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Kuwajima K, Yagi-Utsumi M, Yanaka S, Kato K. DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123748. [PMID: 35744871 PMCID: PMC9230524 DOI: 10.3390/molecules27123748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
Hydrogen/deuterium (H/D) exchange combined with two-dimensional (2D) NMR spectroscopy has been widely used for studying the structure, stability, and dynamics of proteins. When we apply the H/D-exchange method to investigate non-native states of proteins such as equilibrium and kinetic folding intermediates, H/D-exchange quenching techniques are indispensable, because the exchange reaction is usually too fast to follow by 2D NMR. In this article, we will describe the dimethylsulfoxide (DMSO)-quenched H/D-exchange method and its applications in protein science. In this method, the H/D-exchange buffer is replaced by an aprotic DMSO solution, which quenches the exchange reaction. We have improved the DMSO-quenched method by using spin desalting columns, which are used for medium exchange from the H/D-exchange buffer to the DMSO solution. This improvement has allowed us to monitor the H/D exchange of proteins at a high concentration of salts or denaturants. We describe methodological details of the improved DMSO-quenched method and present a case study using the improved method on the H/D-exchange behavior of unfolded human ubiquitin in 6 M guanidinium chloride.
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Affiliation(s)
- Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Correspondence: (K.K.); (K.K.)
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
- Correspondence: (K.K.); (K.K.)
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2
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Rösner HI, Caldarini M, Prestel A, Vanoni MA, Broglia RA, Aliverti A, Tiana G, Kragelund BB. Cold Denaturation of the HIV-1 Protease Monomer. Biochemistry 2017; 56:1029-1032. [DOI: 10.1021/acs.biochem.6b01141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Heike I. Rösner
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
- Biotech
Research and Innovation Centre (BRIC), Faculty of Health and Medical
Sciences, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
| | - Martina Caldarini
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Andreas Prestel
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
| | - Maria A. Vanoni
- Department
of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Ricardo A. Broglia
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
- Niels Bohr Institute, Blegdamsvej
17, 2100 Copenhagen Ø, Denmark
| | - Alessandro Aliverti
- Department
of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Guido Tiana
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Birthe B. Kragelund
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
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3
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Gomaa AI, Nsonzi F, Sedman J, Ismail AA. Enhanced Unfolding of Bovine β-Lactoglobulin Structure Using Microwave Treatment: a Multi-Spectroscopic Study. FOOD BIOPHYS 2016. [DOI: 10.1007/s11483-016-9451-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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4
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Honda RP, Yamaguchi KI, Kuwata K. Acid-induced molten globule state of a prion protein: crucial role of Strand 1-Helix 1-Strand 2 segment. J Biol Chem 2014; 289:30355-30363. [PMID: 25217639 DOI: 10.1074/jbc.m114.559450] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The conversion of a cellular prion protein (PrP(C)) to its pathogenic isoform (PrP(Sc)) is a critical event in the pathogenesis of prion diseases. Pathogenic conversion is usually associated with the oligomerization process; therefore, the conformational characteristics of the pre-oligomer state may provide insights into the conversion process. Previous studies indicate that PrP(C) is prone to oligomer formation at low pH, but the conformation of the pre-oligomer state remains unknown. In this study, we systematically analyzed the acid-induced conformational changes of PrP(C) and discovered a unique acid-induced molten globule state at pH 2.0 termed the "A-state." We characterized the structure of the A-state using far/near-UV CD, 1-anilino-8-naphthalene sulfonate fluorescence, size exclusion chromatography, and NMR. Deuterium exchange experiments with NMR detection revealed its first unique structure ever reported thus far; i.e. the Strand 1-Helix 1-Strand 2 segment at the N terminus was preferentially unfolded, whereas the Helix 2-Helix 3 segment at the C terminus remained marginally stable. This conformational change could be triggered by the protonation of Asp(144), Asp(147), and Glu(196), followed by disruption of key salt bridges in PrP(C). Moreover, the initial population of the A-state at low pH (pH 2.0-5.0) was well correlated with the rate of the β-rich oligomer formation, suggesting that the A-state is the pre-oligomer state. Thus, the specific conformation of the A-state would provide crucial insights into the mechanisms of oligomerization and further pathogenic conversion as well as facilitating the design of novel medical chaperones for treating prion diseases.
