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Hervø-Hansen S, Lin D, Kasahara K, Matubayasi N. Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects. Chem Sci 2024; 15:477-489. [PMID: 38179544 PMCID: PMC10763565 DOI: 10.1039/d3sc04617f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/20/2023] [Indexed: 01/06/2024] Open
Abstract
The roles of cations and anions are different in the perturbation on solvation, and thus, the analyses of the separated contributions from cations and anions are useful to establish molecular pictures of ion-specific effects. In this work, we investigate the effects of cations, anions, and water separately in the solvation of n-alcohols and n-alkanes by free-energy decomposition. By utilising energy-representation theory of solvation, we address the contributions arising from the direct solute-solvent interactions and the excluded-volume effects. It is found that the change in solvation of n-alcohols and n-alkanes upon addition of salt depends primarily on the anion species. The direct interaction between the anion and solute is in agreement with the Setschenow coefficient in terms of the ranking of salting-in and salting-out for n-alkanes, which corresponds to the extent of accumulation of the anion on the solute surface. For each of the n-alcohols and n-alkanes examined, the excluded-volume component in the Setschenow coefficient is well correlated to the (total) Setschenow coefficient when the salt effects are concerned. The ranking of the excluded-volume component in the variation of the salt species is parallel to the water contribution, which is correlated further to the change in the water density upon the addition of the salt.
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Affiliation(s)
- Stefan Hervø-Hansen
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
| | - Daoyang Lin
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
| | - Kento Kasahara
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
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2
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Chadda R, Lee T, Mahoney-Kruszka R, Kelley EG, Bernhardt N, Sandal P, Robertson JL. A thermodynamic analysis of CLC transporter dimerization in lipid bilayers. Proc Natl Acad Sci U S A 2023; 120:e2305100120. [PMID: 37788312 PMCID: PMC10576108 DOI: 10.1073/pnas.2305100120] [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: 03/28/2023] [Accepted: 08/17/2023] [Indexed: 10/05/2023] Open
Abstract
The CLC-ec1 chloride/proton antiporter is a membrane-embedded homodimer with subunits that can dissociate and associate, but the thermodynamic driving forces favor the assembled dimer at biological densities. Yet, the physical reasons for this stability are confounding as dimerization occurs via the burial of hydrophobic interfaces away from the lipid solvent. For binding of nonpolar surfaces in aqueous solution, the driving force is often attributed to the hydrophobic effect, but this should not apply in the membrane since there is very little water. To investigate this further, we quantified the thermodynamic changes associated with CLC dimerization in membranes by carrying out a van 't Hoff analysis of the temperature dependency of the free energy of dimerization, ΔG°. To ensure that the reaction reached equilibrium at different temperatures, we utilized a Förster resonance energy transfer assay to report on relaxation kinetics of subunit exchange as a function of temperature. Equilibration times were then applied to measure CLC-ec1 dimerization isotherms at different temperatures using the single-molecule subunit-capture photobleaching analysis approach. The results demonstrate that the dimerization free energy of CLC in Escherichia coli-like membranes exhibits a nonlinear temperature dependency corresponding to a large, negative change in heat capacity, a signature of solvent ordering effects such as the hydrophobic effect. Consolidating this with our previous molecular analyses suggests that the nonbilayer defect required to solvate the monomeric state is one source of the observed change in heat capacity and indicates the existence of a generalizable driving force for protein association in membranes.
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Affiliation(s)
- Rahul Chadda
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO63110
| | - Taeho Lee
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO63110
- Department of Physics, Washington University, St. Louis, MO63130
| | - Robyn Mahoney-Kruszka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO63110
| | - Elizabeth G. Kelley
- Center for Neutron Research, National Institute for Standards and Technology, Gaithersburg, MD20899
| | - Nathan Bernhardt
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, NIH, Bethesda, MD20894
| | - Priyanka Sandal
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA52242
| | - Janice L. Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO63110
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3
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Dayhoff GW, Uversky VN. Rapid prediction and analysis of protein intrinsic disorder. Protein Sci 2022; 31:e4496. [PMID: 36334049 PMCID: PMC9679974 DOI: 10.1002/pro.4496] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/07/2022]
Abstract
Protein intrinsic disorder is found in all kingdoms of life and is known to underpin numerous physiological and pathological processes. Computational methods play an important role in characterizing and identifying intrinsically disordered proteins and protein regions. Herein, we present a new high-efficiency web-based disorder predictor named Rapid Intrinsic Disorder Analysis Online (RIDAO) that is designed to facilitate the application of protein intrinsic disorder analysis in genome-scale structural bioinformatics and comparative genomics/proteomics. RIDAO integrates six established disorder predictors into a single, unified platform that reproduces the results of individual predictors with near-perfect fidelity. To demonstrate the potential applications, we construct a test set containing more than one million sequences from one hundred organisms comprising over 420 million residues. Using this test set, we compare the efficiency and accessibility (i.e., ease of use) of RIDAO to five well-known and popular disorder predictors, namely: AUCpreD, IUPred3, metapredict V2, flDPnn, and SPOT-Disorder2. We show that RIDAO yields per-residue predictions at a rate two to six orders of magnitude greater than the other predictors and completely processes the test set in under an hour. RIDAO can be accessed free of charge at https://ridao.app.
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Affiliation(s)
- Guy W. Dayhoff
- Department of ChemistryUniversity of South FloridaTampaFloridaUSA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research InstituteUniversity of South FloridaTampaFloridaUSA
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4
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Kuroda Y. Biophysical studies of amorphous protein aggregation and in vivo immunogenicity. Biophys Rev 2022; 14:1495-1501. [PMID: 36465085 PMCID: PMC9684872 DOI: 10.1007/s12551-022-01011-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/26/2022] [Indexed: 11/27/2022] Open
Abstract
Amorphous protein aggregates are oligomers that lack specific, high-order structures. Soluble amorphous aggregates are smaller than ~1 µm. Despite their lack of high-order structure, amorphous protein aggregates exhibit specific biophysical properties such as reversibility of formation, density, conformation, and biochemical stability. Our mutational analysis using a Solubility Controlling Peptide (SCP) tag strongly suggests that amorphous aggregation of small globular proteins can significantly increase in vivo immune response and that the magnitude of enhanced immune responses depends on the aggregates' biophysical and biochemical properties. We propose that SCP tags might help develop subunit (protein) adjuvant-free (immunostimulant-free) vaccines by controlling the aggregation propensity of target proteins.
