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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Xie S, Saba L, Jiang H, Bringas OR, Oghbaie M, Stefano LD, Sherman V, LaCava J. Multiparameter screen optimizes immunoprecipitation. Biotechniques 2024; 76:145-152. [PMID: 38425263 PMCID: PMC11091867 DOI: 10.2144/btn-2023-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
Immunoprecipitation (IP) coupled with mass spectrometry effectively maps protein-protein interactions when genome-wide, affinity-tagged cell collections are used. Such studies have recorded significant portions of the compositions of physiological protein complexes, providing draft 'interactomes'; yet many constituents of protein complexes still remain uncharted. This gap exists partly because high-throughput approaches cannot optimize each IP. A key challenge for IP optimization is stabilizing in vivo interactions during the transfer from cells to test tubes; failure to do so leads to the loss of genuine interactions during the IP and subsequent failure to detect. Our high-content screening method explores the relationship between in vitro chemical conditions and IP outcomes, enabling rapid empirical optimization of conditions for capturing target macromolecular assemblies.
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Affiliation(s)
- Shaoshuai Xie
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, Groningen, 9713AV, The Netherlands
| | - Leila Saba
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, Groningen, 9713AV, The Netherlands
| | - Hua Jiang
- Laboratory of Cellular & Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Omar R Bringas
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, Groningen, 9713AV, The Netherlands
| | - Mehrnoosh Oghbaie
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, Groningen, 9713AV, The Netherlands
- Laboratory of Cellular & Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Luciano Di Stefano
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, Groningen, 9713AV, The Netherlands
| | - Vadim Sherman
- High Energy Physics Instrument Shop, The Rockefeller University, New York, NY 10065, USA
| | - John LaCava
- European Research Institute for the Biology of Ageing, University Medical Centre Groningen, Groningen, 9713AV, The Netherlands
- Laboratory of Cellular & Structural Biology, The Rockefeller University, New York, NY 10065, USA
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3
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Kaur H, Garg M, Tomar D, Singh S, Jena KC. Role of tungsten disulfide quantum dots in specific protein-protein interactions at air-water interface. J Chem Phys 2024; 160:084705. [PMID: 38411235 DOI: 10.1063/5.0187563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
The intriguing network of antibody-antigen (Ab-Ag) interactions is highly governed by environmental perturbations and the nature of biomolecular interaction. Protein-protein interactions (PPIs) have potential applications in developing protein-adsorption-based sensors and nano-scale materials. Therefore, characterizing PPIs in the presence of a nanomaterial at the molecular level becomes imperative. The present work involves the investigation of antiferritin-ferritin (Ab-Ag) protein interactions under the influence of tungsten disulfide quantum dots (WS2 QDs). Isothermal calorimetry and contact angle measurements validated the strong influence of WS2 QDs on Ab-Ag interactions. The interfacial signatures of nano-bio-interactions were evaluated using sum frequency generation vibration spectroscopy (SFG-VS) at the air-water interface. Our SFG results reveal a variation in the tilt angle of methyl groups by ∼12° ± 2° for the Ab-Ag system in the presence of WS2 QDs. The results illustrated an enhanced ordering of water molecules in the presence of QDs, which underpins the active role of interfacial water molecules during nano-bio-interactions. We have also witnessed a differential impact of QDs on Ab-Ag by raising the concentration of the Ab-Ag combination, which showcased an increased inter-molecular interaction among the Ab and Ag molecules and a minimal influence on the methyl tilt angle. These findings suggest the formation of stronger and ordered Ab-Ag complexes upon introducing WS2 QDs in the aqueous medium and signify the potentiality of WS2 QDs relevant to protein-based sensing assays.