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Affiliation(s)
- Ryo P Honda
- School of Medicine and Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Kei-Ichi Yamaguchi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Kazuo Kuwata
- School of Medicine and Gifu University, Yanagido 1-1, Gifu 501-1193, Japan; United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan; Department of Gene and Development, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan and.
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5
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Ikeguchi M. Transient non-native helix formation during the folding of β-lactoglobulin. Biomolecules 2014; 4:202-16. [PMID: 24970212 PMCID: PMC4030977 DOI: 10.3390/biom4010202] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/05/2014] [Accepted: 02/10/2014] [Indexed: 11/20/2022] Open
Abstract
In ideal proteins, only native interactions are stabilized step-by-step in a smooth funnel-like energy landscape. In real proteins, however, the transient formation of non-native structures is frequently observed. In this review, the transient formation of non-native structures is described using the non-native helix formation during the folding of β-lactoglobulin as a prominent example. Although β-lactoglobulin is a predominantly β-sheet protein, it has been shown to form non-native helices during the early stage of folding. The location of non-native helices, their stabilization mechanism, and their role in the folding reaction are discussed.
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Affiliation(s)
- Masamichi Ikeguchi
- Department of Bioinformatics, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo 192-8577, Japan.
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6
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Eberini I, Emerson A, Sensi C, Ragona L, Ricchiuto P, Pedretti A, Gianazza E, Tramontano A. Simulation of urea-induced protein unfolding: A lesson from bovine β-lactoglobulin. J Mol Graph Model 2011; 30:24-30. [DOI: 10.1016/j.jmgm.2011.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 06/01/2011] [Accepted: 06/02/2011] [Indexed: 01/16/2023]
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7
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Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proc Natl Acad Sci U S A 2009; 106:20740-5. [PMID: 19933333 DOI: 10.1073/pnas.0900622106] [Citation(s) in RCA: 189] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With single-molecule FRET, this question can be addressed even under near-native conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both the presence and the absence of denaturant, with good agreement between the results from single-molecule FRET and dynamic light scattering. Although dissociation of denaturant from the polypeptide chain with increasing temperature accounts for part of the compaction, the results indicate an important role for additional temperature-dependent interactions within the unfolded chain. The observation of a collapse of a similar extent in the extremely hydrophilic, intrinsically disordered protein prothymosin alpha suggests that the hydrophobic effect is not the sole source of the underlying interactions. Circular dichroism spectroscopy and replica exchange molecular dynamics simulations in explicit water show changes in secondary structure content with increasing temperature and suggest a contribution of intramolecular hydrogen bonding to unfolded state collapse.
