51
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Das P, Matysiak S. Direct Characterization of Hydrophobic Hydration during Cold and Pressure Denaturation. J Phys Chem B 2012; 116:5342-8. [DOI: 10.1021/jp211832c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Payel Das
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742,
United States
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52
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Bianco V, Iskrov S, Franzese G. Understanding the role of hydrogen bonds in water dynamics and protein stability. J Biol Phys 2012; 38:27-48. [PMID: 23277668 PMCID: PMC3285729 DOI: 10.1007/s10867-011-9235-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 08/07/2011] [Indexed: 11/30/2022] Open
Abstract
The mechanisms of cold and pressure denaturation of proteins are a matter of debate, but it is commonly accepted that water plays a fundamental role in the process. It has been proposed that the denaturation process is related to an increase of hydrogen bonds among hydration water molecules. Other theories suggest that the causes of denaturation are the density fluctuations of surface water, or the destabilization of hydrophobic contacts as a consequence of water molecule inclusions inside the protein, especially at high pressures. We review some theories that have been proposed to give insight into this problem, and we describe a coarse-grained model of water that compares well with experiments for proteins' hydration water. We introduce its extension for a homopolymer in contact with the water monolayer and study it by Monte Carlo simulations in an attempt to understand how the interplay of water cooperativity and interfacial hydrogen bonds affects protein stability.
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Affiliation(s)
- Valentino Bianco
- Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain
| | - Svilen Iskrov
- École Normale Supérieure de Cachan, 61, avenue du Président Wilson, 94235 Cachan cedex, France
| | - Giancarlo Franzese
- Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain
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53
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Revealing conformational substates of lipidated N-Ras protein by pressure modulation. Proc Natl Acad Sci U S A 2011; 109:460-5. [PMID: 22203965 DOI: 10.1073/pnas.1110553109] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Regulation of protein function is often linked to a conformational switch triggered by chemical or physical signals. To evaluate such conformational changes and to elucidate the underlying molecular mechanisms of subsequent protein function, experimental identification of conformational substates and characterization of conformational equilibria are mandatory. We apply pressure modulation in combination with FTIR spectroscopy to reveal equilibria between spectroscopically resolved substates of the lipidated signaling protein N-Ras. Pressure has the advantage that its thermodynamic conjugate is volume, a parameter that is directly related to structure. The conformational dynamics of N-Ras in its different nucleotide binding states in the absence and presence of a model biomembrane was probed by pressure perturbation. We show that not only nucleotide binding but also the presence of the membrane has a drastic effect on the conformational dynamics and selection of conformational substates of the protein, and a new substate appearing upon membrane binding could be uncovered. Population of this new substate is accompanied by structural reorientations of the G domain, as also indicated by complementary ATR-FTIR and IRRAS measurements. These findings thus illustrate that the membrane controls signaling conformations by acting as an effective interaction partner, which has consequences for the G-domain orientation of membrane-associated N-Ras, which in turn is known to be critical for its effector and modulator interactions. Finally, these results provide insights into the influence of pressure on Ras-controlled signaling events in organisms living under extreme environmental conditions as they are encountered in the deep sea where pressures reach the kbar range.
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54
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55
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Voloshin VP, Medvedev NN, Andrews MN, Burri RR, Winter R, Geiger A. Volumetric Properties of Hydrated Peptides: Voronoi–Delaunay Analysis of Molecular Simulation Runs. J Phys Chem B 2011; 115:14217-28. [DOI: 10.1021/jp2050788] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir P. Voloshin
- Institute of Chemical Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia
| | - Nikolai N. Medvedev
- Institute of Chemical Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | | | - R. Reddy Burri
- Physikalische Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Roland Winter
- Physikalische Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Alfons Geiger
- Physikalische Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
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56
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Applications of pressure perturbation calorimetry in biophysical studies. Biophys Chem 2011; 156:13-23. [DOI: 10.1016/j.bpc.2010.12.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 12/29/2010] [Accepted: 12/29/2010] [Indexed: 10/18/2022]
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57
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Schroer MA, Paulus M, Jeworrek C, Krywka C, Schmacke S, Zhai Y, Wieland DCF, Sahle CJ, Chimenti M, Royer CA, Garcia-Moreno B, Tolan M, Winter R. High-pressure SAXS study of folded and unfolded ensembles of proteins. Biophys J 2010; 99:3430-7. [PMID: 21081092 PMCID: PMC2980736 DOI: 10.1016/j.bpj.2010.09.046] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 09/19/2010] [Accepted: 09/23/2010] [Indexed: 11/29/2022] Open
Abstract
A structural interpretation of the thermodynamic stability of proteins requires an understanding of the structural properties of the unfolded state. High-pressure small-angle x-ray scattering was used to measure the effects of temperature, pressure, denaturants, and stabilizing osmolytes on the radii of gyration of folded and unfolded state ensembles of staphylococcal nuclease. A set of variants with the internal Val-66 replaced with Ala, Tyr, or Arg was used to examine how changes in the volume and polarity of an internal microcavity affect the dimensions of the native state and the pressure sensitivity of the ensemble. The unfolded state ensembles achieved for these proteins with high pressure were more compact than those achieved at high temperature, and were all very sensitive to the presence of urea and glycerol. Substitutions at the hydrophobic core detectably altered the conformation of the protein, even in the folded state. The introduction of a charged residue, such as Arg, inside the hydrophobic interior of a protein could dramatically alter the structural properties, even those of the unfolded state. The data suggest that a charge at an internal position can interfere with the formation of transient hydrophobic clusters in the unfolded state, and ensure that the pressure-unfolded form of a protein occupies the maximum volume possible. Only at high temperatures does the radius of gyration of the unfolded state ensemble approach the value for a statistical random coil.
