1
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Kariyawasam NL, Ploetz EA, Swint-Kruse L, Smith PE. Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes. Biophys Chem 2024; 304:107126. [PMID: 37924711 PMCID: PMC10842697 DOI: 10.1016/j.bpc.2023.107126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023]
Abstract
The functions of many proteins are associated with interconversions among conformational substates. However, these substates can be difficult to measure experimentally, and determining contributions from hydration changes can be especially difficult. Here, we assessed the use of pressure perturbations to sample the substates accessible to the Escherichia coli lactose repressor protein (LacI) in various liganded forms. In the presence of DNA, the regulatory domain of LacI adopts an Open conformation that, in the absence of DNA, changes to a Closed conformation. Increasing the simulation pressure prevented the transition from an Open to a Closed conformation, in a similar manner to the binding of DNA and anti-inducer, ONPF. The results suggest the hydration of specific residues play a significant role in determining the population of different LacI substates and that simulating pressure perturbation could be useful for assessing the role of hydration changes that accompany functionally-relevant amino acid substitutions.
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Affiliation(s)
- Nilusha L Kariyawasam
- Department of Chemistry, 213 CBC Building, 1212 Mid-Campus Dr. North, Kansas State University, Manhattan, KS 66506, USA
| | - Elizabeth A Ploetz
- Department of Chemistry, 213 CBC Building, 1212 Mid-Campus Dr. North, Kansas State University, Manhattan, KS 66506, USA
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, MSN 3030, 3901 Rainbow Blvd, The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Paul E Smith
- Department of Chemistry, 213 CBC Building, 1212 Mid-Campus Dr. North, Kansas State University, Manhattan, KS 66506, USA.
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2
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Houlleberghs M, Helsper S, Dom D, Dubroca T, Trociewitz B, Schurko RW, Radhakrishnan S, Breynaert E. Building a Cost-Efficient High-Pressure Cell for Online High-Field NMR and MRI Using Standard Static Probe Heads: An In Situ Demonstration on Clathrate Hydrate Formation. Anal Chem 2023; 95:16936-16942. [PMID: 37931115 PMCID: PMC10666082 DOI: 10.1021/acs.analchem.3c03050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/29/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023]
Abstract
High-pressure nuclear magnetic resonance (NMR) spectroscopy finds remarkable applications in catalysis, protein biochemistry and biophysics, analytical chemistry, material science, energy, and environmental control but requires expensive probe heads and/or sample cells. This contribution describes the design, construction, and testing of a low-cost 5 mm NMR tube suitable for high-pressure NMR measurements of up to 30 MPa. The sample cell comprises a standard, 5 mm single-crystal sapphire tube that has been fitted to a section of a relatively inexpensive polyether ether ketone (PEEK) HPLC column. PEEK HPLC tubing and connectors enable integration with a gas rig or a standard HPLC pump located outside the stray field of the magnet. The cell is compatible with any 5 mm static NMR probe head, exhibits almost zero background in NMR experiments, and is compatible with any liquid, gas, temperature, or pressure range encountered in HPLC experimentation. A specifically designed transport case enables the safe handling of the pressurized tube outside the probe head. The performance of the setup was evaluated using in situ high-field NMR spectroscopy and MRI performed during the formation of bulk and nanoconfined clathrate hydrates occluding methane, ethane, and hydrogen.