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Affiliation(s)
- Harsharan Kaur
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Mayank Garg
- CSIR-Central Scientific Instruments Organisation (CSIR-CSIO), Chandigarh 160030, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Deepak Tomar
- Department of Physics, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Suman Singh
- CSIR-Central Scientific Instruments Organisation (CSIR-CSIO), Chandigarh 160030, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kailash C Jena
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
- Department of Physics, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
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4
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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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5
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Maiti S, Heyden M. Model-Dependent Solvation of the K-18 Domain of the Intrinsically Disordered Protein Tau. J Phys Chem B 2023; 127:7220-7230. [PMID: 37556237 DOI: 10.1021/acs.jpcb.3c01726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
A known imbalance between intra-protein and protein-water interactions in many empirical force fields results in collapsed conformational ensembles of intrinsically disordered proteins in explicit solvent simulations that disagree with experiments. Multiple strategies have been introduced in the literature to modify protein-water interactions, which improve agreement between experiments and simulations. In this work, we combine simulations with standard and modified force fields with a spatially resolved analysis of solvation free energy contributions and compare the consequences of each strategy. We find that enhanced Lennard-Jones (LJ) interactions between protein atoms and water oxygens primarily improve the solvation of nonpolar functional groups of the protein. In contrast, modified electrostatics in the water model or strengthened LJ interactions between the protein and water hydrogens mainly affect the hydration of polar functional groups. Modified electrostatics further impact the average orientation of water molecules in the hydration shell. As a result, protein-water interactions with the first hydration layers are strengthened, while interactions with water molecules in higher hydration shells are weakened. Hence, distinct strategies to balance intra-protein and protein-water interactions in simulations have qualitatively different effects on protein solvation. These differences are not necessarily captured by comparisons to experiments that report on global parameters describing protein conformational ensembles, e.g., the radius of gyration, but will influence the tendency of a protein to form aggregates or phase-separated droplets.
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Affiliation(s)
- Sthitadhi Maiti
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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6
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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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7
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Shin S, Willard AP. Quantifying the Molecular Polarization Response of Liquid Water Interfaces at Heterogeneously Charged Surfaces. J Chem Theory Comput 2023; 19:1843-1852. [PMID: 36866865 DOI: 10.1021/acs.jctc.2c01256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The hydration shells of proteins mediate interactions, such as small molecule binding, that are vital to their biological function or in some cases their dysfunction. However, even when the structure of a protein is known, the properties of its hydration environment cannot be easily predicted due to the complex interplay between protein surface heterogeneity and the collective structure of water's hydrogen bonding network. This manuscript presents a theoretical study of the influence of surface charge heterogeneity on the polarization response of the liquid water interface. We focus our attention on classical point charge models of water, where the polarization response is limited to molecular reorientation. We introduce a new computational method for analyzing simulation data that is capable of quantifying water's collective polarization response and determining the effective surface charge distribution of hydrated surfaces over atomistic length scales. To illustrate the utility of this method, we present the results of molecular dynamics simulations of liquid water in contact with a heterogeneous model surface and the CheY protein.
