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Zhang B, Kang C, Davydov DR. Conformational Rearrangements in the Redox Cycling of NADPH-Cytochrome P450 Reductase from Sorghum bicolor Explored with FRET and Pressure-Perturbation Spectroscopy. BIOLOGY 2022; 11:biology11040510. [PMID: 35453709 PMCID: PMC9030436 DOI: 10.3390/biology11040510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 12/01/2022]
Abstract
Simple Summary NADPH-cytochrome P450 reductase (CPR) enzymes are known to undergo an ample conformational transition between the closed and open states in the process of their redox cycling. To explore the conformational landscape of CPR from the potential biofuel crop Sorghum bicolor (SbCPR), we incorporated a FRET donor/acceptor pair into the enzyme and employed rapid scanning stop-flow and pressure perturbation spectroscopy to characterize the equilibrium between its open and closed states at different stages of the redox cycle. Our results suggest the presence of several open conformational sub-states differing in the system volume change associated with the opening transition (ΔV0). Although the closed conformation always predominates in the conformational landscape, the population of the open conformations increases by order of magnitude upon the two-electron reduction and the formation of the disemiquinone state of the enzyme. In addition to elucidating the functional choreography of plant CPRs, our study demonstrates the high exploratory potential of a combination of the pressure-perturbation approach with the FRET-based monitoring of protein conformational transitions. Abstract NADPH-cytochrome P450 reductase (CPR) from Sorghum bicolor (SbCPR) serves as an electron donor for cytochrome P450 essential for monolignol and lignin production in this biofuel crop. The CPR enzymes undergo an ample conformational transition between the closed and open states in their functioning. This transition is triggered by electron transfer between the FAD and FMN and provides access of the partner protein to the electron-donating FMN domain. To characterize the electron transfer mechanisms in the monolignol biosynthetic pathway better, we explore the conformational transitions in SbCPR with rapid scanning stop-flow and pressure-perturbation spectroscopy. We used FRET between a pair of donor and acceptor probes incorporated into the FAD and FMN domains of SbCPR, respectively, to characterize the equilibrium between the open and closed states and explore its modulation in connection with the redox state of the enzyme. We demonstrate that, although the closed conformation always predominates in the conformational landscape, the population of open state increases by order of magnitude upon the formation of the disemiquinone state. Our results are consistent with several open conformation sub-states differing in the volume change (ΔV0) of the opening transition. While the ΔV0 characteristic of the oxidized enzyme is as large as −88 mL/mol, the interaction of the enzyme with the nucleotide cofactor and the formation of the double-semiquinone state of CPR decrease this value to −34 and −18 mL/mol, respectively. This observation suggests that the interdomain electron transfer in CPR increases protein hydration, while promoting more open conformation. In addition to elucidating the functional choreography of plant CPRs, our study demonstrates the high exploratory potential of a combination of the pressure-perturbation approach with the FRET-based monitoring of protein conformational transitions.
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Gerringer ME, Yancey PH, Tikhonova OV, Vavilov NE, Zgoda VG, Davydov DR. Pressure tolerance of deep-sea enzymes can be evolved through increasing volume changes in protein transitions: a study with lactate dehydrogenases from abyssal and hadal fishes. FEBS J 2020; 287:5394-5410. [PMID: 32250538 PMCID: PMC7818408 DOI: 10.1111/febs.15317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 03/15/2020] [Accepted: 03/27/2020] [Indexed: 11/28/2022]
Abstract
We explore the principles of pressure tolerance in enzymes of deep-sea fishes using lactate dehydrogenases (LDH) as a case study. We compared the effects of pressure on the activities of LDH from hadal snailfishes Notoliparis kermadecensis and Pseudoliparis swirei with those from a shallow-adapted Liparis florae and an abyssal grenadier Coryphaenoides armatus. We then quantified the LDH content in muscle homogenates using mass-spectrometric determination of the LDH-specific conserved peptide LNLVQR. Existing theory suggests that adaptation to high pressure requires a decrease in volume changes in enzymatic catalysis. Accordingly, evolved pressure tolerance must be accompanied with an important reduction in the volume change associated with pressure-promoted alteration of enzymatic activity ( Δ V PP ∘ ). Our results suggest an important revision to this paradigm. Here, we describe an opposite effect of pressure adaptation-a substantial increase in the absolute value of Δ V PP ∘ in deep-living species compared to shallow-water counterparts. With this change, the enzyme activities in abyssal and hadal species do not substantially decrease their activity with pressure increasing up to 1-2 kbar, well beyond full-ocean depth pressures. In contrast, the activity of the enzyme from the tidepool snailfish, L. florae, decreases nearly linearly from 1 to 2500 bar. The increased tolerance of LDH activity to pressure comes at the expense of decreased catalytic efficiency, which is compensated with increased enzyme contents in high-pressure-adapted species. The newly discovered strategy is presumably used when the enzyme mechanism involves the formation of potentially unstable excited transient states associated with substantial changes in enzyme-solvent interactions.