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Affiliation(s)
- Maarten Houlleberghs
- NMR/X-Ray
Platform for Convergence Research (NMRCoRe), KU Leuven, Leuven 3001, Belgium
- Centre
for Surface Chemistry and Catalysis: Characterization and Application
Team (COK-kat), Leuven 3001, Belgium
| | - Shannon Helsper
- Biomedical
MRI, Department of Imaging & Pathology, KU Leuven, Leuven B-3000, Belgium
- National
High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Dirk Dom
- NMR/X-Ray
Platform for Convergence Research (NMRCoRe), KU Leuven, Leuven 3001, Belgium
- Centre
for Surface Chemistry and Catalysis: Characterization and Application
Team (COK-kat), Leuven 3001, Belgium
| | - Thierry Dubroca
- National
High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Bianca Trociewitz
- National
High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Robert W. Schurko
- National
High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Department
of Chemistry and Biochemistry, Florida State
University, Tallahassee, Florida 32306, United States
| | - Sambhu Radhakrishnan
- NMR/X-Ray
Platform for Convergence Research (NMRCoRe), KU Leuven, Leuven 3001, Belgium
- Centre
for Surface Chemistry and Catalysis: Characterization and Application
Team (COK-kat), Leuven 3001, Belgium
| | - Eric Breynaert
- NMR/X-Ray
Platform for Convergence Research (NMRCoRe), KU Leuven, Leuven 3001, Belgium
- Centre
for Surface Chemistry and Catalysis: Characterization and Application
Team (COK-kat), Leuven 3001, Belgium
- National
High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Centre for
Molecular Water Science (CMWS), 22607 Hamburg, Germany
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3
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Necelis M, McDermott C, Belcher Dufrisne M, Baryiames C, Columbus L. Solution NMR investigations of integral membrane proteins: Challenges and innovations. Curr Opin Struct Biol 2023; 82:102654. [PMID: 37542910 PMCID: PMC10529709 DOI: 10.1016/j.sbi.2023.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 06/20/2023] [Indexed: 08/07/2023]
Abstract
Compared to soluble protein counterparts, the understanding of membrane protein stability, solvent interactions, and function are not as well understood. Recent advancements in labeling, expression, and stabilization of membrane proteins have enabled solution nuclear magnetic resonance spectroscopy to investigate membrane protein conformational states, ligand binding, lipid interactions, stability, and folding. This review highlights these advancements and new understandings and provides examples of recent applications.
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Affiliation(s)
- Matthew Necelis
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Connor McDermott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | | | - Linda Columbus
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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4
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Rezaei-Ghaleh N, Amininasab M, Giller K, Becker S. Familial Alzheimer's Disease-Related Mutations Differentially Alter Stability of Amyloid-Beta Aggregates. J Phys Chem Lett 2023; 14:1427-1435. [PMID: 36734539 PMCID: PMC9940190 DOI: 10.1021/acs.jpclett.2c03729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Amyloid-beta (Aβ) deposition as senile plaques is a pathological hallmark of Alzheimer's disease (AD). AD is characterized by a large level of heterogeneity in amyloid pathology, whose molecular origin is poorly understood. Here, we employ NMR spectroscopy and MD simulation at ambient and high pressures and investigate how AD-related mutations in Aβ peptide influence the stability of Aβ aggregates. The pressure-induced monomer dissociation from Aβ aggregates monitored by NMR demonstrated that the Iowa (D23N), Arctic (E22G), and Osaka (ΔE22) mutations altered the pressure stability of Aβ40 aggregates in distinct manners. While the NMR data of monomeric Aβ40 showed only small localized effects of mutations, the MD simulation of mutated Aβ fibrils revealed their distinct susceptibility to elevated pressure. Our data propose a structural basis for the distinct stability of various Aβ fibrils and highlights "stability" as a molecular property potentially contributing to the large heterogeneity of amyloid pathology in AD.
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Affiliation(s)
- Nasrollah Rezaei-Ghaleh
- Institute
of Physical Biology, Heinrich Heine University
Düsseldorf, D-40225 Düsseldorf, Germany
- Institute
of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, D-52428 Jülich, Germany
- Department
of NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
| | - Mehriar Amininasab
- Department
of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, 1417466191 Tehran, Iran
| | - Karin Giller
- Department
of NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
| | - Stefan Becker
- Department
of NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
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5
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Gelenter M, Bax A. Recombinant Expression and Chemical Amidation of Isotopically Labeled Native Melittin. J Am Chem Soc 2023; 145:3850-3854. [PMID: 36753641 PMCID: PMC9951214 DOI: 10.1021/jacs.2c12631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Indexed: 02/10/2023]
Abstract
Post-translational modifications are ubiquitous in the eukaryotic proteome. However, these modifications are rarely incorporated in NMR studies of eukaryotic proteins, which are typically produced through recombinant expression in E. coli. Melittin is the primary peptide in honey bee venom. Its native C-terminal amide significantly affects its equilibrium structure and dynamics in solution and is thus a prerequisite for studying its native structure and function. Here, we present a method for producing triply isotopically labeled (2H, 13C, and 15N) native melittin through recombinant expression followed by chemical amidation. We then show that structural models produced with AlphaFold-Multimer are in even better agreement with experimental residual dipolar couplings than the 2.0 Å resolution X-ray crystal structure for residues G3-K23.
