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Sun Q, Fu Y, Wang W. Temperature effects on hydrophobic interactions: Implications for protein unfolding. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Morel J, Md Zain SN, Archer R. Comparison of drying techniques for bovine lactoferrin: Iron binding and antimicrobial properties of dried lactoferrin. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2021.105142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Tajoddin NN, Konermann L. Analysis of Temperature-Dependent H/D Exchange Mass Spectrometry Experiments. Anal Chem 2020; 92:10058-10067. [DOI: 10.1021/acs.analchem.0c01828] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nastaran N. Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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Daschakraborty S. How do glycerol and dimethyl sulphoxide affect local tetrahedral structure of water around a nonpolar solute at low temperature? Importance of preferential interaction. J Chem Phys 2018; 148:134501. [PMID: 29626866 DOI: 10.1063/1.5019239] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Glycerol and dimethyl sulphoxide (DMSO) have vital roles in cryoprotection of living cells, tissues, etc. The above action has been directly linked with disruption of hydrogen (H-) bond structure and dynamics of water by these cosolvents at bulk region and around various complex units, such as peptide, amino acid, protein, and lipid membrane. However, the disruption of the local structure of the water solvent around a purely hydrophobic solute is still not studied extensively. The latter is also important in the context of stabilization of protein from cold denaturation. Through all-atom molecular dynamics simulation, we have investigated the comparative effect of glycerol and DMSO on the orientational order of water around a nonpolar solute at -5 °C. A steady reduction of the tetrahedral order of water is observed at bulk (>10 Å distance from the solute) and solute interface (<5.5 Å distance from the solute) with increasing the cosolvent concentration. Contrasting roles of glycerol and DMSO have been evidenced. While DMSO affects the H-bond structure of the interfacial water more than that of the bulk water, glycerol affects the water structure almost uniformly at all regions around the solute. Furthermore, while glycerol helps to retain water molecules at the interface, DMSO significantly reduces the water content in that region. We have put forward a plausible mechanism for these contrasting roles of these cosolvents. The solute-cosolvent hydrophobic-interaction-induced orientational alignment of an interfacial cosolvent molecule determines whether the involvement of the cosolvent molecules in H-bonding with solvent water in the interface is akin to the bulk region or not.
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Espinosa YR, Grigera JR, Caffarena ER. Essential dynamics of the cold denaturation: pressure and temperature effects in yeast frataxin. Proteins 2017; 85:125-136. [PMID: 27802581 DOI: 10.1002/prot.25205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/19/2016] [Accepted: 10/25/2016] [Indexed: 11/09/2022]
Abstract
The cold denaturation of globular proteins is a process that can be caused by increasing pressure or decreasing the temperature. Currently, the action mechanism of this process has not been clearly understood, raising an interesting debate on the matter. We have studied the process of cold denaturation using molecular dynamics simulations of the frataxin system Yfh1, which has a dynamic experimental characterization of unfolding at low and high temperatures. The frataxin model here studied allows a comparative analysis using experimental data. Furthermore, we monitored the cold denaturation process of frataxin and also investigated the effect under the high-pressure regime. For a better understanding of the dynamics and structural properties of the cold denaturation, we also analyzed the MD trajectories using essentials dynamic. The results indicate that changes in the structure of water by the effect of pressure and low temperatures destabilize the hydrophobic interaction modifying the solvation and the system volume leading to protein denaturation. Proteins 2016; 85:125-136. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yanis R Espinosa
- CEQUINOR (CONICET-UNLP), 120 e/61 y 62, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - J Raúl Grigera
- CEQUINOR (CONICET-UNLP), 120 e/61 y 62, Universidad Nacional de La Plata, La Plata, 1900, Argentina
- Departmento de Biología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Ernesto R Caffarena
- Fundação Oswaldo Cruz., Rio de Janeiro, Programa de Computação Científica (PROCC), CEP, 21040-360, Rio de Janeiro, Brazil
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Chatterjee P, Sengupta N. Signatures of protein thermal denaturation and local hydrophobicity in domain specific hydration behavior: a comparative molecular dynamics study. MOLECULAR BIOSYSTEMS 2016; 12:1139-50. [PMID: 26876051 DOI: 10.1039/c6mb00017g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We investigate, using atomistic molecular dynamics simulations, the association of surface hydration accompanying local unfolding in the mesophilic protein Yfh1 under a series of thermal conditions spanning its cold and heat denaturation temperatures. The results are benchmarked against the thermally stable protein, Ubq, and behavior at the maximum stability temperature. Local unfolding in Yfh1, predominantly in the beta sheet regions, is in qualitative agreement with recent solution NMR studies; the corresponding Ubq unfolding is not observed. Interestingly, all domains, except for the beta sheet domains of Yfh1, show increased effective surface hydrophobicity with increase in temperature, as reflected by the density fluctuations of the hydration layer. Velocity autocorrelation functions (VACF) of oxygen atoms of water within the hydration layers and the corresponding vibrational density of states (VDOS) are used to characterize alteration in dynamical behavior accompanying the temperature dependent local unfolding. Enhanced caging effects accompanying transverse oscillations of the water molecules are found to occur with the increase in temperature preferentially for the beta sheet domains of Yfh1. Helical domains of both proteins exhibit similar trends in VDOS with changes in temperature. This work demonstrates the existence of key signatures of the local onset of protein thermal denaturation in solvent dynamical behavior.