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Zhang BW, Matubayasi N, Levy RM. Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals. J Phys Chem B 2020; 124:5220-5237. [PMID: 32469519 DOI: 10.1021/acs.jpcb.0c02721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Endpoints density functional theory (DFT) provides a framework for calculating the excess chemical potential of a solute in solution using solvent distribution functions obtained from both physical endpoints of a hypothetical charging process which transforms the solvent density from that of the pure liquid to the solution state. In this work, the endpoints DFT equations are formulated in terms of the indirect (solvent-mediated) contribution ω(x) to the solute-solvent potential of mean force, and their connections are established with the conventional DFT expressions which are based on the use of direct correlation functions. ω actually corresponds to the free-energy cost to move a cavity particle (a tagged solvent molecule which interacts with the other solvent molecules but not the solute) from the bulk to the configuration x of a solvent molecule relative to the solute and is a suitable variable to describe the solvent effects on the solute-solvent interactions. HNC and PY type approximations are then used to integrate the DFT charging integral involved in the exact expression for the excess chemical potential. With these approximations, molecular simulations are to be performed at the two endpoints of solute insertion: pure solvent without the solute and the solution system with the fully coupled solute-solvent interaction. An endpoints method thus utilizes the ensembles of intermolecular configurations of physical interest, which are often readily accessible with MD simulations given the present computational power. To illustrate properties of the formulation, we perform simulations of model systems consisting of a cavity particle in an aqueous solution containing a spherical hydrophobic solute of three different sizes from which ω(x) and the solute chemical potential can be calculated using endpoints DFT expressions. These are compared with corresponding results obtained using the approximations needed in order to evaluate the endpoints DFT charging integral when cavity particle simulation data is not available. We analyze a new approximation (two-points quadratic HNC) to the DFT charging integral which captures the correct behavior of the cavity distributions at both endpoints of the solute insertion. The behavior of the cavity particle in simple and complex liquids plays an important role in various theoretical treatments of the solute chemical potential. For pure Lennard-Jones fluids, the free energy to bring a cavity particle from the bulk to the center of a fluid particle is negative. However, for solutes of varying size, this is not generally true for Lennard-Jones fluids or the systems studied in this work. We carry out energetic and structural analyses of the cavity particle in aqueous solution with hydrophobic solutes of varying size and discuss the results in the context of the hydrophobic effect.
