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Humphreys JM, Teixeira LR, Akella R, He H, Kannangara AR, Sekulski K, Pleinis J, Liwocha J, Jiou J, Servage KA, Orth K, Joachimiak L, Rizo J, Cobb MH, Brautigam CA, Rodan AR, Goldsmith EJ. Hydrostatic Pressure Sensing by WNK kinases. Mol Biol Cell 2023; 34:ar109. [PMID: 37585288 PMCID: PMC10559305 DOI: 10.1091/mbc.e23-03-0113] [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: 05/22/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Previous study has demonstrated that the WNK kinases 1 and 3 are direct osmosensors consistent with their established role in cell-volume control. WNK kinases may also be regulated by hydrostatic pressure. Hydrostatic pressure applied to cells in culture with N2 gas or to Drosophila Malpighian tubules by centrifugation induces phosphorylation of downstream effectors of endogenous WNKs. In vitro, the autophosphorylation and activity of the unphosphorylated kinase domain of WNK3 (uWNK3) is enhanced to a lesser extent than in cells by 190 kPa applied with N2 gas. Hydrostatic pressure measurably alters the structure of uWNK3. Data from size exclusion chromatography in line with multi-angle light scattering (SEC-MALS), SEC alone at different back pressures, analytical ultracentrifugation (AUC), NMR, and chemical crosslinking indicate a change in oligomeric structure in the presence of hydrostatic pressure from a WNK3 dimer to a monomer. The effects on the structure are related to those seen with osmolytes. Potential mechanisms of hydrostatic pressure activation of uWNK3 and the relationships of pressure activation to WNK osmosensing are discussed.
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Affiliation(s)
- John M. Humphreys
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Liliana R. Teixeira
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Radha Akella
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Haixia He
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Ashari R. Kannangara
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kamil Sekulski
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - John Pleinis
- Department of Internal Medicine, Division of Nephrology and Hypertension and Department of Human Genetics, University of Utah, Salt Lake City UT 84112
| | - Joanna Liwocha
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Jenny Jiou
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kelly A. Servage
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lukasz Joachimiak
- Center for Alzheimer’s and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Josep Rizo
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Melanie H. Cobb
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Aylin R. Rodan
- Department of Internal Medicine, Division of Nephrology and Hypertension and Department of Human Genetics, University of Utah, Salt Lake City UT 84112
| | - Elizabeth J. Goldsmith
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390
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2
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Pastore A, Temussi PA. Unfolding under Pressure: An NMR Perspective. Chembiochem 2023; 24:e202300164. [PMID: 37154795 DOI: 10.1002/cbic.202300164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/10/2023]
Abstract
This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides important information about the forces that keep protein structure together. We first analyse what pressure unfolding is, then provide a critical overview of how NMR spectroscopy has contributed to the field and evaluate the observables used in these studies. Finally, we discuss the commonalities and differences between pressure-, cold- and heat-induced unfolding. We conclude that, despite specific peculiarities, in both cold and pressure denaturation the important contribution of the state of hydration of nonpolar side chains is a major factor that determines the pressure dependence of the conformational stability of proteins.
