1
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Dreydoppel M, Dorn B, Modig K, Akke M, Weininger U. Transition-State Compressibility and Activation Volume of Transient Protein Conformational Fluctuations. JACS AU 2021; 1:833-842. [PMID: 34467336 PMCID: PMC8395657 DOI: 10.1021/jacsau.1c00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 06/13/2023]
Abstract
Proteins are dynamic entities that intermittently depart from their ground-state structures and undergo conformational transitions as a critical part of their functions. Central to understanding such transitions are the structural rearrangements along the connecting pathway, where the transition state plays a special role. Using NMR relaxation at variable temperature and pressure to measure aromatic ring flips inside a protein core, we obtain information on the structure and thermodynamics of the transition state. We show that the isothermal compressibility coefficient of the transition state is similar to that of short-chain hydrocarbon liquids, implying extensive local unfolding of the protein. Our results further indicate that the required local volume expansions of the protein can occur not only with a net positive activation volume of the protein, as expected from previous studies, but also with zero activation volume by compaction of remote void volume, when averaged over the ensemble of states.
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Affiliation(s)
- Matthias Dreydoppel
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Britta Dorn
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Kristofer Modig
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Mikael Akke
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Ulrich Weininger
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06120 Halle (Saale), Germany
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2
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Dubois C, Herrada I, Barthe P, Roumestand C. Combining High-Pressure Perturbation with NMR Spectroscopy for a Structural and Dynamical Characterization of Protein Folding Pathways. Molecules 2020; 25:E5551. [PMID: 33256081 PMCID: PMC7731413 DOI: 10.3390/molecules25235551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
High-hydrostatic pressure is an alternative perturbation method that can be used to destabilize globular proteins. Generally perfectly reversible, pressure exerts local effects on regions or domains of a protein containing internal voids, contrary to heat or chemical denaturant that destabilize protein structures uniformly. When combined with NMR spectroscopy, high pressure (HP) allows one to monitor at a residue-level resolution the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. The use of HP-NMR has long been hampered by technical difficulties. Owing to the recent development of commercially available high-pressure sample cells, HP-NMR experiments can now be routinely performed. This review summarizes recent advances of HP-NMR techniques for the characterization at a quasi-atomic resolution of the protein folding energy landscape.
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Affiliation(s)
| | | | | | - Christian Roumestand
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université de Montpellier, 34090 Montpellier, France; (C.D.); (I.H.); (P.B.)
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3
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Stenzoski NE, Zou J, Piserchio A, Ghose R, Holehouse AS, Raleigh DP. The Cold-Unfolded State Is Expanded but Contains Long- and Medium-Range Contacts and Is Poorly Described by Homopolymer Models. Biochemistry 2020; 59:3290-3299. [PMID: 32786415 DOI: 10.1021/acs.biochem.0c00469] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cold unfolding of proteins is predicted by the Gibbs-Helmholtz equation and is thought to be driven by a strongly temperature-dependent interaction of protein nonpolar groups with water. Studies of the cold-unfolded state provide insight into protein energetics, partially structured states, and folding cooperativity and are of practical interest in biotechnology. However, structural characterization of the cold-unfolded state is much less extensive than studies of thermally or chemically denatured unfolded states, in large part because the midpoint of the cold unfolding transition is usually below freezing. We exploit a rationally designed point mutation (I98A) in the hydrophobic core of the C-terminal domain of the ribosomal protein L9 that allows the cold denatured state ensemble to be observed above 0 °C at near neutral pH and ambient pressure in the absence of added denaturants. A combined approach consisting of paramagnetic relaxation enhancement measurements, analysis of small-angle X-ray scattering data, all-atom simulations, and polymer theory provides a detailed description of the cold-unfolded state. Despite a globally expanded ensemble, as determined by small-angle X-ray scattering, sequence-specific medium- and long-range interactions in the cold-unfolded state give rise to deviations from homopolymer-like behavior. Our results reveal that the cold-denatured state is heterogeneous with local and long-range intramolecular interactions that may prime the folded state and also demonstrate that significant long-range interactions are compatible with expanded unfolded ensembles. The work also highlights the limitations of homopolymer-based descriptions of unfolded states of proteins.
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Affiliation(s)
- Natalie E Stenzoski
- Graduate Program in Biochemistry & Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Junjie Zou
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States.,Graduate Programs in Biochemistry, Chemistry and Physics, The Graduate Center of CUNY, New York, New York 10016, United States
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States.,Center for Science and Engineering of Living Systems, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Daniel P Raleigh
- Graduate Program in Biochemistry & Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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4
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Cheng L, Zhu Z, Sun DW. Impacts of high pressure assisted freezing on the denaturation of polyphenol oxidase. Food Chem 2020; 335:127485. [PMID: 32763785 DOI: 10.1016/j.foodchem.2020.127485] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/22/2020] [Accepted: 07/01/2020] [Indexed: 02/08/2023]
Abstract
The mechanism of enzyme protein denaturation induced by high pressure freezing is complicated and unclear as this process involves Pressure-Factors (pressure and time) and Freezing-Factors (temperature, phase transition, recrystallization, and ice crystal types). In this study, the thermodynamics and conformation changes of mushroom polyphenol oxidase (PPO) under high pressure freezing treatments (HPF, 100,150,200,300,400,500MPaP-20°C/30min) and high pressure processes (HPP) followed with normal pressure immersion freezing (HPP-IF, 100-500MPaP25°C/30min - 0.1MPaP-20°C/30min) are investigated as compared with that processed under high pressure processes (HPP, 100-500MPaP25°C/30min) and normal pressure immersion freezing process (IF, 0.1MPaP-20°C/30min). The results suggested that the treated PPO with the same enzyme activity may have various thermodynamic characteristics and conformations; Pressure-Factors play the main roles in the denaturation of the PPO during the HPF treatment, and Freezing-Factors can weak the effect of Pressure-Factors on PPO denaturation; The treated PPO may be transferred into a partially fold intermediate state.
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Affiliation(s)
- Lina Cheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Sericulture & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products Processing, Guangzhou 510610, China
| | - Zhiwei Zhu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Belfield, Dublin 4, Ireland.