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Affiliation(s)
- Yutaka Kuroda
- Department of Biotechnology and Life Sciences, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-Shi, Tokyo, 184-8588 Japan
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5
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Lattanzi V, André I, Gasser U, Dubackic M, Olsson U, Linse S. Amyloid β 42 fibril structure based on small-angle scattering. Proc Natl Acad Sci U S A 2021; 118:e2112783118. [PMID: 34815346 PMCID: PMC8640717 DOI: 10.1073/pnas.2112783118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Amyloid fibrils are associated with a number of neurodegenerative diseases, including fibrils of amyloid β42 peptide (Aβ42) in Alzheimer's disease. These fibrils are a source of toxicity to neuronal cells through surface-catalyzed generation of toxic oligomers. Detailed knowledge of the fibril structure may thus facilitate therapeutic development. We use small-angle scattering to provide information on the fibril cross-section dimension and shape for Aβ42 fibrils prepared in aqueous phosphate buffer at pH = 7.4 and pH 8.0 under quiescent conditions at 37 °C from pure recombinant Aβ42 peptide. Fitting the data using a continuum model reveals an elliptical cross-section and a peptide mass-per-unit length compatible with two filaments of two monomers, four monomers per plane. To provide a more detailed atomistic model, the data were fitted using as a starting state a high-resolution structure of the two-monomer arrangement in filaments from solid-state NMR (Protein Data Bank ID 5kk3). First, a twofold symmetric model including residues 11 to 42 of two monomers in the filament was optimized in terms of twist angle and local packing using Rosetta. A two-filament model was then built and optimized through fitting to the scattering data allowing the two N-termini in each filament to take different conformations, with the same conformation in each of the two filaments. This provides an atomistic model of the fibril with twofold rotation symmetry around the fibril axis. Intriguingly, no polydispersity as regards the number of filaments was observed in our system over separate samples, suggesting that the two-filament arrangement represents a free energy minimum for the Aβ42 fibril.
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Affiliation(s)
- Veronica Lattanzi
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden;
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Ingemar André
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
| | - Urs Gasser
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Marija Dubackic
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Ulf Olsson
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
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Kieserling H, Giefer P, Uttinger MJ, Lautenbach V, Nguyen T, Sevenich R, Lübbert C, Rauh C, Peukert W, Fritsching U, Drusch S, Maria Wagemans A. Structure and adsorption behavior of high hydrostatic pressure-treated β-lactoglobulin. J Colloid Interface Sci 2021; 596:173-183. [PMID: 33839350 DOI: 10.1016/j.jcis.2021.03.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/24/2021] [Accepted: 03/09/2021] [Indexed: 12/18/2022]
Abstract
HYPOTHESIS High hydrostatic pressure treatment causes structural changes in interfacial-active β-lactoglobulin (β-lg). We hypothesized that the pressure-induced structural changes affect the intra- and intermolecular interactions which determine the interfacial activity of β-lg. The conducted experimental and numerical investigations could contribute to the mechanistic understanding of the adsorption behavior of proteins in food-related emulsions. EXPERIMENTS We treated β-lg in water at pH 7 with high hydrostatic pressures up to 600 MPa for 10 min at 20 °C. The secondary structure was characterized with Fourier-transform infrared spectroscopy (FTIR) and circular dichroism (CD), the surface hydrophobicity and charge with fluorescence-spectroscopy and ζ-potential, and the quaternary structure with membrane-osmometry, analytical ultracentrifugation (AUC) and mass spectrometry (MS). Experimental analyses were supported through molecular dynamic (MD) simulations. The adsorption behavior was investigated with pendant drop analysis. FINDINGS MD simulation revealed a pressure-induced molten globule state of β-lg, confirmed by an unfolding of β-sheets with FTIR, a stabilization of α-helices with CD and loss in tertiary structure induced by an increase in surface hydrophobicity. Membrane-osmometry, AUC and MS indicated the formation of non-covalently linked dimers that migrated slower through the water phase, adsorbed more quickly due to hydrophobic interactions with the oil, and lowered the interfacial tension more strongly than reference β-lg.
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Affiliation(s)
- Helena Kieserling
- Technische Universität Berlin, Department of Food Colloids, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Patrick Giefer
- Leibniz Institute for Materials Engineering-IWT, Particles and Process Engineering, Badgasteiner Str. 3, 28359 Bremen, Germany.
| | - Maximilian J Uttinger
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Haberstrasse 9a, 91058 Erlangen, Germany.
| | - Vanessa Lautenbach
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Haberstrasse 9a, 91058 Erlangen, Germany.
| | - Thu Nguyen
- Technische Universität Berlin, Department of Food Colloids, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Robert Sevenich
- Technische Universität Berlin, Department of Food Biotechnology and Process Engineering, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Christian Lübbert
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Haberstrasse 9a, 91058 Erlangen, Germany.
| | - Cornelia Rauh
- Technische Universität Berlin, Department of Food Biotechnology and Process Engineering, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Wolfgang Peukert
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Particle Technology, Interdisciplinary Center for Functional Particle Systems, Haberstrasse 9a, 91058 Erlangen, Germany.
| | - Udo Fritsching
- Leibniz Institute for Materials Engineering-IWT, Particles and Process Engineering, Badgasteiner Str. 3, 28359 Bremen, Germany; University of Bremen, Particles and Process Engineering, Bibliothekstraße 1, 28359 Bremen, Germany.
| | - Stephan Drusch
- Technische Universität Berlin, Department of Food Technology and Food Material Science, Straße des 17. Juni 135, 10623 Berlin, Germany.
| | - Anja Maria Wagemans
- Technische Universität Berlin, Department of Food Colloids, Straße des 17. Juni 135, 10623 Berlin, Germany.
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7
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Ashbaugh HS, Vats M, Garde S. Bridging Gaussian Density Fluctuations from Microscopic to Macroscopic Volumes: Applications to Non-Polar Solute Hydration Thermodynamics. J Phys Chem B 2021; 125:8152-8164. [PMID: 34283590 PMCID: PMC8389927 DOI: 10.1021/acs.jpcb.1c04087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The hydration of
hydrophobic solutes is intimately related to the
spontaneous formation of cavities in water through ambient density
fluctuations. Information theory-based modeling and simulations have
shown that water density fluctuations in small volumes are approximately
Gaussian. For limiting cases of microscopic and macroscopic volumes,
water density fluctuations are known exactly and are rigorously related
to the density and isothermal compressibility of water. Here, we develop
a theory—interpolated gaussian fluctuation theory (IGFT)—that
builds an analytical bridge to describe water density fluctuations
from microscopic to molecular scales. This theory requires no detailed
information about the water structure beyond the effective size of
a water molecule and quantities that are readily obtained from water’s
equation-of-state—namely, the density and compressibility.
Using simulations, we show that IGFT provides a good description of
density fluctuations near the mean, that is, it characterizes the
variance of occupancy fluctuations over all solute sizes. Moreover,
when combined with the information theory, IGFT reproduces the well-known
signatures of hydrophobic hydration, such as entropy convergence and
solubility minima, for atomic-scale solutes smaller than the crossover
length scale beyond which the Gaussian assumption breaks down. We
further show that near hydrophobic and hydrophilic self-assembled
monolayer surfaces in contact with water, the normalized solvent density
fluctuations within observation volumes depend similarly on size as
observed in the bulk, suggesting the feasibility of a modified version
of IGFT for interfacial systems. Our work highlights the utility of
a density fluctuation-based approach toward understanding and quantifying
the solvation of non-polar solutes in water and the forces that drive
them toward surfaces with different hydrophobicities.