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Affiliation(s)
- Martin A. Schroer
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | - Michael Paulus
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | | | - Christina Krywka
- Institut für Experimentelle und Angewandte Physik, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Saskia Schmacke
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | - Yong Zhai
- Fakultät Chemie, Technische Universität Dortmund, Dortmund, Germany
| | | | - Christoph J. Sahle
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | - Michael Chimenti
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Catherine A. Royer
- Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale U554, Centre National de la Recherche Scientifique/Unite Mixte de Recherche, 5048 Université de Montpellier, Montpellier, France
| | | | - Metin Tolan
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | - Roland Winter
- Fakultät Chemie, Technische Universität Dortmund, Dortmund, Germany
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58
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Sarupria S, Ghosh T, García AE, Garde S. Studying pressure denaturation of a protein by molecular dynamics simulations. Proteins 2010; 78:1641-51. [PMID: 20146357 DOI: 10.1002/prot.22680] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This "unfolding-up-on-squeezing" is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results-that pressure denatured states are water-swollen, and theoretical results-that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states-their water-swollen nature, retention of secondary structure, and overall compactness-mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately -60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500-2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties and pressure stability of proteins, and can be potentially extended for applications to protein complexes and assemblies.
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Affiliation(s)
- Sapna Sarupria
- Howard P Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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59
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Schweiker KL, Fitz VW, Makhatadze GI. Universal Convergence of the Specific Volume Changes of Globular Proteins upon Unfolding. Biochemistry 2009; 48:10846-51. [DOI: 10.1021/bi901220u] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katrina L. Schweiker
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033
| | - Victoria W. Fitz
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - George I. Makhatadze
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180
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60
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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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61
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Aswal VK, Chodankar S, Kohlbrecher J, Vavrin R, Wagh AG. Small-angle neutron scattering study of protein unfolding and refolding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:011924. [PMID: 19658746 DOI: 10.1103/physreve.80.011924] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 04/02/2009] [Indexed: 05/28/2023]
Abstract
Small-angle neutron scattering has been used to study protein unfolding and refolding in protein bovine serum albumin (BSA) due to perturbation in its native structure as induced by three different protein denaturating agents: urea, surfactant, and pressure. The BSA protein unfolds for urea concentrations greater than 4 M and is observed to be independent of the protein concentration. The addition of surfactant unfolds the protein by the formation of micellelike aggregates of surfactants along the unfolded polypeptide chains of the protein and depends on the ratio of surfactant to protein concentration. We make use of the dilution method to show the refolding of unfolded proteins in the presence of urea and surfactant. BSA does not show any protein unfolding up to the pressure of 450 MPa. The presence of urea and surfactant (for concentrations prior to inducing their own unfolding) has been used to examine pressure-induced unfolding of the protein at lower pressures. The protein unfolds at 200 MPa pressure in the presence of urea; however, no unfolding is observed with surfactant. The protein unfolding is shown to be reversible in all the above denaturating methods.
