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Polita AR, Bagdonaitė RT, Shivabalan AP, Valinčius G. Influence of Simvastatin and Pravastatin on the Biophysical Properties of Model Lipid Bilayers and Plasma Membranes of Live Cells. ACS Biomater Sci Eng 2024. [PMID: 39180473 DOI: 10.1021/acsbiomaterials.4c00911] [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: 08/26/2024]
Abstract
Statins are among the most widely used drugs for the inhibition of cholesterol biosynthesis, prevention of cardiovascular diseases, and treatment of hypercholesterolemia. Additionally, statins also exhibit cholesterol-independent benefits in various diseases, including neuroprotective properties in Alzheimer's disease, anti-inflammatory effects in coronary artery disease, and antiproliferative activities in cancer, which likely result from the statins' interaction and alteration of lipid bilayers. However, the membrane-modulatory effects of statins and the mechanisms by which statins alter lipid bilayers remain poorly understood. In this work, we explore the membrane-modulating effects of statins on model lipid bilayers and live cells. Through the use of fluorescence lifetime imaging microscopy (FLIM) combined with viscosity-sensitive environmental probes, we demonstrate that hydrophobic, but not hydrophilic, statins are capable of changing the microviscosity and lipid order in model and live cell membranes. Furthermore, we show that hydrophobic simvastatin is capable of forming nanoscale cholesterol-rich domains and homogenizing the cholesterol concentrations in lipid bilayers. Our results provide a mechanistic framework for understanding the bimodal effects of simvastatin on the lipid order and the lateral organization of cholesterol in lipid bilayers. Finally, we demonstrate that simvastatin temporarily decreases the microviscosity of live cell plasma membranes, making them more permeable and increasing the level of intracellular chemotherapeutic drug accumulation.
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Affiliation(s)
- Artu Ras Polita
- Department of Biospectroscopy and bioelectrochemistry, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Ru Ta Bagdonaitė
- Department of Biospectroscopy and bioelectrochemistry, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Arun Prabha Shivabalan
- Department of Biospectroscopy and bioelectrochemistry, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
| | - Gintaras Valinčius
- Department of Biospectroscopy and bioelectrochemistry, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius LT-10257, Lithuania
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2
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Siar EH, Abellanas-Perez P, Rocha-Martin J, Fernandez-Lafuente R. Support Enzyme Loading Influences the Effect of Aldehyde Dextran Modification on the Specificity of Immobilized Ficin for Large Proteins. Molecules 2024; 29:3674. [PMID: 39125078 PMCID: PMC11314007 DOI: 10.3390/molecules29153674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/29/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
It has been reported that the modification of immobilized glyoxyl-ficin with aldehyde dextran can promote steric hindrances that greatly reduce the activity of the immobilized protease against hemoglobin, while the protease still maintained a reasonable level of activity against casein. In this paper, we studied if this effect may be different depending on the amount of ficin loaded on the support. For this purpose, both the moderately loaded and the overloaded glyoxyl-ficin biocatalysts were prepared and modified with aldehyde dextran. While the moderately loaded biocatalyst had a significantly reduced activity, mainly against hemoglobin, the activity of the overloaded biocatalyst was almost maintained. This suggests that aldehyde dextran was able to modify areas of the moderately loaded enzyme that were not available when the enzyme was overloaded. This modification promoted a significant increase in biocatalyst stability for both biocatalysts, but the stability was higher for the overloaded biocatalyst (perhaps due to a combination of inter- and intramolecular crosslinking).
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Affiliation(s)
- El Hocine Siar
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain; (E.H.S.); (P.A.-P.)
- Agri-Food Engineering Laboratory (GENIAAL), Institute of Food, Nutrition and Agri-Food Technologies (INATAA), University of Brothers Mentouri Constantine 1, Constantine 25017, Algeria
| | - Pedro Abellanas-Perez
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC, 28049 Madrid, Spain; (E.H.S.); (P.A.-P.)
| | - Javier Rocha-Martin
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University of Madrid, José Antonio Novais 12, 28040 Madrid, Spain
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3
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Becker M, Loche P, Rezaei M, Wolde-Kidan A, Uematsu Y, Netz RR, Bonthuis DJ. Multiscale Modeling of Aqueous Electric Double Layers. Chem Rev 2024; 124:1-26. [PMID: 38118062 PMCID: PMC10785765 DOI: 10.1021/acs.chemrev.3c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 11/17/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023]
Abstract
From the stability of colloidal suspensions to the charging of electrodes, electric double layers play a pivotal role in aqueous systems. The interactions between interfaces, water molecules, ions and other solutes making up the electrical double layer span length scales from Ångströms to micrometers and are notoriously complex. Therefore, explaining experimental observations in terms of the double layer's molecular structure has been a long-standing challenge in physical chemistry, yet recent advances in simulations techniques and computational power have led to tremendous progress. In particular, the past decades have seen the development of a multiscale theoretical framework based on the combination of quantum density functional theory, force-field based simulations and continuum theory. In this Review, we discuss these theoretical developments and make quantitative comparisons to experimental results from, among other techniques, sum-frequency generation, atomic-force microscopy, and electrokinetics. Starting from the vapor/water interface, we treat a range of qualitatively different types of surfaces, varying from soft to solid, from hydrophilic to hydrophobic, and from charged to uncharged.