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Affiliation(s)
- Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Mayank Vats
- Center for Biotechnology and Interdisciplinary Studies and the Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Shekhar Garde
- Center for Biotechnology and Interdisciplinary Studies and the Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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8
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Harisna AH, Nurdiansyah R, Syaifie PH, Nugroho DW, Saputro KE, Firdayani, Prakoso CD, Rochman NT, Maulana NN, Noviyanto A, Mardliyati E. In silico investigation of potential inhibitors to main protease and spike protein of SARS-CoV-2 in propolis. Biochem Biophys Rep 2021; 26:100969. [PMID: 33681482 PMCID: PMC7914023 DOI: 10.1016/j.bbrep.2021.100969] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Docking analysis of propolis's natural compound was successfully performed against SARS-CoV-2 main protease (Mpro) and spike protein subunit 2 (S2). Initially, the propolis's protein was screened using chromatography analysis and successfully identified 22 compounds in the propolis. Four compounds were further investigated, i.e., neoblavaisoflavone, methylophiopogonone A, 3'-Methoxydaidzin, and genistin. The binding affinity of 3'-Methoxydaidzin was -7.7 kcal/mol, which is similar to nelfinavir (control), while the others were -7.6 kcal/mol. However, we found the key residue of Glu A:166 in the methylophiopogonone A and genistin, even though the predicted binding energy slightly higher than nelfinavir. In contrast, the predicted binding affinity of neoblavaisoflavone, methylophiopogonone A, 3'-Methoxydaidzin, and genistin against S2 were -8.1, -8.2, -8.3, and -8.3 kcal/mol, respectively, which is far below of the control (pravastatin, -7.3 kcal/mol). Instead of conventional hydrogen bonding, the π bonding influenced the binding affinity against S2. The results reveal that this is the first report about methylophiopogonone A, 3'-Methoxydaidzin, and genistin as candidates for anti-viral agents. Those compounds can then be further explored and used as a parent backbone molecule to develop a new supplementation for preventing SARS-CoV-2 infections during COVID-19 outbreaks.
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Affiliation(s)
- Azza Hanif Harisna
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | - Rizky Nurdiansyah
- Department of Bioinformatics, Indonesia International Institute for Life Sciences, Jakarta, 13210, Indonesia
| | - Putri Hawa Syaifie
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | - Dwi Wahyu Nugroho
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | | | - Firdayani
- Center for Pharmaceutical and Medical Technology, Agency for the Assessment and Application of Technology, PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | - Chandra Dwi Prakoso
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | - Nurul Taufiqu Rochman
- Research Center for Metallurgy and Materials, Indonesian Institute of Sciences, PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | | | - Alfian Noviyanto
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
- Department of Mechanical Engineering, Mercu Buana University, Jl. Meruya Selatan, Kebun Jeruk, Jakarta, 11650, Indonesia
| | - Etik Mardliyati
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
- Center for Pharmaceutical and Medical Technology, Agency for the Assessment and Application of Technology, PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
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9
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Paananen A, Weich S, Szilvay GR, Leitner M, Tappura K, Ebner A. Quantifying biomolecular hydrophobicity: Single molecule force spectroscopy of class II hydrophobins. J Biol Chem 2021; 296:100728. [PMID: 33933454 PMCID: PMC8164047 DOI: 10.1016/j.jbc.2021.100728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/25/2021] [Accepted: 04/28/2021] [Indexed: 11/30/2022] Open
Abstract
Hydrophobins are surface-active proteins produced by filamentous fungi. The amphiphilic structure of hydrophobins is very compact, containing a distinct hydrophobic patch on one side of the molecule, locked by four intramolecular disulfide bridges. Hydrophobins form dimers and multimers in solution to shield these hydrophobic patches from water exposure. Multimer formation in solution is dynamic, and hydrophobin monomers can be exchanged between multimers. Unlike class I hydrophobins, class II hydrophobins assemble into highly ordered films at the air-water interface. In order to increase our understanding of the strength and nature of the interaction between hydrophobins, we used atomic force microscopy for single molecule force spectroscopy to explore the molecular interaction forces between class II hydrophobins from Trichoderma reesei under different environmental conditions. A genetically engineered hydrophobin variant, NCys-HFBI, enabled covalent attachment of proteins to the apex of the atomic force microscopy cantilever tip and sample surfaces in controlled orientation with sufficient freedom of movement to measure molecular forces between hydrophobic patches. The measured rupture force between two assembled hydrophobins was ∼31 pN, at a loading rate of 500 pN/s. The results indicated stronger interaction between hydrophobins and hydrophobic surfaces than between two assembling hydrophobin molecules. Furthermore, this interaction was stable under different environmental conditions, which demonstrates the dominance of hydrophobicity in hydrophobin-hydrophobin interactions. This is the first time that interaction forces between hydrophobin molecules, and also between naturally occurring hydrophobic surfaces, have been measured directly at a single-molecule level.
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Affiliation(s)
- Arja Paananen
- Industrial Biotechnology and Food, VTT Technical Research Centre of Finland Ltd, Espoo, Finland.
| | - Sabine Weich
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Géza R Szilvay
- Industrial Biotechnology and Food, VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Michael Leitner
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Kirsi Tappura
- Industrial Biotechnology and Food, VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Andreas Ebner
- Department of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria.
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10
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Ganguly P, Polák J, van der Vegt NFA, Heyda J, Shea JE. Protein Stability in TMAO and Mixed Urea–TMAO Solutions. J Phys Chem B 2020; 124:6181-6197. [DOI: 10.1021/acs.jpcb.0c04357] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, United States
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11
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Greffe VRG, Michiels J. Desiccation-induced cell damage in bacteria and the relevance for inoculant production. Appl Microbiol Biotechnol 2020; 104:3757-3770. [PMID: 32170388 DOI: 10.1007/s00253-020-10501-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 12/21/2022]
Abstract
Plant growth-promoting bacteria show great potential for use in agriculture although efficient application remains challenging to achieve. Cells often lose viability during inoculant production and application, jeopardizing the efficacy of the inoculant. Since desiccation has been documented to be the primary stress factor affecting the decrease in survival, obtaining xerotolerance in plant growth-promoting bacteria is appealing. The molecular damage that occurs by drying bacteria has been broadly investigated, although a complete view is still lacking due to the complex nature of the process. Mechanic, structural, and metabolic changes that occur as a result of water depletion may potentially afflict lethal damage to membranes, DNA, and proteins. Bacteria respond to these harsh conditions by increasing production of exopolysaccharides, changing composition of the membrane, improving the stability of proteins, reducing oxidative stress, and repairing DNA damage. This review provides insight into the complex nature of desiccation stress in bacteria in order to facilitate strategic choices to improve survival and shelf life of newly developed inoculants. KEY POINTS: Desiccation-induced damage affects most major macromolecules in bacteria. Most bacteria are not xerotolerant despite multiple endogenous adaption mechanisms. Sensitivity to drying severely hampers inoculant quality.
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Affiliation(s)
- Vincent Robert Guy Greffe
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium. .,VIB Center for Microbiology, Flanders Institute for Biotechnology, Leuven, Belgium.
