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Tan CY, Xu CH, Wong J, Shen JR, Sakuma S, Yamamoto Y, Lange R, Balny C, Ruan KC. Pressure equilibrium and jump study on unfolding of 23-kDa protein from spinach photosystem II. Biophys J 2004; 88:1264-75. [PMID: 15531632 PMCID: PMC1305128 DOI: 10.1529/biophysj.104.050435] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pressure-induced unfolding of 23-kDa protein from spinach photosystem II has been systematically investigated at various experimental conditions. Thermodynamic equilibrium studies indicate that the protein is very sensitive to pressure. At 20 degrees C and pH 5.5, 23-kDa protein shows a reversible two-state unfolding transition under pressure with a midpoint near 160 MPa, which is much lower than most natural proteins studied to date. The free energy (DeltaG(u)) and volume change (DeltaV(u)) for the unfolding are 5.9 kcal/mol and -160 ml/mol, respectively. It was found that NaCl and sucrose significantly stabilize the protein from unfolding and the stabilization is associated not only with an increase in DeltaG(u) but also with a decrease in DeltaV(u). The pressure-jump studies of 23-kDa protein reveal a negative activation volume for unfolding (-66.2 ml/mol) and a positive activation volume for refolding (84.1 ml/mol), indicating that, in terms of system volume, the protein transition state lies between the folded and unfolded states. Examination of the temperature effect on the unfolding kinetics indicates that the thermal expansibility of the transition state and the unfolded state of 23-kDa protein are closer to each other and they are larger than that of the native state. The diverse pressure-refolding pathways of 23-kDa protein in some conditions were revealed in pressure-jump kinetics.
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Affiliation(s)
- Cui-Yan Tan
- Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, China
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Torrent J, Alvarez-Martinez MT, Harricane MC, Heitz F, Liautard JP, Balny C, Lange R. High pressure induces scrapie-like prion protein misfolding and amyloid fibril formation. Biochemistry 2004; 43:7162-70. [PMID: 15170353 DOI: 10.1021/bi049939d] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Our understanding of conformational conversion of proteins in diseases is essential for any diagnostic and therapeutic approach. Although not fully understood, misfolding of the prion protein (PrP) is implicated in the pathogenesis of prion diseases. Despite several efforts to produce the pathologically misfolded conformation in vitro from a recombinant PrP, no positive result has yet been obtained. Within the "protein-only hypothesis", the reason for this hindrance may be that the experimental conditions used did not allow selection of the pathway adopted in vivo resulting in conversion into the infectious form. Here, using a pressure perturbation approach, we show that recombinant PrP is converted to a novel misfolded conformer, which is prone to aggregate and ultimately form amyloid fibrils. A short incubation at high pressure (600 MPa) of the truncated form of hamster prion protein (SHaPrP(90-231)) resulted in the formation of pre-amyloid structures. The mostly globular aggregates were characterized by ThT and ANS binding, and by a beta-sheet-rich secondary structure. After overnight incubation at 600 MPa, amyloid fibrils were formed. In contrast to pre-amyloid structures, they showed birefringency of polarized light after Congo red staining and a strongly decreased ANS binding capacity, but enhanced ThT binding. Both aggregate types were resistant to digestion by PK, and can be considered as potential scrapie-like forms or precursors. These results may be useful for the search for compounds preventing pathogenic PrP misfolding and aggregation.
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Affiliation(s)
- Joan Torrent
- Université de Montpellier 2, EA3763, Place Eugène Bataillon, F-34095 Montpellier cédex 5, France
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54
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Xu Q, Keiderling TA. Optical spectroscopic differentiation of various equilibrium denatured states of horse cytochrome c. Biopolymers 2004; 73:716-26. [PMID: 15048775 DOI: 10.1002/bip.20011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Thermal unfolding of cytochrome c (cyt c) from several states has been studied using equilibrium spectroscopic techniques. CD in the uv, vibrational circular dichroism, infrared, and uv-vis absorption spectra measured at various temperatures, pHs, salt concentrations, and GuHCl concentrations are used to show the conformational as well as heme structural differences between native and various denatured states. The difference in thermal denaturation behaviors of cyt c starting from acid denatured, molten globule (MG), and the A and native states are explored. Different final high temperature states were observed for cytochrome c unfolding from four different initial states (native, MG, A, and acid denatured state) by electronic CD, Fourier transform infrared (FTIR), and vibrational CD (VCD). Consistent with this, different thermal unfolding pathways for the MG and A states are suggested by the FTIR and VCD data for this process.
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Affiliation(s)
- Qi Xu
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c 111), Chicago, IL 60607-7061, USA
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55
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Akasaka K. Highly fluctuating protein structures revealed by variable-pressure nuclear magnetic resonance. Biochemistry 2003; 42:10875-85. [PMID: 12974621 DOI: 10.1021/bi034722p] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although our knowledge of basic folded structures of proteins has dramatically improved, the extent of our corresponding knowledge of higher-energy conformers remains extremely slim. The latter information is crucial for advancing our understanding of mechanisms of protein function, folding, and conformational diseases. Direct spectroscopic detection and analysis of structures of higher-energy conformers are limited, particularly under physiological conditions, either because their equilibrium populations are small or because they exist only transiently in the folding process. A new experimental strategy using pressure perturbation in conjunction with multidimensional NMR spectroscopy is being used to overcome this difficulty. A number of rare conformers are detected under pressure for a variety of proteins such as the Ras-binding domain of RalGDS, beta-lactoglobulin, dihydrofolate reductase, ubiquitin, apomyoglobin, p13(MTCP1), and prion, which disclose a rich world of protein structure between basically folded and globally unfolded states. Specific structures suggest that these conformers are designed for function and are closely identical to kinetic intermediates. Detailed structural determination of higher-energy conformers with variable-pressure NMR will extend our knowledge of protein structure and conformational fluctuation over most of the biologically relevant conformational space.