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Affiliation(s)
| | - Philip Loche
- Fachbereich
Physik, Freie Universität Berlin, 14195 Berlin, Germany
- Laboratory
of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Majid Rezaei
- Fachbereich
Physik, Freie Universität Berlin, 14195 Berlin, Germany
- Institute
of Theoretical Chemistry, Ulm University, 89081 Ulm, Germany
| | | | - Yuki Uematsu
- Department
of Physics and Information Technology, Kyushu
Institute of Technology, 820-8502 Iizuka, Japan
- PRESTO,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Roland R. Netz
- Fachbereich
Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Douwe Jan Bonthuis
- Institute
of Theoretical and Computational Physics, Graz University of Technology, 8010 Graz, Austria
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4
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Jana PK, Bačová P, Schneider L, Kobayashi H, Hollborn KU, Polińska P, Burkhart C, Harmandaris VA, Müller M. Wall-Spring Thermostat: A Novel Approach for Controlling the Dynamics of Soft Coarse-Grained Polymer Fluids at Surfaces. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pritam Kumar Jana
- Institute for Theoretical Physics, Georg-August University, Friedrich-Hund-Platz 1, 37977 Göttingen, Germany
| | - Petra Bačová
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology─Hellas, Heraklion GR-71110, Greece
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias, IMEYMAT, Campus Universitario Río San Pedro s/n, Puerto Real, Cádiz 11510, Spain
| | - Ludwig Schneider
- Institute for Theoretical Physics, Georg-August University, Friedrich-Hund-Platz 1, 37977 Göttingen, Germany
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Hideki Kobayashi
- Institute for Theoretical Physics, Georg-August University, Friedrich-Hund-Platz 1, 37977 Göttingen, Germany
| | - Kai-Uwe Hollborn
- Institute for Theoretical Physics, Georg-August University, Friedrich-Hund-Platz 1, 37977 Göttingen, Germany
| | | | - Craig Burkhart
- Goodyear Research, The Goodyear Tire and Rubber Company, 142 Goodyear Boulevard, Akron, Ohio 44305, United States
| | - Vagelis A. Harmandaris
- Institute of Applied and Computational Mathematics, Foundation for Research and Technology─Hellas, Heraklion GR-71110, Greece
- Department of Mathematics and Applied Mathematics, University of Crete, Heraklion GR-71110, Greece
- Computation-based Science and Technology Research Center, The Cyprus Institute, Nicosia 2121, Cyprus
| | - Marcus Müller
- Institute for Theoretical Physics, Georg-August University, Friedrich-Hund-Platz 1, 37977 Göttingen, Germany
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5
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Hossain MI, Blanchard GJ. The effect of dilution on induced free charge density gradients in room temperature ionic liquids. Phys Chem Chem Phys 2022; 24:3844-3853. [PMID: 35088776 DOI: 10.1039/d1cp05027c] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on changes in the magnitude and length scale of the induced free charge density gradient, ρf, in three imidazolium room temperature ionic liquids (RTILs) with dilution by methanol and acetonitrile. Using depth- and time-resolved fluorescence measurements of cresyl violet rotational diffusion, we find that ρf persists in RTILs to varying degrees depending on RTIL and diluent identity, and in all cases the functional form of ρf is not a smooth monotonic diminution in either magnitude or persistence length with increasing diluent, but a stepwise collapse. This finding is consistent with changes in the bulk RTIL as a function of dilution seen using rotational diffusion measurements that show the rotating entity in bulk RTILs exhibits a larger effective hydrodynamic volume than would be expected based on bulk viscosity data for the diluted RTILs. This excess hydrodynamic volume can be understood in the context of aggregation of RTIL ion pairs in the diluted RTIL system. The size of the aggregates is seen to depend on RTIL identity and diluent, and in all cases aggregate size increases with increasing dilution. This finding is consistent with the ρf dependence on dilution data. The collapse of ρf is seen to correlate with the onset of RTIL ion pair dimer formation, a condition that may facilitate dissociated RTIL ion mobility in the binary system.
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Affiliation(s)
- Md Iqbal Hossain
- Michigan State University, Department of Chemistry, East Lansing, MI 48824, USA.
| | - G J Blanchard
- Michigan State University, Department of Chemistry, East Lansing, MI 48824, USA.
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6
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Stabilization and operational selectivity alteration of Lipozyme 435 by its coating with polyethyleneimine: Comparison of the biocatalyst performance in the synthesis of xylose fatty esters. Int J Biol Macromol 2021; 192:665-674. [PMID: 34656534 DOI: 10.1016/j.ijbiomac.2021.10.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/09/2021] [Accepted: 10/08/2021] [Indexed: 01/13/2023]
Abstract
Differently modified Lipozyme 435 (L435) (immobilized lipase B from Candida antarctica) preparations were used as biocatalysts in the esterification reaction to synthesize sugar fatty acid esters (SFAEs) from xylose (acyl acceptor) and lauric/palmitic acids (acyl donors) in methyl ethyl ketone (MEK) solvent. The L435 treatment with polyethyleneimine (PEI) (2; 25; and 750 KDa) prevented the enzyme leakage in the crude sugar ester reaction product. The 2 KDa PEI coating of this enzyme preparation produced the highest enzyme stability in MEK, buffer solutions (pHs 5 and 7), and methanol aqueous phosphate buffer at pH 7. Using an excess of the acyl donor (1:5 xylose: fatty acid molar ratio), high xylose conversions (70-84%) were obtained after 24 h-reaction using both, non-modified and PEI (2 KDa) coated L435, but the PEI treated biocatalyst afforded a higher xylose modification degree. After 5 reuse cycles with the L435 coated with PEI 2 KDa, the xylose conversions only decreased 10%, while with the non-treated biocatalyst they decreased by 37%. The formation of SFAEs was confirmed by mass spectrometry, which showed the presence of xylose mono-, di-, and triesters. They exhibited emulsion capacities close to that of a commercial sucrose monolaurate.
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7
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Fuentes-Lemus E, Reyes JS, Gamon LF, López-Alarcón C, Davies MJ. Effect of macromolecular crowding on protein oxidation: Consequences on the rate, extent and oxidation pathways. Redox Biol 2021; 48:102202. [PMID: 34856437 PMCID: PMC8640551 DOI: 10.1016/j.redox.2021.102202] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/02/2022] Open
Abstract
Biological systems are heterogeneous and crowded environments. Such packed milieus are expected to modulate reactions both inside and outside the cell, including protein oxidation. In this work, we explored the effect of macromolecular crowding on the rate and extent of oxidation of Trp and Tyr, in free amino acids, peptides and proteins. These species were chosen as they are readily oxidized and contribute to damage propagation. Dextran was employed as an inert crowding agent, as this polymer decreases the fraction of volume available to other (macro)molecules. Kinetic analysis demonstrated that dextran enhanced the rate of oxidation of free Trp, and peptide Trp, elicited by AAPH-derived peroxyl radicals. For free Trp, the rates of oxidation were 15.0 ± 2.1 and 30.5 ± 3.4 μM min-1 without and with dextran (60 mg mL-1) respectively. Significant increases were also detected for peptide-incorporated Trp. Dextran increased the extent of Trp consumption (up to 2-fold) and induced short chain reactions. In contrast, Tyr oxidation was not affected by the presence of dextran. Studies on proteins, using SDS-PAGE and LC-MS, indicated that oxidation was also affected by crowding, with enhanced amino acid loss (45% for casein), chain reactions and altered extents of oligomer formation. The overall effects of dextran-mediated crowding were however dependent on the protein structure. Overall, these data indicate that molecular crowding, as commonly encountered in biological systems affect the rates, and extents of oxidation, and particularly of Trp residues, illustrating the importance of appropriate choice of in vitro systems to study biological oxidations.
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Affiliation(s)
- Eduardo Fuentes-Lemus
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark.
| | - Juan Sebastián Reyes
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luke F Gamon
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark
| | - Camilo López-Alarcón
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, 2200, Denmark.
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8
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Rodrigues RC, Berenguer-Murcia Á, Carballares D, Morellon-Sterling R, Fernandez-Lafuente R. Stabilization of enzymes via immobilization: Multipoint covalent attachment and other stabilization strategies. Biotechnol Adv 2021; 52:107821. [PMID: 34455028 DOI: 10.1016/j.biotechadv.2021.107821] [Citation(s) in RCA: 207] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 08/21/2021] [Indexed: 12/22/2022]
Abstract
The use of enzymes in industrial processes requires the improvement of their features in many instances. Enzyme immobilization, a requirement to facilitate the recovery and reuse of these water-soluble catalysts, is one of the tools that researchers may utilize to improve many of their properties. This review is focused on how enzyme immobilization may improve enzyme stability. Starting from the stabilization effects that an enzyme may experience by the mere fact of being inside a solid particle, we detail other possibilities to stabilize enzymes: generation of favorable enzyme environments, prevention of enzyme subunit dissociation in multimeric enzymes, generation of more stable enzyme conformations, or enzyme rigidification via multipoint covalent attachment. In this last point, we will discuss the features of an "ideal" immobilization protocol to maximize the intensity of the enzyme-support interactions. The most interesting active groups in the support (glutaraldehyde, epoxide, glyoxyl and vinyl sulfone) will be also presented, discussing their main properties and uses. Some instances in which the number of enzyme-support bonds is not directly related to a higher stabilization will be also presented. Finally, the possibility of coupling site-directed mutagenesis or chemical modification to get a more intense multipoint covalent immobilization will be discussed.
