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Bhagat S, Pal S. A Heteronuclear NMR Study of Aqueous Lithium Salt Solutions of l-Alanine: Revealing Solute Hydrophobic Association through the NMR B' Coefficient. J Phys Chem B 2023; 127:7027-7034. [PMID: 37526300 DOI: 10.1021/acs.jpcb.3c04144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
In the present study, a set of heteronuclear NMR approaches has been adopted to investigate the solution behavior of a small hydrophobic solute l-alanine in the presence of lithium (Li) salts. The presence of salts plays a major role in determining the structure and solvation of biomolecules. It therefore evokes interest to understand the effect of Li salts on amino acids (alanine), the building block of biomolecules. The ionic solute dynamics in the present case has been probed using 1H, 7Li, and 13C nuclei available in the aqueous Li salt solution of l-alanine. Nuclear longitudinal spin relaxation of alanine protons was examined at a variable concentration range of three lithium salts, i.e., LiCl, Li2SO4 and LiClO4, to introduce the NMR B' coefficient for each salt defining ionic solute/solvent interaction in the solution. Analysis of the active relaxation mechanism of 7Li spin-lattice relaxation further revealed the presence of alanine in the solvation shell of Li ion depending on the anionic counterpart.
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Affiliation(s)
- Sakshi Bhagat
- Department of Chemistry, Indian Institute of Technology, Jodhpur, India 342037
| | - Samanwita Pal
- Department of Chemistry, Indian Institute of Technology, Jodhpur, India 342037
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2
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Asakereh I, Lee K, Francisco OA, Khajehpour M. Hofmeister Effects of Group II Cations as Seen in the Unfolding of Ribonuclease A. Chemphyschem 2022; 23:e202100884. [PMID: 35421259 DOI: 10.1002/cphc.202100884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/14/2022] [Indexed: 11/06/2022]
Abstract
This work studies the effects of alkaline-earth cation addition upon the unfolding free energy of a model protein, pancreatic Ribonuclease A (RNase A) by DSC analysis. RNase A was chosen because it: a) does not specifically bind Mg 2+ , Ca 2+ and Sr 2+ cations and b) maintains its structural integrity throughout a large pH range. We have measured and compared the effects of NaCl, MgCl 2 , CaCl 2 and SrCl 2 addition on the melting point of RNase A. Our results show that even though the addition of group II cations to aqueous solvent reduces the solubility of nonpolar residues (and enhances the hydrophobic effect), their interactions with the amide moieties are strong enough to "salt-them-in" the solvent, thereby causing an overall reduction in protein stability. We demonstrate that amide-cation interactions are a major contributor to the observed "Hofmeister Effects" of group II cations in protein folding. Our analysis suggests that protein folding "Hofmeister Effects" of group II cations, are mostly the aggregate sum of how cation addition simultaneously salts-out hydrophobic moieties through increasing the cavitation free energy, while promoting the salting-in of amide moieties through contact pair formation.
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Affiliation(s)
- Iman Asakereh
- University of Manitoba, Chemistry, Dept of Chemistry, University of Manitob, Winnipeg, R3T2N2, Winnipeg, CANADA
| | - Katherine Lee
- University of Manitoba, Chemistry, Dept of Chemistry, University of Manitob, Winnipeg, R3T2N2, Winnipeg, CANADA
| | - Olga A Francisco
- University of Manitoba, Chemistry, Dept of Chemistry, University of Manitob, Winnipeg, R3T2N2, Winnipeg, CANADA
| | - Mazdak Khajehpour
- University of Manitoba, Chemistry, Dept of Chemistry, University of Manitob, R3T2N2, Winnipeg, CANADA
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3
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Abstract
The intrinsic nature of macrocyclic molecules to preferentially absorb a specific solute has been opening up supramolecular chemistry. Nevertheless, the determinant factor with molecular perspectives in promoting host-guest complexations remains inconclusive, due to the lack of rigorous thermodynamic examination on the guest solubility inside the host. Here, we quantify the solute-solvent energetic and entropic contributions between the end states and on the docking route during inclusion of noble gases in cucurbit[5]uril, cucurbit[6]uril, and α-cyclodextrin, using molecular dynamics simulations in combination with the potential distribution theorem. Results show that in all of the pairs examined both the solute-solvent energy and entropy favor the inclusion, while the former is rather dominant. The frequency of interior drying, which pertains to the entropic contribution, differs between the hosts and is controlled by the existence of lid water at portal and the flexibility of host framework. Moreover, the hosts exhibit various types of absorption manners, involving non-, single-, and double-free-energy barriers.