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Affiliation(s)
- Martin
D. Gelenter
- 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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6
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Akke M, Weininger U. NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins. J Phys Chem B 2023; 127:591-599. [PMID: 36640108 PMCID: PMC9884080 DOI: 10.1021/acs.jpcb.2c07258] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180° rotations, or flips, which are mediated by transient and large-scale "breathing" motions that generate sufficient void volume around the aromatic ring. Forty years after the seminal work by Wagner and Wüthrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. Recent developments of improved NMR methods and isotope labeling schemes have enabled a number of advances in addressing the mechanisms and energetics of aromatic ring flips. The nature of the transition states associated with ring flips can be described by thermodynamic activation parameters, including the activation enthalpy, activation entropy, activation volume, and also the isothermal volume compressibility of activation. Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. The field is beginning to gather such data for aromatic residues in a variety of environments, ranging from surface exposed to buried. In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. In this Perspective, we highlight recent developments and provide an outlook toward the future.
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Affiliation(s)
- Mikael Akke
- Division
of Biophysical Chemistry, Center for Molecular Protein Science, Department
of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden,(M.A.)
| | - Ulrich Weininger
- Institute
of Physics, Biophysics, Martin-Luther-University
Halle-Wittenberg, D-06129 Halle (Saale), Germany,(U.W.)
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7
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Pressure, motion, and conformational entropy in molecular recognition by proteins. BIOPHYSICAL REPORTS 2022; 3:100098. [PMID: 36647534 PMCID: PMC9840116 DOI: 10.1016/j.bpr.2022.100098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
The thermodynamics of molecular recognition by proteins is a central determinant of complex biochemistry. For over a half-century, detailed cryogenic structures have provided deep insight into the energetic contributions to ligand binding by proteins. More recently, a dynamical proxy based on NMR-relaxation methods has revealed an unexpected richness in the contributions of conformational entropy to the thermodynamics of ligand binding. Here, we report the pressure dependence of fast internal motion within the ribonuclease barnase and its complex with the protein barstar. In what we believe is a first example, we find that protein dynamics are conserved along the pressure-binding thermodynamic cycle. The femtomolar affinity of the barnase-barstar complex exists despite a penalty by -TΔSconf of +11.7 kJ/mol at ambient pressure. At high pressure, however, the overall change in side-chain dynamics is zero, and binding occurs with no conformational entropy penalty, suggesting an important role of conformational dynamics in the adaptation of protein function to extreme environments. Distinctive clustering of the pressure sensitivity is observed in response to both pressure and binding, indicating the presence of conformational heterogeneity involving less efficiently packed alternative conformation(s). The structural segregation of dynamics observed in barnase is striking and shows how changes in both the magnitude and the sign of regional contributions of conformational entropy to the thermodynamics of protein function are possible.
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8
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Pozza A, Giraud F, Cece Q, Casiraghi M, Point E, Damian M, Le Bon C, Moncoq K, Banères JL, Lescop E, Catoire LJ. Exploration of the dynamic interplay between lipids and membrane proteins by hydrostatic pressure. Nat Commun 2022; 13:1780. [PMID: 35365643 PMCID: PMC8975810 DOI: 10.1038/s41467-022-29410-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Cell membranes represent a complex and variable medium in time and space of lipids and proteins. Their physico-chemical properties are determined by lipid components which can in turn influence the biological function of membranes. Here, we used hydrostatic pressure to study the close dynamic relationships between lipids and membrane proteins. Experiments on the β–barrel OmpX and the α–helical BLT2 G Protein-Coupled Receptor in nanodiscs of different lipid compositions reveal conformational landscapes intimately linked to pressure and lipids. Pressure can modify the conformational landscape of the membrane protein per se, but also increases the gelation of lipids, both being monitored simultaneously at high atomic resolution by NMR. Our study also clearly shows that a membrane protein can modulate, at least locally, the fluidity of the bilayer. The strategy proposed herein opens new perspectives to scrutinize the dynamic interplay between membrane proteins and their surrounding lipids. Direct information on the dynamic interplay between membrane proteins and lipids is scarce. Here the authors report a detailed description of these close relationships by combining lipid nanodiscs and high-pressure NMR. They report the link between pressure and lipid compositions to the conformational landscape of the β-barrel OmpX and the α-helical BLT2 G Protein-Coupled Receptor in nanodiscs.