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Affiliation(s)
- Sucheol Shin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Poudel H, Leitner DM. Locating dynamic contributions to allostery via determining rates of vibrational energy transfer. J Chem Phys 2023; 158:015101. [PMID: 36610954 DOI: 10.1063/5.0132089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Determining rates of energy transfer across non-covalent contacts for different states of a protein can provide information about dynamic and associated entropy changes during transitions between states. We investigate the relationship between rates of energy transfer across polar and nonpolar contacts and contact dynamics for the β2-adrenergic receptor, a rhodopsin-like G-protein coupled receptor, in an antagonist-bound inactive state and agonist-bound active state. From structures sampled during molecular dynamics (MD) simulations, we find the active state to have, on average, a lower packing density, corresponding to generally more flexibility and greater entropy than the inactive state. Energy exchange networks (EENs) are computed for the inactive and active states from the results of the MD simulations. From the EENs, changes in the rates of energy transfer across polar and nonpolar contacts are found for contacts that remain largely intact during activation. Change in dynamics of the contact, and entropy associated with the dynamics, can be estimated from the change in rates of energy transfer across the contacts. Measurement of change in the rates of energy transfer before and after the transition between states thereby provides information about dynamic contributions to activation and allostery.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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9
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Kalayan J, Chakravorty A, Warwicker J, Henchman RH. Total free energy analysis of fully hydrated proteins. Proteins 2023; 91:74-90. [PMID: 35964252 PMCID: PMC10087023 DOI: 10.1002/prot.26411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of thermodynamic stability or instability. The free energies of four hydrated globular proteins with different net charges are calculated from a molecular dynamics simulation, with the energy coming from the system Hamiltonian and entropy using multiscale cell correlation. Water is found to be most stable around anionic residues, intermediate around cationic and polar residues, and least stable near hydrophobic residues, especially when more buried, with stability displaying moderate entropy-enthalpy compensation. Conversely, anionic residues in the proteins are energetically destabilized relative to singly solvated amino acids, while trends for other residues are less clear-cut. Almost all residues lose intraresidue entropy when in the protein, enthalpy changes are negative on average but may be positive or negative, and the resulting overall stability is moderate for some proteins and negligible for others. The free energy of water around single amino acids is found to closely match existing hydrophobicity scales. Regarding the effect of secondary structure, water is slightly more stable around loops, of intermediate stability around β strands and turns, and least stable around helices. An interesting asymmetry observed is that cationic residues stabilize a residue when bonded to its N-terminal side but destabilize it when on the C-terminal side, with a weaker reversed trend for anionic residues.
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Affiliation(s)
- Jas Kalayan
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Arghya Chakravorty
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jim Warwicker
- Manchester Institute of Biotechnology and School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Richard H Henchman
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
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10
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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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11
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Poudel H, Leitner DM. Energy Transport in Class B GPCRs: Role of Protein-Water Dynamics and Activation. J Phys Chem B 2022; 126:8362-8373. [PMID: 36256609 DOI: 10.1021/acs.jpcb.2c03960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We compute energy exchange networks (EENs) through glucagon-like peptide-1 receptor (GLP-1R), a class B G-protein-coupled receptor (GPCR), in inactive and two active states, one activated by a peptide ligand and the other by a small molecule agonist, from results of molecular dynamics simulations. The reorganized network upon activation contains contributions from structural as well as from dynamic changes and corresponding entropic contributions to the free energy of activation, which are estimated in terms of the change in rates of energy transfer across non-covalent contacts. The role of water in the EENs and in activation of GLP-1R is also investigated. The dynamics of water in contact with the central polar network of the transmembrane region is found to be significantly slower for both activated states compared to the inactive state. This result is consistent with the contribution of water molecules to activation of GLP-1R previously suggested and resembles water dynamics in parts of the transmembrane region found in earlier studies of rhodopsin-like GPCRs.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
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12
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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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13
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Reid KM, Leitner DM. Enhanced Mobility during Diels-Alder Reaction: Results of Molecular Simulations. J Phys Chem Lett 2022; 13:3763-3769. [PMID: 35446035 DOI: 10.1021/acs.jpclett.2c00886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Recent measurements indicate enhanced mobility of solvent molecules during Diels-Alder (DA) and other common chemical reactions. We present results of molecular dynamics simulations of the last stages of the DA cycloaddition reaction, from the transition state configuration to product, of furfurylamine and maleimide in acetonitrile at reactant concentrations studied experimentally. We find enhanced mobility of solvent and reactant molecules up to at least a nanometer from the DA product over hundreds of picoseconds. Local heating is ruled out as a factor in the enhanced mobility observed in the simulations, which is instead found to be due to solvent relaxation following the formation of the DA product.
