueous solvents, based on the mobility of solvents within the solvation layer. We suggest that Kramers' theory may be used in future work to model protein conformational transitions in different solvents by incorporating local viscosity effects.
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