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Affiliation(s)
- Bin W Zhang
- Center for Biophysics and Computational Biology, and Department of Chemistry, 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
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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Krupskaya TV, Elagina NV, Borisenko NV, Turov VV. Features of the Hydration of Consolidated Methyl Silica and a Composite Based on It and Succinic Acid. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2019. [DOI: 10.1134/s0036024419070136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gun'ko VM, Turov VV, Pakhlov EM, Krupska TV, Borysenko MV, Kartel MT, Charmas B. Water Interactions with Hydrophobic versus Hydrophilic Nanosilica. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:12145-12153. [PMID: 30212631 DOI: 10.1021/acs.langmuir.8b03110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It is well-known that interaction of hydrophobic powders with water is weak, and upon mixing, they typically form separated phases. Preparation of hydrophobic nanosilica AM1 with a relatively large content of bound water with no formation of separated phases was the aim of this study. Unmodified nanosilica A-300 and initial AM1 (A-300 completely hydrophobized by dimethyldichlorosilane), compacted A-300 (cA-300), and compacted AM1 (cAM1) containing 50-58 wt % of bound water were studied using low-temperature 1H NMR spectroscopy, thermogravimetry, infrared spectroscopy, microscopy, small-angle X-ray scattering, nitrogen adsorption, and theoretical modeling. After mechanical activation (∼20 atm) upon stirring of AM1/water mixture at the degree of hydration h = 1.0 or 1.4 g of distilled water per gram of dry silica, all water is bound and the blend has the bulk density of 0.7 g/cm3. The temperature and interfacial behaviors of bound water depend strongly on a dispersion media type (air, chloroform, and chloroform with trifluoroacetic acid (4:1)) because the boundary area between immiscible water and chloroform should be minimal. Water and chloroform molecules are of different sizes affecting their distribution in pores (voids between silica nanoparticles in their aggregates) of different sizes. Structural, morphological, and textural characteristics of silicas, and environmental features affect not only the distribution of bound water, but also the amounts of strongly (frozen at T < 260 K) and weakly (frozen at 260 K < T < 273 K) bound and strongly (chemical shift δH = 4-6 ppm) and weakly (δH = 1-2 ppm) associated waters. Despite the changes in the characteristics of cAM1, it demonstrates a flotation effect. The developed system with cAM1/bound water could be of interest from a practical point of view due to controlled interactions with aqueous surroundings.
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Affiliation(s)
- Volodymyr M Gun'ko
- Chuiko Institute of Surface Chemistry , 17 General Naumov Street , Kyiv 03164 , Ukraine
| | - Volodymyr V Turov
- Chuiko Institute of Surface Chemistry , 17 General Naumov Street , Kyiv 03164 , Ukraine
| | - Evgeniy M Pakhlov
- Chuiko Institute of Surface Chemistry , 17 General Naumov Street , Kyiv 03164 , Ukraine
| | - Tetyana V Krupska
- Chuiko Institute of Surface Chemistry , 17 General Naumov Street , Kyiv 03164 , Ukraine
| | - Mykola V Borysenko
- Chuiko Institute of Surface Chemistry , 17 General Naumov Street , Kyiv 03164 , Ukraine
| | - Mykola T Kartel
- Chuiko Institute of Surface Chemistry , 17 General Naumov Street , Kyiv 03164 , Ukraine
| | - Barbara Charmas
- Faculty of Chemistry , Maria Curie-Skłodowska University , 20031 Lublin , Poland
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Shibuta S, Imamura H. Hydration Promoted by a Methylene Group: A Volumetric Study on Alkynes in Water. J Phys Chem B 2018; 122:2985-2991. [PMID: 29486128 DOI: 10.1021/acs.jpcb.8b00843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrocarbons including a methylene group are generally considered a hydrophobic building block, in the sense that the density of their hydration water is lower than that of bulk water. However, is the methylene group always hydrophobic? In this study, we experimentally determined the partial molar volume of a methylene group in water as 14.01 ± 0.46 cm3 mol-1 for 1-alkyne, 9.83 ± 0.35 cm3 mol-1 for 2-alkyne, and 11.39 ± 0.55 cm3 mol-1 for 3-alkyne. These values are all unusually small compared to the ∼16 cm3 mol-1 for model compounds from the literature. The subsequent volumetric analysis on the basis of the Kirkwood-Buff parameter indicates that the hydration water is enriched by the addition of a methylene group for 2-alkyne, while it is depleted for the reported model compounds that contain hydrophilic functional groups, 1-alkyne, and 3-alkyne. Our findings suggest that the triple bonded carbons in 2-alkyne that reduce hydration water act as a hydrophobic group in 2-alkyne. Thus, the methylene group should be called "hydrophilic" in this case because it actually recovers the hydration water when placed next to more hydrophobic groups. Therefore, we conclude that the hydrophobicity of a methylene group varies depending on its hydration environment due to other functional groups in the solute.