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Affiliation(s)
- Kazuyuki Akasaka
- Department of Biotechnological Science, School of Biology-Oriented Science and Technology, Kinki University, Wakayama 649-6493, Japan.
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Alexeev D, Barlow PN, Bury SM, Charrier JD, Cooper A, Hadfield D, Jamieson C, Kelly SM, Layfield R, Mayer RJ, McSparron H, Price NC, Ramage R, Sawyer L, Starkmann BA, Uhrin D, Wilken J, Young DW. Synthesis, structural and biological studies of ubiquitin mutants containing (2S, 4S)-5-fluoroleucine residues strategically placed in the hydrophobic core. Chembiochem 2003; 4:894-6. [PMID: 12964166 DOI: 10.1002/cbic.200300699] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dmitriy Alexeev
- Institute of Cell Molecular Biology (ICMB), University of Edinburgh, Michael Swann Building, Mayfield Road, Edinburgh EH9 3RJ, Scotland, UK
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57
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Williamson MP, Akasaka K, Refaee M. The solution structure of bovine pancreatic trypsin inhibitor at high pressure. Protein Sci 2003; 12:1971-9. [PMID: 12930996 PMCID: PMC2323994 DOI: 10.1110/ps.0242103] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The solution structure of bovine pancreatic trypsin inhibitor (BPTI) at a pressure of 2 kbar is presented. The structure was calculated as a change from an energy-minimized low-pressure structure, using (1)H chemical shifts as restraints. The structure has changed by 0.24 A RMS, and has almost unchanged volume. The largest changes as a result of pressure are in the loop 10-16, which contains the active site of BPTI, and residues 38-42, which are adjacent to buried water molecules. Hydrogen bonds are compressed by 0.029 +/- 0.117 A, with the longer hydrogen bonds, including those to internal buried water molecules, being compressed more. The hydrophobic core is also compressed, largely from reduction of packing defects. The parts of the structure that have the greatest change are close to buried water molecules, thus highlighting the importance of water molecules as the nucleation sites for volume fluctuation of proteins in native conditions.
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Affiliation(s)
- Michael P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
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Refaee M, Tezuka T, Akasaka K, Williamson MP. Pressure-dependent changes in the solution structure of hen egg-white lysozyme. J Mol Biol 2003; 327:857-65. [PMID: 12654268 DOI: 10.1016/s0022-2836(03)00209-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The "rules" governing protein structure and stability are still poorly understood. Important clues have come from proteins that operate under extreme conditions, because these clarify the physical constraints on proteins. One obvious extreme is pressure, but so far little is known of the behavior of proteins under pressure, largely for technical reasons. We have therefore developed new methodology for calculating structure change in solution with pressure, using NMR chemical shift changes, and we report the change in structure of lysozyme on going from 30 bar to 2000 bar, this being the first solution structure of a globular protein under pressure. The alpha-helical domain is compressed by approximately 1%, due to tighter packing between helices. The interdomain region is also compressed. By contrast, the beta-sheet domain displays very little overall compression, but undergoes more structural distortion than the alpha-domain. The largest volume changes tend to occur close to hydrated cavities. Because isothermal compressibility is related to volume fluctuation, this suggests that buried water molecules play an important role in conformational fluctuation at normal pressures, and are implicated as the nucleation sites for structural changes leading to pressure denaturation or channel opening.
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Affiliation(s)
- Mohamed Refaee
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, PO Box 594, Sheffiled S10 2UH, UK
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Lübke M, Guichard E, Tromelin A, Le Quéré JL. Nuclear magnetic resonance spectroscopic study of beta-lactoglobulin interactions with two flavor compounds, gamma-decalactone and beta-ionone. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2002; 50:7094-7099. [PMID: 12428965 DOI: 10.1021/jf020513k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Interactions between a well-characterized protein, beta-lactoglobulin, and two flavor compounds, beta-ionone and gamma-decalactone, were studied by 2D NMR spectroscopy. NMR spectra were recorded in aqueous solution (pH 2.0, 12 mM NaCl, 10% D(2)O) under conditions such that beta-lactoglobulin is present in a monomeric state. TOCSY and NOESY spectra were recorded on the protein and the complexes between protein and ligands. The spectra of the NH-CH(alpha) region showed the cross-signals due to the coupling between N- and C-bonded protons in the polypeptide backbone. The observed chemical shift variations in the presence of ligands can be assigned to changes in the protein conformation. It appears that the side chains of several amino acids are affected by binding of gamma-decalactone point into the central cavity (Leu46, Ile56, Met107, and Gln120), whereas binding of beta-ionone affects amino acids located in a groove near the outer surface of the protein (Leu104, Tyr120, and Asp129), as illustrated by molecular visualization. This NMR study provides precise information of the location of binding and confirms the existence of two different binding sites for aroma compounds on beta-lactoglobulin, which was suggested in previous competition studies by fluorometry or affinity chromatography and by structural information obtained from infrared spectroscopy.
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Affiliation(s)
- Markus Lübke
- INRA-UMRA, 17 rue Sully, 21065 Dijon Cedex, France
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Balny C, Masson P, Heremans K. High pressure effects on biological macromolecules: from structural changes to alteration of cellular processes. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:3-10. [PMID: 11983383 DOI: 10.1016/s0167-4838(01)00331-4] [Citation(s) in RCA: 205] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Claude Balny
- INSERM Unité 128, IFR 24, CNRS, 1919, route de Mende, Montpellier, France.
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