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Affiliation(s)
- Korey M Reid
- 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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14
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Rizzuti B. Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140757. [PMID: 35051666 DOI: 10.1016/j.bbapap.2022.140757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulation is the most popular computational technique for investigating the structural and dynamical behaviour of proteins, in search of the molecular basis of their function. Far from being a completely settled field of research, simulations are still evolving to best capture the essential features of the atomic interactions that govern a protein's inner motions. Modern force fields are becoming increasingly accurate in providing a physical description adequate to this purpose, and allow us to model complex biological systems under fairly realistic conditions. Furthermore, the use of accelerated sampling techniques is improving our access to the observation of progressively larger molecular structures, longer time scales, and more hidden functional events. In this review, the basic principles of molecular dynamics simulations and a number of key applications in the area of protein science are summarized, and some of the most important results are discussed. Examples include the study of the structure, dynamics and binding properties of 'difficult' targets, such as intrinsically disordered proteins and membrane receptors, and the investigation of challenging phenomena like hydration-driven processes and protein aggregation. The findings described provide an overall picture of the current state of this research field, and indicate new perspectives on the road ahead to the upcoming future of molecular simulations.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, University of Zaragoza, 50018 Zaragoza, Spain.
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15
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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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16
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Roy P, Sengupta N. Hydration of a small protein under carbon nanotube confinement: Adsorbed substates induce selective separation of the dynamical response. J Chem Phys 2021; 154:204702. [PMID: 34241160 DOI: 10.1063/5.0047078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The co-involvement of biological molecules and nanomaterials has increasingly come to the fore in modern-day applications. While the "bio-nano" (BN) interface presents physico-chemical characteristics that are manifestly different from those observed in isotropic bulk conditions, the underlying molecular reasons remain little understood; this is especially true of anomalies in interfacial hydration. In this paper, we leverage atomistic simulations to study differential adsorption characteristics of a small protein on the inner (concave) surface of a single-walled carbon nanotube whose diameter exceeds dimensions conducive to single-file water movement. Our findings indicate that the extent of adsorption is decided by the degree of foldedness of the protein conformational substate. Importantly, we find that partially folded substates, but not the natively folded one, induce reorganization of the protein hydration layer into an inner layer water closer to the nanotube axis and an outer layer water in the interstitial space near the nanotube walls. Further analyses reveal sharp dynamical differences between water molecules in the two layers as observed in the onset of increased heterogeneity in rotational relaxation and the enhanced deviation from Fickian behavior. The vibrational density of states reveals that the dynamical distinctions are correlated with differences in crucial bands in the power spectra. The current results set the stage for further systematic studies of various BN interfaces vis-à-vis control of hydration properties.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
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17
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Päslack C, Das CK, Schlitter J, Schäfer LV. Spectrally Resolved Estimation of Water Entropy in the Active Site of Human Carbonic Anhydrase II. J Chem Theory Comput 2021; 17:5409-5418. [PMID: 34259506 DOI: 10.1021/acs.jctc.1c00554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A major challenge in understanding ligand binding to biomacromolecules lies in dissecting the underlying thermodynamic driving forces at the atomic level. Quantifying the contributions of water molecules is often especially demanding, although they can play important roles in biomolecular recognition and binding processes. One example is human carbonic anhydrase II, whose active site harbors a conserved network of structural water molecules that are essential for enzymatic catalysis. Inhibitor binding disrupts this water network and changes the hydrogen-bonding patterns in the active site. Here, we use atomistic molecular dynamics simulations to compute the absolute entropy of the individual water molecules confined in the active site of hCAII using a spectrally resolved estimation (SRE) approach. The entropy decrease of water molecules that remain in the active site upon binding of a dorzolamide inhibitor is caused by changes in hydrogen bonding and stiffening of the hydrogen-bonding network. Overall, this entropy decrease is overcompensated by the gain due to the release of three water molecules from the active site upon inhibitor binding. The spectral density calculations enable the assignment of the changes to certain vibrational modes. In addition, the range of applicability of the SRE approximation is systematically explored by exploiting the gradually changing degree of immobilization of water molecules as a function of the distance to a phospholipid bilayer surface, which defines an "entropy ruler". These results demonstrate the applicability of SRE to biomolecular solvation, and we expect it to become a useful method for entropy calculations in biomolecular systems.