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Affiliation(s)
- Yifeng Yao
- Department of Chemistry, Zhejiang University, Hangzhou, 310028, P. R. China
| | - Xuan Zhang
- Department of Chemistry, Zhejiang University, Hangzhou, 310028, P. R. China
| | - Kenji Mochizuki
- Department of Chemistry, Zhejiang University, Hangzhou, 310028, P. R. China
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Effect of salinity on the zinc(II) binding efficiency of siderophore functional groups and implications for salinity tolerance mechanisms in barley. Sci Rep 2021; 11:16704. [PMID: 34408172 PMCID: PMC8373983 DOI: 10.1038/s41598-021-95736-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/23/2021] [Indexed: 12/02/2022] Open
Abstract
Bacteria, fungi and grasses use siderophores to access micronutrients. Hence, the metal binding efficiency of siderophores is directly related to ecosystem productivity. Salinization of natural solutions, linked to climate change induced sea level rise and changing precipitation patterns, is a serious ecological threat. In this study, we investigate the impact of salinization on the zinc(II) binding efficiency of the major siderophore functional groups, namely the catecholate (for bacterial siderophores), α-hydroxycarboxylate (for plant siderophores; phytosiderophores) and hydroxamate (for fungal siderophores) bidentate motifs. Our analysis suggests that the order of increasing susceptibility of siderophore classes to salinity in terms of their zinc(II) chelating ability is: hydroxamate < catecholate < α-hydroxycarboxylate. Based on this ordering, we predict that plant productivity is more sensitive to salinization than either bacterial or fungal productivity. Finally, we show that previously observed increases in phytosiderophore release by barley plants grown under salt stress in a medium without initial micronutrient deficiencies, are in line with the reduced zinc(II) binding efficiency of the α-hydroxycarboxylate ligand and hence important for the salinity tolerance of whole-plant zinc(II) status.
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Bogunia M, Makowski M. Influence of Ionic Strength on Hydrophobic Interactions in Water: Dependence on Solute Size and Shape. J Phys Chem B 2020; 124:10326-10336. [PMID: 33147018 PMCID: PMC7681779 DOI: 10.1021/acs.jpcb.0c06399] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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Hydrophobicity is a phenomenon of
great importance in biology,
chemistry, and biochemistry. It is defined as the interaction between
nonpolar molecules or groups in water and their low solubility. Hydrophobic
interactions affect many processes in water, for example, complexation,
surfactant aggregation, and coagulation. These interactions play a
pivotal role in the formation and stability of proteins or biological
membranes. In the present study, we assessed the effect of ionic strength,
solute size, and shape on hydrophobic interactions between pairs of
nonpolar particles. Pairs of methane, neopentane, adamantane, fullerene,
ethane, propane, butane, hexane, octane, and decane were simulated
by molecular dynamics in AMBER 16.0 force field. As a solvent, TIP3P
and TIP4PEW water models were used. Potential of mean force (PMF)
plots of these dimers were determined at four values of ionic strength,
0, 0.04, 0.08, and 0.40 mol/dm3, to observe its impact
on hydrophobic interactions. The characteristic shape of PMFs with
three extrema (contact minimum, solvent-separated minimum, and desolvation
maximum) was observed for most of the compounds for hydrophobic interactions.
Ionic strength affected hydrophobic interactions. We observed a tendency
to deepen contact minima with an increase in ionic strength value
in the case of spherical and spheroidal molecules. Additionally, two-dimensional
distribution functions describing water density and average number
of hydrogen bonds between water molecules were calculated in both
water models for adamantane and hexane. It was observed that the density
of water did not significantly change with the increase in ionic strength,
but the average number of hydrogen bonds changed. The latter tendency
strongly depends on the water model used for simulations.
