1
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Frezza E, Laage D, Duboué-Dijon E. Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences. J Phys Chem Lett 2024; 15:4351-4358. [PMID: 38619551 DOI: 10.1021/acs.jpclett.4c00629] [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: 04/16/2024]
Abstract
Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to OR, due to the different phosphate orientations in A-form double helical RNA.
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Affiliation(s)
- Elisa Frezza
- Université Paris Cité, CNRS, CiTCoM, Paris 75006, France
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure-PSL, Sorbonne Université, CNRS, Paris 75005, France
| | - Elise Duboué-Dijon
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, Paris 75005, France
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2
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Ghassemi Z, Leach JB. Impact of Confinement within a Hydrogel Mesh on Protein Thermodynamic Stability and Aggregation Kinetics. Mol Pharm 2024; 21:1137-1148. [PMID: 38277273 DOI: 10.1021/acs.molpharmaceut.3c00677] [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] [Indexed: 01/28/2024]
Abstract
Though protein stability and aggregation have been well characterized in dilute solutions, the influence of a confining environment that exists (e.g., in intercellular and tissue spaces and therapeutic formulations) on the protein structure is largely unknown. Herein, the effects of confinement on stability and aggregation were explored for proteins of different sizes, stability, and hydrophobicity when encapsulated in hydrophilic poly(ethylene glycol) hydrogels. Denaturation curves show linear correlations between confinement size (mesh size) and thermodynamic stability, i.e., unfolding free energy and surface area accessible for solvation (represented by m-value). Two clusters of protein types are identifiable from these correlations; the clusters are defined by differences in protein stability, surface area, and aggregation propensity. Proteins with higher stability, larger surface area, and lower aggregation propensity (e.g., lysozyme and myoglobin) are less affected by the confinement imposed by mesh size than proteins with lower stability, smaller surface area, and higher aggregation propensity (e.g., growth hormone and aldehyde dehydrogenase). According to aggregation kinetics measured by thioflavin T fluorescence, confinement in smaller mesh sizes resulted in slower aggregation rates than that in larger mesh sizes. Compared to that in buffer solution, the confinement of a hydrophobic protein (e.g., human insulin) in the hydrogels accelerates protein aggregation. Conversely, the confinement of a hydrophilic protein (e.g., human amylin) in the hydrogels decelerates or prevents aggregation, with the rates of aggregation inversely proportional to mesh size. These findings provide new insights into protein conformational stability in confined microenvironments relevant to various cellular, tissue, and therapeutics scenarios.
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Affiliation(s)
- Zahra Ghassemi
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, ECS 314, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Jennie B Leach
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, ECS 314, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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3
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Kharche S, Yadav M, Hande V, Prakash S, Sengupta D. Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model. J Chem Inf Model 2024; 64:837-850. [PMID: 38291973 DOI: 10.1021/acs.jcim.3c00802] [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: 02/01/2024]
Abstract
The Martini coarse-grain force-field has emerged as an important framework to probe cellular processes at experimentally relevant time- and length-scales. However, the recently developed version, the Martini3 force-field with the implemented Go̅ model (Martini3Go̅), as well as previous variants of the Martini model have not been benchmarked and rigorously tested for globular proteins. In this study, we consider three globular proteins, ubiquitin, lysozyme, and cofilin, and compare protein dynamics and hydration with observables from experiments and all-atom simulations. We show that the Martini3Go̅ model is able to accurately model the structural and dynamic features of small globular proteins. Overall, the structural integrity of the proteins is maintained, as validated by contact maps, radii of gyration (Rg), and SAXS profiles. The chemical shifts predicted from the ensemble sampled in the simulations are consistent with the experimental data. Further, a good match is observed in the protein-water interaction energetics, and the hydration levels of the residues are similar to atomistic simulations. However, the protein-water interaction dynamics is not accurately represented and appears to depend on the protein structural complexity, residue specificity, and water dynamics. Our work is a step toward testing and assessing the Martini3Go̅ model and provides insights into future efforts to refine Martini models with improved solvation effects and better correspondence to the underlying all-atom systems.
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Affiliation(s)
- Shalmali Kharche
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Manjul Yadav
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Vrushali Hande
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Shikha Prakash
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Durba Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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4
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Vural D, Shrestha UR, Petridis L, Smith JC. Water molecule ordering on the surface of an intrinsically disordered protein. Biophys J 2023; 122:4326-4335. [PMID: 37838830 PMCID: PMC10722392 DOI: 10.1016/j.bpj.2023.10.007] [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: 07/31/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023] Open
Abstract
The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.
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Affiliation(s)
- Derya Vural
- Department of Physics, Marmara University, Istanbul, Türkiye; Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
| | - Utsab R Shrestha
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Loukas Petridis
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
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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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Ishigaki M, Kato Y, Chatani E, Ozaki Y. Variations in the Protein Hydration and Hydrogen-Bond Network of Water Molecules Induced by the Changes in the Secondary Structures of Proteins Studied through Near-Infrared Spectroscopy. J Phys Chem B 2023; 127:7111-7122. [PMID: 37477646 DOI: 10.1021/acs.jpcb.3c01803] [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: 07/22/2023]
Abstract
This study investigated how the secondary structural changes of proteins in aqueous solutions affect their hydration and the hydrogen-bond network of water molecules using near-infrared (NIR) spectroscopy. The aqueous solutions of three types of proteins, i.e., ovalbumin, β-lactoglobulin, and bovine serum albumin, were denatured by heating, and changes in the NIR bands of water reflecting the states of hydrogen bonds induced via protein secondary structural changes were investigated. On heating, the intermolecular hydrogen bonds between water molecules as well as between water and protein molecules were broken, and protein molecules were no longer strongly bound by the surrounding water molecules. Consequently, the denaturation was observed to proceed depending on the thermodynamic properties of the proteins. When the aqueous solutions of proteins were cooled after denaturation, the hydrogen-bond network was reformed. However, the state of protein hydration was changed owing to the secondary structural changes of proteins, and the variation patterns were different depending on the protein species. These changes in protein hydration may be derived from the differences in the surface charges of proteins. The elucidation of the mechanism of protein hydration and the formation of the hydrogen-bond network of water molecules will afford a comprehensive understanding of the protein functioning and dysfunctioning derived from the structural changes in proteins.
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Affiliation(s)
- Mika Ishigaki
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Yoshiki Kato
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu, Matsue, Shimane 690-8504, Japan
| | - Eri Chatani
- Department of Chemistry, Graduate School of Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Yukihiro Ozaki
- School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
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8
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Ivanov YD, Shumov ID, Kozlov AF, Ershova MO, Valueva AA, Ivanova IA, Tatur VY, Lukyanitsa AA, Ivanova ND, Ziborov VS. Stopped Flow of Glycerol Induces the Enhancement of Adsorption and Aggregation of HRP on Mica. MICROMACHINES 2023; 14:mi14051024. [PMID: 37241647 DOI: 10.3390/mi14051024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023]
Abstract
Glycerol is a usable component of heat-transfer fluids, and is thus suitable for the use in microchannel-based heat exchangers in biosensors and microelectronic devices. The flow of a fluid can lead to the generation of electromagnetic fields, which can affect enzymes. Herein, by means of atomic force microscopy (AFM) and spectrophotometry, a long-term effect of stopped flow of glycerol through a coiled heat exchanger on horseradish peroxidase (HRP) has been revealed. Samples of buffered HRP solution were incubated near either the inlet or the outlet sections of the heat exchanger after stopping the flow. It has been found that both the enzyme aggregation state and the number of mica-adsorbed HRP particles increase after such an incubation for 40 min. Moreover, the enzymatic activity of the enzyme incubated near the inlet section has been found to increase in comparison with that of the control sample, while the activity of the enzyme incubated near the outlet section remained unaffected. Our results can find application in the development of biosensors and bioreactors, in which flow-based heat exchangers are employed.
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Affiliation(s)
- Yuri D Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
| | - Ivan D Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
| | - Andrey F Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
| | - Maria O Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
| | - Anastasia A Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
| | - Irina A Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
| | - Vadim Y Tatur
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
| | - Andrei A Lukyanitsa
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, Moscow 119991, Russia
| | - Nina D Ivanova
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, Moscow 109472, Russia
| | - Vadim S Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
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9
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Shi J, Cho JH, Hwang W. Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding. J Chem Theory Comput 2023; 19:1875-1887. [PMID: 36820489 PMCID: PMC10848206 DOI: 10.1021/acs.jctc.2c00776] [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: 07/27/2022] [Indexed: 02/24/2023]
Abstract
Atomistic-level understanding of surface hydration mediating protein-protein interactions and ligand binding has been a challenge due to the dynamic nature of water molecules near the surface. We develop a computational method to evaluate the solvation free energy based on the density map of the first hydration shell constructed from all-atom molecular dynamics simulation and use it to examine the binding of two intrinsically disordered ligands to their target protein domain. One ligand is from the human protein, and the other is from the 1918 Spanish flu virus. We find that the viral ligand incurs a 6.9 kcal/mol lower desolvation penalty upon binding to the target, which is consistent with its stronger binding affinity. The difference arises from the spatially fragmented and nonuniform water density profiles of the first hydration shell. In particular, residues that are distal from the ligand-binding site contribute to a varying extent to the desolvation penalty, among which the "entropy hotspot" residues contribute significantly. Thus, ligand binding alters hydration on remote sites in addition to affecting the binding interface. The nonlocal effect disappears when the conformational motion of the protein is suppressed. The present results elucidate the interplay between protein conformational dynamics and surface hydration. Our approach of measuring the solvation free energy based on the water density of the first hydration shell is tolerant of the conformational fluctuation of protein, and we expect it to be applicable to investigating a broad range of biomolecular interfaces.