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5
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The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth. PLoS Comput Biol 2020; 16:e1007767. [PMID: 32365068 PMCID: PMC7282669 DOI: 10.1371/journal.pcbi.1007767] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/09/2020] [Accepted: 03/02/2020] [Indexed: 11/19/2022] Open
Abstract
Many proteins have the potential to aggregate into amyloid fibrils, protein polymers associated with a wide range of human disorders such as Alzheimer’s and Parkinson’s disease. The thermodynamic stability of amyloid fibrils, in contrast to that of folded proteins, is not well understood: the balance between entropic and enthalpic terms, including the chain entropy and the hydrophobic effect, are poorly characterised. Using a combination of theory, in vitro experiments, simulations of a coarse-grained protein model and meta-data analysis, we delineate the enthalpic and entropic contributions that dominate amyloid fibril elongation. Our prediction of a characteristic temperature-dependent enthalpic signature is confirmed by the performed calorimetric experiments and a meta-analysis over published data. From these results we are able to define the necessary conditions to observe cold denaturation of amyloid fibrils. Overall, we show that amyloid fibril elongation is associated with a negative heat capacity, the magnitude of which correlates closely with the hydrophobic surface area that is buried upon fibril formation, highlighting the importance of hydrophobicity for fibril stability. Most proteins fold in the cell into stable, compact structures. Nevertheless, many proteins also have the ability to stick together, forming long fibrillar structures that are associated with a wide range of human disorders including Alzheimer’s and Parkinson’s disease. The exact nature of the amyloid-causing stickiness is not well understood, nevertheless amyloid fibrils show some very specific thermodynamic characteristics. Some fibrils even destabilise at low temperatures. In this work we translate hydrophobic theory previously used to model protein folding to fibril formation. We combine this theory with experimental measurements, simulations and meta-data analysis of different types of fibrils. This allowed us to unravel the nature of the stickiness in amyloid fibrils by observing the effect of temperature changes, specifically at low temperatures, on hydrophobicity.
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6
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Ramanujam V, Alderson TR, Pritišanac I, Ying J, Bax A. Protein structural changes characterized by high-pressure, pulsed field gradient diffusion NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 312:106701. [PMID: 32113145 PMCID: PMC7153785 DOI: 10.1016/j.jmr.2020.106701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Pulsed-field gradient NMR spectroscopy is widely used to measure the translational diffusion and hydrodynamic radius (Rh) of biomolecules in solution. For unfolded proteins, the Rh provides a sensitive reporter on the ensemble-averaged conformation and the extent of polypeptide chain expansion as a function of added denaturant. Hydrostatic pressure is a convenient and reversible alternative to chemical denaturants for the study of protein folding, and enables NMR measurements to be performed on a single sample. While the impact of pressure on the viscosity of water is well known, and our water diffusivity measurements agree closely with theoretical expectations, we find that elevated pressures increase the Rh of dioxane and other small molecules by amounts that correlate with their hydrophobicity, with parallel increases in rotational friction indicated by 13C longitudinal relaxation times. These data point to a tighter coupling with water for hydrophobic surfaces at elevated pressures. Translational diffusion measurement of the unfolded state of a pressure-sensitized ubiquitin mutant (VA2-ubiquitin) as a function of hydrostatic pressure or urea concentration shows that Rh values of both the folded and the unfolded states remain nearly invariant. At ca 23 Å, the Rh of the fully pressure-denatured state is essentially indistinguishable from the urea-denatured state, and close to the value expected for an idealized random coil of 76 residues. The intrinsically disordered protein (IDP) α-synuclein shows slight compaction at pressures above 2 kbar. Diffusion of unfolded ubiquitin and α-synuclein is significantly impacted by sample concentration, indicating that quantitative measurements need to be carried out under dilute conditions.
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Affiliation(s)
- Venkatraman Ramanujam
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - T Reid Alderson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Iva Pritišanac
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany.
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7
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Mandal M, Das A, Mukhopadhyay C. Ubiquitin folds via a flip-twist-lock mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140299. [DOI: 10.1016/j.bbapap.2019.140299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/14/2019] [Accepted: 10/01/2019] [Indexed: 01/08/2023]
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8
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Abiko LA, Grahl A, Grzesiek S. High Pressure Shifts the β 1-Adrenergic Receptor to the Active Conformation in the Absence of G Protein. J Am Chem Soc 2019; 141:16663-16670. [PMID: 31564099 DOI: 10.1021/jacs.9b06042] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
G protein-coupled receptors (GPCRs) are versatile chemical sensors, which transmit the signal of an extracellular binding event across the plasma membrane to the intracellular side. This function is achieved via the modulation of highly dynamical equilibria of various conformational receptor states. Here we have probed the effect of pressure on the conformational equilibria of a functional thermostabilized β1-adrenergic GPCR (β1AR) by solution NMR. High pressure induces a large shift in the conformational equilibrium (midpoint ∼600 bar) from the preactive conformation of agonist-bound β1AR to the fully active conformation, which under normal pressure is only populated when a G protein or a G protein-mimicking nanobody (Nb) binds to the intracellular side of the β1AR·agonist complex. No such large effects are observed for an antagonist-bound β1AR or the ternary β1AR·agonist·Nb80 complex. The detected structural changes of agonist-bound β1AR around the orthosteric ligand binding pocket indicate that the fully active receptor occupies an ∼100 Å3 smaller volume than that of its preactive form. Most likely, this volume reduction is caused by the compression of empty (nonhydrated) cavities in the ligand binding pocket and the center of the receptor, which increases the ligand receptor interactions and explains the ∼100-fold affinity increase of agonists in the presence of G protein. The finding that isotropic pressure induces a directed motion from the preactive to the fully active GPCR conformation provides evidence of the high mechanical robustness of this important functional switch.
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Affiliation(s)
- Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , CH-4056 Basel , Switzerland
| | - Anne Grahl
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , CH-4056 Basel , Switzerland
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , CH-4056 Basel , Switzerland
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9
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Winnikoff JR, Francis WR, Thuesen EV, Haddock SHD. Combing Transcriptomes for Secrets of Deep-Sea Survival: Environmental Diversity Drives Patterns of Protein Evolution. Integr Comp Biol 2019; 59:786-798. [PMID: 31141128 PMCID: PMC6797910 DOI: 10.1093/icb/icz063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Ctenophores, also known as comb jellies, live across extremely broad ranges of temperature and hydrostatic pressure in the ocean. Because various ctenophore lineages adapted independently to similar environmental conditions, Phylum Ctenophora is an ideal system for the study of protein adaptation to extreme environments in a comparative framework. We present such a study here, using a phylogenetically-informed method to compare sequences of four essential metabolic enzymes across gradients of habitat depth and temperature. This method predicts convergent adaptation to these environmental parameters at the amino acid level, providing a novel view of protein adaptation to extreme environments and demonstrating the power and relevance of phylogenetic comparison applied to multi-species transcriptomic datasets from early-diverging metazoa. Across all four enzymes analyzed, 46 amino acid sites were associated with depth-adaptation, 59 with temperature-adaptation, and 56 with both. Sites predicted to be depth- and temperature-adaptive occurred consistently near Rossmann fold cofactor binding motifs and disproportionately in solvent-exposed regions of the protein. These results suggest that the hydrophobic effect and ligand binding may mediate efficient enzyme function at different hydrostatic pressures and temperatures. Using predicted adaptive site maps, such mechanistic hypotheses can now be tested via mutagenesis.