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8
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Hamada D, Tanaka T, Tartaglia GG, Pawar A, Vendruscolo M, Kawamura M, Tamura A, Tanaka N, Dobson CM. Competition between Folding, Native-State Dimerisation and Amyloid Aggregation in β-Lactoglobulin. J Mol Biol 2009; 386:878-90. [DOI: 10.1016/j.jmb.2008.12.038] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 12/10/2008] [Accepted: 12/15/2008] [Indexed: 11/15/2022]
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9
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Davidovic M, Mattea C, Qvist J, Halle B. Protein Cold Denaturation as Seen From the Solvent. J Am Chem Soc 2008; 131:1025-36. [DOI: 10.1021/ja8056419] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Monika Davidovic
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
| | - Carlos Mattea
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
| | - Johan Qvist
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
| | - Bertil Halle
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
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10
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Hoshino M, Katou H, Yamaguchi KI, Goto Y. Dimethylsulfoxide-quenched hydrogen/deuterium exchange method to study amyloid fibril structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:1886-99. [PMID: 17499210 DOI: 10.1016/j.bbamem.2007.03.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2006] [Revised: 02/07/2007] [Accepted: 03/01/2007] [Indexed: 11/16/2022]
Abstract
A general method to analyze the structure of a supramolecular complex of amyloid fibrils at amino acid residue resolution has been developed. This method combines the NMR-detected hydrogen/deuterium (H/D) exchange technique to detect hydrogen-bonded amide groups and the ability of the aprotic organic solvent dimethylsulfoxide (DMSO) to dissolve amyloid fibrils into NMR-observable, monomeric components while suppressing the undesired H/D exchange reaction. Moreover, this method can be generally applied to amyloid fibrils to elucidate the distribution of hydrogen-bonded amino acid residues in the three-dimensional molecular organization in the amyloid fibrils. In this study, we describe theoretical considerations in the H/D exchange method to obtain the structural information of proteins, and the DMSO-quenched H/D exchange method to study a supramolecular complex of amyloid fibrils. A possible application of this method to study the interaction of a protein/peptide with phospholipid membrane is also discussed.
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Affiliation(s)
- Masaru Hoshino
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi, Kyoto 606-8501, Japan.
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11
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Lee YH, Tamura K, Maeda M, Hoshino M, Sakurai K, Takahashi S, Ikegami T, Hase T, Goto Y. Cores and pH-dependent dynamics of ferredoxin-NADP+ reductase revealed by hydrogen/deuterium exchange. J Biol Chem 2006; 282:5959-67. [PMID: 17192259 DOI: 10.1074/jbc.m608417200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NMR-detected hydrogen/deuterium (H/D) exchange of amide protons is a powerful way for investigating the residue-based conformational stability and dynamics of proteins in solution. Maize ferredoxin-NADP(+) reductase (FNR) is a relatively large protein with 314 amino acid residues, consisting of flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide phosphate (NADP(+))-binding domains. To address the structural stability and dynamics of FNR, H/D exchange of amide protons was performed using heteronuclear NMR at pD(r) values 8.0 and 6.0, physiologically relevant conditions mimicking inside of chloroplasts. At both pD(r) values, the exchange rate varied widely depending on the residues. The profiles of protected residues revealed that the highly protected regions matched well with the hydrophobic cores suggested from the crystal structure, and that the NADP(+)-binding domain can be divided into two subdomains. The global stability of FNR obtained by H/D exchange with NMR was higher than that by chemical denaturation, indicating that H/D exchange is especially useful for analyzing the residue-based conformational stability of large proteins, for which global unfolding is mostly irreversible. Interestingly, more dynamic conformation of the C-terminal subdomain of the NADP(+)-binding domain at pD(r) 8.0, the daytime pH in chloroplasts, than at pD(r) 6.0 is likely to be involved in the increased binding of NADP(+) for elevating the activity of FNR. In light of photosynthesis, the present study provides the first structure-based relationship of dynamics with function for the FNR-type family in solution.
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Affiliation(s)
- Young-Ho Lee
- Institute for Protein Research, Osaka University and CREST, Japan Science and Technology Agency, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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12
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Ahn HC, Le YTH, Nagchowdhuri PS, Derose EF, Putnam-Evans C, London RE, Markley JL, Lim KH. NMR characterizations of an amyloidogenic conformational ensemble of the PI3K SH3 domain. Protein Sci 2006; 15:2552-7. [PMID: 17001038 PMCID: PMC2242406 DOI: 10.1110/ps.062154306] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Amyloid formation is associated with structural changes of native polypeptides to monomeric intermediate states and their self-assembly into insoluble aggregates. Characterizations of the amyloidogenic intermediate state are, therefore, of great importance in understanding the early stage of amyloidogenesis. Here, we present NMR investigations of the structural and dynamic properties of the acid-unfolded amyloidogenic intermediate state of the phosphatidylinositol 3-kinase (PI3K) SH3 domain--a model peptide. The monomeric amyloidogenic state of the SH3 domain studied at pH 2.0 (35 degrees C) was shown to be substantially disordered with no secondary structural preferences. (15)N NMR relaxation experiments indicated that the unfolded polypeptide is highly flexible on a subnanosecond timescale when observed under the amyloidogenic condition (pH 2.0, 35 degrees C). However, more restricted motions were detected in residues located primarily in the beta-strands as well as in a loop in the native fold. In addition, nonnative long-range interactions were observed between the residues with the reduced flexibility by paramagnetic relaxation enhancement (PRE) experiments. These indicate that the acid-unfolded state of the SH3 domain adopts a partly folded conformation through nonnative long-range contacts between the dynamically restricted residues at the amyloid-forming condition.