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Affiliation(s)
- Jie Shi
- Department
of Biomedical Engineering, Texas A&M
University, College
Station, Texas 777843, United States
| | - Jae-Hyun Cho
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas 77843, United States
| | - Wonmuk Hwang
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, United States
- Department
of Materials Science and Engineering, Texas
A&M University, College Station, Texas 77843, United States
- Department
of Physics and Astronomy, Texas A&M
University, College Station, Texas 77843, United States
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10
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Light, Water, and Melatonin: The Synergistic Regulation of Phase Separation in Dementia. Int J Mol Sci 2023; 24:ijms24065835. [PMID: 36982909 PMCID: PMC10054283 DOI: 10.3390/ijms24065835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The swift rise in acceptance of molecular principles defining phase separation by a broad array of scientific disciplines is shadowed by increasing discoveries linking phase separation to pathological aggregations associated with numerous neurodegenerative disorders, including Alzheimer’s disease, that contribute to dementia. Phase separation is powered by multivalent macromolecular interactions. Importantly, the release of water molecules from protein hydration shells into bulk creates entropic gains that promote phase separation and the subsequent generation of insoluble cytotoxic aggregates that drive healthy brain cells into diseased states. Higher viscosity in interfacial waters and limited hydration in interiors of biomolecular condensates facilitate phase separation. Light, water, and melatonin constitute an ancient synergy that ensures adequate protein hydration to prevent aberrant phase separation. The 670 nm visible red wavelength found in sunlight and employed in photobiomodulation reduces interfacial and mitochondrial matrix viscosity to enhance ATP production via increasing ATP synthase motor efficiency. Melatonin is a potent antioxidant that lowers viscosity to increase ATP by scavenging excess reactive oxygen species and free radicals. Reduced viscosity by light and melatonin elevates the availability of free water molecules that allow melatonin to adopt favorable conformations that enhance intrinsic features, including binding interactions with adenosine that reinforces the adenosine moiety effect of ATP responsible for preventing water removal that causes hydrophobic collapse and aggregation in phase separation. Precise recalibration of interspecies melatonin dosages that account for differences in metabolic rates and bioavailability will ensure the efficacious reinstatement of the once-powerful ancient synergy between light, water, and melatonin in a modern world.
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11
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Honegger P, Steinhauser O, Schröder C. Collective Spectroscopy of Solvation Phenomena: Conflicts, Challenges, and Opportunities. J Phys Chem Lett 2023; 14:609-618. [PMID: 36634000 DOI: 10.1021/acs.jpclett.2c03574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Different spectroscopy types reveal different aspects of molecular processes in soft matter. In particular, collective observables can provide insights into intermolecular correlations invisible to the more popular single-particle methods. In this perspective we feature the dielectric relaxation spectroscopy (DRS) with an emphasis on the proper interpretation of this complex observable aided by computational spectroscopy. While we focus on the history and recent advances of DRS in the fields of biomolecular hydration and nanoconfinement, the discussion transcends this particular field and provides a guide for how collective spectroscopy types supported by computational decomposition can be employed to further our understanding of soft matter phenomena.
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Affiliation(s)
- Philipp Honegger
- University of Vienna,Faculty of Chemistry, Department of Computational Biological Chemistry, Wien, 1090, Austria
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, BostonMassachusetts02115, United States
| | - Othmar Steinhauser
- University of Vienna,Faculty of Chemistry, Department of Computational Biological Chemistry, Wien, 1090, Austria
| | - Christian Schröder
- University of Vienna,Faculty of Chemistry, Department of Computational Biological Chemistry, Wien, 1090, Austria
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12
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Mehrabi P, Schulz EC. Sample Preparation for Time-Resolved Serial Crystallography: Practical Considerations. Methods Mol Biol 2023; 2652:361-379. [PMID: 37093487 DOI: 10.1007/978-1-0716-3147-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Time-resolved serial crystallography is an emerging method to elucidate the structure-function relationship of biomolecular systems at up to atomic resolution. However, to make this demanding method a success, a number of experimental requirements have to be met. In this chapter, we summarize general guidelines and protocols towards performing time-resolved crystallography experiments, with a particular emphasis on sample requirements and preparation but also a brief excursion into reaction initiation.
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Affiliation(s)
- Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany.
- Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.
| | - Eike C Schulz
- Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
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13
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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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14
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Abed KM, Hayyan A, Elgharbawy AAM, Hizaddin HF, Hashim MA, Hasan HA, Hamid MD, Zuki FM, Saleh J, Aldaihani AGH. Palm Raceme as a Promising Biomass Precursor for Activated Carbon to Promote Lipase Activity with the Aid of Eutectic Solvents. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248734. [PMID: 36557866 PMCID: PMC9781083 DOI: 10.3390/molecules27248734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
This study concerns the role of activated carbon (AC) from palm raceme as a support material for the enhancement of lipase-catalyzed reactions in an aqueous solution, with deep eutectic solvent (DES) as a co-solvent. The effects of carbonization temperature, impregnation ratio, and carbonization time on lipase activity were studied. The activities of Amano lipase from Burkholderia cepacia (AML) and lipase from the porcine pancreas (PPL) were used to investigate the optimum conditions for AC preparation. The results showed that AC has more interaction with PPL and effectively provides greater enzymatic activity compared with AML. The optimum treatment conditions of AC samples that yield the highest enzymatic activity were 0.5 (NaOH (g)/palm raceme (g)), 150 min, and a carbonization temperature of 400 °C. DES was prepared from alanine/sodium hydroxide and used with AC for the further enhancement of enzymatic activity. Kinetic studies demonstrated that the activity of PPL was enhanced with the immobilization of AC in a DES medium.
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Affiliation(s)
- Khalid M. Abed
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Department of Chemical Engineering, College of Engineering, University of Baghdad, Baghdad 10071, Iraq
- University of Malaya Centre for Ionic Liquids (UMCiL), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Adeeb Hayyan
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- University of Malaya Centre for Ionic Liquids (UMCiL), Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (A.H.); (H.F.H.); (H.A.H.)
| | - Amal A. M. Elgharbawy
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia, Kuala Lumpur 53100, Malaysia
- Bioenvironmental Engineering Research Centre (BERC), Department of Biotechnology Engineering, Faculty of Engineering, International Islamic University Malaysia (IIUM), Kuala Lumpur 53100, Malaysia
| | - Hanee F. Hizaddin
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- University of Malaya Centre for Ionic Liquids (UMCiL), Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (A.H.); (H.F.H.); (H.A.H.)
| | - Mohd Ali Hashim
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Hassimi Abu Hasan
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
- Research Centre for Sustainable Process Technology (CESPRO), Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
- Correspondence: (A.H.); (H.F.H.); (H.A.H.)
| | - Mahar Diana Hamid
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- University of Malaya Centre for Ionic Liquids (UMCiL), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Fathiah M. Zuki
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- University of Malaya Centre for Ionic Liquids (UMCiL), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Jehad Saleh
- Chemical Engineering Department, King Saud University, P.O. Box 800, Riyadh 11421, Saudi Arabia
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15
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Kruchinin SE, Kislinskaya EE, Chuev GN, Fedotova MV. Protein 3D Hydration: A Case of Bovine Pancreatic Trypsin Inhibitor. Int J Mol Sci 2022; 23:ijms232314785. [PMID: 36499117 PMCID: PMC9737982 DOI: 10.3390/ijms232314785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Characterization of the hydrated state of a protein is crucial for understanding its structural stability and function. In the present study, we have investigated the 3D hydration structure of the protein BPTI (bovine pancreatic trypsin inhibitor) by molecular dynamics (MD) and the integral equation method in the three-dimensional reference interaction site model (3D-RISM) approach. Both methods have found a well-defined hydration layer around the protein and revealed the localization of BPTI buried water molecules corresponding to the X-ray crystallography data. Moreover, under 3D-RISM calculations, the obtained positions of waters bound firmly to the BPTI sites are in reasonable agreement with the experimental results mentioned above for the BPTI crystal form. The analysis of the 3D hydration structure (thickness of hydration shell and hydration numbers) was performed for the entire protein and its polar and non-polar parts using various cut-off distances taken from the literature as well as by a straightforward procedure proposed here for determining the thickness of the hydration layer. Using the thickness of the hydration shell from this procedure allows for calculating the total hydration number of biomolecules properly under both methods. Following this approach, we have obtained the thickness of the BPTI hydration layer of 3.6 Å with 369 water molecules in the case of MD simulation and 3.9 Å with 333 water molecules in the case of the 3D-RISM approach. The above procedure was also applied for a more detailed description of the BPTI hydration structure near the polar charged and uncharged radicals as well as non-polar radicals. The results presented for the BPTI as an example bring new knowledge to the understanding of protein hydration.