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Affiliation(s)
- Alexandre Pozza
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France
| | - François Giraud
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Quentin Cece
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France.,Laboratoire Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), UMR 8038, CNRS/Université de Paris, Faculté de Pharmacie, 75270, Paris, Cedex 06, France
| | - Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 94305, Stanford, CA, USA
| | - Elodie Point
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France
| | - Marjorie Damian
- Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Pôle Chimie Balard Recherche, 34293, Montpellier, cedex 5, France
| | - Christel Le Bon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France
| | - Jean-Louis Banères
- Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Pôle Chimie Balard Recherche, 34293, Montpellier, cedex 5, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.
| | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS/Université de Paris, Institut de Biologie Physico-Chimique (IBPC, FRC 550), 75005, Paris, France.
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9
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Cardone C, Caseau CM, Bardiaux B, Thureaux A, Galloux M, Bajorek M, Eléouët JF, Litaudon M, Bontems F, Sizun C. A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein. Biomolecules 2021; 11:biom11081225. [PMID: 34439894 PMCID: PMC8392014 DOI: 10.3390/biom11081225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The phosphoprotein P of Mononegavirales (MNV) is an essential co-factor of the viral RNA polymerase L. Its prime function is to recruit L to the ribonucleocapsid composed of the viral genome encapsidated by the nucleoprotein N. MNV phosphoproteins often contain a high degree of disorder. In Pneumoviridae phosphoproteins, the only domain with well-defined structure is a small oligomerization domain (POD). We previously characterized the differential disorder in respiratory syncytial virus (RSV) phosphoprotein by NMR. We showed that outside of RSV POD, the intrinsically disordered N-and C-terminal regions displayed a structural and dynamic diversity ranging from random coil to high helical propensity. Here we provide additional insight into the dynamic behavior of PCα, a domain that is C-terminal to POD and constitutes the RSV L-binding region together with POD. By using small phosphoprotein fragments centered on or adjacent to POD, we obtained a structural picture of the POD–PCα region in solution, at the single residue level by NMR and at lower resolution by complementary biophysical methods. We probed POD–PCα inter-domain contacts and showed that small molecules were able to modify the dynamics of PCα. These structural properties are fundamental to the peculiar binding mode of RSV phosphoprotein to L, where each of the four protomers binds to L in a different way.
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Affiliation(s)
- Christophe Cardone
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Claire-Marie Caseau
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, 78015 Paris, France;
| | | | - Marie Galloux
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Monika Bajorek
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Jean-François Eléouët
- Unité de Virologie et Immunologie Moléculaires, INRAE, Université Paris Saclay, 78352 Jouy-en-Josas, France; (M.G.); (M.B.); (J.-F.E.)
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay, 91190 Gif-sur-Yvette, France; (C.C.); (C.-M.C.); (M.L.); (F.B.)
- Correspondence:
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10
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Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR. BIOLOGY 2021; 10:biology10070656. [PMID: 34356511 PMCID: PMC8301334 DOI: 10.3390/biology10070656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022]
Abstract
Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CαHα groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CαHα, and CH3 groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CαHα when compared to amide groups.
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11
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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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12
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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13
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Structure elucidation of the elusive Enzyme I monomer reveals the molecular mechanisms linking oligomerization and enzymatic activity. Proc Natl Acad Sci U S A 2021; 118:2100298118. [PMID: 33975952 DOI: 10.1073/pnas.2100298118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Enzyme I (EI) is a phosphotransferase enzyme responsible for converting phosphoenolpyruvate (PEP) into pyruvate. This reaction initiates a five-step phosphorylation cascade in the bacterial phosphotransferase (PTS) transduction pathway. Under physiological conditions, EI exists in an equilibrium between a functional dimer and an inactive monomer. The monomer-dimer equilibrium is a crucial factor regulating EI activity and the phosphorylation state of the overall PTS. Experimental studies of EI's monomeric state have yet been hampered by the dimer's high thermodynamic stability, which prevents its characterization by standard structural techniques. In this study, we modified the dimerization domain of EI (EIC) by mutating three amino acids involved in the formation of intersubunit salt bridges. The engineered variant forms an active dimer in solution that can bind and hydrolyze PEP. Using hydrostatic pressure as an additional perturbation, we were then able to study the complete dissociation of the variant from 1 bar to 2.5 kbar in the absence and the presence of EI natural ligands. Backbone residual dipolar couplings collected under high-pressure conditions allowed us to determine the conformational ensemble of the isolated EIC monomeric state in solution. Our calculations reveal that three catalytic loops near the dimerization interface become unstructured upon monomerization, preventing the monomeric enzyme from binding its natural substrate. This study provides an atomic-level characterization of EI's monomeric state and highlights the role of the catalytic loops as allosteric connectors controlling both the activity and oligomerization of the enzyme.