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Affiliation(s)
- V K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
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62
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Giovambattista N, Rossky PJ, Debenedetti PG. Effect of Temperature on the Structure and Phase Behavior of Water Confined by Hydrophobic, Hydrophilic, and Heterogeneous Surfaces. J Phys Chem B 2009; 113:13723-34. [DOI: 10.1021/jp9018266] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicolas Giovambattista
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210, Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544-5263, and Department of Chemistry and Biochemistry, Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712
| | - Peter J. Rossky
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210, Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544-5263, and Department of Chemistry and Biochemistry, Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712
| | - Pablo G. Debenedetti
- Department of Physics, Brooklyn College of the City University of New York, Brooklyn, New York 11210, Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544-5263, and Department of Chemistry and Biochemistry, Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712
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63
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Maeno A, Matsuo H, Akasaka K. The pressure-temperature phase diagram of hen lysozyme at low pH. Biophysics (Nagoya-shi) 2009; 5:1-9. [PMID: 27857574 PMCID: PMC5036640 DOI: 10.2142/biophysics.5.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Accepted: 01/20/2009] [Indexed: 12/01/2022] Open
Abstract
The equilibrium unfolding of hen lysozyme at pH 2 was studied as a function of pressure (0.1~700MPa) and temperature (−10°C~50°C) using Trp fluorescence as monitor supplemented by variable pressure 1H NMR spectroscopy (0.1~400MPa). The unfolding profiles monitored by the two methods allowed the two-state equilibrium analysis between the folded (N) and unfolded (U) conformers. The free energy differences ΔG (=GU–GN) were evaluated from changes in the wavelength of maximum fluorescence intensity (λmax) as a function of pressure and temperature. The dependence of ΔG on temperature exhibits concave curvatures against temperature, showing positive heat capacity changes (ΔCp=CpU–CpN= 1.8–1.9 kJ mol−1 deg−1) at all pressures studied (250~400 MPa), while the temperature TS for maximal ΔG increased from about 10°C at 250MPa to about 40°C at 550MPa. The dependence of ΔG on pressure gave negative volume changes (ΔV=VU–VN) upon unfolding at all temperatures studied (−86~−17 mlmol−1 for −10°C~50°C), which increase significantly with increasing temperature, giving a positive expansivity change (Δα~1.07mlmol−1 deg−1). A phase-diagram between N and U (for ΔG=0) is drawn of hen lysozyme at pH 2 on the pressure-temperature plane. Finally, a three-dimensional free energy landscape (ΔG) is presented on the p-T plane.
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Affiliation(s)
- Akihiro Maeno
- Graduate School of Biology-Oriented Science and Technology, Kinki University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hiroshi Matsuo
- Niigata Industrial Creation Organization, 5-1 Bandaijima, Chuo-ku, Niigata 950-0078, Japan; High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Kazuyuki Akasaka
- Graduate School of Biology-Oriented Science and Technology, Kinki University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
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64
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Mitra L, Rouget JB, Garcia-Moreno B, Royer CA, Winter R. Towards a quantitative understanding of protein hydration and volumetric properties. Chemphyschem 2009; 9:2715-21. [PMID: 18814170 DOI: 10.1002/cphc.200800405] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Herein, we probe by pressure perturbation calorimetry (PPC) the coefficient of thermal expansion, the volumetric and the hydration properties of variants of a hyperstable variant of staphylococcal nuclease (SNase), Delta+PHS. The temperature-dependent volumetric properties of the folded and unfolded states of the wild-type protein are calculated with previously published data. The present PPC results are used to interpret the volume diagram and expansivity at a molecular level. We conclude that the expansivity of the unfolded state is, to a first approximation, temperature independent, while that of the folded state decreases with increasing temperature. Our data suggest that at low temperature the defining contribution to DeltaV comes mainly from excluded volume differences and DeltaV for unfolding is negative. In contrast, at high temperatures, differential solvation due to the increased exposed surface area of the unfolded state and, in particular, its larger thermal volume linked to the increased conformational dynamics of the unfolded state ensemble takes over and DeltaV for unfolding eventually becomes positive.
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Affiliation(s)
- Lally Mitra
- Dortmund University of Technology, Department of Chemistry, Physical Chemistry I-Biophysical Chemistry, Otto-Hahn Str. 6, 44227 Dortmund, Germany
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65
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Paschek D, Hempel S, García AE. Computing the stability diagram of the Trp-cage miniprotein. Proc Natl Acad Sci U S A 2008; 105:17754-9. [PMID: 19004791 PMCID: PMC2582582 DOI: 10.1073/pnas.0804775105] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Indexed: 11/18/2022] Open
Abstract
We report molecular dynamics simulations of the equilibrium folding/unfolding thermodynamics of an all-atom model of the Trp-cage miniprotein in explicit solvent. Simulations are used to sample the folding/unfolding free energy difference and its derivatives along 2 isochores. We model the DeltaG(u)(P,T) landscape using the simulation data and propose a stability diagram model for Trp-cage. We find the proposed diagram to exhibit features similar to globular proteins with increasing hydrostatic pressure destabilizing the native fold. The observed energy differences DeltaE(u) are roughly linearly temperature-dependent and approach DeltaE(u) = 0 with decreasing temperature, suggesting that the system approached the region of cold denaturation. In the low-temperature denatured state, the native helical secondary structure elements are largely preserved, whereas the protein conformation changes to an "open-clamp" configuration. A tighter packing of water around nonpolar sites, accompanied by an increasing solvent-accessible surface area of the unfolded ensemble, seems to stabilize the unfolded state at elevated pressures.