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Affiliation(s)
- Hee-Chul Ahn
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706-1544, USA
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13
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Hattori M, Hiramatsu K, Kurata T, Nishiura M, Takahashi K, Ametani A, Kaminogawa S. Complete refolding of bovine beta-lactoglobulin requires disulfide bond formation under strict conditions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1752:154-65. [PMID: 16143573 DOI: 10.1016/j.bbapap.2005.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2005] [Revised: 07/04/2005] [Accepted: 07/19/2005] [Indexed: 10/25/2022]
Abstract
beta-Lactoglobulin (beta-LG) denatured with 6 M guanidine hydrochloride (GdnHCl) containing a reducing agent and subsequently dialysed against phosphate-buffered saline (PBS) resulted in incomplete refolding of this protein despite the fact that the biological activity for retinol-binding was recovered to almost the same degree as that of the native molecule [Hattori, M., Ametani, A., Katakura, Y., Shimizu, M., Kaminogawa, S. J., Biol. Chem. 268 (1993) 22414-22419]. The enzyme probe method, evaluation of hydrophilicity values, in-gel mobility on SDS-PAGE, and evaluation of disulfide bonds with the Ellman method showed exposure of the hydrophobic region(s) and incorrect disulfide bond formation in such dialyzed beta-LG molecules. We reveal in this present work that complete refolding could be attained by diluting denatured beta-LG with PBS containing a reducing agent, before slow reoxidation of the sulfhydryl groups upon dialysis for gradient removal of the reducing agent in 6 steps. Complete renaturation was confirmed by analyzing the retinol-binding activity, CD spectra, intrinsic fluorescence, binding ability of monoclonal antibodies (mAbs), and SDS-PAGE. Step-by-step disulfide bond formation was considered to be critical for the complete refolding of denatured beta-LG. Our method can contribute to establish a procedure for complete refolding of useful recombinant proteins in vitro without such biological aids as chaperones.
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Affiliation(s)
- Makoto Hattori
- Institute of Symbiotic Science and Technology, Division of Agriscience and Bioscience, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu-City, Tokyo 183-8509, Japan.
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14
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Paci E, Greene LH, Jones RM, Smith LJ. Characterization of the molten globule state of retinol-binding protein using a molecular dynamics simulation approach. FEBS J 2005; 272:4826-38. [PMID: 16156801 DOI: 10.1111/j.1742-4658.2005.04898.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Retinol-binding protein transports retinol, and circulates in the plasma as a macromolecular complex with the protein transthyretin. Under acidic conditions retinol-binding protein undergoes a transition to the molten globule state, and releases the bound retinol ligand. A biased molecular dynamics simulation method has been used to generate models for the ensemble of conformers populated within this molten globule state. Simulation conformers, with a radius of gyration at least 1.1 A greater than that of the native state, contain on average 37%beta-sheet secondary structure. In these conformers the central regions of the two orthogonal beta-sheets that make up the beta-barrel in the native protein are highly persistent. However, there are sizable fluctuations for residues in the outer regions of the beta-sheets, and large variations in side chain packing even in the protein core. Significant conformational changes are seen in the simulation conformers for residues 85-104 (beta-strands E and F and the E-F loop). These changes give an opening of the retinol-binding site. Comparisons with experimental data suggest that the unfolding in this region may provide a mechanism by which the complex of retinol-binding protein and transthyretin dissociates, and retinol is released at the cell surface.