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Affiliation(s)
- Rafael C Rodrigues
- Biocatalysis and Enzyme Technology Lab, Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500, P.O. Box 15090, Porto Alegre, RS, Brazil
| | | | - Diego Carballares
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC Cantoblanco, Madrid, Spain
| | | | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Campus UAM-CSIC Cantoblanco, Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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9
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Enzyme co-immobilization: Always the biocatalyst designers' choice…or not? Biotechnol Adv 2021; 51:107584. [DOI: 10.1016/j.biotechadv.2020.107584] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 01/08/2023]
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10
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Liu H, Xiang S, Zhu H, Li L. The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation. Molecules 2021; 26:molecules26175403. [PMID: 34500836 PMCID: PMC8434405 DOI: 10.3390/molecules26175403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/01/2022] Open
Abstract
The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.
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Affiliation(s)
- Hangxin Liu
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
| | - Shuqing Xiang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
| | - Haomiao Zhu
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
- Correspondence: (H.Z.); (L.L.)
| | - Li Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
- Correspondence: (H.Z.); (L.L.)
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11
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Mutual diffusion of proteins in cold concentration gradients measured by holographic interferometry. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2021.116478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Lan Q, Zhang Z, Xu F, Wei M, Wang Y. Nanomeshes with Sub-10 nm Pores by Glycerol-Triggered 2D Assembly in Liquid Phases for Fast and Selective Membranes. NANO LETTERS 2021; 21:3302-3309. [PMID: 33792318 DOI: 10.1021/acs.nanolett.1c00826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nanomeshes having ultrathin thicknesses and penetrating nanopores promise fast diffusion and precise selectivity and are highly desired in diffusion-involved processes such as separation. Herein, we report a liquid-phase two-dimensional (2D) assembly strategy to synthesize phenolic and carbonaceous nanomeshes with sub-10 nm pores and thicknesses. The synthesis is enabled simply by introducing glycerol in the thermopolymerization of resol/polyether micelles dispersed in ethanol. Experimental and simulation results reveal that glycerol's strong ability to form hydrogen bonds constrain the motion of the micelles, directing them to pack and merge exclusively in the lateral direction. Upon removal of polyether, we obtain phenolic nanomeshes with lateral sizes up to hundreds of micrometers, which can be further converted to carbonaceous nanomeshes. As a proof of concept, we use stacked phenolic and carbonaceous nanomeshes as separation membranes. They show superior permselectivity to nanosized solutes with permeance ∼2-110 times higher than that of other membranes.
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Affiliation(s)
- Qianqian Lan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, People's Republic of China
| | - Zhipeng Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, People's Republic of China
| | - Fang Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, People's Republic of China
| | - Mingjie Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, People's Republic of China
| | - Yong Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, People's Republic of China
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13
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Modulation of the Biocatalytic Properties of a Novel Lipase from Psychrophilic Serratia sp. (USBA-GBX-513) by Different Immobilization Strategies. Molecules 2021; 26:molecules26061574. [PMID: 33809323 PMCID: PMC8001504 DOI: 10.3390/molecules26061574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 01/26/2023] Open
Abstract
In this work, the effect of different immobilization procedures on the properties of a lipase obtained from the extremophilic microorganism Serratia sp. USBA-GBX-513, which was isolated from Paramo soils of Los Nevados National Natural Park (Colombia), is reported. Different Shepharose beads were used: octyl-(OC), octyl-glyoxyl-(OC-GLX), cyanogen bromide (BrCN)-, and Q-Sepharose. The performance of the different immobilized extremophile lipase from Serratia (ESL) was compared with that of the lipase B from Candida antarctica (CALB). In all immobilization tests, hyperactivation of ESL was observed. The highest hyperactivation (10.3) was obtained by immobilization on the OC support. Subsequently, the thermal stability at pH 5, 7, and 9 and the stability in the presence of 50% (v/v) acetonitrile, 50% dioxane, and 50% tetrahydrofuran solvents at pH 7 and 40 °C were evaluated. ESL immobilized on octyl-Sepharose was the most stable biocatalyst at 90 °C and pH 9, while the most stable preparation at pH 5 was ESL immobilized on OC-GLX-Sepharose supports. Finally, in the presence of 50% (v/v) tetrahydrofuran (THF) or dioxane at 40 °C, ESL immobilized on OC-Sepharose was the most stable biocatalyst, while the immobilized preparation of ESL on Q-Sepharose was the most stable one in 40% (v/v) acetonitrile.
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14
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Haridasan N, Sathian SP. Rotational dynamics of proteins in nanochannels: role of solvent's local viscosity. NANOTECHNOLOGY 2021; 32:225102. [PMID: 33621966 DOI: 10.1088/1361-6528/abe906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Viscosity variation of solvent in local regions near a solid surface, be it a biological surface of a protein or an engineered surface of a nanoconfinement, is a direct consequence of intermolecular interactions between the solid body and the solvent. The current coarse-grained molecular dynamics study takes advantage of this phenomenon to investigate the anomaly in a solvated protein's rotational dynamics confined using a representative solid matrix. The concept of persistence time, the characteristic time of structural reordering in liquids, is used to compute the solvent's local viscosity. With an increase in the degree of confinement, the confining matrix significantly influences the solvent molecule's local viscosity present in the protein hydration layer through intermolecular interactions. This effect contributes to the enhanced drag force on protein motion, causing a reduction in the rotational diffusion coefficient. Simulation results suggest that the direct matrix-protein non-bonded interaction is responsible for the occasional jump and discontinuity in orientational motion when the protein is in very tight confinement.