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Affiliation(s)
- Satoshi Shibuta
- Chiba Institute of Technology , 2-1-1 Shibazono , Narashino , Chiba 275-0023 , Japan
| | - Hiroshi Imamura
- Department of Applied Chemistry , College of Life Sciences, Ritsumeikan University , 1-1-1 Noji-Higashi , Kusatsu , Shiga 525-8577 , Japan
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Davydov DR, Yang Z, Davydova N, Halpert JR, Hubbell WL. Conformational Mobility in Cytochrome P450 3A4 Explored by Pressure-Perturbation EPR Spectroscopy. Biophys J 2016; 110:1485-1498. [PMID: 27074675 DOI: 10.1016/j.bpj.2016.02.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 12/04/2015] [Accepted: 02/15/2016] [Indexed: 11/18/2022] Open
Abstract
We used high hydrostatic pressure as a tool for exploring the conformational landscape of human cytochrome P450 3A4 (CYP3A4) by electron paramagnetic resonance and fluorescence spectroscopy. Site-directed incorporation of a luminescence resonance energy transfer donor-acceptor pair allowed us to identify a pressure-dependent equilibrium between two states of the enzyme, where an increase in pressure increased the spatial separation between the two distantly located fluorophores. This transition is characterized by volume change (ΔV°) and P1/2 values of -36.8 ± 5.0 mL/mol and 1.45 ± 0.33 kbar, respectively, which corresponds to a Keq° of 0.13 ± 0.06, so that only 15% of the enzyme adopts the pressure-promoted conformation at ambient pressure. This pressure-promoted displacement of the equilibrium is eliminated by the addition of testosterone, an allosteric activator. Using site-directed spin labeling, we demonstrated that the pressure- and testosterone-sensitive transition is also revealed by pressure-induced changes in the electron paramagnetic resonance spectra of a nitroxide side chain placed at position 85 or 409 of the enzyme. Furthermore, we observed a pressure-induced displacement of the emission maxima of a solvatochromic fluorophore (7-diethylamino-3-((((2-maleimidyl)ethyl)amino)carbonyl) coumarin) placed at the same positions, which suggests a relocation to a more polar environment. Taken together, the results reveal an effector-dependent conformational equilibrium between open and closed states of CYP3A4 that involves a pronounced change at the interface between the region of α-helices A/A' and the meander loop of the enzyme, where residues 85 and 409 are located. Our study demonstrates the high potential of pressure-perturbation strategies for studying protein conformational landscapes.
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Affiliation(s)
- Dmitri R Davydov
- Department of Chemistry, Washington State University, Pullman, Washington; V. N. Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, Russia.
| | - Zhongyu Yang
- Jules Stein Eye Institute, University of California, Los Angeles, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
| | - Nadezhda Davydova
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - James R Halpert
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - Wayne L Hubbell
- Jules Stein Eye Institute, University of California, Los Angeles, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California
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Partial molar volume of nonionic surfactants in aqueous solution studied by the KB/3D-RISM–KH theory. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Aguilar K, Garvín A, Azuara E, Ibarz A. Rate-Controlling Mechanisms in the Photo-degradation of 5-Hydroxymethylfurfural. FOOD BIOPROCESS TECH 2016. [DOI: 10.1007/s11947-016-1729-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Distinct configurations of cations and water in the selectivity filter of the KcsA potassium channel probed by 3D-RISM theory. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.03.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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Yoshida N. Efficient implementation of the three-dimensional reference interaction site model method in the fragment molecular orbital method. J Chem Phys 2014; 140:214118. [DOI: 10.1063/1.4879795] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Phongphanphanee S, Yoshida N, Oiki S, Hirata F. Probing “ambivalent” snug-fit sites in the KcsA potassium channel using three-dimensional reference interaction site model (3D-RISM) theory. PURE APPL CHEM 2014. [DOI: 10.1515/pac-2014-5018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The potassium channel is highly selective for K+ over Na+, and the mechanism underlying this selectivity remains unclear. We show the three-dimensional distribution functions (3D-DFs) of small cations (Li+, Na+, and K+) and the free energy profile of ions inside the open selectivity filter (SF) of the KcsA channel. Our previous results [S. Phongphanphanee, N. Yoshida, S. Oiki, F. Hirata. Abstract Book of 5th International Symposium on Molecular Science of Fluctuations toward Biological Functions, P062 (2012)] indicate that the 3D-DF for K+ exhibits distinct peaks at the sites formed by the eight carbonyl oxygen atoms belonging to the surrounding peptide-backbone and residues (the cage site). Li+ has sharp distributions in the 3D-DF at the center of a quadruplex composed of four carbonyl oxygen atoms (the plane site). Na+ has a rather diffuse distribution throughout the SF region with peaks both in the plane and in cage sites. The results provide microscopic evidence of the phenomenological findings that Li+ and Na+ are not excluded from the SF region and that the binding affinity alone does not cause the ion selectivity of KcsA. In the present study, with an ion placed explicitly along the pore axis, the free energy profiles of the ions inside the SF were calculated; from these profiles we suggest a new mechanism for selective K+ permeation. According to the model, a K+ ion must overcome a free energy barrier that is approximately half that of Na+ to exit from either of the SF mouths due to the existence of an intermediate local minimum along the route for climbing the barriers.