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Affiliation(s)
- Sergey E. Kruchinin
- G.A. Krestov Institute of Solution Chemistry, The Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
| | - Ekaterina E. Kislinskaya
- Department of Fundamental and Applied Chemistry, Institute of Mathematics, Information Technology and Science, Ivanovo State University, Ermak St., 39, 153025 Ivanovo, Russia
| | - Gennady N. Chuev
- Institute of Theoretical and Experimental Biophysics, The Russian Academy of Sciences, Institutskaya St., Pushchino, 142290 Moscow, Russia
- Correspondence: (G.N.C.); (M.V.F.)
| | - Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry, The Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
- Correspondence: (G.N.C.); (M.V.F.)
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16
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Ivanov YD, Shumov ID, Tatur VY, Valueva AA, Kozlov AF, Ivanova IA, Ershova MO, Ivanova ND, Stepanov IN, Lukyanitsa AA, Ziborov VS. AFM Investigation of the Influence of Steam Flow through a Conical Coil Heat Exchanger on Enzyme Properties. MICROMACHINES 2022; 13:2041. [PMID: 36557340 PMCID: PMC9784692 DOI: 10.3390/mi13122041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
The present study is aimed at the revelation of subtle effects of steam flow through a conical coil heat exchanger on an enzyme, incubated near the heat exchanger, at the nanoscale. For this purpose, atomic force microscopy (AFM) has been employed. In our experiments, horseradish peroxidase (HRP) was used as a model enzyme. HRP is extensively employed as a model in food science in order to determine the influence of electromagnetic fields on enzymes. Adsorption properties of HRP on mica have been studied by AFM at the level of individual enzyme macromolecules, while the enzymatic activity of HRP has been studied by spectrophotometry. The solution of HRP was incubated either near the top or at the side of the conically wound aluminium pipe, through which steam flow passed. Our AFM data indicated an increase in the enzyme aggregation on mica after its incubation at either of the two points near the heat exchanger. At the same time, in the spectrophotometry experiments, a slight change in the shape of the curves, reflecting the HRP-catalyzed kinetics of ABTS oxidation by hydrogen peroxide, has also been observed after the incubation of the enzyme solution near the heat exchanger. These effects on the enzyme adsorption and kinetics can be explained by alterations in the enzyme hydration caused by the influence of the electromagnetic field, induced triboelectrically by the flow of steam through the heat exchanger. Our findings should thus be considered in the development of equipment involving conical heat exchangers, intended for either research or industrial use (including miniaturized bioreactors and biosensors). The increased aggregation of the HRP enzyme, observed after its incubation near the heat exchanger, should also be taken into account in analysis of possible adverse effects from steam-heated industrial equipment on the human body.
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Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, Moscow 109472, Russia
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, Moscow 119991, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
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17
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Effect of hemoglobin hydration on the physical properties of erythrocyte cytoplasm and whole blood. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.141560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Li W, Whitcomb KL, Warncke K. Confinement dependence of protein-associated solvent dynamics around different classes of proteins, from the EPR spin probe perspective. Phys Chem Chem Phys 2022; 24:23919-23928. [PMID: 36165617 PMCID: PMC10371532 DOI: 10.1039/d2cp03047k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein function is modulated by coupled solvent fluctuations, subject to the degree of confinement from the surroundings. To identify universal features of the external confinement effect, the temperature dependence of the dynamics of protein-associated solvent over 200-265 K for proteins representative of different classes and sizes is characterized by using the rotational correlation time (detection bandwidth, 10-10-10-7 s) of the electron paramagnetic resonance (EPR, X-band) spin probe, TEMPOL, which is restricted to regions vicinal to protein in frozen aqueous solution. Weak (protein surrounded by aqueous-dimethylsulfoxide cryosolvent mesodomain) and strong (no added crysolvent) conditions of ice boundary confinement are imposed. The panel of soluble proteins represents large and small oligomeric (ethanolamine ammonia-lyase, 488 kDa; streptavidin, 52.8 kDa) and monomeric (myoglobin, 16.7 kDa) globular proteins, an intrinsically disordered protein (IDP, β-casein, 24.0 kDa), an unstructured peptide (protamine, 4.38 kDa) and a small peptide with partial backbone order (amyloid-β residues 1-16, 1.96 kDa). Expanded and condensate structures of β-casein and protamine are resolved by the spin probe under weak and strong confinement, respectively. At each confinement condition, the soluble globular proteins display common T-dependences of rotational correlation times and normalized weights, for two mobility components, protein-associated domain, PAD, and surrounding mesodomain. Strong confinement induces a detectable PAD component and emulation of globular protein T-dependence by the amyloid-β peptide. Confinement uniformly impacts soluble globular protein PAD dynamics, and is therefore a generic control parameter for modulation of soluble globular protein function.
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Affiliation(s)
- Wei Li
- Department of Physics, Emory University, Atlanta, Georgia, 30322.
| | | | - Kurt Warncke
- Department of Physics, Emory University, Atlanta, Georgia, 30322.
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19
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The Effect of a Dodecahedron-Shaped Structure on the Properties of an Enzyme. J Funct Biomater 2022; 13:jfb13040166. [PMID: 36278635 PMCID: PMC9590084 DOI: 10.3390/jfb13040166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/26/2022] Open
Abstract
In this research, the influence of a dodecahedron-shaped structure on the adsorption behavior of a horseradish peroxidase (HRP) enzyme glycoprotein onto mica substrates was studied. In the experiments, samples of an aqueous HRP solution were incubated at various distances (0.03 m, 2 m, 5 m, and control at 20 m) from the dodecahedron surface. After the incubation, the direct adsorption of HRP onto mica substrates immersed in the solutions was performed, and the mica-adsorbed HRP particles were visualized via atomic force microscopy (AFM). The effect of the increased HRP aggregation was only observed after the incubation of the enzyme solution at the 2 m distance from the dodecahedron. In addition, with respect to the control sample, spectrophotometric measurements revealed no change in the HRP enzymatic activity after the incubation at any of the distances studied. The results reported herein can be of use in the modeling of the possible influences of various spatial structures on biological objects in the development of biosensors and other electronic equipment.
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20
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Renault JP, Huart L, Milosavljević AR, Bozek JD, Palaudoux J, Guigner JM, Marichal L, Leroy J, Wien F, Hervé Du Penhoat MA, Nicolas C. Electronic Structure and Solvation Effects from Core and Valence Photoelectron Spectroscopy of Serum Albumin. Int J Mol Sci 2022; 23:ijms23158227. [PMID: 35897833 PMCID: PMC9331649 DOI: 10.3390/ijms23158227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/07/2022] Open
Abstract
X-ray photoelectron spectroscopy of bovine serum albumin (BSA) in a liquid jet is used to investigate the electronic structure of a solvated protein, yielding insight into charge transfer mechanisms in biological systems in their natural environment. No structural damage was observed in BSA following X-ray photoelectron spectroscopy in a liquid jet sample environment. Carbon and nitrogen atoms in different chemical environments were resolved in the X-ray photoelectron spectra of both solid and solvated BSA. The calculations of charge distributions demonstrate the difficulty of assigning chemical contributions in complex systems in an aqueous environment. The high-resolution X-ray core electron spectra recorded are unchanged upon solvation. A comparison of the valence bands of BSA in both phases is also presented. These bands display a higher sensitivity to solvation effects. The ionization energy of the solvated BSA is determined at 5.7 ± 0.3 eV. Experimental results are compared with theoretical calculations to distinguish the contributions of various molecular components to the electronic structure. This comparison points towards the role of water in hole delocalization in proteins.
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Affiliation(s)
- Jean-Philippe Renault
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
- Correspondence: (J.-P.R.); (C.N.)
| | - Lucie Huart
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 75252 Paris, France; (J.-M.G.); (M.-A.H.D.P.)
| | | | - John D. Bozek
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
| | - Jerôme Palaudoux
- Laboratoire de Chimie Physique-Matière et Rayonnement, Sorbonne Université, UMR CNRS 7614, 75252 Paris, France;
| | - Jean-Michel Guigner
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 75252 Paris, France; (J.-M.G.); (M.-A.H.D.P.)
| | - Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
| | - Jocelyne Leroy
- Université Paris-Saclay, CEA, CNRS, NIMBE, CEA Saclay, 91191 Gif-sur-Yvette, France; (L.H.); (L.M.); (J.L.)
| | - Frank Wien
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
| | - Marie-Anne Hervé Du Penhoat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, MNHN, 75252 Paris, France; (J.-M.G.); (M.-A.H.D.P.)
| | - Christophe Nicolas
- Synchrotron SOLEIL, 91192 Saint Aubin, France; (A.R.M.); (J.D.B.); (F.W.)
- Correspondence: (J.-P.R.); (C.N.)