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Affiliation(s)
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | | | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
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18
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Tokunaga Y, Tanaka M, Iida H, Kinoshita M, Tojima Y, Takeuchi K, Imashimizu M. Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin. Biophys J 2021; 120:2386-2393. [PMID: 33894216 PMCID: PMC8390810 DOI: 10.1016/j.bpj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/23/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
Water dynamics in the hydration layers of biomolecules play crucial roles in a wide range of biological functions. A hydrated protein contains multiple components of diffusional and vibrational dynamics of water and protein, which may be coupled at ∼0.1-THz frequency (10-ps timescale) at room temperature. However, the microscopic description of biomolecular functions based on various modes of protein-water-coupled motions remains elusive. A novel approach for perturbing the hydration dynamics in the subterahertz frequency range and probing them at the atomic level is therefore warranted. In this study, we investigated the effect of klystron-based, intense 0.1-THz excitation on the slow dynamics of ubiquitin using NMR-based measurements of hydrogen-deuterium exchange. We demonstrated that the subterahertz irradiation accelerated the hydrogen-deuterium exchange of the amides located in the interior of the protein and hydrophobic surfaces while decelerating this exchange in the amides located in the surface loop and short 310 helix regions. This subterahertz-radiation-induced effect was qualitatively contradictory to the increased-temperature-induced effect. Our results suggest that the heterogeneous water dynamics occurring at the protein-water interface include components that are nonthermally excited by the subterahertz radiation. Such subterahertz-excited components may be linked to the slow function-related dynamics of the protein.
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Affiliation(s)
- Yuji Tokunaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Tanaka
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hitoshi Iida
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Moto Kinoshita
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yuya Tojima
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
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19
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Steinrücken E, Wissel T, Brodrecht M, Breitzke H, Regentin J, Buntkowsky G, Vogel M. 2H NMR study on temperature-dependent water dynamics in amino-acid functionalized silica nanopores. J Chem Phys 2021; 154:114702. [PMID: 33752372 DOI: 10.1063/5.0044141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We prepare various amino-acid functionalized silica pores with diameters of ∼6 nm and study the temperature-dependent reorientation dynamics of water in these confinements. Specifically, we link basic Lys, neutral Ala, and acidic Glu to the inner surfaces and combine 2H nuclear magnetic resonance spin-lattice relaxation and line shape analyses to disentangle the rotational motions of the surfaces groups and the crystalline and liquid water fractions coexisting below partial freezing. Unlike the crystalline phase, the liquid phase shows reorientation dynamics, which strongly depends on the chemistry of the inner surfaces. The water reorientation is slowest for the Lys functionalization, followed by Ala and Glu and, finally, the native silica pores. In total, the rotational correlation times of water at the different surfaces vary by about two orders of magnitude, where this span is largely independent of the temperature in the range ∼200-250 K.
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Affiliation(s)
- Elisa Steinrücken
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Till Wissel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Martin Brodrecht
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Hergen Breitzke
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Julia Regentin
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Michael Vogel
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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20
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Mirror-image antiparallel β-sheets organize water molecules into superstructures of opposite chirality. Proc Natl Acad Sci U S A 2020; 117:32902-32909. [PMID: 33318168 DOI: 10.1073/pnas.2015567117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Biomolecular hydration is fundamental to biological functions. Using phase-resolved chiral sum-frequency generation spectroscopy (SFG), we probe molecular architectures and interactions of water molecules around a self-assembling antiparallel β-sheet protein. We find that the phase of the chiroptical response from the O-H stretching vibrational modes of water flips with the absolute chirality of the (l-) or (d-) antiparallel β-sheet. Therefore, we can conclude that the (d-) antiparallel β-sheet organizes water solvent into a chiral supermolecular structure with opposite handedness relative to that of the (l-) antiparallel β-sheet. We use molecular dynamics to characterize the chiral water superstructure at atomic resolution. The results show that the macroscopic chirality of antiparallel β-sheets breaks the symmetry of assemblies of surrounding water molecules. We also calculate the chiral SFG response of water surrounding (l-) and (d-) LK7β to confirm the presence of chiral water structures. Our results offer a different perspective as well as introduce experimental and computational methodologies for elucidating hydration of biomacromolecules. The findings imply potentially important but largely unexplored roles of water solvent in chiral selectivity of biomolecular interactions and the molecular origins of homochirality in the biological world.