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Affiliation(s)
- Dietmar Paschek
- Fakultät Bio- und Chemieingenieurwesen, Emil-Figge-Strasse 70, Technische Universität Dortmund, D-44227 Dortmund, Germany; and
| | - Sascha Hempel
- Fakultät Bio- und Chemieingenieurwesen, Emil-Figge-Strasse 70, Technische Universität Dortmund, D-44227 Dortmund, Germany; and
| | - Angel E. García
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY 12180-3590
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66
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Krywka C, Sternemann C, Paulus M, Tolan M, Royer C, Winter R. Effect of Osmolytes on Pressure-Induced Unfolding of Proteins: A High-Pressure SAXS Study. Chemphyschem 2008; 9:2809-15. [DOI: 10.1002/cphc.200800522] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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67
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Kamerzell TJ, Russell Middaugh C. The Complex Inter-Relationships Between Protein Flexibility and Stability. J Pharm Sci 2008; 97:3494-517. [DOI: 10.1002/jps.21269] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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68
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Mishra R, Winter R. Cold- and Pressure-Induced Dissociation of Protein Aggregates and Amyloid Fibrils. Angew Chem Int Ed Engl 2008; 47:6518-21. [DOI: 10.1002/anie.200802027] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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69
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Mishra R, Winter R. Kälte- und druckinduzierte Dissoziation von Proteinaggregaten und Amyloidfibrillen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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70
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Clark GNI, Galindo A, Jackson G, Rogers S, Burgess AN. Modeling and Understanding Closed-Loop Liquid−Liquid Immiscibility in Aqueous Solutions of Poly(ethylene glycol) Using the SAFT-VR Approach with Transferable Parameters. Macromolecules 2008. [DOI: 10.1021/ma8007898] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gary N. I. Clark
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K., and ICI Strategic Technology Group, Wilton Centre, PO Box 90, Redcar TS90 8JE, U.K
| | - Amparo Galindo
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K., and ICI Strategic Technology Group, Wilton Centre, PO Box 90, Redcar TS90 8JE, U.K
| | - George Jackson
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K., and ICI Strategic Technology Group, Wilton Centre, PO Box 90, Redcar TS90 8JE, U.K
| | - Steve Rogers
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K., and ICI Strategic Technology Group, Wilton Centre, PO Box 90, Redcar TS90 8JE, U.K
| | - Andrew N. Burgess
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K., and ICI Strategic Technology Group, Wilton Centre, PO Box 90, Redcar TS90 8JE, U.K
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71
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Lopes DHJ, Smirnovas V, Winter R. Islet amyloid polypeptide and high hydrostatic pressure: towards an understanding of the fibrillization process. ACTA ACUST UNITED AC 2008. [DOI: 10.1088/1742-6596/121/11/112002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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72
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Patel BA, Debenedetti PG, Stillinger FH, Rossky PJ. The effect of sequence on the conformational stability of a model heteropolymer in explicit water. J Chem Phys 2008; 128:175102. [PMID: 18465941 DOI: 10.1063/1.2909974] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the properties of a two-dimensional lattice heteropolymer model for a protein in which water is explicitly represented. The model protein distinguishes between hydrophobic and polar monomers through the effect of the hydrophobic monomers on the entropy and enthalpy of the hydrogen bonding of solvation shell water molecules. As experimentally observed, model heteropolymer sequences fold into stable native states characterized by a hydrophobic core to avoid unfavorable interactions with the solvent. These native states undergo cold, pressure, and thermal denaturation into distinct configurations for each type of unfolding transition. However, the heteropolymer sequence is an important element, since not all sequences will fold into stable native states at positive pressures. Simulation of a large collection of sequences indicates that these fall into two general groups, those exhibiting highly stable native structures and those that do not. Statistical analysis of important patterns in sequences shows a strong tendency for observing long blocks of hydrophobic or polar monomers in the most stable sequences. Statistical analysis also shows that alternation of hydrophobic and polar monomers appears infrequently among the most stable sequences. These observations are not absolute design rules and, in practice, these are not sufficient to rationally design very stable heteropolymers. We also study the effect of mutations on improving the stability of the model proteins, and demonstrate that it is possible to obtain a very stable heteropolymer from directed evolution of an initially unstable heteropolymer.
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Affiliation(s)
- Bryan A Patel
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, USA
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73
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Dias CL, Ala-Nissila T, Karttunen M, Vattulainen I, Grant M. Microscopic mechanism for cold denaturation. PHYSICAL REVIEW LETTERS 2008; 100:118101. [PMID: 18517830 DOI: 10.1103/physrevlett.100.118101] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Indexed: 05/26/2023]
Abstract
We elucidate the mechanism of cold denaturation through constant-pressure simulations for a model of hydrophobic molecules in an explicit solvent. We find that the temperature dependence of the hydrophobic effect induces, facilitates, and is the driving force for cold denaturation. The physical mechanism underlying this phenomenon is identified as the destabilization of hydrophobic contact in favor of solvent-separated configurations, the same mechanism seen in pressure-induced denaturation. A phenomenological explanation proposed for the mechanism is suggested as being responsible for cold denaturation in real proteins.