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12
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Abstract
Proteins with a high degree of sequence similarity representing different structures provide a key to understand how protein sequence codes for 3D structure. An analysis using the fuzzy oil drop model was carried out on two pairs of proteins with different secondary structures and with high sequence identities. It has been shown that distributions of hydrophobicity for these proteins are approximated well using single 3D Gaussian function. In other words, the similar sequences fold into different 3D structures, however, alternative structures also have symmetric and monocentric hydrophobic cores. It should be noted that a significant change in the helical to beta-structured form in the N-terminal section takes places in the fragment much preceding the location of the mutated regions. It can be concluded that the final structure is the result of a complicated synergy effect in which the whole chain participates simultaneously.
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13
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Gómez-Velasco H, Rojo-Domínguez A, García-Hernández E. Enthalpically-driven ligand recognition and cavity solvation of bovine odorant binding protein. Biophys Chem 2020; 257:106315. [DOI: 10.1016/j.bpc.2019.106315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/05/2019] [Accepted: 12/08/2019] [Indexed: 11/29/2022]
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14
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The Amyloid as a Ribbon-Like Micelle in Contrast to Spherical Micelles Represented by Globular Proteins. Molecules 2019; 24:molecules24234395. [PMID: 31816829 PMCID: PMC6930452 DOI: 10.3390/molecules24234395] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 01/18/2023] Open
Abstract
Selected amyloid structures available in the Protein Data Bank have been subjected to a comparative analysis. Classification is based on the distribution of hydrophobicity in amyloids that differ with respect to sequence, chain length, the distribution of beta folds, protofibril structure, and the arrangement of protofibrils in each superfibril. The study set includes the following amyloids: Aβ (1-42), which is listed as Aβ (15-40) and carries the D23N mutation, and Aβ (11-42) and Aβ (1-40), both of which carry the E22Δ mutation, tau amyloid, and α-synuclein. Based on the fuzzy oil drop model (FOD), we determined that, despite their conformational diversity, all presented amyloids adopt a similar structural pattern that can be described as a ribbon-like micelle. The same model, when applied to globular proteins, results in structures referred to as "globular micelles," emerging as a result of interactions between the proteins' constituent residues and the aqueous solvent. Due to their composition, amyloids are unable to attain entropically favorable globular forms and instead attempt to limit contact between hydrophobic residues and water by producing elongated structures. Such structures typically contain quasi hydrophobic cores that stretch along the fibril's long axis. Similar properties are commonly found in ribbon-like micelles, with alternating bands of high and low hydrophobicity emerging as the fibrils increase in length. Thus, while globular proteins are generally consistent with a 3D Gaussian distribution of hydrophobicity, the distribution instead conforms to a 2D Gaussian distribution in amyloid fibrils.
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Pan H, Han MY, Li P, Wang L. “On Water” Direct Catalytic Vinylogous Aldol Reaction of Silyl Glyoxylates. J Org Chem 2019; 84:14281-14290. [DOI: 10.1021/acs.joc.9b01945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hong Pan
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Man-Yi Han
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Pinhua Li
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
| | - Lei Wang
- Department of Chemistry, Huaibei Normal University, Huaibei, Anhui 235000, P.R. China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, P.R. China
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16
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Selenko P. Quo Vadis Biomolecular NMR Spectroscopy? Int J Mol Sci 2019; 20:ijms20061278. [PMID: 30875725 PMCID: PMC6472163 DOI: 10.3390/ijms20061278] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) spectroscopy offers the possibility to study proteins and other biomolecules at atomic resolution directly in cells. As such, it provides compelling means to complement existing tools in cellular structural biology. Given the dominance of electron microscopy (EM)-based methods in current structure determination routines, I share my personal view about the role of biomolecular NMR spectroscopy in the aftermath of the revolution in resolution. Specifically, I focus on spin-off applications that in-cell NMR has helped to develop and how they may provide broader and more generally applicable routes for future NMR investigations. I discuss the use of ‘static’ and time-resolved solution NMR spectroscopy to detect post-translational protein modifications (PTMs) and to investigate structural consequences that occur in their response. I argue that available examples vindicate the need for collective and systematic efforts to determine post-translationally modified protein structures in the future. Furthermore, I explain my reasoning behind a Quinary Structure Assessment (QSA) initiative to interrogate cellular effects on protein dynamics and transient interactions present in physiological environments.
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Affiliation(s)
- Philipp Selenko
- Weizmann Institute of Science, Department of Biological Regulation, 234 Herzl Street, Rehovot 76100, Israel.
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17
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Williams LJ, Schendt BJ, Fritz ZR, Attali Y, Lavroff RH, Yarmush ML. A protein interaction free energy model based on amino acid residue contributions: Assessment of point mutation stability of T4 lysozyme. TECHNOLOGY 2019; 7:12-39. [PMID: 32211456 PMCID: PMC7093156 DOI: 10.1142/s233954781950002x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Here we present a model to estimate the interaction free energy contribution of each amino acid residue of a given protein. Protein interaction energy is described in terms of per-residue interaction factors, μ. Multibody interactions are implicitly captured in μ through the combination of amino acid terms (γ) guided by local conformation indices (σ). The model enables construction of an interaction factor heat map for a protein in a given fold, allows prima facie assessment of the degree of residue-residue interaction, and facilitates a qualitative and quantitative evaluation of protein association properties. The model was used to compute thermal stability of T4 bacteriophage lysozyme mutants across seven sites. Qualitative assessment of mutational effects provides a straightforward rationale regarding whether a particular site primarily perturbs native or non-native states, or both. The presented model was found to be in good agreement with experimental mutational data (R 2 = 0.73) and suggests an approach by which to convert structure space into energy space.
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Affiliation(s)
- Lawrence J Williams
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Rd., Piscataway, NJ 08854, USA
| | - Brian J Schendt
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Rd., Piscataway, NJ 08854, USA
| | - Zachary R Fritz
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, 599 Taylor Road, Piscataway, NJ 08854, USA
| | - Yonatan Attali
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Rd., Piscataway, NJ 08854, USA
| | - Robert H Lavroff
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Rd., Piscataway, NJ 08854, USA
| | - Martin L Yarmush
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, 599 Taylor Road, Piscataway, NJ 08854, USA
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18
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19
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Martin YC. How medicinal chemists learned about log P. J Comput Aided Mol Des 2018; 32:809-819. [PMID: 30019206 DOI: 10.1007/s10822-018-0127-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/14/2018] [Indexed: 11/24/2022]
Abstract
Although log P is now recognized to be a key factor that determines the bioactivity of a molecule, the focus of medicinal chemists on hydrophobicity and log P started with the quantitative structure-activity relationships (QSAR) publications of Hansch and Fujita. Their original publication represents a dramatic change of focus to incorporate consideration of log P after a decade of work unsuccessfully attempting to use the Hammett equation to explain the structure-activity relationships of plant growth regulators. QSAR allows one to explore the quantitative relationship between log P and biological activity even when other factors also influence potency. In particular, Hansch's publications of thousands of QSAR equations demonstrate that a relationship of biological activity with log P is indeed a general phenomenon. Hansch's group also provided data and tools that enable others to explore the relationship between log P and the biological activity of compounds of interest.