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Affiliation(s)
- J R Winnikoff
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd., Moss Landing, CA 95039, USA
- Ecology and Evolutionary Biology, University of California at Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - W R Francis
- Department of Biology, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - E V Thuesen
- The Evergreen State College, Laboratory I, Olympia, WA 98505, USA
| | - S H D Haddock
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd., Moss Landing, CA 95039, USA
- Ecology and Evolutionary Biology, University of California at Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
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10
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Uralcan B, Debenedetti PG. Computational Investigation of the Effect of Pressure on Protein Stability. J Phys Chem Lett 2019; 10:1894-1899. [PMID: 30939023 DOI: 10.1021/acs.jpclett.9b00545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Previous studies show parabolic or elliptical regions of protein stability in the pressure-temperature ( P, T) plane. The construction of stability diagrams requires accessing a sufficiently broad ( P, T) range, which is often frustrated by ice formation in experiments and sampling challenges in simulations. We perform a fully atomistic computational study of the miniprotein Trp-cage over the range of temperatures 210 ≤ T ≤ 420 K and pressures P ≤ 5 kbar and construct the corresponding stability diagram. At ambient temperature, pressure shifts the conformational states toward unfolding. Below 250 K, the native fold's stability depends nonmonotonically on pressure. While cold unfolding and thermal denaturation differ significantly at ambient pressure, they exhibit progressive similarity at elevated pressures. At ambient pressure, cold denaturation is an enthalpically driven process that preserves significant elements of Trp-cage's secondary structure. In contrast, cold unfolding at elevated pressures involves a more substantial loss of secondary and tertiary structure, similar to thermal denaturation.
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Affiliation(s)
- Betul Uralcan
- Department of Chemical and Biological Engineering , Princeton University , Princeton , New Jersey 08544 , United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering , Princeton University , Princeton , New Jersey 08544 , United States
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11
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Taricska N, Bokor M, Menyhárd DK, Tompa K, Perczel A. Hydration shell differentiates folded and disordered states of a Trp-cage miniprotein, allowing characterization of structural heterogeneity by wide-line NMR measurements. Sci Rep 2019; 9:2947. [PMID: 30814556 PMCID: PMC6393587 DOI: 10.1038/s41598-019-39121-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 12/10/2018] [Indexed: 12/12/2022] Open
Abstract
Hydration properties of folded and unfolded/disordered miniproteins were monitored in frozen solutions by wide-line 1H-NMR. The amount of mobile water as function of T (-80 °C < T < 0 °C) was found characteristically different for folded (TC5b), semi-folded (pH < 3, TCb5(H+)) and disordered (TC5b_N1R) variants. Comparing results of wide-line 1H-NMR and molecular dynamics simulations we found that both the amount of mobile water surrounding proteins in ice, as well as their thaw profiles differs significantly as function of the compactness and conformational heterogeneity of their structure. We found that (i) at around -50 °C ~50 H2Os/protein melt (ii) if the protein is well-folded then this amount of mobile water remains quasi-constant up to -20 °C, (iii) if disordered then the quantity of the lubricating mobile water increases with T in a constant manner up to ~200 H2Os/protein by reaching -20 °C. Especially in the -55 °C ↔ -15 °C temperature range, wide-line 1H-NMR detects the heterogeneity of protein fold, providing the size of the hydration shell surrounding the accessible conformers at a given temperature. Results indicate that freezing of protein solutions proceeds by the gradual selection of the enthalpically most favored states that also minimize the number of bridging waters.
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Affiliation(s)
- Nóra Taricska
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Mónika Bokor
- Institute for Solid State Physics and Optics, Wigner RCP of the HAS, 1121, Budapest, Hungary
| | - Dóra K Menyhárd
- MTA-ELTE Protein Modelling Research Group, Pázmány Péter st. 1A, 1117, Budapest, Hungary
| | - Kálmán Tompa
- Institute for Solid State Physics and Optics, Wigner RCP of the HAS, 1121, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, 1117, Hungary.
- MTA-ELTE Protein Modelling Research Group, Pázmány Péter st. 1A, 1117, Budapest, Hungary.
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12
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Klamt A, Nagarathinam K, Tanabe M, Kumar A, Balbach J. Hyperbolic Pressure-Temperature Phase Diagram of the Zinc-Finger Protein apoKti11 Detected by NMR Spectroscopy. J Phys Chem B 2019; 123:792-801. [PMID: 30608169 DOI: 10.1021/acs.jpcb.8b11019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For a comprehensive understanding of the thermodynamic state functions describing the stability of a protein, the influence of the intensive properties of temperature and pressure has to be known. With the zinc-finger-containing Kti11, we found a suitable protein for this purpose because folding and unfolding transitions occur at an experimentally accessible temperature (280-330 °K) and pressure (0.1-240 MPa) range. We solved the crystal structure of the apo form of Kti11 to reveal two disulfide bonds at the metal-binding site, which seals off a cavity in the β-barrel part of the protein. From a generally applicable proton NMR approach, we could determine the populations of folded and unfolded chains under all conditions, leading to a hyperbolic pressure-temperature phase diagram rarely observed for proteins. A global fit of a two-state model to all derived populations disclosed reliable values for the change in Gibbs free energy, volume, entropy, heat capacity, compressibility, and thermal expansion upon unfolding. The unfolded state of apoKti11 has a lower compressibility compared to the native state and a smaller volume at ambient pressure. Therefore, a pressure increase up to 200 MPa reduces the population of the native state, and above this value, the native population increases again. Pressure-induced chemical-shift changes in two-dimensional 1H-15N NMR spectra could be employed for a molecular interpretation of the thermodynamic properties of apoKti11.
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Affiliation(s)
- Andi Klamt
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany
| | - Kumar Nagarathinam
- HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany.,Institute of Virology , Hannover Medical School , Carl-Neuberg-Straße 1 , D-30625 Hannover , Germany
| | - Mikio Tanabe
- HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany.,Structural Biology Research Center, Institute of Materials Structure Science , KEK/High Energy Accelerator Research Organization , 1-1 Oho , Tsukuba , Ibaraki , 305-0801 , Japan
| | - Amit Kumar
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany.,Department of Diabetes, Faculty of Lifesciences and Medicine , King's College London , Great Maze Pond , London SE1 1UL , U.K
| | - Jochen Balbach
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany.,HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany
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13
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Cold survival strategies for bacteria, recent advancement and potential industrial applications. Arch Microbiol 2018; 201:1-16. [PMID: 30478730 DOI: 10.1007/s00203-018-1602-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/04/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022]
Abstract
Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.