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14
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Ratkova EL, Fedorov MV. On a relationship between molecular polarizability and partial molar volume in water. J Chem Phys 2011; 135:244109. [DOI: 10.1063/1.3672094] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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15
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Rouha M, Nezbeda I. Excess properties of aqueous solutions: hard spheres versus pseudo-hard bodies. Mol Phys 2011. [DOI: 10.1080/00268976.2010.542779] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Grigera JR, McCarthy AN. The behavior of the hydrophobic effect under pressure and protein denaturation. Biophys J 2010; 98:1626-31. [PMID: 20409483 DOI: 10.1016/j.bpj.2009.12.4298] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2009] [Revised: 11/18/2009] [Accepted: 12/07/2009] [Indexed: 11/25/2022] Open
Abstract
It is well known that proteins denature under high pressure. The mechanism that underlies such a process is still not clearly understood, however, giving way to controversial interpretations. Using molecular dynamics simulation on systems that may be regarded experimentally as limiting examples of the effect of high pressure on globular proteins, such as lysozyme and apomyoglobin, we have effectively reproduced such similarities and differences in behavior as are interpreted from experiment. From the analysis of such data, we explain the experimental evidence at hand through the effect of pressure on the change of water structure, and hence the weakening of the hydrophobic effect that is known to be the main driving force in protein folding.
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Affiliation(s)
- J Raúl Grigera
- Institute of Physics of Fluids and Biological Systems, (La Plata UNLP-CONICET) 59-789, B1900BTE, La Plata, Argentina.
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Kasezawa K, Kato M. Effect of Pressure on Conformational Equilibria of 1-Chloropropane and 1-Bromopropane in Water and Organic Solvents: A Raman Spectroscopic Study. J Phys Chem B 2009; 113:8607-12. [DOI: 10.1021/jp900073p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kunihiro Kasezawa
- Graduate School of Science and Engineering, and Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Minoru Kato
- Graduate School of Science and Engineering, and Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
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Noé F, Daidone I, Smith JC, di Nola A, Amadei A. Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation. J Phys Chem B 2008; 112:11155-63. [DOI: 10.1021/jp801391t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Frank Noé
- DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831-6255, Department of Chemistry, University of Rome “La Sapienza”, P. le Aldo Moro 5, 00185 Rome, Italy, and Department of Chemical
| | - Isabella Daidone
- DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831-6255, Department of Chemistry, University of Rome “La Sapienza”, P. le Aldo Moro 5, 00185 Rome, Italy, and Department of Chemical
| | - Jeremy C. Smith
- DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831-6255, Department of Chemistry, University of Rome “La Sapienza”, P. le Aldo Moro 5, 00185 Rome, Italy, and Department of Chemical
| | - Alfredo di Nola
- DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831-6255, Department of Chemistry, University of Rome “La Sapienza”, P. le Aldo Moro 5, 00185 Rome, Italy, and Department of Chemical
| | - Andrea Amadei
- DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany, Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany, Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, Tennessee 37831-6255, Department of Chemistry, University of Rome “La Sapienza”, P. le Aldo Moro 5, 00185 Rome, Italy, and Department of Chemical
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Imai T, Hisadomi Y, Sawamura S, Taniguchi Y. Uncovering the physical origin of the difference between aliphatic chain and aromatic ring in the “hydrophobic” effects on partial molar volume. J Chem Phys 2008; 128:044502. [DOI: 10.1063/1.2828768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Mikheev YA, Guseva LN, Davydov EY, Ershov YA. The hydration of hydrophobic substances. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2007. [DOI: 10.1134/s0036024407120011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Takekiyo T, Yoshimura Y. Raman spectroscopic study on the hydration structures of tetraethylammonium cation in water. J Phys Chem A 2007; 110:10829-33. [PMID: 16970378 DOI: 10.1021/jp062911m] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational changes of tetraethylammonium ion (Et4N+) in aqueous solution have been studied by Raman spectroscopy as functions of pressure and concentration. The difference in the partial molar volume (Delta V(tg x tg-->tt x tt)) between the trans-gauche x trans-gauche (tg x tg) and trans-trans x trans-trans (tt x tt) conformers of Et4N+ ion has been calculated from the pressure dependence of the relative Raman intensity ratio between the conformers. We discuss about the Delta V(tg x tg-->tt x tt) with two contributions from the molecular and hydration volumes. Delta V(tg x tg-->tt x tt) is found to be negative, and this is mainly due to the large molecular volume contribution. The value of Delta V(tg x tg-->tt x tt) becomes smaller with increasing R probably due to the hydration volume contribution. In view of the pressure and concentration dependences, the water molecules around Et4N+ ions at R = 19 (R= moles of water/moles of salt) mainly form the hydrophobic hydration. The hydrophobic hydration may prefer the tt x tt conformer to the tg x tg conformer. On the other hand, the hydration structure at R = 4 no longer forms the hydrophobic hydration and changes to another type of hydration, where the medium H-bond component is the dominant species. The increase of the ion-ion interactions with decreasing R induces large fractions of the tg x tg conformer.
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Affiliation(s)
- Takahiro Takekiyo
- Department of Applied Chemistry, National Defense Academy, Yokosuka, Kanagawa 239-8686, Japan.
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Imai T, Ohyama S, Kovalenko A, Hirata F. Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin. Protein Sci 2007; 16:1927-33. [PMID: 17660257 PMCID: PMC2206979 DOI: 10.1110/ps.072909007] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The partial molar volume (PMV) change associated with the pressure-induced structural transition of ubiquitin is analyzed by the three-dimensional reference interaction site model (3D-RISM) theory of molecular solvation. The theory predicts that the PMV decreases upon the structural transition, which is consistent with the experimental observation. The volume decomposition analysis demonstrates that the PMV reduction is primarily caused by the decrease in the volume of structural voids in the protein, which is partially canceled by the volume expansion due to the hydration effects. It is found from further analysis that the PMV reduction is ascribed substantially to the penetration of water molecules into a specific part of the protein. Based on the thermodynamic relation, this result implies that the water penetration causes the pressure-induced structural transition. It supports the water penetration model of pressure denaturation of proteins proposed earlier.
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Affiliation(s)
- Takashi Imai
- Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
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Sumi T, Sekino H. Integral equation study of hydrophobic interaction: A comparison between the simple point charge model for water and a Lennard-Jones model for solvent. J Chem Phys 2007; 126:144508. [PMID: 17444724 DOI: 10.1063/1.2718520] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hydrophobic interaction that is characterized by a potential of mean force (PMF) between spherical apolar solutes immersed in the simple point charge (SPCE) model for water was studied using an interaction site model integral equation based on a density-functional theory for molecular fluids. For comparison with the PMFs for various size solutes in the SPCE model, the PMFs in a Lennard-Jones (LJ) model for a solvent whose diameter is same as the SPCE model were also studied using a hypernetted chain integral equation. It is noted in the LJ model that the hydrogen bond and its network structure are completely ignored, but the translational entropy is taken into account. Both PMFs obtained from the SPCE model and from the LJ model have a large first minimum at a contact distance of solutes. In the case that the solute size is about three times larger than water, these PMFs also have a large maximum at a longer distance than the contact position. The strong attraction is attributed to the translational entropy of the solvent, and that the large activation barrier is arising from the weak attraction between the solute and the solvent. The comparison between the SPCE model and the LJ solvent model suggests that the qualitative description of the hydrophobic interaction is possible by using the LJ solvent model. On the other hand, the dewetting tendency on the surface of the apolar solute in a room condition is observed only on the SPCE model. These results indicate that the characteristics of water such as the hydrogen bond affect rather the hydrophobic hydration than the hydrophobic interaction.