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21
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Hu K, Matsuura H, Shirakashi R. Stochastic Analysis of Molecular Dynamics Reveals the Rotation Dynamics Distribution of Water around Lysozyme. J Phys Chem B 2022; 126:4520-4530. [PMID: 35675630 DOI: 10.1021/acs.jpcb.2c00970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water dynamics is essential to biochemical processes by mediating all such reactions, including biomolecular degeneration in solutions. To disentangle the molecular-scale distribution of water dynamics around a solute biomolecule, we investigated here the rotational dynamics of water around lysozyme by combining molecular dynamics (MD) simulations and broadband dielectric spectroscopy (BDS). A statistical analysis using the relaxation times and trajectories of every single water molecule was proposed, and the two-dimensional probability distribution of water at a distance from the lysozyme surface with a rotational relaxation time was given. For the observed lysozyme solutions of 34-284 mg/mL, we discovered that the dielectric relaxation time obtained from this distribution agrees well with the measured γ relaxation time, which suggests that rotational self-correlation of water molecules underlies the gigahertz domain of the dielectric spectra. Regardless of protein concentration, water rotational relaxation time versus the distance from the lysozyme surface revealed that the water rotation is severely retarded within 3 Å from the lysozyme surface and is nearly comparable to pure water when farther than 10 Å. The dimension of the first hydration layer was subsequently identified in terms of the relationship between the acceleration of water rotation and the distance from the protein surface.
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Affiliation(s)
- Kang Hu
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo 153-8505, Japan.,Department of Mechanical Engineering, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Matsuura
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo 153-8505, Japan.,Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Ryo Shirakashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo 153-8505, Japan
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22
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Yu H, Zhang Q, Zhuang W. Comparative analysis of hydration layer reorientation dynamics of antifreeze protein and protein cytochrome P450. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2203038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Antifreeze proteins (AFPs) inhibit ice re-crystallization by a mechanism remaining largely elusive. Dynamics of AFPs’ hydration water and its involvement in the antifreeze activity have not been identified conclusively. We herein, by simulation and theory, examined the water reorientation dynamics in the first hydration layer of an AFP from the spruce budworm, Choristoneura fumiferana, compared with a protein cytochrome P450 (CYP). The increase of potential acceptor water molecules around donor water molecules leads to the acceleration of hydrogen bond exchange between water molecules. Therefore, the jump reorientation of water molecules around the AFP active region is accelerated. Due to the mutual coupling and excitation of hydrogen bond exchange, with the acceleration of hydrogen bond exchange, the rearrangement of the hydrogen bond network and the frame reorientation of water are accelerated. Therefore, the water reorientation dynamics of AFP is faster than that of CYP. The results of this study provide a new physical image of antifreeze protein and a new understanding of the antifreeze mechanism of antifreeze proteins.
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Affiliation(s)
- Hongfeng Yu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhang
- College of Chemistry and Material Sciences, Inner Mongolia Minzu University, Tongliao 028043, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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23
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Horstmann R, Hecht L, Kloth S, Vogel M. Structural and Dynamical Properties of Liquids in Confinements: A Review of Molecular Dynamics Simulation Studies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6506-6522. [PMID: 35580166 DOI: 10.1021/acs.langmuir.2c00521] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Molecular dynamics (MD) simulations are a powerful tool for detailed studies of altered properties of liquids in confinement, in particular, of changed structures and dynamics. They allow, on one hand, for perfect control and systematic variation of the geometries and interactions inherent in confinement situations and, on the other hand, for type-selective and position-resolved analyses of a huge variety of structural and dynamical parameters. Here, we review MD simulation studies on various types of liquids and confinements. The main focus is confined aqueous systems, but also ionic liquids and polymer and silica melts are discussed. Results for confinements featuring different interactions, sizes, shapes, and rigidity will be presented. Special attention will be given to situations in which the confined liquid and the confining matrix consist of the same type of particles and, hence, disparate liquid-matrix interactions are absent. Findings for the magnitude and the range of wall effects on molecular positions and orientations and on molecular dynamics, including vibrational motion and structural relaxation, are reviewed. Moreover, their dependence on the parameters of the confinement and their relevance to theoretical approaches to the glass transition are addressed.
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Affiliation(s)
- Robin Horstmann
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Lukas Hecht
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Sebastian Kloth
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Michael Vogel
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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24
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Bongini P, Niccolai N, Trezza A, Mangiavacchi G, Santucci A, Spiga O, Bianchini M, Gardini S. Structural Bioinformatic Survey of Protein-Small Molecule Interfaces Delineates the Role of Glycine in Surface Pocket Formation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1881-1886. [PMID: 33095703 DOI: 10.1109/tcbb.2020.3033384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
With a structural bioinformatic approach, we have explored amino acid compositions at PISA defined interfaces between small molecules and proteins that are contained in an optimized subset of 11,351 PDB files. The use of a series of restrictions, to prevent redundancy and biases from interactions between amino acids with charged side chains and ions, yielded a final data set of 45,230 protein-small molecule interfaces. We have compared occurrences of natural amino acids in surface exposed regions and binding sites for all the proteins of our data set. From our structural bioinformatic survey, the most relevant signal arose from the unexpected Gly abundance at enzyme catalytic sites. This finding suggested that Gly must have a fundamental role in stabilizing concave protein surface moieties. Subsequently, we have tried to predict the effect of in silico Gly mutations in hen egg white lysozyme to optimize those conditions that can reshape the protein surface with the appearance of new pockets. Replacing amino acids having bulky side chains with Gly in specific protein regions seems a feasible way for designing proteins with additional surface pockets, which can alter protein surface dynamics, therefore, representing controllable switches for protein activity.
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25
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Abstract
In this study, we examine the spectral dielectric properties of liquid water in charged nanopores over a wide range of frequencies (0.3 GHz to 30 THz) and pore widths (0.3 to 5 nm). This has been achieved using classical molecular dynamics simulations of hydrated Na-smectite, the prototypical swelling clay mineral. We observe a drastic (20-fold) and anisotropic decrease in the static relative permittivity of the system as the pore width decreases. This large decrement in static permittivity reflects a strong attenuation of the main Debye relaxation mode of liquid water. Remarkably, this strong attenuation entails very little change in the time scale of the collective relaxation. Our results indicate that water confined in charged nanopores is a distinct solvent with a much weaker collective nature than bulk liquid water, in agreement with recent observations of water in uncharged nanopores. Finally, we observe remarkable agreement between the dielectric properties of the simulated clay system against a compiled set of soil samples at various volumetric water contents. This implies that saturation may not be the sole property dictating the dielectric properties of soil samples, rather that the pore-size distribution of fully saturated nanopores may also play a critically important role.
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Affiliation(s)
- Thomas R Underwood
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Ian C Bourg
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States.,High Meadows Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
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26
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Karjalainen J, Henschel H, Nissi MJ, Nieminen MT, Hanni M. Dipolar Relaxation of Water Protons in the Vicinity of a Collagen-like Peptide. J Phys Chem B 2022; 126:2538-2551. [PMID: 35343227 PMCID: PMC8996236 DOI: 10.1021/acs.jpcb.2c00052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Quantitative magnetic
resonance imaging is one of the few available
methods for noninvasive diagnosis of degenerative changes in articular
cartilage. The clinical use of the imaging data is limited by the
lack of a clear association between structural changes at the molecular
level and the measured magnetic relaxation times. In anisotropic,
collagen-containing tissues, such as articular cartilage, the orientation
dependency of nuclear magnetic relaxation can obscure the content
of the images. Conversely, if the molecular origin of the phenomenon
would be better understood, it would provide opportunities for diagnostics
as well as treatment planning of degenerative changes in these tissues.
We study the magnitude and orientation dependence of the nuclear magnetic
relaxation due to dipole–dipole coupling of water protons in
anisotropic, collagenous structures. The water–collagen interactions
are modeled with molecular dynamics simulations of a small collagen-like
peptide dissolved in water. We find that in the vicinity of the collagen-like
peptide, the dipolar relaxation of water hydrogen nuclei is anisotropic,
which can result in orientation-dependent relaxation times if the
water remains close to the peptide. However, the orientation-dependency
of the relaxation is different from the commonly observed magic-angle
phenomenon in articular cartilage MRI.
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Affiliation(s)
- Jouni Karjalainen
- Research Unit of Medical Imaging Physics and Technology, University of Oulu, P.O. Box 5000, Oulu 90014, Finland
| | - Henning Henschel
- Research Unit of Medical Imaging Physics and Technology, University of Oulu, P.O. Box 5000, Oulu 90014, Finland
| | - Mikko J Nissi
- Research Unit of Medical Imaging Physics and Technology, University of Oulu, P.O. Box 5000, Oulu 90014, Finland.,Department of Applied Physics, University of Eastern Finland, Kuopio 70210, Finland
| | - Miika T Nieminen
- Research Unit of Medical Imaging Physics and Technology, University of Oulu, P.O. Box 5000, Oulu 90014, Finland.,Department of Diagnostic Radiology, Oulu University Hospital, Oulu 90014, Finland.,Medical Research Center, University of Oulu and Oulu University Hospital, Oulu 90014, Finland
| | - Matti Hanni
- Research Unit of Medical Imaging Physics and Technology, University of Oulu, P.O. Box 5000, Oulu 90014, Finland.,Department of Diagnostic Radiology, Oulu University Hospital, Oulu 90014, Finland.,Medical Research Center, University of Oulu and Oulu University Hospital, Oulu 90014, Finland
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27
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Gasparotto P, Fitzner M, Cox SJ, Sosso GC, Michaelides A. How do interfaces alter the dynamics of supercooled water? NANOSCALE 2022; 14:4254-4262. [PMID: 35244128 DOI: 10.1039/d2nr00387b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The structure of liquid water in the proximity of an interface can deviate significantly from that of bulk water, with surface-induced structural perturbations typically converging to bulk values at about ∼1 nm from the interface. While these structural changes are well established it is, in contrast, less clear how an interface perturbs the dynamics of water molecules within the liquid. Here, through an extensive set of molecular dynamics simulations of supercooled bulk and interfacial water films and nano-droplets, we observe the formation of persistent, spatially extended dynamical domains in which the average mobility varies as a function of the distance from the interface. This is in stark contrast with the dynamical heterogeneity observed in bulk water, where these domains average out spatially over time. We also find that the dynamical response of water to an interface depends critically on the nature of the interface and on the choice of interface definition. Overall these results reveal a richness in the dynamics of interfacial water that opens up the prospect of tuning the dynamical response of water through specific modifications of the interface structure or confining material.