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21
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Shiraga K, Urabe M, Matsui T, Kikuchi S, Ogawa Y. Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor. Phys Chem Chem Phys 2020; 22:19468-19479. [PMID: 32761010 DOI: 10.1039/d0cp02265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.
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Affiliation(s)
- Keiichiro Shiraga
- RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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22
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Leitner DM, Hyeon C, Reid KM. Water-mediated biomolecular dynamics and allostery. J Chem Phys 2020; 152:240901. [DOI: 10.1063/5.0011392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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23
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Hayes MA. Dielectrophoresis of proteins: experimental data and evolving theory. Anal Bioanal Chem 2020; 412:3801-3811. [PMID: 32314000 PMCID: PMC7250158 DOI: 10.1007/s00216-020-02623-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/28/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023]
Abstract
The ability to selectively move and trap proteins is core to their effective use as building blocks and for their characterization. Analytical and preparative strategies for proteins have been pursued and modeled for nearly a hundred years, with great advances and success. Core to all of these studies is the separation, isolation, purification, and concentration of pure homogeneous fractions of a specific protein in solution. Processes to accomplish this useful solution include biphasic equilibrium (chromatographies, extractions), mechanical, bulk property, chemical equilibria, and molecular recognition. Ultimately, the goal of all of these is to physically remove all non-like protein molecules-to the finest detail: all atoms in the full three-dimensional structure being identical down the chemical bond and bulk structure chirality. One strategy which has not been effectively pursued is exploiting the higher order subtle electrical properties of the protein-solvent system. The advent of microfluidic systems has enabled the use of very high electric fields and well-defined gradients such that extremely high resolution separations of protein mixtures are possible. These advances and recognition of these capabilities have caused a re-evaluation of the underlying theoretical models and they were found to be inadequate. New theoretical descriptions are being considered which align more closely to the total forces present and the subtlety of differences between similar proteins. These are focused on the interfacial area between the protein and hydrating solvent molecules, as opposed to the macroscale assumptions of homogeneous solutions and particles. This critical review examines all data which has been published that place proteins in electric field gradients which induce collection of those proteins, demonstrating a force greater than dispersive effects or countering forces. Evolving theoretical constructs are presented and discussed, and a general estimate of future capabilities using the higher order effects and the high fields and precise gradients of microfluidic systems is discussed. Graphical abstract.
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Affiliation(s)
- Mark A Hayes
- School of Molecular Sciences, Arizona State University, Mail Stop 1604, Tempe, AZ, 85287, USA.
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24
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Tendong E, Dasgupta TS, Chakrabarti J. Dynamics of water trapped in transition metal oxide-graphene nano-confinement. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:325101. [PMID: 32191936 DOI: 10.1088/1361-648x/ab814f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/19/2020] [Indexed: 06/10/2023]
Abstract
Motivated by practical implementation of transition-metal oxide-graphene heterostructures, we use all atom molecular dynamics simulations to study dynamics of water in a nano slit bounded by a transition metal oxide surface, namely, TiO2termination of SrTiO3, and graphene. The resultant asymmetric, strong confinement produces square ice-like crystallites of water pinned at TiO2surface and drives enhanced hydrophobicity of graphene via the proximity effect to the hydrophilic TiO2surface. This importantly brings in dynamic heterogeneity, both in translational and rotational degrees of freedom, due to coupling between the slow relaxing, strongly adsorbed water layer at the hydrophilic oxide surface, and faster relaxation of subsequent water layers. The heterogeneity is signalled in the ruggedness of the effective free energy landscapes. We discuss possible implications of our findings in drug delivery.