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Affiliation(s)
- Emanuele Paci
- Institute of Molecular Biophysics, School of Physics and Astronomy, University of Leeds, UK.
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15
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Szyperski T, Mills JL, Perl D, Balbach J. Combined NMR-observation of cold denaturation in supercooled water and heat denaturation enables accurate measurement of deltaC(p) of protein unfolding. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2005; 35:363-6. [PMID: 16240113 DOI: 10.1007/s00249-005-0028-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Revised: 09/23/2005] [Accepted: 09/28/2005] [Indexed: 10/25/2022]
Abstract
Cold and heat denaturation of the double mutant Arg 3-->Glu/Leu 66-->Glu of cold shock protein Csp of Bacillus caldolyticus was monitored using 1D (1)H NMR spectroscopy in the temperature range from -12 degrees C in supercooled water up to +70 degrees C. The fraction of unfolded protein, f (u), was determined as a function of the temperature. The data characterizing the unfolding transitions could be consistently interpreted in the framework of two-state models: cold and heat denaturation temperatures were determined to be -11 degrees C and 39 degrees C, respectively. A joint fit to both cold and heat transition data enabled the accurate spectroscopic determination of the heat capacity difference between native and denatured state, DeltaC(p) of unfolding. The approach described in this letter, or a variant thereof, is generally applicable and promises to be of value for routine studies of protein folding.
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Affiliation(s)
- Thomas Szyperski
- Department of Chemistry, The State University of New York, Buffalo, NY 14260, USA.
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16
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Seshasayee ASN, Raghunathan K, Sivaraman K, Pennathur G. Role of hydrophobic interactions and salt-bridges in β-hairpin folding. J Mol Model 2005; 12:197-204. [PMID: 16231193 DOI: 10.1007/s00894-005-0018-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2005] [Accepted: 06/27/2005] [Indexed: 11/30/2022]
Abstract
Beta-hairpins are the simplest form of beta-sheets which, due to the presence of long-range interactions, can be considered as tertiary structures. Molecular dynamics simulation is a powerful tool that can unravel whole pathways of protein folding/unfolding at atomic resolution. We have performed several molecular dynamics simulations, to a total of over 250 ns, of a beta-hairpin peptide in water using GROMACS. We show that hydrophobic interactions are necessary for initiating the folding of the peptide. Once formed, the peptide is stabilized by hydrogen bonds and disruption of hydrophobic interactions in the folded peptide does not denature the structure. In the absence of hydrophobic interactions, the peptide fails to fold. However, the introduction of a salt-bridge compensates for the loss of hydrophobic interactions to a certain extent.
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17
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Dyer RB, Maness SJ, Franzen S, Fesinmeyer RM, Olsen KA, Andersen NH. Hairpin Folding Dynamics: The Cold-Denatured State Is Predisposed for Rapid Refolding. Biochemistry 2005; 44:10406-15. [PMID: 16042418 DOI: 10.1021/bi050698z] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cold denaturation is a general phenomenon in globular proteins, and the associated cold-denatured states of proteins have important fundamental and practical significance. Here, we have characterized the cold-denatured state of a beta-hairpin forming peptide, MrH3a, in 8% hexafluoro-2-propanol (HFIP) and the dynamics of its refolding following a laser-induced T-jump. Beta-hairpins constitute an important class of protein structural elements, yet their folding mechanisms are not fully understood. Characterization of MrH3a using NMR, CD, and IR spectroscopies reveals residual structure in the cold-denatured state, in contrast with the highly disordered heat-denatured state. The residual structure in the cold-denatured state comprises relatively compact and solvent protected conformations. Furthermore, we find a substantial acceleration in the rate of folding from the cold-denatured state compared to that of the heat-denatured state. In addition, the cold-denatured state is not populated in 20% HFIP; folding occurs only from the fully unfolded state and is significantly slower. We interpret the acceleration of the folding rate of MrH3a in 8% HFIP as a direct consequence of the collapsed conformations of the cold-denatured state. Finally, there may be some reduction of the loop search cost when starting from the cold-denatured state, since this state may have some of the stabilizing cross-strand interactions already formed.