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Affiliation(s)
- Navaneeth Haridasan
- Micro and Nanoscale Transport Lab, Applied Mechanics Department, Indian Institute of Technology Madras, Chennai, India
| | - Sarith P Sathian
- Micro and Nanoscale Transport Lab, Applied Mechanics Department, Indian Institute of Technology Madras, Chennai, India
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15
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Pandey A, Murmu K, Gooh Pattader PS. Non-equilibrium thermal annealing of a polymer blend in bilayer settings for complex micro/nano-patterning. RSC Adv 2021; 11:10183-10193. [PMID: 35423522 PMCID: PMC8695700 DOI: 10.1039/d1ra00017a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 02/26/2021] [Indexed: 01/30/2023] Open
Abstract
Micro phase separation in a thin film of a polymer blend leads to interesting patterns on different substrates. A plethora of studies in this field discussed the effect of the surface energy of the underlying tethered polymer brush or substrate on the final morphology of the polymer blend. The conventional process toward the final morphology is rather slow. Here, aiming fast lithography, we induce the kinetically driven morphological evolution by rapid thermal annealing (RTA) of the polymer blend of polystyrene (PS) and polymethylmethacrylate (PMMA) in bilayer settings at a very high temperature. The underlying film consists of untethered constituent homopolymers or their blend or random-co-polymer (RCP). Apart from the phase inversion of the blend on the PS homopolymer, a rich morphology of the blend on the RCP underlayer is uncovered with systematic investigation of the film using sequential washing with selective solvents. The dissolution characteristics and the thermal stability of the constituent polymers corroborated the observation. Based on the understanding of the morphological evolution, fabrication of a complex shaped micro/nano-pattern with multiple length scales is demonstrated using this blend/RCP system. This study shows a novel methodology for easy fabrication of hierarchical small length scale complex structures.
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Affiliation(s)
- Ankur Pandey
- Department of Chemical Engineering, Indian Institute of Technology Guwahati 781039 India
| | - Kaniska Murmu
- Department of Chemical Engineering, Indian Institute of Technology Guwahati 781039 India
| | - Partho Sarathi Gooh Pattader
- Department of Chemical Engineering, Indian Institute of Technology Guwahati 781039 India
- Center for Nanotechnology, Indian Institute of Technology Guwahati 781039 India
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16
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Monteiro RR, Virgen-Ortiz JJ, Berenguer-Murcia Á, da Rocha TN, dos Santos JC, Alcántara AR, Fernandez-Lafuente R. Biotechnological relevance of the lipase A from Candida antarctica. Catal Today 2021. [DOI: 10.1016/j.cattod.2020.03.026] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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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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18
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Multi-Combilipases: Co-Immobilizing Lipases with Very Different Stabilities Combining Immobilization via Interfacial Activation and Ion Exchange. The Reuse of the Most Stable Co-Immobilized Enzymes after Inactivation of the Least Stable Ones. Catalysts 2020. [DOI: 10.3390/catal10101207] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The lipases A and B from Candida antarctica (CALA and CALB), Thermomyces lanuginosus (TLL) or Rhizomucor miehei (RML), and the commercial and artificial phospholipase Lecitase ultra (LEU) may be co-immobilized on octyl agarose beads. However, LEU and RML became almost fully inactivated under conditions where CALA, CALB and TLL retained full activity. This means that, to have a five components co-immobilized combi-lipase, we should discard 3 fully active and immobilized enzymes when the other two enzymes are inactivated. To solve this situation, CALA, CALB and TLL have been co-immobilized on octyl-vinyl sulfone agarose beads, coated with polyethylenimine (PEI) and the least stable enzymes, RML and LEU have been co-immobilized over these immobilized enzymes. The coating with PEI is even favorable for the activity of the immobilized enzymes. It was checked that RML and LEU could be released from the enzyme-PEI coated biocatalyst, although this also produced some release of the PEI. That way, a protocol was developed to co-immobilize the five enzymes, in a way that the most stable could be reused after the inactivation of the least stable ones. After RML and LEU inactivation, the combi-biocatalysts were incubated in 0.5 M of ammonium sulfate to release the inactivated enzymes, incubated again with PEI and a new RML and LEU batch could be immobilized, maintaining the activity of the three most stable enzymes for at least five cycles of incubation at pH 7.0 and 60 °C for 3 h, incubation on ammonium sulfate, incubation in PEI and co-immobilization of new enzymes. The effect of the order of co-immobilization of the different enzymes on the co-immobilized biocatalyst activity was also investigated using different substrates, finding that when the most active enzyme versus one substrate was immobilized first (nearer to the surface of the particle), the activity was higher than when this enzyme was co-immobilized last (nearer to the particle core).
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19
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Willems K, Ruić D, L R Lucas F, Barman U, Verellen N, Hofkens J, Maglia G, Van Dorpe P. Accurate modeling of a biological nanopore with an extended continuum framework. NANOSCALE 2020; 12:16775-16795. [PMID: 32780087 DOI: 10.1039/d0nr03114c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Despite the broad success of biological nanopores as powerful instruments for the analysis of proteins and nucleic acids at the single-molecule level, a fast simulation methodology to accurately model their nanofluidic properties is currently unavailable. This limits the rational engineering of nanopore traits and makes the unambiguous interpretation of experimental results challenging. Here, we present a continuum approach that can faithfully reproduce the experimentally measured ionic conductance of the biological nanopore Cytolysin A (ClyA) over a wide range of ionic strengths and bias potentials. Our model consists of the extended Poisson-Nernst-Planck and Navier-Stokes (ePNP-NS) equations and a computationally efficient 2D-axisymmetric representation for the geometry and charge distribution of the nanopore. Importantly, the ePNP-NS equations achieve this accuracy by self-consistently considering the finite size of the ions and the influence of both the ionic strength and the nanoscopic scale of the pore on the local properties of the electrolyte. These comprise the mobility and diffusivity of the ions, and the density, viscosity and relative permittivity of the solvent. Crucially, by applying our methodology to ClyA, a biological nanopore used for single-molecule enzymology studies, we could directly quantify several nanofluidic characteristics difficult to determine experimentally. These include the ion selectivity, the ion concentration distributions, the electrostatic potential landscape, the magnitude of the electro-osmotic flow field, and the internal pressure distribution. Hence, this work provides a means to obtain fundamental new insights into the nanofluidic properties of biological nanopores and paves the way towards their rational engineering.
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Affiliation(s)
- Kherim Willems
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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20
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Becaro AA, Mendes AA, Adriano WS, Lopes LA, Vanzolini KL, Fernandez-Lafuente R, Tardioli PW, Cass QB, Giordano RDLC. Immobilization and stabilization of d-hydantoinase from Vigna angularis and its use in the production of N-carbamoyl-d-phenylglycine. Improvement of the reaction yield by allowing chemical racemization of the substrate. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Arana-Peña S, Rios NS, Mendez-Sanchez C, Lokha Y, Gonçalves LR, Fernández-Lafuente R. Use of polyethylenimine to produce immobilized lipase multilayers biocatalysts with very high volumetric activity using octyl-agarose beads: Avoiding enzyme release during multilayer production. Enzyme Microb Technol 2020; 137:109535. [DOI: 10.1016/j.enzmictec.2020.109535] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/15/2020] [Accepted: 02/14/2020] [Indexed: 10/25/2022]
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22
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Glyoxyl-Activated Agarose as Support for Covalently Link Novo-Pro D: Biocatalysts Performance in the Hydrolysis of Casein. Catalysts 2020. [DOI: 10.3390/catal10050466] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This study aimed to evaluate the performance of a commercial protease (Novo-Pro D (NPD)), both in soluble and immobilized forms, in the hydrolysis of proteins (using casein as model protein). Immobilization of the protease NPD on 6% agarose activated with glyoxyl groups for 24 h at 20 °C and pH 10.0 allowed preparing immobilized biocatalyst with around 90% immobilization yield, 92% recovered activity versus small substrate, and a thermal stability 5.3-fold higher than the dialyzed soluble enzyme at 50 °C and pH 8.0. Immobilization times longer than 24 h lead to a decrease in the recovered activity and did not improve the biocatalyst stability. At 50 °C and pH 6.5, the immobilized NPD was around 20-fold more stable than the dialyzed soluble protease. Versus casein, the immobilized NDP presented a 10% level of activity, but it allowed hydrolyzing casein (26 g/L) at 50 °C and pH 6.5 up to a 40% degree of hydrolysis (DH) after 2 h reaction, while under the same conditions, only a 34% DH was achieved with soluble NPD. In addition, the immobilized NPD showed good reusability, maintaining the DH of casein for at least ten 2h-reaction batches.