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Affiliation(s)
- Piero Gasparotto
- Scientific Computing Division, Paul Scherrer Institute, Villigen 5232, Switzerland.
| | - Martin Fitzner
- Thomas Young Centre, London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Stephen James Cox
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Gabriele Cesare Sosso
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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28
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Santra S, Jana M. Influence of Aqueous Arginine Solution on Regulating Conformational Stability and Hydration Properties of the Secondary Structural Segments of a Protein at Elevated Temperatures: A Molecular Dynamics Study. J Phys Chem B 2022; 126:1462-1476. [PMID: 35147426 DOI: 10.1021/acs.jpcb.1c09583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effects of aqueous arginine solution on the conformational stability of the secondary structural segments of a globular protein, ubiquitin, and the structure and dynamics of the surrounding water and arginine were examined by performing atomistic molecular dynamics (MD) simulations. Attempts have been made to identify the osmolytic efficacy of arginine solution, and its influence in guiding the hydration properties of the protein at an elevated temperature of 450 K. The similar properties of the protein in pure water at elevated temperatures were computed and compared. Replica exchange MD simulation was performed to explore the arginine solution's sensitivity in stabilizing the protein conformations for a wide range of temperatures (300-450 K). It was observed that although all the helices and strands of the protein undergo unfolding at elevated temperature in pure water, they exhibited native-like conformational dynamics in the presence of arginine at both ambient and elevated temperatures. We find that the higher free energy barrier between the folded native and unfolded states of the protein primarily arises from the structural transformation of α-helix, relative to the strands. Our study revealed that the water structure around the secondary segments depends on the nature of amino acid compositions of the helices and strands. The reorientation of water dipoles around the helices and strands was found hindered due to the presence of arginine in the solution; such hindrance reduces the possibility of exchange of hydrogen bonds that formed between the secondary segments of protein and water (PW), and as a result, PW hydrogen bonds take longer time to relax than in pure water. On the other hand, the origin of slow relaxation of protein-arginine (PA) hydrogen bonds was identified to be due to the presence of different types of protein-bound arginine molecules, where arginine interacts with the secondary structural segments of the protein through multiple/bifurcated hydrogen bonds. These protein-bound arginine formed different kinds of bridged PA hydrogen bonds between amino acid residues of the same secondary segments or among multiple bonds and helped protein to conserve its native folded form firmly.
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Affiliation(s)
- Santanu Santra
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
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29
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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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30
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Belyanchikov M, Bedran Z, Savinov M, Bednyakov P, Proschek P, Prokleska J, Abalmasov V, Zhukova E, Thomas VG, Dudka A, Zhugayevych A, Petzelt J, Prokhorov A, Anzin V, Kremer R, Fischer JKH, Lunkenheimer P, Loidl A, Uykur E, Dressel M, Gorshunov B. Single-particle and collective excitations of polar water molecules confined in nano-pores within cordierite crystal lattice. Phys Chem Chem Phys 2022; 24:6890-6904. [DOI: 10.1039/d1cp05338h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently, the low-temperature phase of water molecules confined within nanocages formed by the crystalline lattice of water-containing cordierite crystals was reported to comprise domains with ferroelectrically ordered dipoles within the...
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31
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Mollazadeh S, Yazdimamaghani M, Yazdian-Robati R, Pirhadi S. New insight into the structural changes of apoferritin pores in the process of doxorubicin loading at an acidic pH: Molecular dynamics simulations. Comput Biol Med 2021; 141:105158. [PMID: 34952337 DOI: 10.1016/j.compbiomed.2021.105158] [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: 10/19/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/19/2022]
Abstract
Apoferritin (APO-Fr) is one of the most investigated proteins proposed as an advanced structure for drug delivery systems. Herein, molecular dynamics simulation was employed to compare the opening of 3-fold and 4-fold pores in APO-Fr during the partial disassembly process at an acidic pH. We showed that more hydrophilic residues in the surface of 3-fold pores compared to 4-fold pores facilitate increased flexibility and a higher tendency to open. In particular, dissociation is induced by the presence of Doxorubicin (DOX) close to 3-fold pores. Our simulations showed loaded DOXs on the APO-Fr surface were mainly involved in the hydrogen bond interactions with the hydrophilic residues, suggesting the difficulty of hydrophobic drugs loading in APO-Fr with the partial disassembly process. However, π-π interactions as well as hydrogen bonds between protein and DOXs were mediated by the basic and acidic amino acids such as HIP128, GLU17, and LYS143 at the open pores, providing penetration of DOXs into the H-Apo-Fr. We conclude that increased drug encapsulations and loading capacity of hydrophobic drugs into the cavity of APO-Fr are feasible by further disassembly of openings to access the internal hydrophobic portions of the protein.
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Affiliation(s)
- Shirin Mollazadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical, Iran
| | - Mostafa Yazdimamaghani
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Rezvan Yazdian-Robati
- Pharmaceutical Sciences Research Centre, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Somayeh Pirhadi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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32
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Scollo F, Evci H, Amaro M, Jurkiewicz P, Sykora J, Hof M. What Does Time-Dependent Fluorescence Shift (TDFS) in Biomembranes (and Proteins) Report on? Front Chem 2021; 9:738350. [PMID: 34778202 PMCID: PMC8586494 DOI: 10.3389/fchem.2021.738350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022] Open
Abstract
The organization of biomolecules and bioassemblies is highly governed by the nature and extent of their interactions with water. These interactions are of high intricacy and a broad range of methods based on various principles have been introduced to characterize them. As these methods view the hydration phenomena differently (e.g., in terms of time and length scales), a detailed insight in each particular technique is to promote the overall understanding of the stunning “hydration world.” In this prospective mini-review we therefore critically examine time-dependent fluorescence shift (TDFS)—an experimental method with a high potential for studying the hydration in the biological systems. We demonstrate that TDFS is very useful especially for phospholipid bilayers for mapping the interfacial region formed by the hydrated lipid headgroups. TDFS, when properly applied, reports on the degree of hydration and mobility of the hydrated phospholipid segments in the close vicinity of the fluorophore embedded in the bilayer. Here, the interpretation of the recorded TDFS parameters are thoroughly discussed, also in the context of the findings obtained by other experimental techniques addressing the hydration phenomena (e.g., molecular dynamics simulations, NMR spectroscopy, scattering techniques, etc.). The differences in the interpretations of TDFS outputs between phospholipid biomembranes and proteins are also addressed. Additionally, prerequisites for the successful TDFS application are presented (i.e., the proper choice of fluorescence dye for TDFS studies, and TDFS instrumentation). Finally, the effects of ions and oxidized phospholipids on the bilayer organization and headgroup packing viewed from TDFS perspective are presented as application examples.
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Affiliation(s)
- Federica Scollo
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
| | - Hüseyin Evci
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
| | - Mariana Amaro
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
| | - Piotr Jurkiewicz
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
| | - Jan Sykora
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the CAS, Prague, Czechia
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33
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Leo L, Bridelli MG, Polverini E. Reversible processes in collagen dehydration: A molecular dynamics study. Arch Biochem Biophys 2021; 714:109079. [PMID: 34748734 DOI: 10.1016/j.abb.2021.109079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/11/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022]
Abstract
Collagen dehydration is an unavoidable damaging process that causes the lack of fibers' physical properties and it is usually irreversible. However, the identification of low hydration conditions that permit a recovering of initial collagen features after a rehydration treatment is particularly of interest. Monitoring structural changes by means of MD simulations, we investigated the hydration-dehydration-rehydration cycle of two microfibril models built on different fragments of the sequence of rat tail collagen type I. The microfibrils have different hydropathic features, to investigate the influence of amino acid composition on the whole process. We showed that with low hydration at a level corresponding to the first shell, microfibril gains in compactness and tubularity. Crucially, some water molecules remain trapped inside the fibrils, allowing, by rehydrating, a recovery of the initial collagen structural features. Water rearranges in cluster around the protein, and its first layer is more anchored to the surface. However, these changes in distribution and mobility in low hydration conditions get back with rehydration.
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Affiliation(s)
- Ludovica Leo
- Department of Mathematical, Physical and Computer Science, University of Parma, Parco Area Delle Scienze, 7/A, 43124, Parma, Italy.
| | - Maria Grazia Bridelli
- Department of Mathematical, Physical and Computer Science, University of Parma, Parco Area Delle Scienze, 7/A, 43124, Parma, Italy.
| | - Eugenia Polverini
- Department of Mathematical, Physical and Computer Science, University of Parma, Parco Area Delle Scienze, 7/A, 43124, Parma, Italy.