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20
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Zhang BW, Cui D, Matubayasi N, Levy RM. The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations. J Phys Chem B 2018; 122:4700-4707. [PMID: 29634902 DOI: 10.1021/acs.jpcb.8b02666] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We use end point simulations to estimate the excess chemical potential of water in the homogeneous liquid and at the interface with a protein in solution. When the pure liquid is taken as the reference, the excess chemical potential of interfacial water is the difference between the solvation free energy of a water molecule at the interface and in the bulk. Using the homogeneous liquid as an example, we show that the solvation free energy for growing a water molecule can be estimated by applying UWHAM to the simulation data generated from the initial and final states (i.e., "the end points") instead of multistate free energy perturbation simulations because of the possible overlaps of the configurations sampled at the end points. Then end point simulations are used to estimate the solvation free energy of water at the interface with a protein in solution. The estimate of the solvation free energy at the interface from two simulations at the end points agrees with the benchmark using 32 states within a 95% confidence interval for most interfacial locations. The ability to accurately estimate the excess chemical potential of water from end point simulations facilitates the statistical thermodynamic analysis of diverse interfacial phenomena. Our focus is on analyzing the excess chemical potential of water at protein receptor binding sites with the goal of using this information to assist in the design of tight binding ligands.
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Affiliation(s)
- Bin W Zhang
- Center for Biophysics and Computational Biology , Department of Chemistry , and Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Di Cui
- Center for Biophysics and Computational Biology , Department of Chemistry , and Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science , Osaka University , Toyonaka , Osaka 560-8531 , Japan.,Elements Strategy Initiative for Catalysts and Batteries , Kyoto University , Katsura , Kyoto 615-8520 , Japan
| | - Ronald M Levy
- Center for Biophysics and Computational Biology , Department of Chemistry , and Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
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21
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Meti MD, Dixit MK, Tembe BL. Salting-in of neopentane in the aqueous solutions of urea and glycine-betaine. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1431834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manjunath D. Meti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Mayank K. Dixit
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Bhalachandra L. Tembe
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
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22
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Biophysical studies of protein solubility and amorphous aggregation by systematic mutational analysis and a helical polymerization model. Biophys Rev 2018; 10:473-480. [PMID: 29302914 DOI: 10.1007/s12551-017-0342-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/13/2017] [Indexed: 01/04/2023] Open
Abstract
At concentrations above solubility, a protein aggregates, most often into amorphous aggregates, and loses its function. However, unlike amyloidogenic aggregates, which are β-sheeted fibrillar aggregates often related to neurodegenerative diseases, amorphous aggregates, where proteins aggregate/oligomerize without forming specific high-order structures, are rarely the focus of biophysical studies. Hence, protein solubility with respect to amorphous aggregation remains to be fully characterized from a biophysical viewpoint. Here, I briefly describe the structural nature of proteins in amorphous aggregates before discussing systematic mutational analyses that aim to rationalize the contribution of individual amino acids to the solubility of a protein. The discussion is expected to demonstrate that protein solubility, and, accordingly, amorphous aggregation, can be understood using thermodynamic and biophysical rationales similar to those used in the study of protein stability or, more recently, amyloidogenesis. Finally, I will argue that the mathematical formalism of the helical polymerization model (HPM) proposed by Oosawa, Kasai, and Asakura's group can be readily adapted to provide a thermodynamic description of a system containing amorphous aggregates and soluble particles. The HPM and HPM-derived models imply the presence of nuclei or seeds for amorphous aggregates, similar to those hypothesized in crystallogenesis and amyloidogenesis.
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23
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Nishio M. Myths in Modern Science: The Hydrogen Bond and its Surroundings Part 2. The Hydrophobic-Bond-Myth. CHEM-BIO INFORMATICS JOURNAL 2018. [DOI: 10.1273/cbij.18.10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Li MS, Li T, Lu X, Sun LC, Chen YL, Liu H, Cao MJ, Liu GM. Site-directed mutagenesis of myofibril-bound serine proteinase from Crucian carp : possible role of Pro95, A127 and I130 on thermal stability. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Pérez-Fuentes L, Drummond C, Faraudo J, Bastos-González D. Interaction of organic ions with proteins. SOFT MATTER 2017; 13:1120-1131. [PMID: 28093583 DOI: 10.1039/c6sm02048h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this study we have investigated how different proteins interact with big organic ions. Two ions that are similar in size and chemical structure (Ph4B- anion and Ph4As+ cation) were studied. The proteins chosen are the two major allergenic proteins of cow's milk, β-lactoglobulin and β-casein, and bovine serum albumin, BSA, as the reference protein. First, a quantitative study to determine the hydrophobic degree of the proteins was performed. Then, electrokinetic and stability measurements on protein-coated polystyrene (PS) microspheres as a function of the tetraphenyl ion concentration were carried out. Our results show that the affinity of the organic ions depends on the hydrophobicity of the interface. Big charge inversions and re-stabilization patterns were observed at very low concentrations of tetraphenyl ions for the most hydrophobic protein studied (with β-casein). Besides, the ionic concentrations needed to destabilize these colloidal systems were roughly one order of magnitude lower for the anion than for the cation. In addition, we studied conformational changes of the adsorbed proteins with a quartz crystal microbalance. Proteins were adsorbed onto hydrophobic flat substrates and then exposed to the tetraphenyl ions. The protein films swelled or collapsed as a function of the accumulation of tetraphenyl ions. Similarly to the electrokinetic/stability studies, the ionic concentration necessary to trigger structural changes of the protein films was one order of magnitude larger for the cation than for the anion. All the results evidence that the accumulation of these organic ions on an interface depends directly on its degree of hydrophobicity. We attribute the different interactions of the anion and the cation with these interfaces to their dissimilar hydration, which makes the anion show a more hydrophobic behaviour than the cation.
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Affiliation(s)
- Leonor Pérez-Fuentes
- Biocolloid and Fluid Physics Group, Department of Applied Physics. University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
| | - Carlos Drummond
- CNRS, Centre de Recherche Paul Pascal (CRPP), UPR 8641, F3300, Pessac, France. and Université de Bordeaux, CRPP, UPR 8641, F-33600 Pessac, France
| | - Jordi Faraudo
- Institut de Ciència dels Materials de Barcelona (ICMAB-CSIC), Carrer dels Tillers s/n, Campus de la UAB, E-08193 Bellaterra, Barcelona, Spain
| | - Delfi Bastos-González
- Biocolloid and Fluid Physics Group, Department of Applied Physics. University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
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26
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Dixit M, Hajari T, Tembe B. The effect of urea and taurine osmolytes on hydrophobic association and solvation of methane and neopentane molecules. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.08.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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27
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Ganguly P, van der Vegt NFA, Shea JE. Hydrophobic Association in Mixed Urea-TMAO Solutions. J Phys Chem Lett 2016; 7:3052-9. [PMID: 27440555 DOI: 10.1021/acs.jpclett.6b01344] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The formation of a hydrophobic core is key to the folding and resulting function of most proteins in the cell. In several organisms, as well as in many in vitro experiments, protein folding is modulated by the presence of osmolytes, but the mechanism by which hydrophobic association occurs is not well understood. We present a study of the solvation thermodynamics of hydrophobic self-association in mixed-osmolyte urea-TMAO solutions, with neopentane as a model hydrophobic molecule. Using molecular dynamics simulations and the Kirkwood-Buff theory of solutions, we show that a sensitive balance between the TMAO-water and the TMAO-urea interactions governs the osmolyte-induced changes in hydrophobic association in mixed urea-TMAO solutions. This balance must be correctly incorporated in force-field parametrization because hydrophobic association can be either enhanced or prevented all together by slightly increasing or decreasing the osmolyte-water affinity and osmolyte-osmolyte self-affinity of TMAO molecules.