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Affiliation(s)
- Małgorzata Bogunia
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Mariusz Makowski
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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Zhao L, Damodaran S. Hofmeister Order of Anions on Protein Stability Originates from Lifshitz-van der Waals Dispersion Interaction with the Protein Phase. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:12993-13002. [PMID: 31512478 DOI: 10.1021/acs.langmuir.9b00486] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mechanism underpinning the Hofmeister order of anions on protein stability and other physical and biological processes has been a mystery since its discovery in 1888. In the present study, we investigated electrostatic and Lifshitz-van der Waals (L-vdW) dispersion (electrodynamic) interactions between Hofmeister salts and four monomeric globular proteins. It is shown that structure-stabilizing salts exerted positive L-vdW pressure, whereas structure-destabilizing salts exerted negative L-vdW pressure on proteins. The relative order of the L-vdW pressure followed the Hofmeister series and it overshadowed the electrostatic pressure at high salt concentrations. The net change in the thermal denaturation temperature (ΔTd) of proteins in 0.8 M Hofmeister salt solutions followed a linear relationship (r2 > 0.8) with the net electrodynamic pressure regardless of the physicochemical differences between proteins. This study also revealed that segregation of anions into structure stabilizers and destabilizers depended on the dielectric susceptibility of the anion in the ultraviolet region: ions having absorbtion spectrum in the ultraviolet region (e.g., Cl-, Br-, I-, and SCN-) exerted a negative electrodynamic pressure, whereas those with absorbtion spectrum only in the infrared region, for example, SO42-, exerted a positive electrodynamic pressure. The lack of ultraviolet absorption of SO42- ions was because of quenching of ultraviolet radiation by water at below 170 nm.
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Affiliation(s)
- Lei Zhao
- Department of Food Science, College of Agriculture and Life Sciences , University of Wisconsin-Madison , Madison 53706 , Wisconsin , United States
| | - Srinivasan Damodaran
- Department of Food Science, College of Agriculture and Life Sciences , University of Wisconsin-Madison , Madison 53706 , Wisconsin , United States
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Mochizuki K, Sumi T, Koga K. Influence of co-non-solvency on hydrophobic molecules driven by excluded volume effect. Phys Chem Chem Phys 2017; 19:23915-23918. [DOI: 10.1039/c7cp04152g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We demonstrate by molecular dynamics simulation that co-non-solvency of hydrophobic molecules arises from solvent-excluded volume effect.
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Affiliation(s)
- Kenji Mochizuki
- Department of Chemistry
- The University of Utah
- Salt Lake City
- USA
- Research Institute for Interdisciplinary Science
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science
- Okayama University
- Okayama 700-8530
- Japan
- Department of Chemistry
| | - Kenichiro Koga
- Research Institute for Interdisciplinary Science
- Okayama University
- Okayama 700-8530
- Japan
- Department of Chemistry
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8
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Hatano I, Mochizuki K, Sumi T, Koga K. Hydrophobic Polymer Chain in Water That Undergoes a Coil-to-Globule Transition Near Room Temperature. J Phys Chem B 2016; 120:12127-12134. [DOI: 10.1021/acs.jpcb.6b08347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- I. Hatano
- Research
Institute for Interdisciplinary Science and ‡Department of Chemistry, Faculty
of Science, Okayama University, Okayama 700-8530, Japan
| | - K. Mochizuki
- Research
Institute for Interdisciplinary Science and ‡Department of Chemistry, Faculty
of Science, Okayama University, Okayama 700-8530, Japan
| | - T. Sumi
- Research
Institute for Interdisciplinary Science and ‡Department of Chemistry, Faculty
of Science, Okayama University, Okayama 700-8530, Japan
| | - K. Koga
- Research
Institute for Interdisciplinary Science and ‡Department of Chemistry, Faculty
of Science, Okayama University, Okayama 700-8530, Japan
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Macdonald RD, Khajehpour M. Effects of the protein denaturant guanidinium chloride on aqueous hydrophobic contact-pair interactions. Biophys Chem 2014; 196:25-32. [PMID: 25268875 DOI: 10.1016/j.bpc.2014.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/20/2014] [Accepted: 08/20/2014] [Indexed: 11/19/2022]
Abstract
Guanidinium chloride (GdmCl) is one of the most common protein denaturants. Although GdmCl is well known in the field of protein folding, the mechanism by which it denatures proteins is not well understood. In fact, there are few studies looking at its effects on hydrophobic interactions. In this work the effect of GdmCl on hydrophobic interactions has been studied by observing how the denaturant influences model systems of phenyl and alkyl hydrophobic contact pairs. Contact pair formation is monitored through the use of fluorescence spectroscopy, i.e., measuring the intrinsic phenol fluorescence being quenched by carboxylate ions. Hydrophobic interactions are isolated from other interactions through a previously developed methodology. The results show that GdmCl does not significantly affect hydrophobic interactions between small moieties such as methyl groups and phenol; while on the other hand, the interaction of larger hydrophobes such as hexyl and heptyl groups with phenol is significantly destabilized.