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23
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Baksi A, Ghorai PK, Biswas R. Dynamic Susceptibility and Structural Heterogeneity of Large Reverse Micellar Water: An Examination of the Core–Shell Model via Probing the Layer-wise Features. J Phys Chem B 2020; 124:2848-2863. [DOI: 10.1021/acs.jpcb.9b11895] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Atanu Baksi
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector-III, Salt Lake, Kolkata 700106, India
| | - Pradip Kr. Ghorai
- Indian Institute of Science Education and Research, Mohanpur, Nadia, Kolkata 741246, India
| | - Ranjit Biswas
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector-III, Salt Lake, Kolkata 700106, India
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24
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25
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Srivastava A, Karmakar S, Debnath A. Quantification of spatio-temporal scales of dynamical heterogeneity of water near lipid membranes above supercooling. SOFT MATTER 2019; 15:9805-9815. [PMID: 31746927 DOI: 10.1039/c9sm01725a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308 K to determine the physical sources of universal slow relaxations of hydration layers and length-scale of the spatially heterogeneous dynamics. Continuously residing interface water (IW) molecules hydrogen bonded to different moieties of lipid heads in the membrane are identified. The non-Gaussian parameters of all classes of IW molecules show a cross-over from cage vibration to translational diffusion. A significant non-Gaussianity is observed for the IW molecules exhibiting large length correlations in translational van Hove functions. Two time-scales for the ballistic motions and hopping transitions are obtained from the self intermediate scattering functions of the IW molecules with an additional long relaxation, which disappears for bulk water. The long relaxation time-scales for the IW molecules obtained from the self intermediate scattering functions are in good accordance with the hydrogen bond relaxation time-scales irrespective of the nature of the chemical confinement and the confinement lifetime. Employing a block analysis approach, the length-scale of dynamical heterogeneities is captured from a transition from non-Gaussianity to Gaussianity in van Hove correlation functions of the IW molecules. The heterogeneity length-scale is comparable to the wave-length of the small and weak undulations of the membrane calculated by Fourier transforms of lipid tilts. This opens up a new avenue towards a possible correlation between heterogeneity length-scale and membrane curvature more significant for rippled membranes. Thus, our analyses provide a measure towards the spatio-temporal scale of dynamical heterogeneity of confined water near membranes.
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Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India.
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26
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Tan S, Pan Y, Wei Q, Jiang Y, Xiong F, Yao X, Cai Z, An Q, Zhou L, Mai L. Polyol Solvation Effect on Tuning the Universal Growth of Binary Metal Oxide Nanodots@Graphene Oxide Heterostructures for Electrochemical Applications. Chemistry 2019; 25:14604-14612. [DOI: 10.1002/chem.201902697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Shuangshuang Tan
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070 Hubei P. R. China
| | - Yexin Pan
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070 Hubei P. R. China
| | - Qiulong Wei
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070 Hubei P. R. China
| | - Yalong Jiang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070 Hubei P. R. China
| | - Fangyu Xiong
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070 Hubei P. R. China
| | - Xuhui Yao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070 Hubei P. R. China
| | - Zhijun Cai
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070 Hubei P. R. China
| | - Qinyou An
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070 Hubei P. R. China
| | - Liang Zhou
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070 Hubei P. R. China
| | - Liqiang Mai
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering Wuhan University of Technology, Wuhan 430070 Hubei P. R. China
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27
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Qaisrani MN, Grisanti L, Gebauer R, Hassanali A. Structural and dynamical heterogeneities at glutamine-water interfaces. Phys Chem Chem Phys 2019; 21:16083-16094. [PMID: 31298261 DOI: 10.1039/c9cp02259g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The behavior of water at the surfaces of solid amino acid crystals has received little attention despite its importance in nucleation processes. In this work, we take a first step to fill this gap by using molecular dynamics simulations to study the structural and dynamical properties of water near the (100), (010) and (001) surfaces of l-glutamine crystals. These highly hydrophilic surfaces serve as excellent model systems for interrogating the behavior of water. Despite having the same molecular composition, water at each surface displays characteristic structural, orientational and dynamical correlations. This behavior is tuned by how the different chemical groups of amino acids make contact with the liquid phase. All three surfaces yield a glassy layer of interfacial water which is reflected in different ways such as the presence of a rotationally arrested layer of water molecules and substantial slow down of the diffusion of water near the interface. By increasing the concentration of molecules in solution, we show that the binding of glutamine molecules to the crystal surface creates a crowded environment involving pockets of trapped water molecules altering the water dynamics in a highly non-trivial manner suggesting that the solvent dynamics may have important implications on crystal nucleation.
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Affiliation(s)
- Muhammad Nawaz Qaisrani
- International School for Advanced Studies, Via Bonomea 265, 34136 Trieste, Italy and The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy.
| | - Luca Grisanti
- Divison of Theoretical Physics - Institut Ruer Bošković (IRB), Bijenička cesta 54, 10000, Zagreb, Croatia.
| | - Ralph Gebauer
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy.
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy.
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28
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Umeda K, Kobayashi K, Minato T, Yamada H. Atomic-Level Viscosity Distribution in the Hydration Layer. PHYSICAL REVIEW LETTERS 2019; 122:116001. [PMID: 30951327 DOI: 10.1103/physrevlett.122.116001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Indexed: 05/24/2023]
Abstract
The viscosity of solvation structures is crucial for the development of energy-efficient biofunctional and electrochemical devices. Elucidating their subnanoscale distributions can cause the formation of a sustainable energy society. Here, we visualize the site-specific three-dimensional damping distribution on a CaCO_{3} surface composed of binary ion species using ultra-low-noise frequency modulation atomic force microscopy. With the support from molecular dynamics simulation, we found a strikingly large damping at the calcium sites, which demonstrates the capability of this methodology to visualize atomic-scale viscosity in the hydration layers. Our finding will expedite the evolutions of various functional devices.
