1
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Kang WY, Mondal A, Bonney JR, Perez A, Prentice BM. Structural Elucidation of Ubiquitin via Gas-Phase Ion/Ion Cross-Linking Reactions Using Sodium-Cationized Reagents Coupled with Infrared Multiphoton Dissociation. Anal Chem 2024; 96:8518-8527. [PMID: 38711366 PMCID: PMC11161031 DOI: 10.1021/acs.analchem.4c00442] [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] [Indexed: 05/08/2024]
Abstract
Accurate structural determination of proteins is critical to understanding their biological functions and the impact of structural disruption on disease progression. Gas-phase cross-linking mass spectrometry (XL-MS) via ion/ion reactions between multiply charged protein cations and singly charged cross-linker anions has previously been developed to obtain low-resolution structural information on proteins. This method significantly shortens experimental time relative to conventional solution-phase XL-MS but has several technical limitations: (1) the singly deprotonated N-hydroxysulfosuccinimide (sulfo-NHS)-based cross-linker anions are restricted to attachment at neutral amine groups of basic amino acid residues and (2) analyzing terminal cross-linked fragment ions is insufficient to unambiguously localize sites of linker attachment. Herein, we demonstrate enhanced structural information for alcohol-denatured A-state ubiquitin obtained from an alternative gas-phase XL-MS approach. Briefly, singly sodiated ethylene glycol bis(sulfosuccinimidyl succinate) (sulfo-EGS) cross-linker anions enable covalent cross-linking at both ammonium and amine groups. Additionally, covalently modified internal fragment ions, along with terminal b-/y-type counterparts, improve the determination of linker attachment sites. Molecular dynamics simulations validate experimentally obtained gas-phase conformations of denatured ubiquitin. This method has identified four cross-linking sites across 8+ ubiquitin, including two new sites in the N-terminal region of the protein that were originally inaccessible in prior gas-phase XL approaches. The two N-terminal cross-linking sites suggest that the N-terminal half of ubiquitin is more compact in gas-phase conformations. By comparison, the two C-terminal linker sites indicate the signature transformation of this region of the protein from a native to a denatured conformation. Overall, the results suggest that the solution-phase secondary structures of the A-state ubiquitin are conserved in the gas phase. This method also provides sufficient sensitivity to differentiate between two gas-phase conformers of the same charge state with subtle structural variations.
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Affiliation(s)
| | - Arup Mondal
- Department of Chemistry, University of Florida
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2
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Sharif D, Rahman M, Mahmud S, Sultana MN, Attanayake K, DeBastiani A, Foroushani SH, Li P, Valentine SJ. In-droplet hydrogen-deuterium exchange to examine protein/peptide solution conformer heterogeneity. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9593. [PMID: 37430450 DOI: 10.1002/rcm.9593] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/25/2023] [Accepted: 05/22/2023] [Indexed: 07/12/2023]
Abstract
RATIONALE Many different structure analysis techniques are not capable of probing the heterogeneity of solution conformations. Here, we examine the ability of in-droplet hydrogen-deuterium exchange (HDX) to directly probe solution conformer heterogeneity of a protein with mass spectrometry (MS) detection. METHODS Two vibrating capillary vibrating sharp-edge spray ionization (cVSSI) devices have been arranged such that they generate microdroplet plumes of the analyte and D2 O reagent, which coalesce to form reaction droplets where HDX takes place in the solution environment. The native HDX-MS setup has been first explored for two model peptides that have distinct structural compositions in solution. The effectiveness of the multidevice cVSSI-HDX in illustrating structural details has been further exploited to investigate coexisting solution-phase conformations of the protein ubiquitin. RESULTS In-droplet HDX reveals decreased backbone exchange for a model peptide that has a greater helix-forming propensity. Differences in intrinsic rates of the alanine and serine residues may account for much of the observed protection. The data allow the first estimates of backbone exchange rates for peptides undergoing in-droplet HDX. That said, the approach may hold greater potential for investigating the tertiary structure and structural transitions of proteins. For ubiquitin protein, HDX reactivity differences suggest that multiple conformers are present in native solutions. The addition of methanol to buffered aqueous solutions of ubiquitin results in increased populations of solution conformers of higher reactivity. Data analysis suggests that partially folded conformers such as the A-state of ubiquitin increase with methanol content; the native state may be preserved to a limited degree even under stronger denaturation conditions. CONCLUSION The deuterium uptake after in-droplet HDX has been observed to correspond to some degree with peptide backbone hydrogen protection based on differences in intrinsic rates of exchange. The presence of coexisting protein solution structures under native and denaturing solution conditions has been distinguished by the isotopic distributions of deuterated ubiquitin ions.