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Affiliation(s)
- E Tendong
- Department of Condensed Matter Physics and Material Sciences & Department of Chemical Biological and Macromoleculer Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata - 700106, India
| | - T Saha Dasgupta
- Department of Condensed Matter Physics and Material Sciences & Department of Chemical Biological and Macromoleculer Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata - 700106, India
| | - J Chakrabarti
- Department of Condensed Matter Physics and Material Sciences,Thematic Unit of Excellence for Material Science & Technology Research Centre, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata - 700106, India
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25
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Yamada SA, Hung ST, Thompson WH, Fayer MD. Effects of pore size on water dynamics in mesoporous silica. J Chem Phys 2020; 152:154704. [DOI: 10.1063/1.5145326] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Steven A. Yamada
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Samantha T. Hung
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Ward H. Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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26
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Baksi A, Ghorai PK, Biswas R. Dynamic Susceptibility and Structural Heterogeneity of Large Reverse Micellar Water: An Examination of the Core–Shell Model via Probing the Layer-wise Features. J Phys Chem B 2020; 124:2848-2863. [DOI: 10.1021/acs.jpcb.9b11895] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Atanu Baksi
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector-III, Salt Lake, Kolkata 700106, India
| | - Pradip Kr. Ghorai
- Indian Institute of Science Education and Research, Mohanpur, Nadia, Kolkata 741246, India
| | - Ranjit Biswas
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector-III, Salt Lake, Kolkata 700106, India
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27
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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: 33] [Impact Index Per Article: 8.3] [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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28
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Feng S, Peters GHJ, Ohtake S, Schöneich C, Shalaev E. Water Distribution and Clustering on the Lyophilized IgG1 Surface: Insight from Molecular Dynamics Simulations. Mol Pharm 2020; 17:900-908. [PMID: 31990562 DOI: 10.1021/acs.molpharmaceut.9b01150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water has a critical role in the stability of the higher-order structure of proteins. In addition, it is considered to be a major destabilization factor for the physical and chemical stability of freeze-dried proteins and peptides. Physical and chemical aspects of protein/water relationships are commonly studied with the use of water vapor sorption isotherms for amorphous lyophilized proteins, which, in turn, are commonly analyzed using the Brunauer-Emmett-Teller (BET) equation to obtain the parameters, Wm and CB. The parameter Wm is generally referred to as the "monolayer limit of adsorption" and has a narrow range of 6-8% for most proteins. In this study, the water distribution on an IgG1 surface is investigated by molecular dynamics (MD) simulations at different water contents. The monolayer of water molecules was found to have limited coverage of the protein surface, and the true monolayer coverage of the protein globule actually occurs at a hydration level above 30%. The distribution of water molecules on the IgG1 surface is also highly heterogeneous, and the heterogeneity is not considered in the BET theory. In this study, a mechanistic model has been developed to describe the water vapor sorption isotherm. This model is based on the analysis of the hydrogen bonding network extracted from the MD simulations. The model is consistent with the experimental Type-II isotherm, which is usually observed for proteins. The physical meaning of the BET monolayer was redefined as the onset of water cluster formation. A simple model to calculate the onset water level, Wm, is proposed based on the hydration of different amino acids, as determined from the MD simulations.