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14
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Ando N, Barquera B, Bartlett DH, Boyd E, Burnim AA, Byer AS, Colman D, Gillilan RE, Gruebele M, Makhatadze G, Royer CA, Shock E, Wand AJ, Watkins MB. The Molecular Basis for Life in Extreme Environments. Annu Rev Biophys 2021; 50:343-372. [PMID: 33637008 DOI: 10.1146/annurev-biophys-100120-072804] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.
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Affiliation(s)
- Nozomi Ando
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Blanca Barquera
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202, USA
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Audrey A Burnim
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Amanda S Byer
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Daniel Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Richard E Gillilan
- Center for High Energy X-ray Sciences (CHEXS), Ithaca, New York 14853, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Department of Physics, University of Illinois, Urbana-Champaign, Illinois 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - George Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA;
| | - Everett Shock
- GEOPIG, School of Earth & Space Exploration, School of Molecular Sciences, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona 85287, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77845, USA.,Department of Chemistry, Texas A&M University, College Station, Texas 77845, USA.,Department of Molecular & Cellular Medicine, Texas A&M University, College Station, Texas 77845, USA
| | - Maxwell B Watkins
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York 14853, USA.,Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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15
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Rai DK, Gillilan RE, Huang Q, Miller R, Ting E, Lazarev A, Tate MW, Gruner SM. High-pressure small-angle X-ray scattering cell for biological solutions and soft materials. J Appl Crystallogr 2021; 54:111-122. [PMID: 33841059 PMCID: PMC7941318 DOI: 10.1107/s1600576720014752] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/06/2020] [Indexed: 11/10/2022] Open
Abstract
Pressure is a fundamental thermodynamic parameter controlling the behavior of biological macromolecules. Pressure affects protein denaturation, kinetic parameters of enzymes, ligand binding, membrane permeability, ion trans-duction, expression of genetic information, viral infectivity, protein association and aggregation, and chemical processes. In many cases pressure alters the molecular shape. Small-angle X-ray scattering (SAXS) is a primary method to determine the shape and size of macromolecules. However, relatively few SAXS cells described in the literature are suitable for use at high pressures and with biological materials. Described here is a novel high-pressure SAXS sample cell that is suitable for general facility use by prioritization of ease of sample loading, temperature control, mechanical stability and X-ray background minimization. Cell operation at 14 keV is described, providing a q range of 0.01 < q < 0.7 Å-1, pressures of 0-400 MPa and an achievable temperature range of 0-80°C. The high-pressure SAXS cell has recently been commissioned on the ID7A beamline at the Cornell High Energy Synchrotron Source and is available to users on a peer-reviewed proposal basis.
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Affiliation(s)
- Durgesh K. Rai
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Richard E. Gillilan
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
| | - Robert Miller
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | - Edmund Ting
- Pressure BioSciences Inc., South Easton, MA 02375, USA
| | | | - Mark W. Tate
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | - Sol M. Gruner
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853, USA
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
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16
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Xu X, Gagné D, Aramini JM, Gardner KH. Volume and compressibility differences between protein conformations revealed by high-pressure NMR. Biophys J 2021; 120:924-935. [PMID: 33524371 DOI: 10.1016/j.bpj.2020.12.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/25/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Proteins often interconvert between different conformations in ways critical to their function. Although manipulating such equilibria for biophysical study is often challenging, the application of pressure is a potential route to achieve such control by favoring the population of lower volume states. Here, we use this feature to study the interconversion of ARNT PAS-B Y456T, which undergoes a dramatic +3 slip in the β-strand register as it switches between two stably folded conformations. Using high-pressure biomolecular NMR approaches, we obtained the first, to our knowledge, quantitative data testing two key hypotheses of this process: the slipped conformation is both smaller and less compressible than the wild-type equivalent, and the interconversion proceeds through a chiefly unfolded intermediate state. Data collected in steady-state pressure and time-resolved pressure-jump modes, including observed pressure-dependent changes in the populations of the two conformers and increased rate of interconversion between conformers, support both hypotheses. Our work exemplifies how these approaches, which can be generally applied to protein conformational switches, can provide unique information that is not easily accessible through other techniques.