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Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California at Santa Barbara , Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt , Alarich-Weiss-Straße 10, Darmstadt 64287, Germany
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California at Santa Barbara , Santa Barbara, California 93106, United States
- Department of Physics, University of California at Santa Barbara , Santa Barbara, California 93106, United States
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28
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29
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Harris RC, Pettitt BM. Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:083003. [PMID: 26836518 PMCID: PMC5370576 DOI: 10.1088/0953-8984/28/8/083003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The idea that a 'hydrophobic energy' drives protein folding, aggregation, and binding by favoring the sequestration of bulky residues from water into the protein interior is widespread. The solvation free energies (ΔGsolv) of small nonpolar solutes increase with surface area (A), and the free energies of creating macroscopic cavities in water increase linearly with A. These observations seem to imply that there is a hydrophobic component (ΔGhyd) of ΔGsolv that increases linearly with A, and this assumption is widely used in implicit solvent models. However, some explicit-solvent molecular dynamics studies appear to contradict these ideas. For example, one definition (ΔG(LJ)) of ΔGhyd is that it is the free energy of turning on the Lennard-Jones (LJ) interactions between the solute and solvent. However, ΔG(LJ) decreases with A for alanine and glycine peptides. Here we argue that these apparent contradictions can be reconciled by defining ΔGhyd to be a near hard core insertion energy (ΔGrep), as in the partitioning proposed by Weeks, Chandler, and Andersen. However, recent results have shown that ΔGrep is not a simple function of geometric properties of the molecule, such as A and the molecular volume, and that the free energy of turning on the attractive part of the LJ potential cannot be computed from first-order perturbation theory for proteins. The theories that have been developed from these assumptions to predict ΔGhyd are therefore inadequate for proteins.
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Affiliation(s)
- Robert C Harris
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0304, USA
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30
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Effect of glycine betaine on the hydrophobic interactions in the presence of denaturant: A molecular dynamics study. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2015.12.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Kenny PW, Montanari CA, Prokopczyk IM, Ribeiro JFR, Sartori GR. Hydrogen Bond Basicity Prediction for Medicinal Chemistry Design. J Med Chem 2016; 59:4278-88. [DOI: 10.1021/acs.jmedchem.5b01946] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter W. Kenny
- Grupo de Estudos em Química
Medicinal—NEQUIMED, Instituto de Química de São
Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, 13560-590 São Carlos, São Paulo, Brazil
| | - Carlos A. Montanari
- Grupo de Estudos em Química
Medicinal—NEQUIMED, Instituto de Química de São
Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, 13560-590 São Carlos, São Paulo, Brazil
| | - Igor M. Prokopczyk
- Grupo de Estudos em Química
Medicinal—NEQUIMED, Instituto de Química de São
Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, 13560-590 São Carlos, São Paulo, Brazil
| | - Jean F. R. Ribeiro
- Grupo de Estudos em Química
Medicinal—NEQUIMED, Instituto de Química de São
Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, 13560-590 São Carlos, São Paulo, Brazil
| | - Geraldo Rodrigues Sartori
- Grupo de Estudos em Química
Medicinal—NEQUIMED, Instituto de Química de São
Carlos, Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, 13560-590 São Carlos, São Paulo, Brazil
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32
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Chaudhari MI, Rempe SB, Asthagiri D, Tan L, Pratt LR. Molecular Theory and the Effects of Solute Attractive Forces on Hydrophobic Interactions. J Phys Chem B 2016; 120:1864-70. [DOI: 10.1021/acs.jpcb.5b09552] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mangesh I. Chaudhari
- Center
for Biological and Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Susan B. Rempe
- Center
for Biological and Material Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - D. Asthagiri
- Department
of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - L. Tan
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - L. R. Pratt
- Department
of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
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35
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Ou SC, Cui D, Patel S. Molecular modeling of ions at interfaces: exploring similarities to hydrophobic solvation through the lens of induced aqueous interfacial fluctuations. Phys Chem Chem Phys 2016; 18:30357-30365. [DOI: 10.1039/c6cp04112d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ion specific effects are ubiquitous in chemistry and biology.
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Affiliation(s)
- Shu-Ching Ou
- Sealy Center for Structural Biology and Molecular Biophysics
- University of Texas Medical Branch
- 301 University Boulevard
- Galveston
- USA
| | - Di Cui
- Department of Chemistry
- Temple University
- Philadelphia
- USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry
- University of Delaware
- Newark
- USA
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36
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Chen K, Liu Q, Ni JP, Zhu HJ, Li YF, Wang Q. Synthesis, insecticidal activities and structure-activity relationship studies of novel anthranilic diamides containing pyridylpyrazole-4-carboxamide. PEST MANAGEMENT SCIENCE 2015; 71:1503-1512. [PMID: 25472809 DOI: 10.1002/ps.3954] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 09/03/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND Anthranilic diamide insecticides containing pyridylpyrazole-5-carboxamide are extremely important in modern agriculture. New structurally modified compounds with high insecticidal activity were discovered by designing a series of novel pyridylpyrazole-4-carboxamides (9I to 9IV) and pyridylpyrazole-4-carboxamides (10I to 10IV), the latter designed by the cyclisation of two amides. The structure-activity relationship (SAR) between the two series is of interest. RESULTS Two series of novel anthranilic diamides containing pyridylpyrazole-4-carboxamide were synthesised and characterised via melting point, (1)H NMR, (13)C NMR, MS and elemental analyses. The insecticidal activities of these compounds against Plutella xylostella were evaluated. At a concentration of 100 mg L(-1), the compounds with unmodified amide moieties (9I to 9IV) exhibited much better larvicidal activities than the other derivative compounds (10I to 10IV). Most of the compounds 9I to 9IV showed over 90% larvicidal activity at 100 mg L(-1). Furthermore, compounds 9IIIa, 9IIIc, 9IIId and 9IVd displayed significant insecticidal activity at 10 mg L(-1). Density functional theory (DFT) calculation was carried out to provide more information regarding SAR. CONCLUSION Thirty-two new anthranlic diamides containing pyridylpyrazole-4-carboxamide were designed and obtained. SAR analysis and DFT calculation results revealed that the amide moiety had a very important effect on bioactivity. This work has provided information that could aid investigations of novel insecticides.