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Affiliation(s)
- Cristiano L Dias
- Physics Department, Rutherford Building, McGill University, 3600 rue University, Montréal, Québec, Canada H3A 2T8
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74
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Kamerzell TJ, Ramsey JD, Middaugh CR. Immunoglobulin Dynamics, Conformational Fluctuations, and Nonlinear Elasticity and Their Effects on Stability. J Phys Chem B 2008; 112:3240-50. [DOI: 10.1021/jp710061a] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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75
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Patel BA, Debenedetti PG, Stillinger FH, Rossky PJ. A water-explicit lattice model of heat-, cold-, and pressure-induced protein unfolding. Biophys J 2007; 93:4116-27. [PMID: 17766342 PMCID: PMC2098741 DOI: 10.1529/biophysj.107.108530] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigate the effect of temperature and pressure on polypeptide conformational stability using a two-dimensional square lattice model in which water is represented explicitly. The model captures many aspects of water thermodynamics, including the existence of density anomalies, and we consider here the simplest representation of a protein: a hydrophobic homopolymer. We show that an explicit treatment of hydrophobic hydration is sufficient to produce cold, pressure, and thermal denaturation. We investigate the effects of the enthalpic and entropic components of the water-protein interactions on the overall folding phase diagram, and show that even a schematic model such as the one we consider yields reasonable values for the temperature and pressure ranges within which highly compact homopolymer configurations are thermodynamically stable.
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Affiliation(s)
- Bryan A Patel
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey, USA.
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76
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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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77
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Pereira B, Jain S, Sarupria S, Yang L, Garde S. Pressure dependence of the compressibility of a micelle and a protein: insights from cavity formation analysis. Mol Phys 2007. [DOI: 10.1080/00268970601140750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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78
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Smirnovas V, Winter R, Funck T, Dzwolak W. Protein Amyloidogenesis in the Context of Volume Fluctuations: A Case Study on Insulin. Chemphyschem 2006; 7:1046-9. [PMID: 16596700 DOI: 10.1002/cphc.200500717] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Vytautas Smirnovas
- University of Dortmund, Department of Chemistry, 44227 Dortmund, Germany
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79
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Meersman F, Smeller L, Heremans K. Protein stability and dynamics in the pressure–temperature plane. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:346-54. [PMID: 16414316 DOI: 10.1016/j.bbapap.2005.11.019] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 11/23/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
The pressure-temperature stability diagram of proteins and the underlying assumptions of the elliptical shape of the diagram are discussed. Possible extensions, such as aggregation and fibril formation, are considered. An important experimental observation is the extreme pressure stability of the mature fibrils. Molecular origins of the diagram in terms of models of the partial molar volume of a protein focus on cavities and hydration. Changes in thermal expansivity, compressibility and heat capacity in terms of fluctuations of the enthalpy and volume change of the unfolding should also focus on these parameters. It is argued that the study of water-soluble polymers might further our understanding of the stability diagram. Whereas the role of water in protein behaviour is unquestioned, the role of cavities is less clear.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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80
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Skouri-Panet F, Quevillon-Cheruel S, Michiel M, Tardieu A, Finet S. sHSPs under temperature and pressure: the opposite behaviour of lens alpha-crystallins and yeast HSP26. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:372-83. [PMID: 16476575 DOI: 10.1016/j.bbapap.2005.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Revised: 11/21/2005] [Accepted: 12/06/2005] [Indexed: 11/25/2022]
Abstract
Small angle X-ray scattering was used to follow the temperature and pressure induced structural transitions of polydisperse native calf lens alpha-crystallins and recombinant human alphaB-crystallins and of monodisperse yeast HSP26. The alpha-crystallins were known to increase in size with increasing temperature, whereas HSP26 partially dissociates into dimers. SAXS intensity curves demonstrated that the average 40-mer calf alpha-crystallin converted into 80-mer in a narrow temperature range, from 60 to 69 degrees C, whereas the average 30-mer alphaB-crystallin was continuously transformed into 60-mer at lower temperature, from 40 to 60 degrees C. These temperature-induced transitions were irreversible. Similar transitions, yet reversible, could be induced with pressure in the 100 to 300 MPa pressure range. Moreover, temperature and pressure could be combined to lower the transition temperatures. On the other hand, SAXS curves recorded during pressure scans from 0.1 to 200 MPa with monodisperse 24-mer HSP26 revealed dissociation of the 24-mer into dimers. This dissociation was complete and reversible. Whatever the sHSP, a decrease of partial specific volume was found to be associated with the pressure induced quaternary structure transitions, in agreement with the hypothesis that such transitions represent a first step on the protein denaturation pathway.