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Affiliation(s)
- Xingjian Xu
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York; Ph.D Program in Biochemistry, The Graduate Center, CUNY, New York, New York
| | - Donald Gagné
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York
| | - James M Aramini
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York; Department of Chemistry and Biochemistry, City College of New York, New York, New York; Ph.D. Programs in Biochemistry, Chemistry, and Biology, The Graduate Center, CUNY, New York, New York.
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17
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Sprangers R. High-pressure NMR measurements provide insights into the different structural states that proteins can adopt. Biophys J 2021; 120:749-751. [PMID: 33561391 DOI: 10.1016/j.bpj.2021.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 10/22/2022] Open
Affiliation(s)
- Remco Sprangers
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
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18
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Le Vay K, Carter BM, Watkins DW, Dora Tang TY, Ting VP, Cölfen H, Rambo RP, Smith AJ, Ross Anderson JL, Perriman AW. Controlling Protein Nanocage Assembly with Hydrostatic Pressure. J Am Chem Soc 2020; 142:20640-20650. [PMID: 33252237 DOI: 10.1021/jacs.0c07285] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Controlling the assembly and disassembly of nanoscale protein cages for the capture and internalization of protein or non-proteinaceous components is fundamentally important to a diverse range of bionanotechnological applications. Here, we study the reversible, pressure-induced dissociation of a natural protein nanocage, E. coli bacterioferritin (Bfr), using synchrotron radiation small-angle X-ray scattering (SAXS) and circular dichroism (CD). We demonstrate that hydrostatic pressures of 450 MPa are sufficient to completely dissociate the Bfr 24-mer into protein dimers, and the reversibility and kinetics of the reassembly process can be controlled by selecting appropriate buffer conditions. We also demonstrate that the heme B prosthetic group present at the subunit dimer interface influences the stability and pressure lability of the cage, despite its location being discrete from the interdimer interface that is key to cage assembly. This indicates a major cage-stabilizing role for heme within this family of ferritins.
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Affiliation(s)
- Kristian Le Vay
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
- Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K
| | - Ben M Carter
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - T-Y Dora Tang
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
| | - Valeska P Ting
- Bristol Composites Institute (ACCIS), Department of Mechanical Engineering, University of Bristol, Queen's Building, Bristol BS8 1TR, U.K
| | - Helmut Cölfen
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Robert P Rambo
- Diamond House, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Fermi Ave., Didcot OX11 0DE, U.K
| | - Andrew J Smith
- Diamond House, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Fermi Ave., Didcot OX11 0DE, U.K
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Adam W Perriman
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, U.K
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19
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Alsiary RA, Alghrably M, Saoudi A, Al-Ghamdi S, Jaremko L, Jaremko M, Emwas AH. Using NMR spectroscopy to investigate the role played by copper in prion diseases. Neurol Sci 2020; 41:2389-2406. [PMID: 32328835 PMCID: PMC7419355 DOI: 10.1007/s10072-020-04321-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/29/2020] [Indexed: 12/31/2022]
Abstract
Prion diseases are a group of rare neurodegenerative disorders that develop as a result of the conformational conversion of normal prion protein (PrPC) to the disease-associated isoform (PrPSc). The mechanism that actually causes disease remains unclear. However, the mechanism underlying the conformational transformation of prion protein is partially understood-in particular, there is strong evidence that copper ions play a significant functional role in prion proteins and in their conformational conversion. Various models of the interaction of copper ions with prion proteins have been proposed for the Cu (II)-binding, cell-surface glycoprotein known as prion protein (PrP). Changes in the concentration of copper ions in the brain have been associated with prion diseases and there is strong evidence that copper plays a significant functional role in the conformational conversion of PrP. Nevertheless, because copper ions have been shown to have both a positive and negative effect on prion disease onset, the role played by Cu (II) ions in these diseases remains a topic of debate. Because of the unique properties of paramagnetic Cu (II) ions in the magnetic field, their interactions with PrP can be tracked even at single atom resolution using nuclear magnetic resonance (NMR) spectroscopy. Various NMR approaches have been utilized to study the kinetic, thermodynamic, and structural properties of Cu (II)-PrP interactions. Here, we highlight the different models of copper interactions with PrP with particular focus on studies that use NMR spectroscopy to investigate the role played by copper ions in prion diseases.