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Affiliation(s)
- Ryan D Macdonald
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Mazdak Khajehpour
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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Manna A, Kumar A. Invoking Pairwise Interactions in Water-Promoted Diels-Alder Reactions by using Ionic Liquids as Cosolvents. Chemphyschem 2014; 15:3067-77. [DOI: 10.1002/cphc.201402338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Indexed: 11/09/2022]
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11
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Graziano G. Hydrostatic pressure effect on hydrophobic hydration and pairwise hydrophobic interaction of methane. J Chem Phys 2014; 140:094503. [DOI: 10.1063/1.4866972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Why Do Tetrapropylammonium Chloride and Sulphate Salts Destabilize the Native State of Globular Proteins? ScientificWorldJournal 2014; 2014:870106. [PMID: 24616650 PMCID: PMC3925590 DOI: 10.1155/2014/870106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 12/04/2013] [Indexed: 11/25/2022] Open
Abstract
It has recently been shown that aqueous solutions of tetrapropylammonium chloride and sulphate salts destabilize the folded conformation of Trp-peptides (Dempsey et al., 2011). This result is rationalized by the application of a statistical thermodynamic approach (Graziano, 2010). It is shown that the magnitude of the solvent-excluded volume effect, the main contribution for the native state stability, decreases in both aqueous 2 M TPACl solution and aqueous 1 M TPA2SO4 solution. This happens because TPA+ ions are so large in size and interact so weakly with water molecules, due to their very low charge density, to be able to counteract the electrostrictive effect of chloride and sulphate ions on the water structure, so that the density of their aqueous solutions is smaller or only slightly larger than that of water.
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13
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Booth JJ, Abbott S, Shimizu S. Mechanism of hydrophobic drug solubilization by small molecule hydrotropes. J Phys Chem B 2012; 116:14915-21. [PMID: 23236952 DOI: 10.1021/jp309819r] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drugs that are poorly soluble in water can be solubilized by the addition of hydrotropes. Albeit known for almost a century, how they work at a molecular basis is still controversial due to the lack of a rigorous theoretical basis. To clear up this situation, a combination of experimental data and Fluctuation Theory of Solutions (FTS) has been employed; information on the interactions between all the molecular species present in the solution has been evaluated directly. FTS has identified two major factors of hydrotrope-induced solubilization: preferential hydrotrope-solute interaction and water activity depression. The former is dominated by hydrotrope-solute association, and the latter is enhanced by ionic dissociation and hindered by the self-aggregation of the hydrotropes. Moreover, in stark contrast to previous hypotheses, neither the change of solute hydration nor the water structure accounts for hydrotropy. Indeed, the rigorous FTS poses serious doubts over the other common hypothesis: self-aggregation of the hydrotrope hinders, rather than promotes, solubilization.
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Affiliation(s)
- Jonathan J Booth
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, United Kingdom
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15
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The application of condensed matter methods to the study of the conformation and elastic properties of biopolymers and the transport of DNA through cell membranes. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1022-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Riccio A, Graziano G. Cold unfolding of β-hairpins: A molecular-level rationalization. Proteins 2011; 79:1739-46. [DOI: 10.1002/prot.22997] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/03/2010] [Accepted: 01/14/2011] [Indexed: 11/11/2022]
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18
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19
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Role of solvent accessible surface area in the conformational equilibrium of n-butane in liquids. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2010.12.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Graziano G. On the molecular origin of cold denaturation of globular proteins. Phys Chem Chem Phys 2010; 12:14245-52. [PMID: 20882232 DOI: 10.1039/c0cp00945h] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A polypeptide chain can adopt very different conformations, a fundamental distinguishing feature of which is the water accessible surface area, WASA, that is a measure of the layer around the polypeptide chain where the center of water molecules cannot physically enter, generating a solvent-excluded volume effect. The large WASA decrease associated with the folding of a globular protein leads to a large decrease in the solvent-excluded volume, and so to a large increase in the configurational/translational freedom of water molecules. The latter is a quantity that depends upon temperature. Simple calculations over the -30 to 150 °C temperature range, where liquid water can exist at 1 atm, show that such a gain decreases significantly on lowering the temperature below 0 °C, paralleling the decrease in liquid water density. There will be a temperature where the destabilizing contribution of the polypeptide chain conformational entropy exactly matches the stabilizing contribution of the water configurational/translational entropy, leading to cold denaturation.
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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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Graziano G. Hydrophobic interaction of two large plates: An analysis of salting-in/salting-out effects. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.03.092] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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