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81
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Mitra L, Smolin N, Ravindra R, Royer C, Winter R. Pressure perturbation calorimetric studies of the solvation properties and the thermal unfolding of proteins in solution—experiments and theoretical interpretation. Phys Chem Chem Phys 2006; 8:1249-65. [PMID: 16633605 DOI: 10.1039/b516608j] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We used pressure perturbation calorimetry (PPC), a relatively new and efficient technique, to study the solvation and volumetric properties of amino acids and peptides as well as of proteins in their native and unfolded state. In PPC, the coefficient of thermal expansion of the partial volume of the protein is deduced from the heat consumed or produced after small isothermal pressure jumps, which strongly depends on the interaction of the protein with the solvent or cosolvent at the protein-solvent interface. Furthermore, the effects of various chaotropic and kosmotropic cosolvents on the volume and expansivity changes of proteins were measured over a wide concentration range with high precision. Depending on the type of cosolvent and its concentration, specific differences were found for the solvation properties and unfolding behaviour of the proteins, and the volume change upon unfolding may even change sign. To yield a molecular interpretation of the different terms contributing to the partial protein volume and its temperature dependence, and hence a better understanding of the PPC data, molecular dynamics computer simulations on SNase were also carried out and compared with the experimental data. The PPC studies introduced aim to obtain more insight into the basic thermodynamic properties of protein solvation and volume effects accompanying structural transformations of proteins in various cosolvents on one hand, as these form the basis for understanding their physiological functions and their use in drug designing and formulations, but also to initiate further valuable applications in studies of other biomolecular and chemical systems.
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Affiliation(s)
- Lally Mitra
- University of Dortmund, Department of Chemistry, Physical Chemistry I--Biophysical Chemistry, Otto-Hahn Str. 6, D-44227 Dortmund, Germany
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82
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Lin SY, Hsieh TF, Wei YS, Li MJ. Mechanical compression affecting the thermal-induced conformational stability and denaturation temperature of human fibrinogen. Int J Biol Macromol 2005; 37:127-33. [PMID: 16257049 DOI: 10.1016/j.ijbiomac.2005.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Revised: 09/26/2005] [Accepted: 09/26/2005] [Indexed: 11/28/2022]
Abstract
Thermal-induced conformational stability and changes in denaturation temperature of human fibrinogen (FBG) after different mechanical compressions were investigated by a simultaneous Fourier transform infrared microspectroscopy equipped with thermal analyzer (thermal FTIR microscopic system). The confocal Raman microspectroscopy was also applied to determine the thermal reversibility of solid FBG. FBG powder was pressed on one KBr pellet (1 KBr method) or sealed within two KBr pellets (2 KBr method) by different mechanical compressions. The result indicates that there was no marked difference in the thermal behavior for the solid FBG samples prepared by 1 KBr method in the heating process even under different mechanical compression pressures, in which the thermal-induced denaturation temperatures from native to denatured state were maintained constant at 66-67 degrees C. However, the denaturation temperature for the solid FBG samples prepared by 2 KBr method was shifted from 55 to 62 degrees C with the increase of mechanical compression pressure. A good linear correlation was also found between the denaturation temperature and mechanical compression pressure for FBG samples prepared by 2 KBr method. The solid FBG sample, whether prepared by 1 KBr or 2 KBr method, was also found to show the thermal-irreversible property.
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Affiliation(s)
- Shan-Yang Lin
- Biopharmaceutics Laboratory, Department of Medical Research and Education, Taipei Veterans General Hospital, Shih-Pai, Taipei, Taiwan, ROC.
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83
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Smirnovas V, Winter R, Funck T, Dzwolak W. Thermodynamic Properties Underlying the α-Helix-to-β-Sheet Transition, Aggregation, and Amyloidogenesis of Polylysine as Probed by Calorimetry, Densimetry, and Ultrasound Velocimetry. J Phys Chem B 2005; 109:19043-5. [PMID: 16853453 DOI: 10.1021/jp053283w] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we performed a detailed thermodynamic study of an aggregation-prone polypeptide, polylysine, to gain a deeper insight into the scenario of physicochemical events during its unfolding, aggregation, and amyloidogenesis. The precise and simultaneous determination of the partial molar volume, the heat capacity, and the coefficients of thermal expansion, as well as adiabatic and isothermal compressibility of the protein upon unfolding and aggregation, yields a thermodynamic picture of the aggregation process highlighting the importance of volume fluctuations during unfolding and amyloidogenesis of proteins.
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84
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Meersman F, Smeller L, Heremans K. Extending the Pressure-Temperature State Diagram of Myoglobin. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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85
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Winter R, Dzwolak W. Exploring the temperature-pressure configurational landscape of biomolecules: from lipid membranes to proteins. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2005; 363:537-563. [PMID: 15664898 DOI: 10.1098/rsta.2004.1507] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hydrostatic pressure has been used as a physical parameter for studying the stability and energetics of biomolecular systems, such as lipid mesophases and proteins, but also because high pressure is an important feature of certain natural membrane environments and because the high-pressure phase behaviour of biomolecules is of biotechnological interest. By using spectroscopic and scattering techniques, the temperature- and pressure-dependent structure and phase behaviour of lipid systems, differing in chain configuration, headgroup structure and concentration, and proteins have been studied and are discussed. A thermodynamic approach is presented for studying the stability of proteins as a function of both temperature and pressure. The results demonstrate that combined temperature-pressure dependent studies can help delineate the free-energy landscape of proteins and hence help elucidate which features and thermodynamic parameters are essential in determining the stability of the native conformational state of proteins. We also introduce pressure as a kinetic variable. Applying the pressure jump relaxation technique in combination with time-resolved synchrotron X-ray diffraction and spectroscopic techniques, the kinetics of un/refolding of proteins has been studied. Finally, recent advances in using pressure for studying misfolding and aggregation of proteins will be discussed.