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Affiliation(s)
- Rawiah A. Alsiary
- King Abdullah International Medical Research Center (KAIMRC), Jeddah, Saudi Arabia/King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Jeddah, Saudi Arabia
| | - Mawadda Alghrably
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Abdelhamid Saoudi
- Oncology, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia. King Abdullah International Medical Research Center (KAIMRC), Jeddah, Saudi Arabia/King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Jeddah, Saudi Arabia
| | - Suliman Al-Ghamdi
- Oncology, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia. King Abdullah International Medical Research Center (KAIMRC), Jeddah, Saudi Arabia/King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Jeddah, Saudi Arabia
| | - Lukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Abdul-Hamid Emwas
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
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20
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Wakamoto T, Kitazawa S, Kameda T, Kitahara R. Dynamic aspects of pressure and temperature-stabilized intermediates of outer surface protein A. Proteins 2020; 88:1423-1433. [PMID: 32519353 DOI: 10.1002/prot.25962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/05/2020] [Accepted: 06/06/2020] [Indexed: 01/18/2023]
Abstract
Structural characterization of alternatively folded and partially disordered protein conformations remains challenging. Outer surface protein A (OspA) is a pivotal protein in Borrelia infection, which is the etiological agent of Lyme disease. OspA exists in equilibrium with intermediate conformations, in which the central and the C-terminal regions of the protein have lower stabilities than the N-terminal. Here, we characterize pressure- and temperature-stabilized intermediates of OspA by nuclear magnetic resonance spectroscopy combined with paramagnetic relaxation enhancement (PRE). We found that although the C-terminal region of the intermediate was partially disordered, it retains weak specific contact with the N-terminal region, owing to a twist of the central β-sheet and increased flexibility in the polypeptide chain. The disordered C-terminal region of the pressure-stabilized intermediate was more compact than that of the temperature-stabilized form. Further, molecular dynamics simulation demonstrated that temperature-induced disordering of the β-sheet was initiated at the C-terminal region and continued through to the central region. An ensemble of simulation snapshots qualitatively described the PRE data from the intermediate and indicated that the intermediate structures of OspA may expose tick receptor-binding sites more readily than does the basic folded conformation.
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Affiliation(s)
- Takuro Wakamoto
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Soichiro Kitazawa
- College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Ryo Kitahara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Japan.,College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
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21
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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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22
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Arthanari H, Takeuchi K, Dubey A, Wagner G. Emerging solution NMR methods to illuminate the structural and dynamic properties of proteins. Curr Opin Struct Biol 2019; 58:294-304. [PMID: 31327528 PMCID: PMC6778509 DOI: 10.1016/j.sbi.2019.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 06/03/2019] [Accepted: 06/10/2019] [Indexed: 12/20/2022]
Abstract
The first recognition of protein breathing was more than 50 years ago. Today, we are able to detect the multitude of interaction modes, structural polymorphisms, and binding-induced changes in protein structure that direct function. Solution-state NMR spectroscopy has proved to be a powerful technique, not only to obtain high-resolution structures of proteins, but also to provide unique insights into the functional dynamics of proteins. Here, we summarize recent technical landmarks in solution NMR that have enabled characterization of key biological macromolecular systems. These methods have been fundamental to atomic resolution structure determination and quantitative analysis of dynamics over a wide range of time scales by NMR. The ability of NMR to detect lowly populated protein conformations and transiently formed complexes plays a critical role in its ability to elucidate functionally important structural features of proteins and their dynamics.
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Affiliation(s)
- Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
| | - Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 135-0064 Tokyo, Japan.
| | - Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States.