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34
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Hamada M, Iwata T, Fuki M, Kandori H, Weber S, Kobori Y. Orientations and water dynamics of photoinduced secondary charge-separated states for magnetoreception by cryptochrome. Commun Chem 2021; 4:141. [PMID: 36697801 PMCID: PMC9814139 DOI: 10.1038/s42004-021-00573-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/02/2021] [Indexed: 01/28/2023] Open
Abstract
In the biological magnetic compass, blue-light photoreceptor protein of cryptochrome is thought to conduct the sensing of the Earth's magnetic field by photoinduced sequential long-range charge-separation (CS) through a cascade of tryptophan residues, WA(H), WB(H) and WC(H). Mechanism of generating the weak-field sensitive radical pair (RP) is poorly understood because geometries, electronic couplings and their modulations by molecular motion have not been investigated in the secondary CS states generated prior to the terminal RP states. In this study, water dynamics control of the electronic coupling is revealed to be a key concept for sensing the direction of weak magnetic field. Geometry and exchange coupling (singlet-triplet energy gap: 2J) of photoinduced secondary CS states composed of flavin adenine dinucleotide radical anion (FAD-•) and radical cation WB(H)+• in the cryptochrome DASH from Xenopus laevis were clarified by time-resolved electron paramagnetic resonance. We found a time-dependent energetic disorder in 2J and was interpreted by a trap CS state capturing one reorientated water molecule at 120 K. Enhanced electron-tunneling by water-libration was revealed for the terminal charge-separation event at elevated temperature. This highlights importance of optimizing the electronic coupling for regulation of the anisotropic RP yield on the possible magnetic compass senses.
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Affiliation(s)
- Misato Hamada
- grid.31432.370000 0001 1092 3077Department of Chemistry, Graduate School of Science, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan
| | - Tatsuya Iwata
- grid.265050.40000 0000 9290 9879Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274‒8510 Japan
| | - Masaaki Fuki
- grid.31432.370000 0001 1092 3077Department of Chemistry, Graduate School of Science, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan ,grid.31432.370000 0001 1092 3077Molecular Photoscience Research Center, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan
| | - Hideki Kandori
- grid.47716.330000 0001 0656 7591Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555 Japan ,grid.47716.330000 0001 0656 7591OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555 Japan
| | - Stefan Weber
- grid.5963.9Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Yasuhiro Kobori
- grid.31432.370000 0001 1092 3077Department of Chemistry, Graduate School of Science, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan ,grid.31432.370000 0001 1092 3077Molecular Photoscience Research Center, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan
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35
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions. Int J Mol Sci 2021; 22:ijms22179350. [PMID: 34502252 PMCID: PMC8431001 DOI: 10.3390/ijms22179350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.
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36
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Kudłacik-Kramarczyk S, Drabczyk A, Głąb M, Gajda P, Czopek A, Zagórska A, Jaromin A, Gubernator J, Makara A, Tyliszczak B. The Development of the Innovative Synthesis Methodology of Albumin Nanoparticles Supported by Their Physicochemical, Cytotoxic and Hemolytic Evaluation. MATERIALS (BASEL, SWITZERLAND) 2021; 14:4386. [PMID: 34442909 PMCID: PMC8400698 DOI: 10.3390/ma14164386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 01/28/2023]
Abstract
Many studies are being performed to develop effective carriers for controlled cytostatic delivery wherein albumin is a promising material due to its tendency to accumulate near cancer cells. The novelty of this work involves the development of the synthesis methodology of albumin nanoparticles and their biological and physicochemical evaluation. Albumin particles were obtained via the salt-induced precipitation and K3PO4 was used as a salting-out agent. Various concentrations of protein and salting-out agent solutions were mixed using a burette or a syringe system. It was proved that the size of the particles depended on the concentrations of the reagents and the methodology applied. As a result of a process performed using a burette and 2 M K3PO4, albumin spheres having a size 5-25 nm were obtained. The size of nanospheres and their spherical shape was confirmed via TEM analysis. The use of a syringe system led to preparation of particles of large polydispersity. The highest albumin concentration allowing for synthesis of homogeneous particles was 2 g/L. The presence of albumin in spheres was confirmed via the FT-IR technique and UV-Vis spectroscopy. All samples showed no cytotoxicity towards normal human dermal fibroblasts and no hemolytic properties against human erythrocytes (the hemolysis did not exceed 2.5%).
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Affiliation(s)
- Sonia Kudłacik-Kramarczyk
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31-864 Krakow, Poland
| | - Anna Drabczyk
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31-864 Krakow, Poland
| | - Magdalena Głąb
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31-864 Krakow, Poland
| | - Paweł Gajda
- Department of Sustainable Energy Development, Faculty of Energy and Fuels, AGH University of Science and Technology, 30 Mickiewicza Av., 30-059 Krakow, Poland;
| | - Anna Czopek
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (A.C.); (A.Z.)
| | - Agnieszka Zagórska
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna St., 30-688 Krakow, Poland; (A.C.); (A.Z.)
| | - Anna Jaromin
- Department of Lipids and Liposomes, Faculty of Biotechnology, University of Wroclaw, 14a Joliot-Curie St., 50-383 Wroclaw, Poland; (A.J.); (J.G.)
| | - Jerzy Gubernator
- Department of Lipids and Liposomes, Faculty of Biotechnology, University of Wroclaw, 14a Joliot-Curie St., 50-383 Wroclaw, Poland; (A.J.); (J.G.)
| | - Agnieszka Makara
- Faculty of Chemical Engineering and Technology, Cracow University of Technology, 24 Warszawska St., 31-155 Krakow, Poland;
| | - Bożena Tyliszczak
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31-864 Krakow, Poland
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Chakraborty I, Kar RK, Sarkar D, Kumar S, Maiti NC, Mandal AK, Bhunia A. Solvent Relaxation NMR: A Tool for Real-Time Monitoring Water Dynamics in Protein Aggregation Landscape. ACS Chem Neurosci 2021; 12:2903-2916. [PMID: 34292711 DOI: 10.1021/acschemneuro.1c00262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Solvent dynamics strongly induce the fibrillation of an amyloidogenic system. Probing the solvation mechanism is crucial as it enables us to predict different proteins' functionalities, such as the aggregation propensity, structural flexibility, and toxicity. This work shows that a straightforward NMR method in conjunction with phenomenological models gives a global and qualitative picture of water dynamics at different concentrations and temperatures. Here, we study amyloid system Aβ40 and its fragment AV20 (A21-V40) and G37L (mutation at Gly37 → Leu of AV20), having different aggregation and toxic properties. The independent validation of this method is elucidated using all-atom classical MD simulation. These two state-of-the-art techniques are pivotal in linking the effect of solvent environment in the near hydration-shell to their aggregation nature. The time-dependent modulation in solvent dynamics probed with the NMR solvent relaxation method can be further adopted to gain insight into amyloidogenesis and link with their toxicity profiles.
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Affiliation(s)
| | - Rajiv K. Kar
- Faculty II-Mathematics and Natural Sciences, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Dibakar Sarkar
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Sourav Kumar
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Nakul C. Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Atin Kumar Mandal
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata 700054, India
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38
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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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39
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Hassan I, Ferraro F, Imhof P. Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide. Molecules 2021; 26:2148. [PMID: 33917998 PMCID: PMC8068333 DOI: 10.3390/molecules26082148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent's effect on the vibrational frequency.
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Affiliation(s)
- Irtaza Hassan
- Institute for Theoretical Physics, Freie Universtiät Berlin, Arnimallee 14, 14195 Berlin, Germany;
| | - Federica Ferraro
- Computer Chemistry Center, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany;
| | - Petra Imhof
- Institute for Theoretical Physics, Freie Universtiät Berlin, Arnimallee 14, 14195 Berlin, Germany;
- Computer Chemistry Center, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany;
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40
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Bansia H, Mahanta P, Yennawar NH, Ramakumar S. Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches. J Chem Inf Model 2021; 61:1322-1333. [PMID: 33570386 DOI: 10.1021/acs.jcim.0c01126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cryptic pockets are visible in ligand-bound protein structures but are occluded in unbound structures. Utilizing these pockets in fragment-based drug-design provides an attractive option for proteins not tractable by classical binding sites. However, owing to their hidden nature, they are difficult to identify. Here, we show that small glycols find cryptic pockets on a diverse set of proteins. Initial crystallography experiments serendipitously revealed the ability of ethylene glycol, a small glycol, to identify a cryptic pocket on the W6A mutant of the RBSX protein (RBSX-W6A). Explicit-solvent molecular dynamics (MD) simulations of RBSX-W6A with the exposed state of the cryptic pocket (ethylene glycol removed) revealed closure of the pocket reiterating that the exposed state of cryptic pockets in general are unstable in the absence of ligands. Also, no change in the pocket was observed for simulations of RBSX-W6A with the occluded state of the cryptic pocket, suggesting that water molecules are not able to open the cryptic pocket. "Cryptic-pocket finding" potential of small glycols was then supported and generalized through additional crystallography experiments, explicit-cosolvent MD simulations, and protein data set construction and analysis. The cryptic pocket on RBSX-W6A was found again upon repeating the crystallography experiments with another small glycol, propylene glycol. Use of ethylene glycol as a probe molecule in cosolvent MD simulations led to the enhanced sampling of the exposed state of experimentally observed cryptic sites on a test set of two proteins (Niemann-Pick C2, Interleukin-2). Further, analyses of protein structures with validated cryptic sites showed that ethylene glycol molecules bind to sites on proteins (Bcl-xL, G-actin, myosin II, and glutamate receptor 2), which become apparent upon binding of biologically relevant ligands. Our study thus suggests potential application of the small glycols in experimental and computational fragment-based approaches to identify cryptic pockets in apparently undruggable and/or difficult targets, making these proteins amenable to drug-design strategies.