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14
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Charlier C, Courtney JM, Anfinrud P, Bax A. Interrupted Pressure-Jump NMR Experiments Reveal Resonances of On-Pathway Protein Folding Intermediate. J Phys Chem B 2018; 122:11792-11799. [PMID: 30256104 DOI: 10.1021/acs.jpcb.8b08456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Previous pressure-jump NMR experiments on a pressure-sensitized double mutant of ubiquitin showed evidence that its folding occurs via two parallel, comparably efficient pathways: a single barrier and a two-barrier pathway. An interrupted folding NMR experiment is introduced, where for a brief period the pressure is dropped to atmospheric conditions (1 bar), followed by a jump back to high pressure for signal detection. Conventional, forward sampling of the indirect dimension during the low-pressure period correlates the 15N or 13C' chemical shifts of the unfolded protein at 1 bar to the 1H frequencies of both the unfolded and folded proteins at high pressure. Remarkably, sampling the data of the same experiment in the reverse direction yields the frequencies of proteins present at the end of the low-pressure interval, which include unfolded, intermediate, and folded species. Although the folding intermediate 15N shifts differ strongly from natively folded protein, its 13C' chemical shifts, which are more sensitive probes for secondary structure, closely match those of the folded protein and indicate that the folding intermediate must have a structure that is quite similar to the native state.
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Affiliation(s)
- Cyril Charlier
- Laboratory of Chemical Physics, NIDDK , National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
| | - Joseph M Courtney
- Laboratory of Chemical Physics, NIDDK , National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
| | - Philip Anfinrud
- Laboratory of Chemical Physics, NIDDK , National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
| | - Ad Bax
- Laboratory of Chemical Physics, NIDDK , National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
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15
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Caro JA, Wand AJ. Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology. Methods 2018; 148:67-80. [PMID: 29964175 PMCID: PMC6133745 DOI: 10.1016/j.ymeth.2018.06.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 01/15/2023] Open
Abstract
Pressure and temperature are the two fundamental variables of thermodynamics. Temperature and chemical perturbation are central experimental tools for the exploration of macromolecular structure and dynamics. Though it has long been recognized that hydrostatic pressure offers a complementary and often unique view of macromolecular structure, stability and dynamics, it has not been employed nearly as much. For solution NMR applications the limited use of high-pressure is undoubtedly traced to difficulties of employing pressure in the context of modern multinuclear and multidimensional NMR. Limitations in pressure tolerant NMR sample cells have been overcome and enable detailed studies of macromolecular energy landscapes, hydration, dynamics and function. Here we review the practical considerations for studies of biological macromolecules at elevated pressure, with a particular emphasis on applications in protein biophysics and structural biology.
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Affiliation(s)
- José A Caro
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6509, United States
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6509, United States.
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16
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Dreydoppel M, Becker P, Raum HN, Gröger S, Balbach J, Weininger U. Equilibrium and Kinetic Unfolding of GB1: Stabilization of the Native State by Pressure. J Phys Chem B 2018; 122:8846-8852. [PMID: 30185038 DOI: 10.1021/acs.jpcb.8b06888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
NMR spectroscopy allows an all-atom view on pressure-induced protein folding, separate detection of different folding states, determination of their population, and the measurement of the folding kinetics at equilibrium. Here, we studied the folding of protein GB1 at pH 2 in a temperature and pressure dependent way. We find that the midpoints of temperature-induced unfolding increase with higher pressure. NMR relaxation dispersion experiments disclosed that the unfolding kinetics slow down at elevated pressure while the folding kinetics stay virtually the same. Therefore, pressure is stabilizing the native state of GB1. These findings extend the knowledge of the influence of pressure on protein folding kinetics, where so far typically a destabilization by increased activation volumes of folding was observed. Our findings thus point toward an exceptional section in the pressure-temperature phase diagram of protein unfolding. The stabilization of the native state could potentially be caused by a shift of p Ka values of glutamates and aspartates in favor of the negatively charged state as judged from pH sensitive chemical shifts.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
| | - Paul Becker
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
| | - Heiner N Raum
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
| | - Stefan Gröger
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
| | - Jochen Balbach
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics , Martin-Luther-University Halle-Wittenberg , D-06120 Halle (Saale) , Germany
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17
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Study of protein folding under native conditions by rapidly switching the hydrostatic pressure inside an NMR sample cell. Proc Natl Acad Sci U S A 2018; 115:E4169-E4178. [PMID: 29666248 PMCID: PMC5939115 DOI: 10.1073/pnas.1803642115] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Development of specialized instrumentation enables rapid switching of the hydrostatic pressure inside an operating NMR spectrometer. This technology allows observation of protein signals during the repeated folding process. Applied to ubiquitin, a previously extensively studied model of protein folding, the methodology reveals an initially highly dynamic state that deviates relatively little from random coil behavior but also provides evidence for numerous repeatedly failed folding events, previously only observed in computer simulations. Above room temperature, direct NMR evidence shows a ∼50% fraction of proteins folding through an on-pathway kinetic intermediate, thereby revealing two equally efficient parallel folding pathways. In general, small proteins rapidly fold on the timescale of milliseconds or less. For proteins with a substantial volume difference between the folded and unfolded states, their thermodynamic equilibrium can be altered by varying the hydrostatic pressure. Using a pressure-sensitized mutant of ubiquitin, we demonstrate that rapidly switching the pressure within an NMR sample cell enables study of the unfolded protein under native conditions and, vice versa, study of the native protein under denaturing conditions. This approach makes it possible to record 2D and 3D NMR spectra of the unfolded protein at atmospheric pressure, providing residue-specific information on the folding process. 15N and 13C chemical shifts measured immediately after dropping the pressure from 2.5 kbar (favoring unfolding) to 1 bar (native) are close to the random-coil chemical shifts observed for a large, disordered peptide fragment of the protein. However, 15N relaxation data show evidence for rapid exchange, on a ∼100-μs timescale, between the unfolded state and unstable, structured states that can be considered as failed folding events. The NMR data also provide direct evidence for parallel folding pathways, with approximately one-half of the protein molecules efficiently folding through an on-pathway kinetic intermediate, whereas the other half fold in a single step. At protein concentrations above ∼300 μM, oligomeric off-pathway intermediates compete with folding of the native state.