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Affiliation(s)
- Kenichi Umeda
- Department of Electronic Science and Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
- Department of Advanced Material Science, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
- Nano Life Science Institute, Institute for Frontier Science Initiative, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan
| | - Kei Kobayashi
- Department of Electronic Science and Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Taketoshi Minato
- Office of Society-Academia Collaboration for Innovation, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
| | - Hirofumi Yamada
- Department of Electronic Science and Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510, Japan
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29
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Lan K, Liu Y, Zhang W, Liu Y, Elzatahry A, Wang R, Xia Y, Al-Dhayan D, Zheng N, Zhao D. Uniform Ordered Two-Dimensional Mesoporous TiO2 Nanosheets from Hydrothermal-Induced Solvent-Confined Monomicelle Assembly. J Am Chem Soc 2018; 140:4135-4143. [DOI: 10.1021/jacs.8b00909] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kun Lan
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Laboratory of Advanced Materials, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Fudan University, Shanghai, 200433, PR China
| | - Yao Liu
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Laboratory of Advanced Materials, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Fudan University, Shanghai, 200433, PR China
| | - Wei Zhang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Laboratory of Advanced Materials, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Fudan University, Shanghai, 200433, PR China
| | - Yong Liu
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Laboratory of Advanced Materials, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Fudan University, Shanghai, 200433, PR China
| | - Ahmed Elzatahry
- Materials Science and Technology Program, College of Arts and Sciences, Qatar University, PO Box 2713, Doha 2713, Qatar
| | - Ruicong Wang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Laboratory of Advanced Materials, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Fudan University, Shanghai, 200433, PR China
| | - Yongyao Xia
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Laboratory of Advanced Materials, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Fudan University, Shanghai, 200433, PR China
| | - Dhaifallah Al-Dhayan
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nanfeng Zheng
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, PR China
| | - Dongyuan Zhao
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Laboratory of Advanced Materials, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), Fudan University, Shanghai, 200433, PR China
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30
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Consolati T, Bolivar JM, Petrasek Z, Berenguer J, Hidalgo A, Guisán JM, Nidetzky B. Biobased, Internally pH-Sensitive Materials: Immobilized Yellow Fluorescent Protein as an Optical Sensor for Spatiotemporal Mapping of pH Inside Porous Matrices. ACS APPLIED MATERIALS & INTERFACES 2018; 10:6858-6868. [PMID: 29384355 DOI: 10.1021/acsami.7b16639] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The pH is fundamental to biological function and its measurement therefore crucial across all biosciences. Unlike homogenous bulk solution, solids often feature internal pH gradients due to partition effects and confined biochemical reactions. Thus, a full spatiotemporal mapping for pH characterization in solid materials with biological systems embedded in them is essential. In here, therefore, a fully biocompatible methodology for real-time optical sensing of pH within porous materials is presented. A genetically encoded ratiometric pH sensor, the enhanced superfolder yellow fluorescent protein (sYFP), is used to functionalize the internal surface of different materials, including natural and synthetic organic polymers as well as silica frameworks. By using controlled, tailor-made immobilization, sYFP is homogenously distributed within these materials and so enables, via self-referenced imaging analysis, pH measurements in high accuracy and with useful spatiotemporal resolution. Evolution of internal pH is monitored in consequence of a proton-releasing enzymatic reaction, the hydrolysis of penicillin by a penicillin acylase, taking place in solution or confined to the solid surface of the porous matrix. Unlike optochemical pH sensors, which often interfere with biological function, labeling with sYFP enables pH sensing without altering the immobilized enzyme's properties in any of the materials used. Fast response of sYFP to pH change permits evaluation of biochemical kinetics within the solid materials. Thus, pH sensing based on immobilized sYFP represents a broadly applicable technique to the study of biology confined to the internally heterogeneous environment of solid matrices.
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Affiliation(s)
- Tanja Consolati
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz , Petersgasse 12, A-8010 Graz, Austria
| | - Juan M Bolivar
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz , Petersgasse 12, A-8010 Graz, Austria
| | - Zdenek Petrasek
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz , Petersgasse 12, A-8010 Graz, Austria
| | - Jose Berenguer
- Department of Molecular Biology, Universidad Autónoma de Madrid, Center for Molecular Biology 'Severo-Ochoa' (UAM-CSIC) , Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Aurelio Hidalgo
- Department of Molecular Biology, Universidad Autónoma de Madrid, Center for Molecular Biology 'Severo-Ochoa' (UAM-CSIC) , Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Jose M Guisán
- Institute of Catalysis and Petroleum Chemistry (ICP-CSIC) , C/Marie Curie, 2, Cantoblanco, 28049 Madrid, Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz , Petersgasse 12, A-8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology , Petersgasse 14, A-8010 Graz, Austria
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31
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Biswas R, Bagchi B. Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:013001. [PMID: 29205175 DOI: 10.1088/1361-648x/aa9b1d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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33
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Wang Y, Xu J, Wang S, Yang C. Quantitative relationship between fluid inhomogeneities and flow enhancement in nanotubes. NANOSCALE 2017; 9:6777-6782. [PMID: 28489106 DOI: 10.1039/c7nr01464c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Flow enhancement in nanotubes is of great potential to achieve ultra-fast fluidic transport. However, the mechanism of such a fast transport and the reduction as the tube enlarges to bulk scale is still unclear. In this study, we establish a model to quantitatively correlate the flow enhancement and the fluid inhomogeneity to describe the enhanced transport and its evolution with the tube dimension. We found the fluid inhomogeneity at the solid-liquid interface in nanotubes and its independence with tube size by dissipative particle dynamics (DPD) simulation. Based on that, we establish novel theoretical models for the penetration rate in nanotubes for the first time with parameters related to the fluid inhomogeneity which can achieve quantitative prediction of nanoflow enhancement and are valid through all scales.
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Affiliation(s)
- Yuying Wang
- Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
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34
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McDaniel JG, Yethiraj A. Coupling between the Dynamics of Water and Surfactants in Lyotropic Liquid Crystals. J Phys Chem B 2017; 121:5048-5057. [DOI: 10.1021/acs.jpcb.7b02551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jesse G. McDaniel
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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35
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Ding H, Jiang H, Hou Z. Study of dynamic heterogeneity of an active particle system. Phys Rev E 2017; 95:052608. [PMID: 28618538 DOI: 10.1103/physreve.95.052608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Indexed: 06/07/2023]
Abstract
We have studied spatial and temporal dynamic heterogeneity (DH) in a system of hard-sphere particles, subjected to active forces with constant amplitude and random direction determined by rotational diffusion with correlation time τ. We have used a variety of observables to characterize the DH behavior, including the deviation from standard Stokes-Einstein (SE) relation, a non-Gaussian parameter α_{2}(Δt) for the distribution of particle displacement within a certain time interval Δt, a four-point susceptibility χ_{4}(Δt,ΔL) for the correlation in dynamics between any two points in space separated by distance ΔL within some time window Δt, and a vector spatial-temporal correlation function S_{vec}(R,Δt) for vector displacements within time interval Δt of particle pairs originally separated by R. By mapping the particle motion into a continuous-time random walk with constant jump length, we can obtain the average waiting time 〈t_{x}〉∝D_{s}^{-1} and persistence time 〈t_{p}〉∝η, with D_{s} the self-diffusion coefficient and η the shear viscosity, such that the observable λ=〈t_{p}〉/〈t_{x}〉∝D_{s}η can be calculated as a function of the control parameter τ to show how it deviates from its SE value λ_{0}. Interestingly, we find λ/λ_{0} shows a nonmonotonic behavior for large volume fraction φ_{a}, wherein λ/λ_{0} undergoes a minimum at a certain intermediate value of τ, indicating that both small and large particle activity may lead to strong DH. Such a reentrance phenomenon is further demonstrated in terms of the non-Gaussian parameters α_{2}, four-point susceptibility χ_{4}, and vector spatiotemporal correlation functions S_{vec}, respectively. Detail analysis shows that it is the competition between the dual roles of particle activity, namely, activity-induced higher effective temperature and activity-induced clustering, that leads to such nontrivial nonmonotonic behaviors. In addition, we find that DH may also show a maximum level at an intermediate value of φ_{a} if τ is large enough, implying that a more crowded system may be less heterogeneous than a less crowded one for a system with high particle activity.