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Affiliation(s)
- Harsh Bansia
- Department of Physics, Indian Institute of Science, Bengaluru 560012, India
| | - Pranjal Mahanta
- Department of Physics, Indian Institute of Science, Bengaluru 560012, India
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, United States
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41
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Nandakumar A, Ito Y, Ueda M. Solvent Effects on the Self-Assembly of an Amphiphilic Polypeptide Incorporating α-Helical Hydrophobic Blocks. J Am Chem Soc 2020; 142:20994-21003. [PMID: 33272014 DOI: 10.1021/jacs.0c03425] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The self-assembly of biological molecules is an important pathway to understanding the molecular basis of complex metabolic events. The presence of a cosolvent in an aqueous solution during the self-assembly process can promote the formation of kinetically trapped metastable intermediates. In nature, a category of cosolvents termed osmolytes can work to strengthen the hydrogen-bond network of water such that the native states of certain proteins are favored, thus modulating their function and stability. However, identifying cosolvents that act as osmolytes in biomimetic applications, such as the self-assembly of soft materials, remains challenging. The present work examined the effects of ethanol (EtOH) and acetonitrile (ACN) as cosolvents on the self-assembly of the amphiphilic polypeptide PSar30-(l-Leu-Aib)6 (S30L12), which incorporates α-helical hydrophobic blocks, in aqueous solution. The results provided a direct observation of morphological behavior of S30L12 as a function of solvent composition. Morphological transitions were investigated using transmission electron microscopy, while the packing of peptide molecules was assessed using circular dichroism analyses and evaluations of membrane fluidity. In the EtOH/H2O mixtures, the EtOH strengthened the hydrogen-bond network of the water, thus limiting the hydrophobic hydration of S30L12 assemblies and enhancing hydrophobic interactions between assemblies. In contrast, ACN formed self-associated nanoclusters in water and at the hydrophobic cores of peptide assemblies to stabilize the edges exposed to bulk water and enhance the assembly kinetics. Fourier transform infrared (FT-IR) analysis indicated that both EtOH and ACN can modify the self-assembly of biomaterials in the same manner as osmolyte protectants or denaturants.
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Affiliation(s)
- Avanashiappan Nandakumar
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Motoki Ueda
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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42
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Destabilisation of the structure of transthyretin is driven by Ca 2. Int J Biol Macromol 2020; 166:409-423. [PMID: 33129902 DOI: 10.1016/j.ijbiomac.2020.10.199] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/08/2020] [Accepted: 10/24/2020] [Indexed: 12/19/2022]
Abstract
Tetrameric transthyretin (TTR) transports thyroid hormones and retinol in plasma and cerebrospinal fluid and performs protective functions under stress conditions. Ageing and mutations result in TTR destabilisation and the formation of the amyloid deposits that dysregulate Ca2+ homeostasis. Our aim was to determine whether Ca2+ affects the structural stability of TTR. We show, using multiple techniques, that Ca2+ does not induce prevalent TTR dissociation and/or oligomerisation. However, in the presence of Ca2+, TTR exhibits altered conformational flexibility and different interactions with the solvent molecules. These structural changes lead to the formation of the sub-populations of non-native TTR conformers and to the destabilisation of the structure of TTR. Moreover, the sub-population of TTR molecules undergoes fragmentation that is augmented by Ca2+. We postulate that Ca2+ constitutes the structural and functional switch between the native and non-native forms of TTR, and therefore tip the balance towards age-dependent pathological calcification.
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43
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Gerig JT. Examination of Interactions of Hexafluoro-2-propanol with Trp-Cage in Hexafluoro-2-propanol-Water by MD Simulations and Intermolecular Nuclear Overhauser Effects. J Phys Chem B 2020; 124:9793-9802. [PMID: 33095591 DOI: 10.1021/acs.jpcb.0c06476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
All-atom molecular dynamic simulations of the peptide Trp-cage in 30% hexafluoro-2-propanol- water (V/V) at 278 K have been carried out with the goal of exploring peptide hydrogen-solvent fluorine nuclear spin cross relaxation. Force field parameters for HFIP reported by Fioroni et al. along with the fluorine parameters of the TFE5 model reported by this lab were used. Water was represented by the TIP5P-Ew model. Peptide modeling used the AMBER99SB-ILDN force field. Translational diffusion coefficients of solution components at 278 K were predicted to within 35% of experimental values using these parameter sets. The simulations indicate that the solvent mixture is not homogeneous, with HFIP molecules clustered into aggregates as large as 53 fluoroalcohol molecules. The solvent environment of surface atoms of Trp-cage fluctuates between being HFIP-rich and more water-rich about every 10 ns. In accord with previous studies by other groups, the average concentration of HFIP near the surface of the peptide is significantly enhanced over the concentration of HFIP in the bulk solvent. In the simulations, ∼7% of the initial contacts between HFIP molecules and Trp-cage develop into peptide-fluoroalcohol interactions that persist for times as long as 8 ns. Most of the available experimental nuclear spin cross-relaxation rates (ΣHF) for hydrogens of the Trp-cage in 30% HFIP-water are reproduced from the MD trajectories to within uncertainties of the experimental data and the simulations. However, a few calculated ΣHF values for hydrogens of the Trp-cage do not agree with experiment. These tend to be situations where long-lived peptide-HFIP interactions are predicted. The disagreements between observed and calculated ΣHF in these instances signal defects in the modeling parameters and procedures that are presently unrecognized.
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Affiliation(s)
- J T Gerig
- Department of Chemistry & Biochemistry University of California, Santa Barbara Santa Barbara, California 93106, United States
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44
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Belousov R, Qaisrani MN, Hassanali A, Roldán É. First-passage fingerprints of water diffusion near glutamine surfaces. SOFT MATTER 2020; 16:9202-9216. [PMID: 32510065 DOI: 10.1039/d0sm00541j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The extent to which biological interfaces affect the dynamics of water plays a key role in the exchange of matter and chemical interactions that are essential for life. The density and the mobility of water molecules depend on their proximity to biological interfaces and can play an important role in processes such as protein folding and aggregation. In this work, we study the dynamics of water near glutamine surfaces-a system of interest in studies of neurodegenerative diseases. Combining molecular-dynamics simulations and stochastic modelling, we study how the mean first-passage time and related statistics of water molecules escaping subnanometer-sized regions vary from the interface to the bulk. Our analysis reveals a dynamical complexity that reflects underlying chemical and geometrical properties of the glutamine surfaces. From the first-passage time statistics of water molecules, we infer their space-dependent diffusion coefficient in directions normal to the surfaces. Interestingly, our results suggest that the mobility of water varies over a longer length scale than the chemical potential associated with the water-protein interactions. The synergy of molecular dynamics and first-passage techniques opens the possibility for extracting space-dependent diffusion coefficients in more complex, inhomogeneous environments that are commonplace in living matter.
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Affiliation(s)
- Roman Belousov
- ICTP - The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy.
| | - Muhammad Nawaz Qaisrani
- ICTP - The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy. and SISSA - International School for Advanced Studies, Via Bonomea 265, 34136 Trieste, Italy
| | - Ali Hassanali
- ICTP - The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy.
| | - Édgar Roldán
- ICTP - The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy.
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45
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Tian R, Hu G, Ou X, Luo M, Li J. Dynamic behaviors of interfacial water on the self-assembly monolayer (SAM) heterogeneous surface. J Chem Phys 2020; 153:124705. [PMID: 33003729 DOI: 10.1063/5.0019135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dynamic behaviors of water molecules near the surface with mixed hydrophobic and hydrophilic areas are studied by molecular dynamics simulation. More specifically, the diffusion coefficient and hydrogen bond lifetime of interfacial water on the self-assembly monolayer composed of hydrophobic and hydrophilic groups and their dependence on the mixing ratio are studied. The diffusion dramatically slows down, and the hydrogen bond lifetime considerably increases when a few hydrophilic groups are added to the hydrophobic surface. When the percentage of hydrophilic groups increases to 25%, the behavior of interfacial water is similar to the case of the pure hydrophilic surface. The sensitivity to the hydrophilic group can be attributed to the fact that the grafted hydrophilic groups can not only retard the directly bound water molecules but also affect indirectly bound water by stabilizing hydrogen bonds among interfacial water molecules.