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Affiliation(s)
- Prathit Chatterjee
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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Chatterjee P, Bagchi S, Sengupta N. The non-uniform early structural response of globular proteins to cold denaturing conditions: a case study with Yfh1. J Chem Phys 2014; 141:205103. [PMID: 25429964 DOI: 10.1063/1.4901897] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The mechanism of cold denaturation in proteins is often incompletely understood due to limitations in accessing the denatured states at extremely low temperatures. Using atomistic molecular dynamics simulations, we have compared early (nanosecond timescale) structural and solvation properties of yeast frataxin (Yfh1) at its temperature of maximum stability, 292 K (Ts), and the experimentally observed temperature of complete unfolding, 268 K (Tc). Within the simulated timescales, discernible "global" level structural loss at Tc is correlated with a distinct increase in surface hydration. However, the hydration and the unfolding events do not occur uniformly over the entire protein surface, but are sensitive to local structural propensity and hydrophobicity. Calculated infrared absorption spectra in the amide-I region of the whole protein show a distinct red shift at Tc in comparison to Ts. Domain specific calculations of IR spectra indicate that the red shift primarily arises from the beta strands. This is commensurate with a marked increase in solvent accessible surface area per residue for the beta-sheets at Tc. Detailed analyses of structure and dynamics of hydration water around the hydrophobic residues of the beta-sheets show a more bulk water like behavior at Tc due to preferential disruption of the hydrophobic effects around these domains. Our results indicate that in this protein, the surface exposed beta-sheet domains are more susceptible to cold denaturing conditions, in qualitative agreement with solution NMR experimental results.
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Affiliation(s)
- Prathit Chatterjee
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Sayan Bagchi
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Neelanjana Sengupta
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
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Abstract
A theoretical rationalization of the occurrence of cold denaturation for globular proteins was devised, assuming that the effective size of water molecules depends upon temperature [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252]. In the present work, it is shown that the latter assumption is not necessary. By performing the same type of calculations in water, 40% (by weight) methanol, methanol, and carbon tetrachloride, it emerges that cold denaturation occurs only in water due to the special temperature dependence of its density and the small size of its molecules. These two coupled factors determine the magnitude and the temperature dependence of the stabilizing term that measures the gain in configurational/translational entropy of water molecules upon folding of the protein. This term has to be contrasted with the destabilizing contribution measuring the loss in conformational entropy of the polypeptide chain upon folding.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11 - 82100 Benevento, Italy.
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Ben-Naim A. Theoretical aspects of pressure and solute denaturation of proteins: A Kirkwood-buff-theory approach. J Chem Phys 2012; 137:235102. [DOI: 10.1063/1.4772463] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Romero-Romero ML, Inglés-Prieto A, Ibarra-Molero B, Sanchez-Ruiz JM. Highly anomalous energetics of protein cold denaturation linked to folding-unfolding kinetics. PLoS One 2011; 6:e23050. [PMID: 21829584 PMCID: PMC3146537 DOI: 10.1371/journal.pone.0023050] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 07/05/2011] [Indexed: 11/29/2022] Open
Abstract
Despite several careful experimental analyses, it is not yet clear whether protein cold-denaturation is just a “mirror image” of heat denaturation or whether it shows unique structural and energetic features. Here we report that, for a well-characterized small protein, heat denaturation and cold denaturation show dramatically different experimental energetic patterns. Specifically, while heat denaturation is endothermic, the cold transition (studied in the folding direction) occurs with negligible heat effect, in a manner seemingly akin to a gradual, second-order-like transition. We show that this highly anomalous energetics is actually an apparent effect associated to a large folding/unfolding free energy barrier and that it ultimately reflects kinetic stability, a naturally-selected trait in many protein systems. Kinetics thus emerges as an important factor linked to differential features of cold denaturation. We speculate that kinetic stabilization against cold denaturation may play a role in cold adaptation of psychrophilic organisms. Furthermore, we suggest that folding-unfolding kinetics should be taken into account when analyzing in vitro cold-denaturation experiments, in particular those carried out in the absence of destabilizing conditions.
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Affiliation(s)
- M. Luisa Romero-Romero
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Alvaro Inglés-Prieto
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Beatriz Ibarra-Molero
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
- * E-mail:
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Badasyan AV, Tonoyan SA, Mamasakhlisov YS, Giacometti A, Benight AS, Morozov VF. Competition for hydrogen-bond formation in the helix-coil transition and protein folding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:051903. [PMID: 21728568 DOI: 10.1103/physreve.83.051903] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Indexed: 05/31/2023]
Abstract
The problem of the helix-coil transition of biopolymers in explicit solvents, such as water, with the ability for hydrogen bonding with a solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress, or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.
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Affiliation(s)
- A V Badasyan
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, Venezia, Italy.
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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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Riccio A, Ascolese E, Graziano G. Cold denaturation in the Schellman–Brandts model of globular proteins. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.12.088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Dias CL, Ala-Nissila T, Wong-ekkabut J, Vattulainen I, Grant M, Karttunen M. The hydrophobic effect and its role in cold denaturation. Cryobiology 2009; 60:91-9. [PMID: 19616532 DOI: 10.1016/j.cryobiol.2009.07.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 07/14/2009] [Accepted: 07/14/2009] [Indexed: 11/19/2022]
Abstract
The hydrophobic effect is considered the main driving force for protein folding and plays an important role in the stability of those biomolecules. Cold denaturation, where the native state of the protein loses its stability upon cooling, is also attributed to this effect. It is therefore not surprising that a lot of effort has been spent in understanding this phenomenon. Despite these efforts, many unresolved fundamental aspects remain. In this paper we review and summarize the thermodynamics of proteins, the hydrophobic effect and cold denaturation. We start by accounting for these phenomena macroscopically then move to their atomic-level description. We hope this review will help the reader gain insights into the role played by the hydrophobic effect in cold denaturation.
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Affiliation(s)
- Cristiano L Dias
- Department of Applied Mathematics, The University of Western Ontario, Middlesex College, 1151 Richmond St. N., London, Ont., Canada N6A 5B7.
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