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Affiliation(s)
- Annalisa Pastore
- European Synchrotron Radiation Facilities, 71 Ave des Martyrs, 38000, Grenoble, France
- The Wohl Institute, King's College London, 5 Cutcombe Rd, SE59RT, London, UK
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3
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Harish B, Wang J, Hayden EJ, Grabe B, Hiller W, Winter R, Royer CA. Hidden intermediates in Mango III RNA aptamer folding revealed by pressure perturbation. Biophys J 2022; 121:421-429. [PMID: 34971617 PMCID: PMC8822612 DOI: 10.1016/j.bpj.2021.12.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/12/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
Fluorescent RNA aptamers have the potential to enable routine quantitation and localization of RNA molecules and serve as models for understanding biologically active aptamers. In recent years, several fluorescent aptamers have been selected and modified to improve their properties, revealing that small changes to the RNA or the ligands can modify significantly their fluorescent properties. Although structural biology approaches have revealed the bound, ground state of several fluorescent aptamers, characterization of low-abundance, excited states in these systems is crucial to understanding their folding pathways. Here we use pressure as an alternative variable to probe the suboptimal states of the Mango III aptamer with both fluorescence and NMR spectroscopy approaches. At moderate KCl concentrations, increasing pressure disrupted the G-quadruplex structure of the Mango III RNA and led to an intermediate with lower fluorescence. These observations indicate the existence of suboptimal RNA structural states that still bind the TO1-biotin fluorophore and moderately enhance fluorescence. At higher KCl concentration as well, the intermediate fluorescence state was populated at high pressure, but the G-quadruplex remained stable at high pressure, supporting the notion of parallel folding and/or binding pathways. These results demonstrate the usefulness of pressure for characterizing RNA folding intermediates.
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Affiliation(s)
| | - Jinqiu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy
| | | | - Bastian Grabe
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy,Corresponding author
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4
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Chen J, Zaer S, Drori P, Zamel J, Joron K, Kalisman N, Lerner E, Dokholyan NV. The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds. Structure 2021; 29:1048-1064.e6. [PMID: 34015255 PMCID: PMC8419013 DOI: 10.1016/j.str.2021.05.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/12/2021] [Accepted: 04/30/2021] [Indexed: 11/22/2022]
Abstract
α-Synuclein plays an important role in synaptic functions by interacting with synaptic vesicle membrane, while its oligomers and fibrils are associated with several neurodegenerative diseases. The specific monomer structures that promote its membrane binding and self-association remain elusive due to its transient nature as an intrinsically disordered protein. Here, we use inter-dye distance distributions from bulk time-resolved Förster resonance energy transfer as restraints in discrete molecular dynamics simulations to map the conformational space of the α-synuclein monomer. We further confirm the generated conformational ensemble in orthogonal experiments utilizing far-UV circular dichroism and cross-linking mass spectrometry. Single-molecule protein-induced fluorescence enhancement measurements show that within this conformational ensemble, some of the conformations of α-synuclein are surprisingly stable, exhibiting conformational transitions slower than milliseconds. Our comprehensive analysis of the conformational ensemble reveals essential structural properties and potential conformations that promote its various functions in membrane interaction or oligomer and fibril formation.
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Affiliation(s)
- Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Sofia Zaer
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Joanna Zamel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Khalil Joron
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA; Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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5
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Chalikian TV, Macgregor RB. Volumetric Properties of Four-Stranded DNA Structures. BIOLOGY 2021; 10:813. [PMID: 34440045 PMCID: PMC8389613 DOI: 10.3390/biology10080813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/27/2022]
Abstract
Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic instability, and regulation of transcription and translation events. To gain an understanding of the molecular determinants underlying the biological role of four-stranded DNA structures, their biophysical properties have been extensively studied. The limited libraries on volume, expansibility, and compressibility accumulated to date have begun to provide insights into the molecular origins of helix-to-coil and helix-to-helix conformational transitions involving four-stranded DNA structures. In this article, we review the recent progress in volumetric investigations of G-quadruplexes and i-motifs, emphasizing how such data can be used to characterize intra-and intermolecular interactions, including solvation. We describe how volumetric data can be interpreted at the molecular level to yield a better understanding of the role that solute-solvent interactions play in modulating the stability and recognition events of nucleic acids. Taken together, volumetric studies facilitate unveiling the molecular determinants of biological events involving biopolymers, including G-quadruplexes and i-motifs, by providing one more piece to the thermodynamic puzzle describing the energetics of cellular processes in vitro and, by extension, in vivo.