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Affiliation(s)
- R Winter
- University of Dortmund, Physical Chemistry I, Otto-Hahn Strasse 6, 44227 Dortmund, Germany.
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86
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Ding Y, Ye X, Zhang G. Microcalorimetric Investigation on Aggregation and Dissolution of Poly(N-isopropylacrylamide) Chains in Water. Macromolecules 2005. [DOI: 10.1021/ma048460q] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yanwei Ding
- Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, Structure Research Laboratory, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiaodong Ye
- Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, Structure Research Laboratory, University of Science and Technology of China, Hefei, Anhui, China
| | - Guangzhao Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, Structure Research Laboratory, University of Science and Technology of China, Hefei, Anhui, China
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87
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Ravindra R, Zhao S, Gies H, Winter R. Protein encapsulation in mesoporous silicate: the effects of confinement on protein stability, hydration, and volumetric properties. J Am Chem Soc 2004; 126:12224-5. [PMID: 15453729 DOI: 10.1021/ja046900n] [Citation(s) in RCA: 171] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
On the basis of the predictions of statistical-thermodynamic models, it is postulated that excluded volume effects may play a significant role in the stability, interaction, and function of proteins. We studied the effects of confinement on protein un/refolding and stability. Our approach was to encapsulate a model protein, RNase A, in a mesoporous silica, MCM-48, with glasslike wall structure and with well-defined pores to create a crowded microenvironment. To the best of our knowledge, this is the first report where pressure perturbation and differential scanning calorimetric techniques are employed to evaluate the stability, hydration, and volumetric properties of the confined protein. A drastic increase in protein stability ( approximately 30 degrees C increase in unfolding temperature) is observed. The increase in stability is probably not only due to a restriction in conformational space (excluded volume effect due to nonspecific interactions) but also due to an increased strength of hydration of the protein within the narrow silica pores.
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Affiliation(s)
- Revanur Ravindra
- University of Dortmund, Department of Chemistry, Physical Chemistry I, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
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88
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Nicolini C, Ravindra R, Ludolph B, Winter R. Characterization of the temperature- and pressure-induced inverse and reentrant transition of the minimum elastin-like polypeptide GVG(VPGVG) by DSC, PPC, CD, and FT-IR spectroscopy. Biophys J 2004; 86:1385-92. [PMID: 14990468 PMCID: PMC1303976 DOI: 10.1016/s0006-3495(04)74209-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We investigated the temperature- and pressure-dependent structure and phase behavior of a solvated oligopeptide, GVG(VPGVG), which serves as a minimalistic elastin-like model system, over a large region of the thermodynamic phase field, ranging from 2 to 120 degrees C and from ambient pressure up to approximately 10 kbar, applying various spectroscopic (CD, FT-IR) and thermodynamic (DSC, PPC) measurements. We find that this octapeptide behaves as a two-state system which undergoes the well-known inverse-temperature folding transition occurring at T approximately 36 degrees C, and, in addition, a slow trend reversal at higher temperatures, finally leading to a reentrant unfolding close to the boiling point of water. Furthermore, the pressure-dependence of the folding/unfolding transition was studied to yield a more complete picture of the p, T-stability diagram of the system. A molecular-level picture of these processes, in particular on the role of water for the folding and unfolding events of the peptide, presented with the help of molecular-dynamics simulations, is presented in a companion article in this issue.
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Affiliation(s)
- C Nicolini
- Department of Chemistry, University of Dortmund, Dortmund, Germany
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89
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Dzwolak W, Ravindra R, Nicolini C, Jansen R, Winter R. The diastereomeric assembly of polylysine is the low-volume pathway for preferential formation of beta-sheet aggregates. J Am Chem Soc 2004; 126:3762-8. [PMID: 15038729 DOI: 10.1021/ja039138i] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interaction of left- and right-handed polylysine chains (poly(D-lysine) and poly(L-lysine)) results in a dramatic increase in the propensity to form aggregated beta-sheet structure (and amyloid-like fibrils), which is reflected by an approximately 15 degrees C decrease of temperature of the alpha-helix-to-beta-sheet transition. While a relative volume expansion of 13-19 mL x mol(-1) accompanies the alpha-to-beta-transition in a single enantiomer, this does not hold true for the mixture, which, along with substantially more negative heat capacity changes, points to a lower solvent-entropy cost of the transition as the possible thermodynamic driving force of the diastereomeric aggregation. The underlying solvational mechanism may be one of the decisive factors responsible for the spontaneous protein aggregation in vivo and, as such, may shed new light on the molecular basis of amyloid-associated diseases.
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Affiliation(s)
- Wojciech Dzwolak
- High Pressure Research Center, Polish Academy of Sciences, Sokolowska 29/37, 01-142 Warsaw, Poland.