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18
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Ploetz EA, Smith PE. Simulated pressure denaturation thermodynamics of ubiquitin. Biophys Chem 2017; 231:135-145. [PMID: 28576277 DOI: 10.1016/j.bpc.2017.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/14/2017] [Accepted: 04/17/2017] [Indexed: 01/09/2023]
Abstract
Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method. Native and fully extended ubiquitin are used as the test conformations. Changes in the protein volumes are then followed as a function of pressure, allowing for conformation-specific protein compressibility values to also be obtained. Residue volume and compressibility values indicate significant contributions to protein denaturation thermodynamics from nonpolar and coil residues, together with a general negative compressibility exhibited by acidic residues.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, 213 CBC Building, 1212 Mid Campus Dr. North, Kansas State University, Manhattan, KS 66506-0401, United States
| | - Paul E Smith
- Department of Chemistry, 213 CBC Building, 1212 Mid Campus Dr. North, Kansas State University, Manhattan, KS 66506-0401, United States.
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19
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Kim SB, Palmer JC, Debenedetti PG. Computational investigation of cold denaturation in the Trp-cage miniprotein. Proc Natl Acad Sci U S A 2016; 113:8991-6. [PMID: 27457961 PMCID: PMC4987839 DOI: 10.1073/pnas.1607500113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The functional native states of globular proteins become unstable at low temperatures, resulting in cold unfolding and impairment of normal biological function. Fundamental understanding of this phenomenon is essential to rationalizing the evolution of freeze-tolerant organisms and developing improved strategies for long-term preservation of biological materials. We present fully atomistic simulations of cold denaturation of an α-helical protein, the widely studied Trp-cage miniprotein. In contrast to the significant destabilization of the folded structure at high temperatures, Trp-cage cold denatures at 210 K into a compact, partially folded state; major elements of the secondary structure, including the α-helix, are conserved, but the salt bridge between aspartic acid and arginine is lost. The stability of Trp-cage's α-helix at low temperatures suggests a possible evolutionary explanation for the prevalence of such structures in antifreeze peptides produced by cold-weather species, such as Arctic char. Although the 310-helix is observed at cold conditions, its position is shifted toward Trp-cage's C-terminus. This shift is accompanied by intrusion of water into Trp-cage's interior and the hydration of buried hydrophobic residues. However, our calculations also show that the dominant contribution to the favorable energetics of low-temperature unfolding of Trp-cage comes from the hydration of hydrophilic residues.
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Affiliation(s)
- Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Jeremy C Palmer
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544;
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20
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Bothe JR, Tonelli M, Ali IK, Dai Z, Frederick RO, Westler WM, Markley JL. The Complex Energy Landscape of the Protein IscU. Biophys J 2016; 109:1019-25. [PMID: 26331259 PMCID: PMC4564936 DOI: 10.1016/j.bpj.2015.07.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/20/2015] [Accepted: 07/28/2015] [Indexed: 11/10/2022] Open
Abstract
IscU, the scaffold protein for iron-sulfur (Fe-S) cluster biosynthesis in Escherichia coli, traverses a complex energy landscape during Fe-S cluster synthesis and transfer. Our previous studies showed that IscU populates two interconverting conformational states: one structured (S) and one largely disordered (D). Both states appear to be functionally important because proteins involved in the assembly or transfer of Fe-S clusters have been shown to interact preferentially with either the S or D state of IscU. To characterize the complex structure-energy landscape of IscU, we employed NMR spectroscopy, small-angle x-ray scattering (SAXS), and differential scanning calorimetry. Results obtained for IscU at pH 8.0 show that its S state is maximally populated at 25°C and that heating or cooling converts the protein toward the D state. Results from NMR and DSC indicate that both the heat- and cold-induced S→D transitions are cooperative and two-state. Low-resolution structural information from NMR and SAXS suggests that the structures of the cold-induced and heat-induced D states are similar. Both states exhibit similar 1H-15N HSQC spectra and the same pattern of peptidyl-prolyl peptide bond configurations by NMR, and both appear to be similarly expanded compared with the S state based on analysis of SAXS data. Whereas in other proteins the cold-denatured states have been found to be slightly more compact than the heat-denatured states, these two states occupy similar volumes in IscU.
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Affiliation(s)
- Jameson R Bothe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ibrahim K Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ziqi Dai
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ronnie O Frederick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - William M Westler
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin.
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21
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Tugarinov V, Libich DS, Meyer V, Roche J, Clore GM. The energetics of a three-state protein folding system probed by high-pressure relaxation dispersion NMR spectroscopy. Angew Chem Int Ed Engl 2016; 54:11157-61. [PMID: 26352026 DOI: 10.1002/anie.201505416] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Indexed: 11/11/2022]
Abstract
The energetic and volumetric properties of a three-state protein folding system, comprising a metastable triple mutant of the Fyn SH3 domain, have been investigated using pressure-dependent (15) N-relaxation dispersion NMR from 1 to 2500 bar. Changes in partial molar volumes (ΔV) and isothermal compressibilities (ΔκT ) between all the states along the folding pathway have been determined to reasonable accuracy. The partial volume and isothermal compressibility of the folded state are 100 mL mol(-1) and 40 μL mol(-1) bar(-1) , respectively, higher than those of the unfolded ensemble. Of particular interest are the findings related to the energetic and volumetric properties of the on-pathway folding intermediate. While the latter is energetically close to the unfolded state, its volumetric properties are similar to those of the folded protein. The compressibility of the intermediate is larger than that of the folded state reflecting the less rigid nature of the former relative to the latter.
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Affiliation(s)
- Vitali Tugarinov
- Laboratory of Chemical Physics, Building 5, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (USA).
| | - David S Libich
- Laboratory of Chemical Physics, Building 5, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (USA)
| | - Virginia Meyer
- Laboratory of Chemical Physics, Building 5, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (USA)
| | - Julien Roche
- Laboratory of Chemical Physics, Building 5, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (USA)
| | - G Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (USA).
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22
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van Dijk E, Varilly P, Knowles TPJ, Frenkel D, Abeln S. Consistent Treatment of Hydrophobicity in Protein Lattice Models Accounts for Cold Denaturation. PHYSICAL REVIEW LETTERS 2016; 116:078101. [PMID: 26943560 DOI: 10.1103/physrevlett.116.078101] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 05/04/2023]
Abstract
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavorable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here, we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.