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Affiliation(s)
- Kai Chen
- Department of Applied Chemistry, College of Sciences, Nanjing Tech University, Nanjing, China
| | - Qi Liu
- Department of Applied Chemistry, College of Sciences, Nanjing Tech University, Nanjing, China
- Jiangsu Pesticide Research Institute Co Ltd, Nanjing, China
| | - Jue-Ping Ni
- Jiangsu Pesticide Research Institute Co Ltd, Nanjing, China
| | - Hong-Jun Zhu
- Department of Applied Chemistry, College of Sciences, Nanjing Tech University, Nanjing, China
- Jiangsu Key Laboratory of Industrial Water Conservation and Emission Reduction, Nanjing, China
| | - Yu-Feng Li
- Department of Applied Chemistry, College of Sciences, Nanjing Tech University, Nanjing, China
| | - Qiang Wang
- Department of Applied Chemistry, College of Sciences, Nanjing Tech University, Nanjing, China
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37
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Dixit MK, Siddique AA, Tembe BL. Salting-Out of Methane in the Aqueous Solutions of Urea and Glycine-Betaine. J Phys Chem B 2015; 119:10941-53. [PMID: 25965507 DOI: 10.1021/acs.jpcb.5b00556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied the hydrophobic association and solvation of methane molecules in aqueous solutions of urea and glycine betaine (GB). We have calculated the potentials of mean force (PMFs) between methane molecules in water, aqueous GB, aqueous urea and aqueous urea-GB mixtures. The PMFs and equilibrium constants indicate that both urea and GB increase the hydrophobic association of methane. Calculation of thermodynamic parameters shows that the association of methane is stabilized by entropy whereas solvation is favored by enthalpy. In the case of the water-urea-GB mixture, both hydrophobic association and solvation are stabilized by entropy. From the investigation of radial distribution functions, running coordination numbers and excess coordination numbers, we infer that both urea and GB are preferentially excluded from methane surface in the mixtures of osmolytes and methane is preferentially solvated by water molecules in all the mixtures. The favorable exclusion of both urea and GB from the methane surface suggests that both urea and GB increase the interaction between methane molecules, i.e., salting-out of methane. We observe that addition of both urea and GB to water enhances local water structure. The calculated values of diffusion constants of water also suggest enhanced water-water interactions in the presence of urea and GB. The calculated free energies of methane in these mixtures show that methane is less soluble in the mixtures of urea and GB than in water. The data on solvation free energies support the observations obtained from the PMFs of methane molecules.
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Affiliation(s)
- Mayank Kumar Dixit
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
| | - Asrar A Siddique
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
| | - B L Tembe
- Department of Chemistry, Indian Institute of Technology Bombay , Powai, Mumbai 400076, India
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38
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Functionalized activated carbon for the adsorptive removal of perchlorate from water solutions. Front Chem Sci Eng 2015. [DOI: 10.1007/s11705-015-1517-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Onofrio A, Parisi G, Punzi G, Todisco S, Di Noia MA, Bossis F, Turi A, De Grassi A, Pierri CL. Distance-dependent hydrophobic-hydrophobic contacts in protein folding simulations. Phys Chem Chem Phys 2015; 16:18907-17. [PMID: 25083519 DOI: 10.1039/c4cp01131g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Successful prediction of protein folding from an amino acid sequence is a challenge in computational biology. In order to reveal the geometric constraints that drive protein folding, highlight those constraints kept or missed by distinct lattices and for establishing which class of intra- and inter-secondary structure element interactions is the most relevant for the correct folding of proteins, we have calculated inter-alpha carbon distances in a set of 42 crystal structures consisting of mainly helix, sheet or mixed conformations. The inter-alpha carbon distances were also calculated in several lattice "hydrophobic-polar" models built from the same protein set. We found that helix structures are more prone to form "hydrophobic-hydrophobic" contacts than beta-sheet structures. At a distance lower than or equal to 3.8 Å (very short-range interactions), "hydrophobic-hydrophobic" contacts are almost absent in the native structures, while they are frequent in all the analyzed lattice models. At distances in-between 3.8 and 9.5 Å (short-/medium-range interactions), the best performing lattice for reproducing mainly helix structures is the body-centered-cubic lattice. If protein structures contain sheet portions, lattice performances get worse, with few exceptions observed for double-tetrahedral and body-centered-cubic lattices. Finally, we can observe that ab initio protein folding algorithms, i.e. those based on the employment of lattices and Monte Carlo simulated annealings, can be improved simply and effectively by preventing the generation of "hydrophobic-hydrophobic" contacts shorter than 3.8 Å, by monitoring the "hydrophobic-hydrophobic/polar-polar" contact ratio in short-/medium distance ranges and by using preferentially a body-centered-cubic lattice.
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Affiliation(s)
- Angelo Onofrio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125, Bari, Italy.
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Dunbar JA, Arthur EJ, White AM, Kubarych KJ. Ultrafast 2D-IR and Simulation Investigations of Preferential Solvation and Cosolvent Exchange Dynamics. J Phys Chem B 2015; 119:6271-9. [DOI: 10.1021/acs.jpcb.5b01952] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Josef A. Dunbar
- Department of Chemistry and
LSA Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 49109, United States
| | - Evan J. Arthur
- Department of Chemistry and
LSA Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 49109, United States
| | - Aaron M. White
- Department of Chemistry and
LSA Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 49109, United States
| | - Kevin J. Kubarych
- Department of Chemistry and
LSA Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 49109, United States
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41
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Kosower EM, Borz G. Low polarity water, a novel transition species at the polyethylene–water interface. Phys Chem Chem Phys 2015; 17:24895-900. [DOI: 10.1039/c5cp04439a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Polyethylene sandwich or a single window cell: dark bars represent polyethylene (PE) windows (double or single) of a cell. Wavy lines are water (W) and low polarity water (LPW). Subtraction of the single window spectrum from the double window spectrum leaves the LPW spectrum as illustrated in the figure.
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Affiliation(s)
| | - Galina Borz
- School of Chemistry
- Tel Aviv University
- Tel Aviv
- 69978 Israel
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42
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Dobberschütz S, Rimmen M, Hassenkam T, Andersson MP, Stipp SLS. Specific ion effects on the hydrophobic interaction of benzene self-assembled monolayers. Phys Chem Chem Phys 2015. [DOI: 10.1039/c5cp01803j] [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
The ions, Ca2+, Mg2+, Na+ and K+, decrease the hydrophobic attraction (in this order) between benzene-terminated self assembled monolayers by affecting the creation of bridging capillaries and by charging the surfaces.