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Affiliation(s)
- Shaoxin Feng
- Department of Pharmaceutical Development, Allegan plc, Irvine, California 92612, United States
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Satoshi Ohtake
- BioTherapeutics Pharmaceutical Sciences, Pfizer, Chesterfield, Missouri 63017, United States
| | - Christian Schöneich
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Evgenyi Shalaev
- Department of Pharmaceutical Development, Allegan plc, Irvine, California 92612, United States
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29
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Heinz LP, Grubmüller H. Computing Spatially Resolved Rotational Hydration Entropies from Atomistic Simulations. J Chem Theory Comput 2019; 16:108-118. [DOI: 10.1021/acs.jctc.9b00926] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Leonard P. Heinz
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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30
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Benderskii A, Morita A. Nonlinear spectroscopy and interfacial structure and dynamics. J Chem Phys 2019; 151:150401. [PMID: 31640380 DOI: 10.1063/1.5129103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alexander Benderskii
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Akihiro Morita
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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31
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Abstract
The conformation of water around proteins is of paramount importance, as it determines protein interactions. Although the average water properties around the surface of proteins have been provided experimentally and computationally, protein surfaces are highly heterogeneous. Therefore, it is crucial to determine the correlations of water to the local distributions of polar and nonpolar protein surface domains to understand functions such as aggregation, mutations, and delivery. By using atomistic simulations, we investigate the orientation and dynamics of water molecules next to 4 types of protein surface domains: negatively charged, positively charged, and charge-neutral polar and nonpolar amino acids. The negatively charged amino acids orient around 98% of the neighboring water dipoles toward the protein surface, and such correlation persists up to around 16 Å from the protein surface. The positively charged amino acids orient around 94% of the nearest water dipoles against the protein surface, and the correlation persists up to around 12 Å. The charge-neutral polar and nonpolar amino acids are also orienting the water neighbors in a quantitatively weaker manner. A similar trend was observed in the residence time of the nearest water neighbors. These findings hold true for 3 technically important enzymes (PETase, cytochrome P450, and organophosphorus hydrolase). Our results demonstrate that the water-amino acid degree of correlation follows the same trend as the amino acid contribution in proteins solubility, namely, the negatively charged amino acids are the most beneficial for protein solubility, then the positively charged amino acids, and finally the charge-neutral amino acids.
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32
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Sheu SY, Liu YC, Zhou JK, Schlag EW, Yang DY. Surface Topography Effects of Globular Biomolecules on Hydration Water. J Phys Chem B 2019; 123:6917-6932. [PMID: 31282162 DOI: 10.1021/acs.jpcb.9b03734] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydration water serves as a microscopic manifestation of structural stability and functions of biomolecules. To develop bio-nanomaterials in applications, it is important to study how the surface topography and heterogeneity of biomolecules result in their diversity of the hydration dynamics and energetics. We here performed molecular dynamics simulations combined with the steered molecular dynamics and umbrella sampling to investigate the dynamics and escape process associated with the free energy change of water molecules close to a globular biomolecule, i.e., hemoglobin (Hb) and G-quadruplex DNA (GDNA). The residence time, power of long-time tail, and dipole relaxation time were found to display drastic changes within the averaged hydration shell of 3.0-5.0 Å. Compared with bulk water, in the inner hydration shell, the water dipole moment displays a slower relaxation process and is more oriented toward GDNA than toward Hb, forming a hedgehog-like structure when it surrounds GDNA. In particular, a spine water structure is observed in the GDNA narrow groove. The water isotope effect not only prolongs the dynamic time scales of libration motion in the inner hydration shell and the dipole relaxation processes in the bulk but also strengthens the DNA spine water structure. The potential of the mean force profile reflects the integrity of the hydration shell structure and enables us to obtain detailed insights into the structures formed by water, such as the caged H-bond network and the edge bridge structures; it also reveals that local hydration shell free energy (LHSFE) depends on H-bond rupture processes and ranges from 0.2 to 4.2 kcal/mol. Our results demonstrate that the surface topography of a biomolecule influences the integrity of the hydration shell structure and LHSFE. Our studies are able to identify various further applications in the areas of microfluid devices and nano-dewetting on bioinspired surfaces.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan.,Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Yu-Cheng Liu
- Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Jia-Kai Zhou
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan
| | - Edward W Schlag
- Institut für Physikalische und Theoretische Chemie , TU-München , Lichtenbergstr. 4 , 85748 Garching , Germany
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
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Pattni V, Heyden M. Pressure Effects on Protein Hydration Water Thermodynamics. J Phys Chem B 2019; 123:6014-6022. [DOI: 10.1021/acs.jpcb.9b04094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Viren Pattni
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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