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Affiliation(s)
- Erik van Dijk
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit, De Boelelaan 1081A, 1081 HV Amsterdam, Netherlands
| | - Patrick Varilly
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Sanne Abeln
- Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit, De Boelelaan 1081A, 1081 HV Amsterdam, Netherlands
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23
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Tugarinov V, Libich DS, Meyer V, Roche J, Clore GM. The Energetics of a Three-State Protein Folding System Probed by High-Pressure Relaxation Dispersion NMR Spectroscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Sirovetz BJ, Schafer NP, Wolynes PG. Water Mediated Interactions and the Protein Folding Phase Diagram in the Temperature–Pressure Plane. J Phys Chem B 2015; 119:11416-27. [DOI: 10.1021/acs.jpcb.5b03828] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Brian J. Sirovetz
- Center
for Theoretical Biological Physics, Rice University, 6500 Main
Street, Houston, Texas 77030, United States
- Department
of Chemistry, Rice University, Space Science 201, Houston, Texas 77251, United States
| | - Nicholas P. Schafer
- Center
for Theoretical Biological Physics, Rice University, 6500 Main
Street, Houston, Texas 77030, United States
| | - Peter G. Wolynes
- Center
for Theoretical Biological Physics, Rice University, 6500 Main
Street, Houston, Texas 77030, United States
- Department
of Chemistry, Rice University, Space Science 201, Houston, Texas 77251, United States
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25
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van Dijk E, Hoogeveen A, Abeln S. The hydrophobic temperature dependence of amino acids directly calculated from protein structures. PLoS Comput Biol 2015; 11:e1004277. [PMID: 26000449 PMCID: PMC4441443 DOI: 10.1371/journal.pcbi.1004277] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 04/12/2015] [Indexed: 12/26/2022] Open
Abstract
The hydrophobic effect is the main driving force in protein folding. One can estimate the relative strength of this hydrophobic effect for each amino acid by mining a large set of experimentally determined protein structures. However, the hydrophobic force is known to be strongly temperature dependent. This temperature dependence is thought to explain the denaturation of proteins at low temperatures. Here we investigate if it is possible to extract this temperature dependence directly from a large set of protein structures determined at different temperatures. Using NMR structures filtered for sequence identity, we were able to extract hydrophobicity propensities for all amino acids at five different temperature ranges (spanning 265-340 K). These propensities show that the hydrophobicity becomes weaker at lower temperatures, in line with current theory. Alternatively, one can conclude that the temperature dependence of the hydrophobic effect has a measurable influence on protein structures. Moreover, this work provides a method for probing the individual temperature dependence of the different amino acid types, which is difficult to obtain by direct experiment. In general, proteins become functional once they fold into a specific globular structure. On folding, hydrophobic amino acids get buried inside the protein such that they are shielded from the water; this hydrophobic effect makes a protein fold stable. However, the strength of the hydrophobicity is known to be strongly temperature dependent, leading for example to lower stability at lower temperatures (cold denaturation). Nevertheless, it is difficult to quantify the temperature dependence for hydrophobic amino acids. Here we are able to estimate the strength of the hydrophobic effect, by analysing the positions of a large number of amino acids from protein structures experimentally determined at different temperatures. For each amino acid type, we use the ratio between the number of residues at the inside and at the surface of the folded structures as a measure for its hydrophobicity. This approach shows that the hydrophobic effect becomes weaker at lower temperatures, as expected from theoretical predictions. Understanding the temperature dependence for amino acids, can help to make proteins (or enzymes) stable at a specific temperature range. For example, the design of enzymes that are stable and functional at low temperatures may benefit from this work.
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Affiliation(s)
- Erik van Dijk
- Computer Science Department, Centre for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, Netherlands
| | - Arlo Hoogeveen
- Computer Science Department, Centre for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, Netherlands
| | - Sanne Abeln
- Computer Science Department, Centre for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, Netherlands
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26
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Fizil Á, Gáspári Z, Barna T, Marx F, Batta G. "Invisible" conformers of an antifungal disulfide protein revealed by constrained cold and heat unfolding, CEST-NMR experiments, and molecular dynamics calculations. Chemistry 2015; 21:5136-44. [PMID: 25676351 PMCID: PMC4464532 DOI: 10.1002/chem.201404879] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Indexed: 12/12/2022]
Abstract
Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two- and three-state analysis of thermal unfolding, that the population of hidden states may weight 20-40 % at 298 K in a disulfide-rich protein. In addition, sensitive (15) N-CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR "dark matter". Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction.
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Affiliation(s)
- Ádám Fizil
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen (Hungary)
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27
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A fully atomistic computer simulation study of cold denaturation of a β-hairpin. Nat Commun 2014; 5:5773. [PMID: 25502835 DOI: 10.1038/ncomms6773] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/04/2014] [Indexed: 11/08/2022] Open
Abstract
Cold denaturation is a fundamental phenomenon in aqueous solutions where the native structure of proteins disrupts on cooling. Understanding this process in molecular details can provide a new insight into the detailed natures of hydrophobic forces governing the stability of proteins in water. We show that the cold-denaturation-like phenomenon can be directly observed at low temperatures using a fully atomistic molecular dynamics simulation method. Using a highly optimized protein force field in conjunction with three different explicit water models, a replica exchange molecular dynamics simulation scheme at constant pressures allows for the computation of the melting profile of an experimentally well-characterized β-hairpin peptide. For all three water models tested, the simulated melting profiles are indicative of possible cold denaturation. From the analysis of simulation ensembles, we find that the most probable cold-denatured structure is structurally compact, with its hydrogen bonds and native hydrophobic packing substantially disrupted.
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28
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Kingsley CN, Bierma JC, Pham V, Martin RW. γS-crystallin proteins from the Antarctic nototheniid toothfish: a model system for investigating differential resistance to chemical and thermal denaturation. J Phys Chem B 2014; 118:13544-53. [PMID: 25372016 PMCID: PMC4254003 DOI: 10.1021/jp509134d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The γS1- and γS2-crystallins,
structural eye lens proteins
from the Antarctic toothfish (Dissostichus mawsoni), are homologues of the human lens protein γS-crystallin.
Although γS1 has the higher thermal stability of the two, it
is more susceptible to chemical denaturation by urea. The lower thermodynamic
stability of both toothfish crystallins relative to human γS-crystallin
is consistent with the current picture of how proteins from organisms
endemic to perennially cold environments have achieved low-temperature
functionality via greater structural flexibility. In some respects,
the sequences of γS1- and γS2-crystallin are typical of
psychrophilic proteins; however, their amino acid compositions also
reflect their selection for a high refractive index increment. Like
their counterparts in the human lens and those of mesophilic fish,
both toothfish crystallins are relatively enriched in aromatic residues
and methionine and exiguous in aliphatic residues. The sometimes contradictory
requirements of selection for cold tolerance and high refractive index
make the toothfish crystallins an excellent model system for further
investigation of the biophysical properties of structural proteins.