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Affiliation(s)
- R Brian Dyer
- Bioscience Division, Mail Stop J586, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
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18
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Yamada Y, Yajima T, Fujiwara K, Arai M, Ito K, Shimizu A, Kihara H, Kuwajima K, Amemiya Y, Ikeguchi M. Helical and Expanded Conformation of Equine β-Lactoglobulin in the Cold-denatured State. J Mol Biol 2005; 350:338-48. [PMID: 15925384 DOI: 10.1016/j.jmb.2005.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2004] [Revised: 04/28/2005] [Accepted: 05/03/2005] [Indexed: 11/26/2022]
Abstract
The thermal unfolding transition of equine beta-lactoglobulin (ELG) was investigated by circular dichroism (CD) over a temperature range of -15 degrees C to 85 degrees C. In the presence of 2 M urea, a cooperative unfolding transition was observed both with increasing and decreasing temperature. The CD spectrum indicated that the heat and cold-denatured states of ELG have substantial secondary structures but lack persistent tertiary packing of the side-chains. In order to clarify the relation between the heat or cold-denatured state and the acid-denatured (A) state characterized previously, we have attempted to observe the temperature dependence of the CD spectrum at pH 1.5. The CD spectrum in the heat-denatured state is similar to that in the A state. The CD spectrum in the A state does not change cooperatively with increasing temperature. These results indicate that the heat-denatured state and the A state are the same structural state. On the other hand, the CD intensity at acid pH cooperatively increased with decreasing temperature. The CD spectrum at low temperature and acid pH is consistent with that in the cold-denatured state. Therefore, the cold-denatured state is distinguished from the heat-denatured state or the A state, and ELG assumes a larger amount of non-native alpha-helices in the cold-denatured state. Small angle X-ray scattering and analytical ultracentrifugation have indicated that ELG assumes an expanded chain-like conformation in the cold-denatured state in contrast to the compact globular conformation in the A state. The relation between the molecular size and the helical content in the partially folded states is discussed.
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Affiliation(s)
- Yoshiteru Yamada
- Department of Bioengineering, Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan
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Gottschalk M, Nilsson H, Roos H, Halle B. Protein self-association in solution: the bovine beta -lactoglobulin dimer and octamer. Protein Sci 2004; 12:2404-11. [PMID: 14573854 PMCID: PMC2366967 DOI: 10.1110/ps.0305903] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have used proton magnetic relaxation dispersion (MRD) to study the self-association of bovine beta-lactoglobulin variant A (BLG-A) as a function of temperature at pH 4.7 (dimer-octamer equilibrium) and as a function of NaCl concentration at pH 2.5 (monomer-dimer equilibrium). The MRD method identifies coexisting oligomers from their rotational correlation times and determines their relative populations from the associated dispersion amplitudes. From MRD-derived correlation times and hydrodynamic model calculations, we confirm that BLG-A dimers associate to octamers below room temperature. The tendency for BLG-A dimers to assemble into octamers is found to be considerably weaker than in previous light scattering studies in the presence of buffer salt. At pH 2.5, the MRD data are consistent with an essentially complete transition from monomers in the absence of salt to dimers in 1 M NaCl. Because of an interfering relaxation dispersion from nanosecond water exchange, we cannot determine the oligomer populations at intermediate salt concentrations. This nanosecond dispersion may reflect intersite exchange of water molecules trapped inside the large binding cavity of BLG-A.