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23
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Abstract
Although many proteins possess a distinct folded structure lying at a minimum in a funneled free energy landscape, thermal energy causes any protein to continuously access lowly populated excited states. The existence of excited states is an integral part of biological function. Although transitions into the excited states may lead to protein misfolding and aggregation, little structural information is currently available for them. Here, we show how NMR spectroscopy, coupled with pressure perturbation, brings these elusive species to light. As pressure acts to favor states with lower partial molar volume, NMR follows the ensuing change in the equilibrium spectroscopically, with residue-specific resolution. For T4 lysozyme L99A, relaxation dispersion NMR was used to follow the increase in population of a previously identified "invisible" folded state with pressure, as this is driven by the reduction in cavity volume by the flipping-in of a surface aromatic group. Furthermore, multiple partly disordered excited states were detected at equilibrium using pressure-dependent H/D exchange NMR spectroscopy. Here, unfolding reduced partial molar volume by the removal of empty internal cavities and packing imperfections through subglobal and global unfolding. A close correspondence was found for the distinct pressure sensitivities of various parts of the protein and the amount of internal cavity volume that was lost in each unfolding event. The free energies and populations of excited states allowed us to determine the energetic penalty of empty internal protein cavities to be 36 cal⋅Å-3.
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24
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Espinosa YR, Caffarena ER, Grigera JR. The role of hydrophobicity in the cold denaturation of proteins under high pressure: A study on apomyoglobin. J Chem Phys 2019; 150:075102. [PMID: 30795674 DOI: 10.1063/1.5080942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An exciting debate arises when microscopic mechanisms involved in the denaturation of proteins at high pressures are explained. In particular, the issue emerges when the hydrophobic effect is invoked, given that hydrophobicity cannot elucidate by itself the volume changes measured during protein unfolding. In this work, we study by the use of molecular dynamics simulations and essential dynamics analysis the relation between the solvation dynamics, volume, and water structure when apomyoglobin is subjected to a hydrostatic pressure regime. Accordingly, the mechanism of cold denaturation of proteins under high-pressure can be related to the disruption of the hydrogen-bond network of water favoring the coexistence of two states, low-density and high-density water, which directly implies in the formation of a molten globule once the threshold of 200 MPa has been overcome.
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Affiliation(s)
- Yanis R Espinosa
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET-UNLP), Calle 59 Nro 789, B1900BTE La Plata, Argentina
| | - Ernesto R Caffarena
- Programa de Computação Científica (PROCC), Fundação Oswaldo Cruz, Manguinhos, CEP 21040-360 Rio de Janeiro, Brazil
| | - J Raúl Grigera
- CEQUINOR, Universidad de La Plata and CONICET, 47 y 115, B1900 La Plata, Argentina
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25
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Abstract
The Tinker-OpenMM package for AMOEBA molecular dynamics on GPU has long been limited to the Monte Carlo barostat due to the lack of virial calculation. In this paper, we report the calculation of the internal virial for the AMOEBA forcefield. This constitutes the first GPU implementation of a polarizable internal virial. This is followed by the implementation of the Berendsen barostat into Tinker-OpenMM as a demonstration of the capability of Tinker-OpenMM to calculate the virial with sufficient accuracy to enable pressure control. These additions enable the further improvement of Tinker-OpenMM to include a wide range of virial-based barostat algorithms.
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26
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Characterization of low-lying excited states of proteins by high-pressure NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:350-358. [PMID: 30366154 DOI: 10.1016/j.bbapap.2018.10.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/17/2018] [Accepted: 10/22/2018] [Indexed: 12/26/2022]
Abstract
Hydrostatic pressure alters the free energy of proteins by a few kJ mol-1, with the amount depending on their partial molar volumes. Because the folded ground state of a protein contains cavities, it is always a state of large partial molar volume. Therefore pressure always destabilises the ground state and increases the population of partially and completely unfolded states. This is a mild and reversible conformational change, which allows the study of excited states under thermodynamic equilibrium conditions. Many of the excited states studied in this way are functionally relevant; they also seem to be very similar to kinetic folding intermediates, thus suggesting that evolution has made use of the 'natural' dynamic energy landscape of the protein fold and sculpted it to optimise function. This includes features such as ligand binding, structural change during the catalytic cycle, and dynamic allostery.
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NMR Methods of Characterizing Biomolecular Structural Dynamics and Conformational Ensembles. Methods 2018; 148:1-3. [DOI: 10.1016/j.ymeth.2018.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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