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Affiliation(s)
- Huai Ding
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huijun Jiang
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhonghuai Hou
- Department of Chemical Physics and Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
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36
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Ricci M, Trewby W, Cafolla C, Voïtchovsky K. Direct observation of the dynamics of single metal ions at the interface with solids in aqueous solutions. Sci Rep 2017; 7:43234. [PMID: 28230209 PMCID: PMC5322364 DOI: 10.1038/srep43234] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 01/23/2017] [Indexed: 01/14/2023] Open
Abstract
The dynamics of ions adsorbed at the surface of immersed charged solids plays a central role in countless natural and industrial processes such as crystal growth, heterogeneous catalysis, electrochemistry, or biological function. Electrokinetic measurements typically distinguish between a so-called Stern layer of ions and water molecules directly adsorbed on to the solid’s surface, and a diffuse layer of ions further away from the surface. Dynamics within the Stern layer remain poorly understood, largely owing to a lack of in-situ atomic-level insights. Here we follow the dynamics of single Rb+ and H3O+ ions at the surface of mica in water using high-resolution atomic force microscopy with 25 ms resolution. Our results suggest that single hydrated Rb+ions reside τ1 = 104 ± 5 ms at a given location, but this is dependent on the hydration state of the surface which evolves on a slower timescale of τ2 = 610 ± 30 ms depending on H3O+ adsorption. Increasing the liquid’s temperature from 5 °C to 65 °C predictably decreases the apparent glassiness of the interfacial water, but no clear effect on the ions’ dynamics was observed, indicating a diffusion-dominated process. These timescales are remarkably slow for individual monovalent ions and could have important implications for interfacial processes in electrolytes.
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Affiliation(s)
- Maria Ricci
- University of Cambridge, Cavendish Laboratory, Cambridge CB3 0HE, UK
| | - William Trewby
- Department of Physics, Durham University, Durham DH1 3LE, UK
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37
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Dhindsa GK, Bhowmik D, Goswami M, O’Neill H, Mamontov E, Sumpter BG, Hong L, Ganesh P, Chu XQ. Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study. J Phys Chem B 2016; 120:10059-10068. [DOI: 10.1021/acs.jpcb.6b07511] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gurpreet K. Dhindsa
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Debsindhu Bhowmik
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Monojoy Goswami
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computer
Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O’Neill
- Biology and
Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eugene Mamontov
- Chemical
and Engineering Materials Division, Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | - Bobby G. Sumpter
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computer
Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Liang Hong
- Institute of Natural Science & Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Panchapakesan Ganesh
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiang-qiang Chu
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
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38
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Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. Biochim Biophys Acta Gen Subj 2016; 1860:1821-35. [PMID: 27241846 DOI: 10.1016/j.bbagen.2016.05.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics. SCOPE OF REVIEW This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties. MAJOR CONCLUSIONS In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration. GENERAL SIGNIFICANCE An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.
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39
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Bellissent-Funel MC, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia AE. Water Determines the Structure and Dynamics of Proteins. Chem Rev 2016; 116:7673-97. [PMID: 27186992 DOI: 10.1021/acs.chemrev.5b00664] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.
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Affiliation(s)
| | - Ali Hassanali
- International Center for Theoretical Physics, Condensed Matter and Statistical Physics 34151 Trieste, Italy
| | - Martina Havenith
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Richard Henchman
- Manchester Institute of Biotechnology The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Pohl
- Johannes Kepler University , Gruberstrasse, 40 4020 Linz, Austria
| | - Fabio Sterpone
- Institut de Biologie Physico-Chimique Laboratoire de Biochimie Théorique 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - David van der Spoel
- Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University , 751 24 Uppsala, Sweden
| | - Yao Xu
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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40
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Chemmi H, Petit D, Levitz P, Denoyel R, Galarneau A, Korb JP. Noninvasive Experimental Evidence of the Linear Pore Size Dependence of Water Diffusion in Nanoconfinement. J Phys Chem Lett 2016; 7:393-398. [PMID: 26751162 DOI: 10.1021/acs.jpclett.5b02718] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We show that nuclear magnetic relaxation experiments at variable magnetic fields (NMRD) provide noninvasive means for probing the spatial dependence of liquid diffusion close to solid interfaces. These experiments performed on samples of cylindrical and spherical nanopore geometries demonstrate that the average diffusion coefficient parallel to the interface is proportional to the pore radii in different dynamics regimes. A master curve method allows extraction of gradients of diffusion coefficients in proximity of the pore surfaces, indicative of the efficiency of coupling between liquid layers. Due to their selectivity in frequency, NMRD experiments are able to differentiate the different water dynamical events induced by heterogeneous surfaces or composed dynamical processes. This analysis relevant in physical and biological confinements highlights the interplay between the molecular and continuous description of fluid dynamics near interfaces.