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Affiliation(s)
- Michael Gottschalk
- Department of Biophysical Chemistry, Lund University, SE-22100 Lund, Sweden
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Shi Z, Woody RW, Kallenbach NR. Is polyproline II a major backbone conformation in unfolded proteins? ADVANCES IN PROTEIN CHEMISTRY 2004; 62:163-240. [PMID: 12418104 DOI: 10.1016/s0065-3233(02)62008-x] [Citation(s) in RCA: 257] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Zhengshuang Shi
- Department of Chemistry, New York University, New York 10003, USA
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Millett IS, Doniach S, Plaxco KW. Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. ADVANCES IN PROTEIN CHEMISTRY 2004; 62:241-62. [PMID: 12418105 DOI: 10.1016/s0065-3233(02)62009-1] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ian S Millett
- Department of Applied Physics, Stanford University, Stanford, California 92343, USA
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Mayor U, Grossmann JG, Foster NW, Freund SMV, Fersht AR. The denatured state of Engrailed Homeodomain under denaturing and native conditions. J Mol Biol 2003; 333:977-91. [PMID: 14583194 DOI: 10.1016/j.jmb.2003.08.062] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Protein folding starts from the elusive form of the denatured state that is present under conditions that favour the native state. We have studied the denatured state of Engrailed Homeodomain (En-HD) under mildly and strongly denaturing conditions at the level of individual residues by NMR and more globally by conventional spectroscopy and solution X-ray scattering. We have compared these states with a destabilized mutant, L16A, which is predominantly denatured under conditions where the wild-type is native. This engineered denatured state, which could be directly studied under native conditions, was in genuine equilibrium with the native state, which could be observably populated by changing the conditions or introducing a stabilizing mutation. The denatured state had extensive native secondary structure and was significantly compact and globular. But, the side-chains and backbone were highly mobile. Non-cooperative melting of the residual structure on the denatured state of En-HD was observed, both at the residue and the molecular level, with increasingly denaturing conditions. The absence of a co-operative transition could result from the denatured state ensemble progressing through a series of intermediates or from a more general slide (second-order transition) from the compact form under native conditions to the more extended at highly denaturing conditions. In either case, the starting point for folding under native conditions is highly structured and already poised to adopt the native structure.
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Affiliation(s)
- Ugo Mayor
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK
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Ragona L, Catalano M, Zetta L, Longhi R, Fogolari F, Molinari H. Peptide models of folding initiation sites of bovine beta-lactoglobulin: identification of nativelike hydrophobic interactions involving G and H strands. Biochemistry 2002; 41:2786-96. [PMID: 11851426 DOI: 10.1021/bi011615r] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In an attempt to characterize the early folding events in bovine beta-lactoglobulin (BLG), a set of peptides, covering the flexible N-terminal region and the stable C-terminus beta-core, was synthesized and analyzed by circular dichroism and by nuclear magnetic resonance in water, trifluoroethanol (TFE), and sodium dodecyl sulfate (SDS) below and above the critical micellar concentration. The role of local and long-range hydrophobic interactions in guiding the folding has been investigated. For the peptide fragment covering the more flexible N-terminal region of BLG (beta-strands A, B), where both theoretical predictions and kinetic refolding experiments suggested the formation of non-native alpha-helix, no native long-range contacts were identified, and a helical secondary structure was stabilized only in the presence of 25 mM SDS. At variance, in 50% (v/v) TFE, native, long-range hydrophobic interactions were observed in the peptide covering the core region comprising G and H beta-strands. The side chains involved in these interactions form a nativelike hydrophobic cluster, thus suggesting that the GH region may act as the folding initiation site for BLG. This result is reinforced by the identification, in the urea denaturated BLG, of residual structure located at the level of the GH interface, as evidenced by NMR analysis. These results, in excellent agreement with kinetic, thermodynamic, and cold denaturation folding data, once more underline the utmost importance of the GH region for the stability and folding of BLG. Severe aggregation effects prevented the structural analysis of the peptide covering the EFGH region, indicating that this larger segment does not represent an independent folding domain and that the terminal alpha-helix is necessary for stabilizing the BLG folding core.