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Affiliation(s)
- Ranran Tian
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Guorong Hu
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Xinwen Ou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Mengbo Luo
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
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46
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Belyanchikov MA, Savinov M, Bedran ZV, Bednyakov P, Proschek P, Prokleska J, Abalmasov VA, Petzelt J, Zhukova ES, Thomas VG, Dudka A, Zhugayevych A, Prokhorov AS, Anzin VB, Kremer RK, Fischer JKH, Lunkenheimer P, Loidl A, Uykur E, Dressel M, Gorshunov B. Dielectric ordering of water molecules arranged in a dipolar lattice. Nat Commun 2020; 11:3927. [PMID: 32764722 PMCID: PMC7411056 DOI: 10.1038/s41467-020-17832-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 07/17/2020] [Indexed: 11/09/2022] Open
Abstract
Intermolecular hydrogen bonds impede long-range (anti-)ferroelectric order of water. We confine H2O molecules in nanosized cages formed by ions of a dielectric crystal. Arranging them in channels at a distance of ~5 Å with an interchannel separation of ~10 Å prevents the formation of hydrogen networks while electric dipole-dipole interactions remain effective. Here, we present measurements of the temperature-dependent dielectric permittivity, pyrocurrent, electric polarization and specific heat that indicate an order-disorder ferroelectric phase transition at T0 ≈ 3 K in the water dipolar lattice. Ab initio molecular dynamics and classical Monte Carlo simulations reveal that at low temperatures the water molecules form ferroelectric domains in the ab-plane that order antiferroelectrically along the channel direction. This way we achieve the long-standing goal of arranging water molecules in polar order. This is not only of high relevance in various natural systems but might open an avenue towards future applications in biocompatible nanoelectronics. Despite the apparent simplicity of a H2O molecule, the mutual ferroelectric ordering of the molecules is unresolved. Here, the authors realize a macroscopic ferroelectric phase transition in a network of dipole-dipole coupled water molecules located in nanopores of gemstone.
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Affiliation(s)
- M A Belyanchikov
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia.
| | - M Savinov
- Institute of Physics, Czech Academy of Sciences, 18221, Praha 8, Czech Republic
| | - Z V Bedran
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia
| | - P Bednyakov
- Institute of Physics, Czech Academy of Sciences, 18221, Praha 8, Czech Republic
| | - P Proschek
- Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, 12116, Prague 2, Czech Republic
| | - J Prokleska
- Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, 12116, Prague 2, Czech Republic
| | - V A Abalmasov
- Institute of Automation and Electrometry SB RAS, 630090, Novosibirsk, Russia
| | - J Petzelt
- Institute of Physics, Czech Academy of Sciences, 18221, Praha 8, Czech Republic
| | - E S Zhukova
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia
| | - V G Thomas
- Sobolev Institute of Geology and Mineralogy, RAS, 630090, Novosibirsk, Russia.,Novosibirsk State University, 630090, Novosibirsk, Russia
| | - A Dudka
- Shubnikov Institute of Crystallography, "Crystallography and Photonics", Russian Academy of Sciences, 119333, Moscow, Russia
| | - A Zhugayevych
- Skolkovo Institute of Science and Technology, 143026, Moscow, Russia
| | - A S Prokhorov
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia.,Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow, Russia
| | - V B Anzin
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia.,Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow, Russia
| | - R K Kremer
- Max-Planck-Institut für Festkörperforschung, 70569, Stuttgart, Germany
| | - J K H Fischer
- Experimental Physics V, University of Augsburg, 86135, Augsburg, Germany.,T. Kimura Lab, Department of Advanced Materials Science, University of Tokyo, Tokyo, Japan
| | - P Lunkenheimer
- Experimental Physics V, University of Augsburg, 86135, Augsburg, Germany
| | - A Loidl
- Experimental Physics V, University of Augsburg, 86135, Augsburg, Germany
| | - E Uykur
- 1.Physikalisches Institut, Universität Stuttgart, 70569, Stuttgart, Germany
| | - M Dressel
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia.,1.Physikalisches Institut, Universität Stuttgart, 70569, Stuttgart, Germany
| | - B Gorshunov
- Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russia.
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47
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Bruckbauer ST, Minkoff BB, Yu D, Cryns VL, Cox MM, Sussman MR. Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli. Mol Cell Proteomics 2020; 19:1375-1395. [PMID: 32536603 PMCID: PMC8015010 DOI: 10.1074/mcp.ra120.002092] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/10/2020] [Indexed: 12/12/2022] Open
Abstract
Recent work has begun to investigate the role of protein damage in cell death because of ionizing radiation (IR) exposure, but none have been performed on a proteome-wide basis, nor have they utilized MS (MS) to determine chemical identity of the amino acid side chain alteration. Here, we use Escherichia coli to perform the first MS analysis of IR-treated intact cells on a proteome scale. From quintuplicate IR-treated (1000 Gy) and untreated replicates, we successfully quantified 13,262 peptides mapping to 1938 unique proteins. Statistically significant, but low in magnitude (<2-fold), IR-induced changes in peptide abundance were observed in 12% of all peptides detected, although oxidative alterations were rare. Hydroxylation (+15.99 Da) was the most prevalent covalent adduct detected. In parallel with these studies on E. coli, identical experiments with the IR-resistant bacterium, Deinococcus radiodurans, revealed orders of magnitude less effect of IR on the proteome. In E. coli, the most significant target of IR by a wide margin was glyceraldehyde 3'-phosphate dehydrogenase (GAPDH), in which the thiol side chain of the catalytic Cys residue was oxidized to sulfonic acid. The same modification was detected in IR-treated human breast carcinoma cells. Sensitivity of GAPDH to reactive oxygen species (ROS) has been described previously in microbes and here, we present GAPDH as an immediate, primary target of IR-induced oxidation across all domains of life.
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Affiliation(s)
- Steven T Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin B Minkoff
- Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Deyang Yu
- Department of Medicine, University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, USA
| | - Vincent L Cryns
- Department of Medicine, University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.
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48
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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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49
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Abstract
The disaccharide trehalose is accumulated in the cytoplasm of some organisms in response to harsh environmental conditions. Trehalose biosynthesis and accumulation are important for the survival of such organisms by protecting the structure and function of proteins and membranes. Trehalose affects the dynamics of proteins and water molecules in the bulk and the protein hydration shell. Enzyme catalysis and other processes dependent on protein dynamics are affected by the viscosity generated by trehalose, as described by the Kramers’ theory of rate reactions. Enzyme/protein stabilization by trehalose against thermal inactivation/unfolding is also explained by the viscosity mediated hindering of the thermally generated structural dynamics, as described by Kramers’ theory. The analysis of the relationship of viscosity–protein dynamics, and its effects on enzyme/protein function and other processes (thermal inactivation and unfolding/folding), is the focus of the present work regarding the disaccharide trehalose as the viscosity generating solute. Finally, trehalose is widely used (alone or in combination with other compounds) in the stabilization of enzymes in the laboratory and in biotechnological applications; hence, considering the effect of viscosity on catalysis and stability of enzymes may help to improve the results of trehalose in its diverse uses/applications.
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50
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Ivanov YD, Pleshakova TO, Shumov ID, Kozlov AF, Ivanova IA, Valueva AA, Tatur VY, Smelov MV, Ivanova ND, Ziborov VS. AFM Imaging of Protein Aggregation in Studying the Impact of Knotted Electromagnetic Field on A Peroxidase. Sci Rep 2020; 10:9022. [PMID: 32488177 PMCID: PMC7265551 DOI: 10.1038/s41598-020-65888-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/12/2020] [Indexed: 11/09/2022] Open
Abstract
The phenomenon of knotted electromagnetic field (KEMF) is now actively studied, as such fields are characterized by a nontrivial topology. The research in this field is mainly aimed at technical applications - for instance, the development of efficient communication systems. Until present, however, the influence of KEMF on biological objects (including enzyme systems) was not considered. Herein, we have studied the influence of KEMF on the aggregation and enzymatic activity of a protein with the example of horseradish peroxidase (HRP). The test HRP solution was irradiated in KEMF (the radiation power density was 10-12 W/cm2 at 2.3 GHz frequency) for 40 min. After the irradiation, the aggregation of HRP was examined by atomic force microscopy (AFM) at the single-molecule level. The enzymatic activity was monitored by conventional spectrophotometry. It has been demonstrated that an increased aggregation of HRP, adsorbed on the AFM substrate surface, was observed after irradiation of the protein sample in KEMF with low (10-12 W/cm2) radiation power density; at the same time, the enzymatic activity remained unchanged. The results obtained herein can be used in the development of models describing the interaction of enzymes with electromagnetic field. The obtained data can also be of importance considering possible pathological factors that can take place upon the influence of KEMF on biological objects- for instance, changes in hemodynamics due to increased protein aggregation are possible; the functionality of protein complexes can also be affected by aggregation of their protein subunits. These effects should also be taken into account in the development of novel highly sensitive systems for human serological diagnostics of breast cancer, prostate cancer, brain cancer and other oncological pathologies, and for diagnostics of diseases in animals, and crops.
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Affiliation(s)
- Yuri D Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia.
| | - Tatyana O Pleshakova
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Ivan D Shumov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Andrey F Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Irina A Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Anastasia A Valueva
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Vadim Yu Tatur
- Foundation of Perspective Technologies and Novations, Moscow, 115682, Russia
| | - Mikhail V Smelov
- Foundation of Perspective Technologies and Novations, Moscow, 115682, Russia
| | - Nina D Ivanova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, 109472, Russia
| | - Vadim S Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia.,Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow, 125412, Russia
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