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Affiliation(s)
- Houria Chemmi
- Physique de la Matière Condensée, Ecole Polytechnique-CNRS , Palaiseau 91128, France
| | - Dominique Petit
- Physique de la Matière Condensée, Ecole Polytechnique-CNRS , Palaiseau 91128, France
| | - Pierre Levitz
- Physicochimie des Electrolytes et Nanosystèmes Interfaciaux, CNRS-UMR 8234, Université Pierre et Marie Curie , 4 place Jussieu, 72522 Paris Cedex 5, France
| | - Renaud Denoyel
- MADIREL, Aix-Marseille Université, CNRS-UMR 7246 , Centre de St Jérôme, 13397 Marseille Cedex 20, France
| | - Anne Galarneau
- Institut Charles Gerhardt Montpellier, UMR 5253 CNRS-UM-ENSCM, ENSCM , 8 rue de l'Ecole Normale, 34296, Montpellier Cedex 05, France
| | - Jean-Pierre Korb
- Physique de la Matière Condensée, Ecole Polytechnique-CNRS , Palaiseau 91128, France
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41
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Sterpone F, Derreumaux P, Melchionna S. Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. J Chem Theory Comput 2015; 11:1843-53. [PMID: 26574390 PMCID: PMC5242371 DOI: 10.1021/ct501015h] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A novel simulation framework that integrates the OPEP coarse-grained (CG) model for proteins with the Lattice Boltzmann (LB) methodology to account for the fluid solvent at mesoscale level is presented. OPEP is a very efficient, water-free and electrostatic-free force field that reproduces at quasi-atomistic detail processes like peptide folding, structural rearrangements, and aggregation dynamics. The LB method is based on the kinetic description of the solvent in order to solve the fluid mechanics under a wide range of conditions, with the further advantage of being highly scalable on parallel architectures. The capabilities of the approach are presented, and it is shown that the strategy is effective in exploring the role of hydrodynamics on protein relaxation and peptide aggregation. The end result is a strategy for modeling systems of thousands of proteins, such as in the case of dense protein suspensions. The future perspectives of the multiscale approach are also discussed.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
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42
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Provasi D, Boz MB, Johnston JM, Filizola M. Preferred supramolecular organization and dimer interfaces of opioid receptors from simulated self-association. PLoS Comput Biol 2015; 11:e1004148. [PMID: 25822938 PMCID: PMC4379167 DOI: 10.1371/journal.pcbi.1004148] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/22/2015] [Indexed: 11/18/2022] Open
Abstract
Substantial evidence in support of the formation of opioid receptor (OR) di-/oligomers suggests previously unknown mechanisms used by these proteins to exert their biological functions. In an attempt to guide experimental assessment of the identity of the minimal signaling unit for ORs, we conducted extensive coarse-grained (CG) molecular dynamics (MD) simulations of different combinations of the three major OR subtypes, i.e., μ-OR, δ-OR, and κ-OR, in an explicit lipid bilayer. Specifically, we ran multiple, independent MD simulations of each homomeric μ-OR/μ-OR, δ-OR/δ-OR, and κ-OR/κ-OR complex, as well as two of the most studied heteromeric complexes, i.e., δ-OR/μ-OR and δ-OR/κ-OR, to derive the preferred supramolecular organization and dimer interfaces of ORs in a cell membrane model. These simulations yielded over 250 microseconds of accumulated data, which correspond to approximately 1 millisecond of effective simulated dynamics according to established scaling factors of the CG model we employed. Analysis of these data indicates similar preferred supramolecular organization and dimer interfaces of ORs across the different receptor subtypes, but also important differences in the kinetics of receptor association at specific dimer interfaces. We also investigated the kinetic properties of interfacial lipids, and explored their possible role in modulating the rate of receptor association and in promoting the formation of filiform aggregates, thus supporting a distinctive role of the membrane in OR oligomerization and, possibly, signaling.
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Affiliation(s)
- Davide Provasi
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Mustafa Burak Boz
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jennifer M. Johnston
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Marta Filizola
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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43
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Ghosh R, Samanta T, Banaerjee S, Biswas R, Bagchi B. Spatio-temporal correlations in aqueous systems: computational studies of static and dynamic heterogeneity by 2D-IR spectroscopy. Faraday Discuss 2015; 177:313-28. [PMID: 25692942 DOI: 10.1039/c4fd00201f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Local heterogeneity is ubiquitous in natural aqueous systems. It can be caused locally by external biomolecular subsystems like proteins, DNA, micelles and reverse micelles, nanoscopic materials etc., but can also be intrinsic to the thermodynamic nature of the aqueous solution itself (like binary mixtures or at the gas-liquid interface). The altered dynamics of water in the presence of such diverse surfaces has attracted considerable attention in recent years. As these interfaces are quite narrow, only a few molecular layers thick, they are hard to study by conventional methods. The recent development of two dimensional infra-red (2D-IR) spectroscopy allows us to estimate length and time scales of such dynamics fairly accurately. In this work, we present a series of interesting studies employing two dimensional infra-red spectroscopy (2D-IR) to investigate (i) the heterogeneous dynamics of water inside reverse micelles of varying sizes, (ii) supercritical water near the Widom line that is known to exhibit pronounced density fluctuations and also study (iii) the collective and local polarization fluctuation of water molecules in the presence of several different proteins. The spatio-temporal correlation of confined water molecules inside reverse micelles of varying sizes is well captured through the spectral diffusion of corresponding 2D-IR spectra. In the case of supercritical water also, we observe a strong signature of dynamic heterogeneity from the elongated nature of the 2D-IR spectra. In this case the relaxation is ultrafast. We find remarkable agreement between the different tools employed to study the relaxation of density heterogeneity. For aqueous protein solutions, we find that the calculated dielectric constant of the respective systems unanimously shows a noticeable increment compared to that of neat water. However, the 'effective' dielectric constant for successive layers shows significant variation, with the layer adjacent to the protein having a much lower value. Relaxation is also slowest at the surface. We find that the dielectric constant achieves the bulk value at distances more than 3 nm from the surface of the protein.
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Affiliation(s)
- Rikhia Ghosh
- SSCU, Indian Institute of Science, Bangalore 560012, India.
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44
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Zhang J, Zhong J, Li W, Wang M, Liu B, Li Z, Yan Y. Molecular insight into the dynamical adsorption behavior of nanoscale water droplets on a heterogeneous surface. RSC Adv 2015. [DOI: 10.1039/c5ra09296e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A heterogeneous surface is constructed by adding one hydrophilic patch at the center of a hydrophobic surface, and the dynamical adsorption process of nanoscale water droplets is investigated adopting molecular dynamics simulations.
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Affiliation(s)
- Jun Zhang
- College of Science
- China University of Petroleum
- 266580 Qingdao
- People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong
| | - Jie Zhong
- College of Science
- China University of Petroleum
- 266580 Qingdao
- People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong
| | - Wen Li
- College of Science
- China University of Petroleum
- 266580 Qingdao
- People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong
| | - Muhan Wang
- College of Science
- China University of Petroleum
- 266580 Qingdao
- People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong
| | - Bing Liu
- College of Science
- China University of Petroleum
- 266580 Qingdao
- People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong
| | - Zhen Li
- College of Science
- China University of Petroleum
- 266580 Qingdao
- People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong
| | - Youguo Yan
- College of Science
- China University of Petroleum
- 266580 Qingdao
- People’s Republic of China
- Key Laboratory of New Energy Physics & Materials Science in Universities of Shandong
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45
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Cao J, Liu S, Xiong J, Chen Y, Zhang Z. Stimuli responsive chiral liquid crystal phases of phenylboronic acid functionalized rodlike viruses and their interaction with biologically important diols. Chem Commun (Camb) 2014; 50:10402-5. [DOI: 10.1039/c4cc04639k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
M13 viruses decorated with phenylboronic acid moieties form pH-responsive chiral LC phases that are regulated by binding with biological diols.
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Affiliation(s)
- Jun Cao
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- and Institute of Polymer Chemistry
- Nankai University
- Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Shuaiyu Liu
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- and Institute of Polymer Chemistry
- Nankai University
- Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Jie Xiong
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- and Institute of Polymer Chemistry
- Nankai University
- Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Yingjun Chen
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- and Institute of Polymer Chemistry
- Nankai University
- Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| | - Zhenkun Zhang
- Key Laboratory of Functional Polymer Materials of Ministry of Education
- and Institute of Polymer Chemistry
- Nankai University
- Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
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