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Affiliation(s)
- Laura Ragona
- Laboratorio NMR, ICM, via Ampère 56, 20131, Milano, Italy, Istituto di Biocatalisi e Riconoscimento Molecolare, CNR, via M. Bianco, 20131 Milano, Italy
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HATTORI M. Functional Improvements in Food Proteins in Multiple Aspects by Conjugation with Saccharides: Case Studies of .BETA.-Lactoglobulin-Acidic Polysaccharides Conjugates. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2002. [DOI: 10.3136/fstr.8.291] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Taulier N, Chalikian TV. Characterization of pH-induced transitions of beta-lactoglobulin: ultrasonic, densimetric, and spectroscopic studies. J Mol Biol 2001; 314:873-89. [PMID: 11734004 DOI: 10.1006/jmbi.2001.5188] [Citation(s) in RCA: 176] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Depending on solution conditions, beta-lactoglobulin can exist in one of its six pH-dependent structural states. We have characterized the acid and basic-induced conformational transitions between these structural states over the pH range of pH 1 to pH 13. To this end, we have employed high-precision ultrasonic and densimetric measurements coupled with fluorescence and CD spectroscopic data. Our combined spectroscopic and volumetric results have revealed five pH-induced transitions of beta-lactoglobulin between pH 1 and pH 13. The first transition starts at pH 2 and is not completed even at pH 1, our lowest experimental pH. This transition is followed by the dimer-to-monomer transition of beta-lactoglobulin between pH 2.5 and pH 4. The dimer-to-monomer transition is accompanied by decreases in volume, v degrees (-0.008(+/-0.003) cm3 x g(-1)), and adiabatic compressibility, k degrees (S) (-(0.7(+/-0.4))x10(-6) cm3 x g(-1) x bar(-1)). We interpret the observed changes in volume and compressibility associated with the dimer-to-monomer transition of beta-lactoglobulin, in conjunction with X-ray crystallographic data, as suggesting a 7 % increase in protein hydration, with the hydration changes being localized in the area of contact between the two monomeric subunits. The so-called N-to-Q transition of beta-lactoglobulin occurs between pH 4.5 and pH 6 and is accompanied by increases in volume, v degrees (0.004(+/-0.003) cm3 x g(-1)), and compressibility, k degrees (S) ((0.7(+/-0.4))x10(-6) cm3 x g(-1) x bar(-1)). The Tanford transition of beta-lactoglobulin is centered at pH 7.5 and is accompanied by a decrease in volume, v degrees (-0.006(+/-0.003) cm3 x g(-1)), and an increase in compressibility, k degrees (S) ((1.5(+/-0.5))x10(-6) cm3 x g(-1) x bar(-1)). Based on these volumetric results, we propose that the Tanford transition is accompanied by a 5 to 10 % increase in the protein hydration and a loosening of the interior packing of beta-lactoglobulin as reflected in a 12 % increase in its intrinsic compressibility. Finally, above pH 9, the protein undergoes irreversible base-induced unfolding which is accompanied by decreases in v degrees (-0.014(+/-0.003) cm3 x g(-1)) and k degrees (S) (-(7.0(+/-0.5))x10(-6) cm3 x g(-1) x bar(-1)). Combining these results with our CD spectroscopic data, we propose that, in the base-induced unfolded state of beta-lactoglobulin, only 80 % of the surface area of the fully unfolded conformation is exposed to the solvent. Thus, in so far as solvent exposure is concerned, the base-induced unfolded states of beta-lactoglobulin retains some order, with 20 % of its amino acid residues remaining solvent inaccessible.
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Affiliation(s)
- N Taulier
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, 19 Russell Street, Toronto, Ontario, M5S 2S2, Canada
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