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Affiliation(s)
- Daud Sharif
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Mohammad Rahman
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Sultan Mahmud
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Mst Nigar Sultana
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Samira Hajian Foroushani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
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3
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Ujma J, Jhingree J, Norgate E, Upton R, Wang X, Benoit F, Bellina B, Barran P. Protein Unfolding in Freeze Frames: Intermediate States are Revealed by Variable-Temperature Ion Mobility-Mass Spectrometry. Anal Chem 2022; 94:12248-12255. [PMID: 36001095 PMCID: PMC9453741 DOI: 10.1021/acs.analchem.2c03066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas phase is an idealized laboratory for the study of protein structure, from which it is possible to examine stable and transient forms of mass-selected ions in the absence of bulk solvent. With ion mobility-mass spectrometry (IM-MS) apparatus built to operate at both cryogenic and elevated temperatures, we have examined conformational transitions that occur to the monomeric proteins: ubiquitin, lysozyme, and α-synuclein as a function of temperature and in source activation. We rationalize the experimental observations with a temperature-dependent framework model and comparison to known conformers. Data from ubiquitin show unfolding transitions that proceed through diverse and highly elongated intermediate states, which converge to more compact structures. These findings contrast with data obtained from lysozyme─a protein where (un)-folding plasticity is restricted by four disulfide linkages, although this is alleviated in its reduced form. For structured proteins, collision activation of the protein ions in-source enables subsequent "freezing" or thermal annealing of unfolding intermediates, whereas disordered proteins restructure substantially at 250 K even without activation, indicating that cold denaturation can occur without solvent. These data are presented in the context of a toy model framework that describes the relative occupancy of the available conformational space.
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Affiliation(s)
- Jakub Ujma
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jacquelyn Jhingree
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Emma Norgate
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rosie Upton
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Xudong Wang
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Florian Benoit
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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4
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Li W, Chaihu L, Jiang J, Wu B, Zheng X, Dai R, Tian Y, Huang Y, Wang G, Men Y. Microfluidic Platform for Time-Resolved Characterization of Protein Higher-Order Structures and Dynamics Using Top-Down Mass Spectrometry. Anal Chem 2022; 94:7520-7527. [PMID: 35584038 DOI: 10.1021/acs.analchem.2c00077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Characterization of protein higher-order structures and dynamics is essential for understanding the biological functions of proteins and revealing the underlying mechanisms. Top-down mass spectrometry (MS) accesses structural information at both the intact protein level and the peptide fragment level. Native top-down MS allows analysis of a protein complex's architecture and subunits' identity and modifications. Top-down hydrogen/deuterium exchange (HDX) MS offers high spatial resolution for conformational or binding interface analysis and enables conformer-specific characterization. A microfluidic chip can provide superior performance for front-end reactions useful for these MS workflows, such as flexibility in manipulating multiple reactant flows, integrating various functional modules, and automation. However, most microchip-MS devices are designed for bottom-up approaches or top-down proteomics. Here, we demonstrate a strategy for designing a microchip for top-down MS analysis of protein higher-order structures and dynamics. It is suitable for time-resolved native MS and HDX MS, with designs aiming for efficient ionization of intact protein complexes, flexible manipulation of multiple reactant flows, and precise control of reaction times over a broad range of flow rates on the submicroliter per minute scale. The performance of the prototype device is demonstrated by measurements of systems including monoclonal antibodies, antibody-antigen complexes, and coexisting protein conformers. This strategy may benefit elaborate structural analysis of biomacromolecules and inspire method development using the microchip-MS approach.