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90
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Cordeiro Y, Kraineva J, Ravindra R, Lima LMTR, Gomes MPB, Foguel D, Winter R, Silva JL. Hydration and packing effects on prion folding and beta-sheet conversion. High pressure spectroscopy and pressure perturbation calorimetry studies. J Biol Chem 2004; 279:32354-9. [PMID: 15173173 DOI: 10.1074/jbc.m404295200] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The main hypothesis for prion diseases proposes that the cellular protein (PrP(C)) can be altered into a misfolded, beta-sheet-rich isoform (PrP(Sc)), which undergoes aggregation and triggers the onset of transmissible spongiform encephalopathies. Here, we compare the stability against pressure and the thermomechanical properties of the alpha-helical and beta-sheet conformations of recombinant murine prion protein, designated as alpha-rPrP and beta-rPrP, respectively. High temperature induces aggregates and a large gain in intermolecular antiparallel beta-sheet (beta-rPrP), a conformation that shares structural similarity with PrP(Sc). alpha-rPrP is highly stable, and only pressures above 5 kilobars (1 kilobar = 100 MegaPascals) cause reversible denaturation, a process that leads to a random and turnrich conformation with concomitant loss of alpha-helix, as measured by Fourier transform infrared spectroscopy. In contrast, aggregates of beta-rPrP are very sensitive to pressure, undergoing transition into a dissociated species that differs from the denatured form derived from alpha-rPrP. The higher susceptibility to pressure of beta-rPrP can be explained by its less hydrated structure. Pressure perturbation calorimetry supports the view that the accessible surface area of alpha-rPrP is much higher than that of beta-rPrP, which explains the lower degree of hydration of beta-rPrP. Our findings shed new light on the mechanism of prion conversion and show how water plays a prominent role. Our results allow us to propose a volume and free energy diagram of the different species involved in the conversion and aggregation. The existence of different folded conformations as well as different denatured states of PrP may explain the elusive character of its conversion into a pathogenic form.
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Affiliation(s)
- Yraima Cordeiro
- Departamento de Bioquímica Médica, Centro Nacional de Ressonāncia Magnética Nuclear de Macromoléculas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil
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91
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Schreiner E, Nicolini C, Ludolph B, Ravindra R, Otte N, Kohlmeyer A, Rousseau R, Winter R, Marx D. Folding and unfolding of an elastinlike oligopeptide: "inverse temperature transition," reentrance, and hydrogen-bond dynamics. PHYSICAL REVIEW LETTERS 2004; 92:148101. [PMID: 15089575 DOI: 10.1103/physrevlett.92.148101] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2003] [Indexed: 05/24/2023]
Abstract
The temperature-dependent behavior of a solvated oligopeptide, GVG(VPGVG), is investigated. Spectroscopic measurements, thermodynamic measurements, and molecular dynamics simulations find that this elastinlike octapeptide behaves as a two-state system that undergoes an "inverse temperature" folding transition and reentrant unfolding close to the boiling point of water. A molecular picture of these processes is presented, emphasizing changes in the dynamics of hydrogen bonding at the protein/water interface and peptide backbone librational entropy.
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Affiliation(s)
- Eduard Schreiner
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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92
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Diab C, Akiyama Y, Kataoka K, Winnik FM. Microcalorimetric Study of the Temperature-Induced Phase Separation in Aqueous Solutions of Poly(2-isopropyl-2-oxazolines). Macromolecules 2004. [DOI: 10.1021/ma0358733] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Charbel Diab
- Faculty of Pharmacy and Department of Chemistry, Université de Montréal, CP 6128 Succursale Centre Ville, Montréal, QC Canada H3C 3J7, and Department of Materials Science, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113 8656, Japan
| | - Yoshitsugu Akiyama
- Faculty of Pharmacy and Department of Chemistry, Université de Montréal, CP 6128 Succursale Centre Ville, Montréal, QC Canada H3C 3J7, and Department of Materials Science, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113 8656, Japan
| | - Kazunori Kataoka
- Faculty of Pharmacy and Department of Chemistry, Université de Montréal, CP 6128 Succursale Centre Ville, Montréal, QC Canada H3C 3J7, and Department of Materials Science, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113 8656, Japan
| | - Françoise M. Winnik
- Faculty of Pharmacy and Department of Chemistry, Université de Montréal, CP 6128 Succursale Centre Ville, Montréal, QC Canada H3C 3J7, and Department of Materials Science, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113 8656, Japan
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93
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Laukkanen A, Valtola L, Winnik FM, Tenhu H. Formation of Colloidally Stable Phase Separated Poly(N-vinylcaprolactam) in Water: A Study by Dynamic Light Scattering, Microcalorimetry, and Pressure Perturbation Calorimetry. Macromolecules 2004. [DOI: 10.1021/ma035124l] [Citation(s) in RCA: 171] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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94
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Dzwolak W, Ravindra R, Winter R. Hydration and structure—the two sides of the insulin aggregation process. Phys Chem Chem Phys 2004. [DOI: 10.1039/b314086e] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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