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Affiliation(s)
- Carolyn N Kingsley
- Department of Chemistry, University of California-Irvine , 1102 Natural Sciences 2, Irvine, California, 92697-2025, United States
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29
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Qin Z, Balasubramanian SK, Wolkers WF, Pearce JA, Bischof JC. Correlated parameter fit of arrhenius model for thermal denaturation of proteins and cells. Ann Biomed Eng 2014; 42:2392-404. [PMID: 25205396 DOI: 10.1007/s10439-014-1100-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/23/2014] [Indexed: 12/12/2022]
Abstract
Thermal denaturation of proteins is critical to cell injury, food science and other biomaterial processing. For example protein denaturation correlates strongly with cell death by heating, and is increasingly of interest in focal thermal therapies of cancer and other diseases at temperatures which often exceed 50 °C. The Arrhenius model is a simple yet widely used model for both protein denaturation and cell injury. To establish the utility of the Arrhenius model for protein denaturation at 50 °C and above its sensitivities to the kinetic parameters (activation energy E a and frequency factor A) were carefully examined. We propose a simplified correlated parameter fit to the Arrhenius model by treating E a, as an independent fitting parameter and allowing A to follow dependently. The utility of the correlated parameter fit is demonstrated on thermal denaturation of proteins and cells from the literature as a validation, and new experimental measurements in our lab using FTIR spectroscopy to demonstrate broad applicability of this method. Finally, we demonstrate that the end-temperature within which the denaturation is measured is important and changes the kinetics. Specifically, higher E a and A parameters were found at low end-temperature (50 °C) and reduce as end-temperatures increase to 70 °C. This trend is consistent with Arrhenius parameters for cell injury in the literature that are significantly higher for clonogenics (45-50 °C) vs. membrane dye assays (60-70 °C). Future opportunities to monitor cell injury by spectroscopic measurement of protein denaturation are discussed.
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Affiliation(s)
- Zhenpeng Qin
- Department of Mechanical Engineering, University of Minnesota, 111 Church St. SE, Minneapolis, MN, 55455, USA
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30
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Abstract
A theoretical rationalization of the occurrence of cold denaturation for globular proteins was devised, assuming that the effective size of water molecules depends upon temperature [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252]. In the present work, it is shown that the latter assumption is not necessary. By performing the same type of calculations in water, 40% (by weight) methanol, methanol, and carbon tetrachloride, it emerges that cold denaturation occurs only in water due to the special temperature dependence of its density and the small size of its molecules. These two coupled factors determine the magnitude and the temperature dependence of the stabilizing term that measures the gain in configurational/translational entropy of water molecules upon folding of the protein. This term has to be contrasted with the destabilizing contribution measuring the loss in conformational entropy of the polypeptide chain upon folding.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11 - 82100 Benevento, Italy.
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31
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Role of cavities and hydration in the pressure unfolding of T4 lysozyme. Proc Natl Acad Sci U S A 2014; 111:13846-51. [PMID: 25201963 DOI: 10.1073/pnas.1410655111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is well known that high hydrostatic pressures can induce the unfolding of proteins. The physical underpinnings of this phenomenon have been investigated extensively but remain controversial. Changes in solvation energetics have been commonly proposed as a driving force for pressure-induced unfolding. Recently, the elimination of void volumes in the native folded state has been argued to be the principal determinant. Here we use the cavity-containing L99A mutant of T4 lysozyme to examine the pressure-induced destabilization of this multidomain protein by using solution NMR spectroscopy. The cavity-containing C-terminal domain completely unfolds at moderate pressures, whereas the N-terminal domain remains largely structured to pressures as high as 2.5 kbar. The sensitivity to pressure is suppressed by the binding of benzene to the hydrophobic cavity. These results contrast to the pseudo-WT protein, which has a residual cavity volume very similar to that of the L99A-benzene complex but shows extensive subglobal reorganizations with pressure. Encapsulation of the L99A mutant in the aqueous nanoscale core of a reverse micelle is used to examine the hydration of the hydrophobic cavity. The confined space effect of encapsulation suppresses the pressure-induced unfolding transition and allows observation of the filling of the cavity with water at elevated pressures. This indicates that hydration of the hydrophobic cavity is more energetically unfavorable than global unfolding. Overall, these observations point to a range of cooperativity and energetics within the T4 lysozyme molecule and illuminate the fact that small changes in physical parameters can significantly alter the pressure sensitivity of proteins.
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32
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Mangini V, Dell'Aglio M, De Stradis A, De Giacomo A, De Pascale O, Natile G, Arnesano F. Amyloid transition of ubiquitin on silver nanoparticles produced by pulsed laser ablation in liquid as a function of stabilizer and single-point mutations. Chemistry 2014; 20:10745-51. [PMID: 25060114 DOI: 10.1002/chem.201402934] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Indexed: 11/05/2022]
Abstract
The interaction of nanoparticles with proteins has emerged as a key issue in addressing the problem of nanotoxicity. We investigated the interaction of silver nanoparticles (AgNPs), produced by laser ablation with human ubiquitin (Ub), a protein essential for degradative processes in cells. The surface plasmon resonance peak of AgNPs indicates that Ub is rapidly adsorbed on the AgNP surface yielding a protein corona; the Ub-coated AgNPs then evolve into clusters held together by an amyloid form of the protein, as revealed by binding of thioflavin T fluorescent dye. Transthyretin, an inhibitor of amyloid-type aggregation, impedes aggregate formation and disrupts preformed AgNP clusters. In the presence of sodium citrate, a common stabilizer that confers an overall negative charge to the NPs, Ub is still adsorbed on the AgNP surface, but no clustering is observed. Ub mutants bearing a single mutation at one edge β strand (i.e. Glu16Val) or in loop (Glu18Val) behave in a radically different manner.