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Affiliation(s)
- Tigran V. Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada;
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6
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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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7
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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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8
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Roche J, Royer CA, Roumestand C. Exploring Protein Conformational Landscapes Using High-Pressure NMR. Methods Enzymol 2019; 614:293-320. [DOI: 10.1016/bs.mie.2018.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Jenkins KA, Fossat MJ, Zhang S, Rai DK, Klein S, Gillilan R, White Z, Gerlich G, McCallum SA, Winter R, Gruner SM, Barrick D, Royer CA. The consequences of cavity creation on the folding landscape of a repeat protein depend upon context. Proc Natl Acad Sci U S A 2018; 115:E8153-E8161. [PMID: 30104366 PMCID: PMC6126725 DOI: 10.1073/pnas.1807379115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effect of introducing internal cavities on protein native structure and global stability has been well documented, but the consequences of these packing defects on folding free-energy landscapes have received less attention. We investigated the effects of cavity creation on the folding landscape of the leucine-rich repeat protein pp32 by high-pressure (HP) and urea-dependent NMR and high-pressure small-angle X-ray scattering (HPSAXS). Despite a modest global energetic perturbation, cavity creation in the N-terminal capping motif (N-cap) resulted in very strong deviation from two-state unfolding behavior. In contrast, introduction of a cavity in the most stable, C-terminal half of pp32 led to highly concerted unfolding, presumably because the decrease in stability by the mutations attenuated the N- to C-terminal stability gradient present in WT pp32. Interestingly, enlarging the central cavity of the protein led to the population under pressure of a distinct intermediate in which the N-cap and repeats 1-4 were nearly completely unfolded, while the fifth repeat and the C-terminal capping motif remained fully folded. Thus, despite modest effects on global stability, introducing internal cavities can have starkly distinct repercussions on the conformational landscape of a protein, depending on their structural and energetic context.
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Affiliation(s)
- Kelly A Jenkins
- Graduate Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Martin J Fossat
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Siwen Zhang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Durgesh K Rai
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853
| | - Sean Klein
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Richard Gillilan
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853
| | - Zackary White
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Grayson Gerlich
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Scott A McCallum
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Roland Winter
- Department of Physical Chemistry, Technical University of Dortmund, 44227 Dortmund, Germany
| | - Sol M Gruner
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853
- Department of Physics, Cornell University, Ithaca, NY 14853
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853
| | - Doug Barrick
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Catherine A Royer
- Graduate Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY 12180;
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180
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10
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Zhang Y, Kitazawa S, Peran I, Stenzoski N, McCallum SA, Raleigh DP, Royer CA. High Pressure ZZ-Exchange NMR Reveals Key Features of Protein Folding Transition States. J Am Chem Soc 2016; 138:15260-15266. [PMID: 27781428 DOI: 10.1021/jacs.6b09887] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding protein folding mechanisms and their sequence dependence requires the determination of residue-specific apparent kinetic rate constants for the folding and unfolding reactions. Conventional two-dimensional NMR, such as HSQC experiments, can provide residue-specific information for proteins. However, folding is generally too fast for such experiments. ZZ-exchange NMR spectroscopy allows determination of folding and unfolding rates on much faster time scales, yet even this regime is not fast enough for many protein folding reactions. The application of high hydrostatic pressure slows folding by orders of magnitude due to positive activation volumes for the folding reaction. We combined high pressure perturbation with ZZ-exchange spectroscopy on two autonomously folding protein domains derived from the ribosomal protein, L9. We obtained residue-specific apparent rates at 2500 bar for the N-terminal domain of L9 (NTL9), and rates at atmospheric pressure for a mutant of the C-terminal domain (CTL9) from pressure dependent ZZ-exchange measurements. Our results revealed that NTL9 folding is almost perfectly two-state, while small deviations from two-state behavior were observed for CTL9. Both domains exhibited large positive activation volumes for folding. The volumetric properties of these domains reveal that their transition states contain most of the internal solvent excluded voids that are found in the hydrophobic cores of the respective native states. These results demonstrate that by coupling it with high pressure, ZZ-exchange can be extended to investigate a large number of protein conformational transitions.