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Affiliation(s)
- Tomonari Sumi
- Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
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Moghaddam MS, Chan HS. Pressure and temperature dependence of hydrophobic hydration: Volumetric, compressibility, and thermodynamic signatures. J Chem Phys 2007; 126:114507. [PMID: 17381220 DOI: 10.1063/1.2539179] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The combined effect of pressure and temperature on hydrophobic hydration of a nonpolar methanelike solute is investigated by extensive simulations in the TIP4P model of water. Using test-particle insertion techniques, free energies of hydration under a range of pressures from 1 to 3000 atm are computed at eight temperatures ranging from 278.15 to 368.15 K. Corresponding enthalpy, entropy, and heat capacity accompanying the hydration process are estimated from the temperature dependence of the free energies. Partial molar and excess volumes calculated using pressure derivatives of the simulated free energies are consistent with those determined by direct volume simulations; but direct volume determination offers more reliable estimates for compressibility. At 298.15 K, partial molar and excess isothermal compressibilities of methane are negative at 1 atm. Partial molar and excess adiabatic (isentropic) compressibilities are estimated to be also negative under the same conditions. But partial molar and excess isothermal compressibilities are positive at high pressures, with a crossover from negative to positive compressibility at approximately 100-1000 atm. This trend is consistent with experiments on aliphatic amino acids and pressure-unfolded states of proteins. For the range of pressures simulated, hydration heat capacity exhibits little pressure dependence, also in apparent agreement with experiment. When pressure is raised at constant room temperature, hydration free energy increases while its entropic component remains essentially constant. Thus, the increasing unfavorability of hydration under raised pressure is seen as largely an enthalpic effect. Ramifications of the findings of the authors for biopolymer conformational transitions are discussed.
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Affiliation(s)
- Maria Sabaye Moghaddam
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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26
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Graziano G. Partial molar volume of n-alcohols at infinite dilution in water calculated by means of scaled particle theory. J Chem Phys 2006; 124:134507. [PMID: 16613461 DOI: 10.1063/1.2186319] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The partial molar volume of n-alcohols at infinite dilution in water is smaller than the molar volume in the neat liquid phase. It is shown that the formula for the partial molar volume at infinite dilution obtained from the scaled particle theory equation of state for binary hard sphere mixtures is able to reproduce in a satisfactory manner the experimental data over a large temperature range. This finding implies that the packing effects play the fundamental role in determining the partial molar volume at infinite dilution in water also for solutes, such as n-alcohols, forming H bonds with water molecules. Since the packing effects in water are largely related to the small size of its molecules, the latter feature is the ultimate cause of the decrease in partial molar volume associated with the hydrophobic effect.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Via Port' Arsa, 11-82100 Benevento, Italy.
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Osaka N, Shibayama M. Pressure-induced phase transitions of hydrophobically solvated block-copolymer solutions. PHYSICAL REVIEW LETTERS 2006; 96:048303. [PMID: 16486903 DOI: 10.1103/physrevlett.96.048303] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2005] [Indexed: 05/06/2023]
Abstract
The structures of poly(2-(2-ethoxy)ethoxyethyl vinyl ether)-block-poly(2-methoxyethyl vinyl ether) in D2O have been investigated with small-angle neutron scattering (SANS) as a function of temperature T and pressure P. At ambient pressure, the solution underwent a two-step transition at 40 and 65 degrees C, both of which were convex-upward functions of P having a maximum around P0 approximately 150 MPa. The first transition was assigned to a microphase separation to form a bcc structure, and the second was to a macrophase separation. Pressurizing at 28 degrees C resulted in a macrophase separation with divergence at 350 MPa. At 45 degrees C, a reentrant microphase separation was observed by increasing P. Differences in the states of hydrophobic solvation in the low (P<P0) and high pressure regions (P>P0) are discussed based on the SANS structure factors.
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Affiliation(s)
- Noboru Osaka
- Neutron Science Laboratory, Institute for Solid State Physics, The University of Tokyo, Tokai, Ibaraki 319-1106, Japan
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Imai T, Hirata F. Reply to “Comment on ‘Hydrophobic effects on partial molar volume’ ” [J. Chem. Phys. 123, 167103 (2005)]. J Chem Phys 2005. [DOI: 10.1063/1.2085029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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30
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Graziano G. Comment on “Hydrophobic effects on partial molar volume” [J. Chem. Phys. 122, 094509 (2005)]. J Chem Phys 2005; 123:167103; author reply 167104. [PMID: 16268729 DOI: 10.1063/1.2085028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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