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Affiliation(s)
- Vincenzo Mangini
- Department of Chemistry, University of Bari "Aldo Moro" via Orabona, 4, 70125, Bari (Italy)
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33
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Dias CL, Chan HS. Pressure-Dependent Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding. J Phys Chem B 2014; 118:7488-7509. [DOI: 10.1021/jp501935f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Cristiano L. Dias
- Department
of Physics, New Jersey Institute of Technology, University Heights, Tiernan Hall, Room 463, Newark, New Jersey 07102, United States
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
| | - Hue Sun Chan
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
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34
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Silva JL, Oliveira AC, Vieira TCRG, de Oliveira GAP, Suarez MC, Foguel D. High-Pressure Chemical Biology and Biotechnology. Chem Rev 2014; 114:7239-67. [DOI: 10.1021/cr400204z] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jerson L. Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Andrea C. Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Tuane C. R. G. Vieira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Guilherme A. P. de Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Marisa C. Suarez
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Debora Foguel
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
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35
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Transition state and ground state properties of the helix-coil transition in peptides deduced from high-pressure studies. Proc Natl Acad Sci U S A 2013; 110:20988-93. [PMID: 24324160 DOI: 10.1073/pnas.1317973110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Volume changes associated with protein folding reactions contain valuable information about the folding mechanism and the nature of the transition state. However, meaningful interpretation of such data requires that overall volume changes be deconvoluted into individual contributions from different structural components. Here we focus on one type of structural element, the α-helix, and measure triplet-triplet energy transfer at high pressure to determine volume changes associated with the helix-coil transition. Our results reveal that the volume of a 21-amino-acid alanine-based peptide shrinks upon helix formation. Thus, helices, in contrast with native proteins, become more stable with increasing pressure, explaining the frequently observed helical structures in pressure-unfolded proteins. Both helix folding and unfolding become slower with increasing pressure. The volume changes associated with the addition of a single helical residue to a preexisting helix were obtained by comparing the experimental results with Monte Carlo simulations based on a kinetic linear Ising model. The reaction volume for adding a single residue to a helix is small and negative (-0.23 cm(3) per mol = -0.38 Å(3) per molecule) implying that intrahelical hydrogen bonds have a smaller volume than peptide-water hydrogen bonds. In contrast, the transition state has a larger volume than either the helical or the coil state, with activation volumes of 2.2 cm(3)/mol (3.7 Å(3) per molecule) for adding and 2.4 cm(3)/mol (4.0 Å(3) per molecule) for removing one residue. Thus, addition or removal of a helical residue proceeds through a transitory high-energy state with a large volume, possibly due to the presence of unsatisfied hydrogen bonds, although steric effects may also contribute.
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36
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Wiktor M, Hartley O, Grzesiek S. Characterization of structure, dynamics, and detergent interactions of the anti-HIV chemokine variant 5P12-RANTES. Biophys J 2013; 105:2586-97. [PMID: 24314089 PMCID: PMC3853082 DOI: 10.1016/j.bpj.2013.10.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/14/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022] Open
Abstract
RANTES (CCL5) is a chemokine that recruits immune cells to inflammatory sites by interacting with the G-protein coupled receptor CCR5, which is also the primary coreceptor used together with CD4 by HIV to enter and infect target cells. Ligands of CCR5, including chemokines and chemokine analogs, are capable of blocking HIV entry, and studies of their structures and interactions with CCR5 will be key to understanding and optimizing HIV inhibition. The RANTES derivative 5P12-RANTES is a highly potent HIV entry inhibitor that is being developed as a topical HIV prevention agent (microbicide). We have characterized the structure and dynamics of 5P12-RANTES by solution NMR. With the exception of the nine flexible N-terminal residues, 5P12-RANTES has the same structure as wild-type RANTES but unlike the wild-type, does not dimerize via its N-terminus. To prepare the ground for interaction studies with detergent-solubilized CCR5, we have also investigated the interaction of RANTES and 5P12-RANTES with various commonly used detergents. Both RANTES variants are stable in Cymal-5, DHPC, Anzergent-3-12, dodecyltrimethylammonium chloride, and a DDM/CHAPS/CHS mixture. Fos-Cholines, dodecyldimethylglycine, and sodium dodecyl-sulfate denature both RANTES variants at low pH, whereas at neutral pH the stability is considerably higher. The onset of Fos-Choline-12-induced denaturation and the denatured state were characterized by circular dichroism and NMR. The detergent interaction starts below the critical micelle concentration at a well-defined mixed hydrophobic/positive surface region of the chemokine, which overlaps with the dimer interface. An increase of Fos-Choline-12 concentration above the critical micelle concentration causes a transition to a denatured state with a high α-helical content.
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Affiliation(s)
- Maciej Wiktor
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
| | - Oliver Hartley
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
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37
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Roche J, Ying J, Maltsev AS, Bax A. Impact of hydrostatic pressure on an intrinsically disordered protein: a high-pressure NMR study of α-synuclein. Chembiochem 2013; 14:1754-61. [PMID: 23813793 PMCID: PMC3874805 DOI: 10.1002/cbic.201300244] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Indexed: 11/06/2022]
Abstract
The impact of pressure on the backbone (15) N, (1) H and (13) C chemical shifts in N-terminally acetylated α-synuclein has been evaluated over a pressure range 1-2500 bar. Even while the chemical shifts fall very close to random coil values, as expected for an intrinsically disordered protein, substantial deviations in the pressure dependence of the chemical shifts are seen relative to those in short model peptides. In particular, the nonlinear pressure response of the (1) H(N) chemical shifts, which commonly is associated with the presence of low-lying "excited states", is much larger in α-synuclein than in model peptides. The linear pressure response of (1) H(N) chemical shift, commonly linked to H-bond length change, correlates well with those in short model peptides, and is found to be anticorrelated with its temperature dependence. The pressure dependence of (13) C chemical shifts shows remarkably large variations, even when accounting for residue type, and do not point to a clear shift in population between different regions of the Ramachandran map. However, a nearly universal decrease in (3) JHN-Hα by 0.22 ± 0.05 Hz suggests a slight increase in population of the polyproline II region at 2500 bar. The first six residues of N-terminally acetylated synuclein show a transient of approximately 15% population of α-helix, which slightly diminishes at 2500 bar. The backbone dynamics of the protein is not visibly affected beyond the effect of slight increase in water viscosity at 2500 bar.
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Affiliation(s)
- Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 (USA)
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38
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Matysiak S, Das P. Effects of sequence and solvation on the temperature-pressure conformational landscape of proteinlike heteropolymers. PHYSICAL REVIEW LETTERS 2013; 111:058103. [PMID: 23952449 DOI: 10.1103/physrevlett.111.058103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Indexed: 06/02/2023]
Abstract
We study the role of sequence and solvation in shaping the temperature-pressure (T, P) conformational landscape of model heteropolymers with a coarse-grained model. We design foldable primarily hydrophobic sequences with fixed polar content in water at physiological conditions, which demonstrate (T, P) dependence of conformational stability similar to biological proteins. Inherent helicity emerges as a result of local polar-polar interactions in the sequences that mimic biological α helices. The helical propensity is reduced upon solvation and remains unaltered at cold T and high P, which is driven by the T-P induced changes of the hydration shell. Consequently, at nonphysiological conditions the weakening of hydrophobic interactions facilitates population of non-native, helical, compact conformations stabilized through direct nonlocal interactions between polar residues.
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Affiliation(s)
- Silvina Matysiak
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA.
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