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Affiliation(s)
- Yi Zhang
- Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Soichiro Kitazawa
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Ivan Peran
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Natalie Stenzoski
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Scott A McCallum
- NMR Core Facility, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Daniel P Raleigh
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Catherine A Royer
- Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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11
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Dellarole M, Caro JA, Roche J, Fossat M, Barthe P, García-Moreno E B, Royer CA, Roumestand C. Evolutionarily Conserved Pattern of Interactions in a Protein Revealed by Local Thermal Expansion Properties. J Am Chem Soc 2015; 137:9354-62. [PMID: 26135981 DOI: 10.1021/jacs.5b04320] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The way in which the network of intramolecular interactions determines the cooperative folding and conformational dynamics of a protein remains poorly understood. High-pressure NMR spectroscopy is uniquely suited to examine this problem because it combines the site-specific resolution of the NMR experiments with the local character of pressure perturbations. Here we report on the temperature dependence of the site-specific volumetric properties of various forms of staphylococcal nuclease (SNase), including three variants with engineered internal cavities, as measured with high-pressure NMR spectroscopy. The strong temperature dependence of pressure-induced unfolding arises from poorly understood differences in thermal expansion between the folded and unfolded states. A significant inverse correlation was observed between the global thermal expansion of the folded proteins and the number of strong intramolecular hydrogen bonds, as determined by the temperature coefficient of the backbone amide chemical shifts. Comparison of the identity of these strong H-bonds with the co-evolution of pairs of residues in the SNase protein family suggests that the architecture of the interactions detected in the NMR experiments could be linked to a functional aspect of the protein. Moreover, the temperature dependence of the residue-specific volume changes of unfolding yielded residue-specific differences in expansivity and revealed how mutations impact intramolecular interaction patterns. These results show that intramolecular interactions in the folded states of proteins impose constraints against thermal expansion and that, hence, knowledge of site-specific thermal expansivity offers insight into the patterns of strong intramolecular interactions and other local determinants of protein stability, cooperativity, and potentially also of function.
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Affiliation(s)
- Mariano Dellarole
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
| | - Jose A Caro
- ‡T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St.. Baltimore, Maryland 21218, United States
| | - Julien Roche
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
| | - Martin Fossat
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
| | - Philippe Barthe
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
| | - Bertrand García-Moreno E
- ‡T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St.. Baltimore, Maryland 21218, United States
| | - Catherine A Royer
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
| | - Christian Roumestand
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
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12
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Cortines JR, Lima LMT, Mohana-Borges R, Millen TDA, Gaspar LP, Lanman JK, Prevelige PE, Silva JL. Structural insights into the stabilization of the human immunodeficiency virus type 1 capsid protein by the cyclophilin-binding domain and implications on the virus cycle. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:341-8. [DOI: 10.1016/j.bbapap.2014.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 11/24/2014] [Accepted: 12/10/2014] [Indexed: 01/01/2023]
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Roche J, Dellarole M, Royer CA, Roumestand C. Exploring the Protein Folding Pathway with High-Pressure NMR: Steady-State and Kinetics Studies. Subcell Biochem 2015; 72:261-278. [PMID: 26174386 DOI: 10.1007/978-94-017-9918-8_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Defining the physical-chemical determinants of protein folding and stability, under normal and pathological conditions has constituted a major subfield in biophysical chemistry for over 50 years. Although a great deal of progress has been made in recent years towards this goal, a number of important questions remain. These include characterizing the structural, thermodynamic and dynamic properties of the barriers between conformational states on the protein energy landscape, understanding the sequence dependence of folding cooperativity, defining more clearly the role of solvation in controlling protein stability and dynamics and probing the high energy thermodynamic states in the native state basin and their role in misfolding and aggregation. Fundamental to the elucidation of these questions is a complete thermodynamic parameterization of protein folding determinants. In this chapter, we describe the use of high-pressure coupled to Nuclear Magnetic Resonance (NMR) spectroscopy to reveal unprecedented details on the folding energy landscape of proteins.