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Affiliation(s)
- S. Dobberschütz
- Nano-Science Center
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen Ø
- Denmark
| | - M. Rimmen
- Nano-Science Center
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen Ø
- Denmark
| | - T. Hassenkam
- Nano-Science Center
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen Ø
- Denmark
| | - M. P. Andersson
- Nano-Science Center
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen Ø
- Denmark
| | - S. L. S. Stipp
- Nano-Science Center
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen Ø
- Denmark
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43
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Ou SC, Patel S. Electrostatic contribution from solvent in modulating single-walled carbon nanotube association. J Chem Phys 2014; 141:114906. [PMID: 25240371 PMCID: PMC4187323 DOI: 10.1063/1.4892566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/28/2014] [Indexed: 11/14/2022] Open
Abstract
We perform all-atom molecular dynamics simulations to compute the potential of mean force (PMF) between two (10,10) single-walled carbon nanotubes solvated in pure nonpolarizable SPC/E and polarizable TIP4P-FQ water, at various temperatures. In general, the reversible work required to bring two nanotubes from a dissociated state (free energy reference) to contact state (free energy minimum) is more favorable and less temperature-dependent in TIP4P-FQ than in SPC/E water models. In contrast, molecular properties and behavior of water such as the spatially-resolved water number density (intertube, intratube, or outer regions), for TIP4P-FQ are more sensitive to temperature than SPC/E. Decomposition of the solvent-induced PMF into different spatial regions suggests that TIP4P-FQ has stronger temperature dependence; the opposing destabilizing/stabilizing contributions from intertube water and more distal water balance each other and suppress the temperature dependence of total association free energy. Further investigation of hydrogen bonding network in intertube water reveals that TIP4P-FQ retains fewer hydrogen bonds than SPC/E, which correlates with the lower water number density in this region. This reduction of hydrogen bonds affects the intertube water dipoles. As the intertube volume decreases, TIP4P-FQ dipole moment approaches the gas phase value; the distribution of dipole magnitude also becomes narrower due to less average polarization/perturbation from other water molecules. Our results imply that the reduction of water under confinement may seem trivial, but underlying effects to structure and free energetics are non-negligible.
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Affiliation(s)
- Shu-Ching Ou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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44
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Dupont S, Rapoport A, Gervais P, Beney L. Survival kit of Saccharomyces cerevisiae for anhydrobiosis. Appl Microbiol Biotechnol 2014; 98:8821-34. [DOI: 10.1007/s00253-014-6028-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/08/2014] [Accepted: 08/10/2014] [Indexed: 01/08/2023]
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45
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Muche S, Levacheva I, Samsonova O, Pham L, Christou G, Bakowsky U, Hołyńska M. A chiral, low-cytotoxic [Ni15]-wheel complex. Inorg Chem 2014; 53:7642-9. [PMID: 24992258 DOI: 10.1021/ic500957y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A new chiral [Ni15] complex with a Schiff-base ligand derived from o-vanillin and L-glutamic acid is presented, emphasizing the properties relevant for biology and materials science. The formation of the complex molecules in solution is confirmed by AFM and dynamic light scattering studies. The compound is weakly antiferromagnetic with considerable admixture of excited states, comprising negligibly interacting [Ni3] units. Studies of the interactions with two cell lines indicate low cytotoxicity.
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Affiliation(s)
- Simon Muche
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW), Philipps-Universität Marburg , Hans-Meerwein-Straße, D-35032 Marburg, Germany
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46
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Nick Pace C, Scholtz JM, Grimsley GR. Forces stabilizing proteins. FEBS Lett 2014; 588:2177-84. [PMID: 24846139 DOI: 10.1016/j.febslet.2014.05.006] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 04/30/2014] [Accepted: 05/05/2014] [Indexed: 11/30/2022]
Abstract
The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic and hydrogen bonding variants. (1) Based on studies of 138 hydrophobic interaction variants in 11 proteins, burying a -CH2- group on folding contributes 1.1±0.5 kcal/mol to protein stability. (2) The burial of non-polar side chains contributes to protein stability in two ways: first, a term that depends on the removal of the side chains from water and, more importantly, the enhanced London dispersion forces that result from the tight packing in the protein interior. (3) Based on studies of 151 hydrogen bonding variants in 15 proteins, forming a hydrogen bond on folding contributes 1.1±0.8 kcal/mol to protein stability. (4) The contribution of hydrogen bonds to protein stability is strongly context dependent. (5) Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. (6) Polar group burial can make a favorable contribution to protein stability even if the polar group is not hydrogen bonded. (7) Hydrophobic interactions and hydrogen bonds both make large contributions to protein stability.
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Affiliation(s)
- C Nick Pace
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, United States.
| | - J Martin Scholtz
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, United States
| | - Gerald R Grimsley
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, United States
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Abstract
In the present article, we provide a brief overview of the main approaches to analysing the sequence-structure relationship of proteins and outline a novel method of structure prediction. The proposed method involves finding a set of rules that describes a correlation between the distribution of residues in a sequence and the essential structural characteristics of a protein structure. The residue distribution rules specify the 'favourable' residues that are required in certain positions of a polypeptide chain in order for it to assume a particular protein fold, and the 'unfavourable' residues incompatible with the given fold. Identification of amino acid distribution rules derives from examination of inter-residue contacts. We describe residue distribution rules for a large group of β-sandwich-like proteins characterized by a specific arrangement of strands in their two β-sheets. It was shown that this method has very high accuracy (approximately 85%). The advantage of the residue rule approach is that it makes possible prediction of protein folding even in polypeptide chains that have very low global sequence similarities, as low as 18%. Another potential benefit is that a better understanding of which residues play essential roles in a given protein fold may facilitate rational protein engineering design.
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48
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Paul S, Paul S. The influence of trehalose on hydrophobic interactions of small nonpolar solute: A molecular dynamics simulation study. J Chem Phys 2013; 139:044508. [DOI: 10.1063/1.4816521] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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49
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Ahmad E, Rabbani G, Zaidi N, Khan MA, Qadeer A, Ishtikhar M, Singh S, Khan RH. Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges. J Biomol Struct Dyn 2013; 31:630-48. [DOI: 10.1080/07391102.2012.706081] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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50
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Negrón LM, Meléndez-Contés Y, Rivera JM. Patchy supramolecules as versatile tools to probe hydrophobicity in nanoglobular systems. J Am Chem Soc 2013; 135:3815-7. [PMID: 23432409 PMCID: PMC3646530 DOI: 10.1021/ja401373h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe precise supramolecules that enable the evaluation of the effective hydrophobicity of amphiphilic or "patchy" nanoglobular systems. These supramolecules exhibit the lower critical solution temperature phenomenon, which provides a quantitative measure of their effective hydrophobicity. Specifically, two isomeric 8-aryl-2'-deoxyguanosine derivatives with a transposed pair of methylene groups self-assemble into hexadecameric nanoglobular supramolecular G-quadruplexes (SGQs) that show large differences in their transition temperatures as determined by turbidity and differential scanning calorimetry studies. Molecular modeling studies suggested that differential clustering of the hydrophobic patches on the surface is responsible for the striking differences between the two isomeric supramolecules.
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Affiliation(s)
- Luis M. Negrón
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, P.R. 00931
| | - Yazmary Meléndez-Contés
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, P.R. 00931
| | - José M. Rivera
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, P.R. 00931
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