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Affiliation(s)
- Julien Roche
- Centre de Biochimie Structurale, UMR UM1&UM2/5048 CNRS/1054 INSERM, 29 rue de Navacelles, 34090, Montpellier, France
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14
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High-pressure SANS and fluorescence unfolding study of calmodulin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1560-8. [DOI: 10.1016/j.bbapap.2014.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/06/2014] [Accepted: 05/16/2014] [Indexed: 11/15/2022]
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Mesnage S, Dellarole M, Baxter NJ, Rouget JB, Dimitrov JD, Wang N, Fujimoto Y, Hounslow AM, Lacroix-Desmazes S, Fukase K, Foster SJ, Williamson MP. Molecular basis for bacterial peptidoglycan recognition by LysM domains. Nat Commun 2014; 5:4269. [PMID: 24978025 PMCID: PMC4083421 DOI: 10.1038/ncomms5269] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/02/2014] [Indexed: 02/06/2023] Open
Abstract
Carbohydrate recognition is essential for growth, cell adhesion and signalling in all living organisms. A highly conserved carbohydrate binding module, LysM, is found in proteins from viruses, bacteria, fungi, plants and mammals. LysM modules recognize polysaccharides containing N-acetylglucosamine (GlcNAc) residues including peptidoglycan, an essential component of the bacterial cell wall. However, the molecular mechanism underpinning LysM-peptidoglycan interactions remains unclear. Here we describe the molecular basis for peptidoglycan recognition by a multimodular LysM domain from AtlA, an autolysin involved in cell division in the opportunistic bacterial pathogen Enterococcus faecalis. We explore the contribution of individual modules to the binding, identify the peptidoglycan motif recognized, determine the structures of free and bound modules and reveal the residues involved in binding. Our results suggest that peptide stems modulate LysM binding to peptidoglycan. Using these results, we reveal how the LysM module recognizes the GlcNAc-X-GlcNAc motif present in polysaccharides across kingdoms.
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Affiliation(s)
- Stéphane Mesnage
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Mariano Dellarole
- Centre de Biochimie Structurale, CNRS UMR 5048—UM 1—INSERM UMR 1054, F-34090 Montpellier, France
- These authors contributed equally to this work
- Present address: Institut Pasteur, Unité de Virologie Structurale, 28 Rue du Docteur Roux, F-75015 Paris, France
| | - Nicola J. Baxter
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- These authors contributed equally to this work
| | - Jean-Baptiste Rouget
- Centre de Biochimie Structurale, CNRS UMR 5048—UM 1—INSERM UMR 1054, F-34090 Montpellier, France
| | - Jordan D. Dimitrov
- INSERM, U872, Centre de Recherche des Cordeliers, Equipe 16, F-75006 Paris, France
- Université Pierre et Marie Curie, UMR-S 872, F-75006 Paris, France
- Université Paris Descartes, UMR-S 872, F-75006 Paris, France
| | - Ning Wang
- Department of Chemistry, Laboratory for Natural Products Chemistry, Osaka University, Osaka 560-0043, Japan
| | - Yukari Fujimoto
- Department of Chemistry, Laboratory for Natural Products Chemistry, Osaka University, Osaka 560-0043, Japan
| | - Andrea M. Hounslow
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Sébastien Lacroix-Desmazes
- INSERM, U872, Centre de Recherche des Cordeliers, Equipe 16, F-75006 Paris, France
- Université Pierre et Marie Curie, UMR-S 872, F-75006 Paris, France
- Université Paris Descartes, UMR-S 872, F-75006 Paris, France
| | - Koichi Fukase
- Department of Chemistry, Laboratory for Natural Products Chemistry, Osaka University, Osaka 560-0043, Japan
| | - Simon J. Foster
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Michael P. Williamson
- Krebs Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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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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