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Affiliation(s)
- Wen Li
- Research Center for Biomedical Optics and Molecular Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lingxiao Chaihu
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.,Institute of Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Jialu Jiang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Bizhu Wu
- Research Center for Biomedical Optics and Molecular Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xuan Zheng
- Research Center for Biomedical Optics and Molecular Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Rongrong Dai
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Ye Tian
- Institute of Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yanyi Huang
- Institute of Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
| | - Guanbo Wang
- Institute of Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
| | - Yongfan Men
- Research Center for Biomedical Optics and Molecular Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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5
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Kit MCS, Carvalho VV, Vilseck JZ, Webb IK. Gas-Phase Ion/Ion Chemistry for Structurally Sensitive Probes of Gaseous Protein Ion Structure: Electrostatic and Electrostatic to Covalent Cross-Linking. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 463:116549. [PMID: 33716558 PMCID: PMC7946065 DOI: 10.1016/j.ijms.2021.116549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Intramolecular interactions within a protein are key in maintaining protein tertiary structure and understanding how proteins function. Ion mobility-mass spectrometry (IM-MS) has become a widely used approach in structural biology since it provides rapid measurements of collision cross sections (CCS), which inform on the gas-phase conformation of the biomolecule under study. Gas-phase ion/ion reactions target amino acid residues with specific chemical properties and the modified sites can be identified by MS. In this study, electrostatically reactive, gas-phase ion/ion chemistry and IM-MS are combined to characterize the structural changes between ubiquitin electrosprayed from aqueous and denaturing conditions. The electrostatic attachment of sulfo-NHS acetate to ubiquitin via ion/ion reactions and fragmentation by electron-capture dissociation (ECD) provide the identification of the most accessible protonated sites within ubiquitin as the sulfonate group forms an electrostatic complex with accessible protonated side chains. The protonated sites identified by ECD from the different solution conditions are distinct and, in some cases, reflect the disruption of interactions such as salt bridges that maintain the native protein structure. This agrees with previously published literature demonstrating that a high methanol concentration at low pH causes the structure of ubiquitin to change from a native (N) state to a more elongated A state. Results using gas-phase, electrostatic cross-linking reagents also point to similar structural changes and further confirm the role of methanol and acid in favoring a more unfolded conformation. Since cross-linking reagents have a distance constraint for the two reactive sites, the data is valuable in guiding computational structures generated by molecular dynamics. The research presented here describes a promising strategy that can detect subtle changes in the local environment of targeted amino acid residues to inform on changes in the overall protein structure.
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Affiliation(s)
- Melanie Cheung See Kit
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
| | - Veronica V. Carvalho
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
| | - Jonah Z. Vilseck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Ian K. Webb
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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6
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Carvalho VV, Cheung See Kit M, Webb IK. Ion Mobility and Gas-Phase Covalent Labeling Study of the Structure and Reactivity of Gaseous Ubiquitin Ions Electrosprayed from Aqueous and Denaturing Solutions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1037-1046. [PMID: 32255627 PMCID: PMC7205579 DOI: 10.1021/jasms.9b00138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Gas-phase ion/ion chemistry was coupled to ion mobility/mass spectrometry analysis to correlate the structure of gaseous ubiquitin to its solution structures with selective covalent structural probes. Collision cross section (CCS) distributions were measured to ensure the ubiquitin ions were not unfolded when they were introduced to the gas phase. Aqueous solutions stabilizing the native state of ubiquitin yielded folded ubiquitin structures with CCS values consistent with previously published literature. Denaturing solutions favored several families of unfolded conformations for most of the charge states evaluated. Gas-phase covalent labeling via ion/ion reactions was followed by collision-induced dissociation of the intact, labeled protein to determine which residues were labeled. Ubiquitin 5+ and 6+ electrosprayed from aqueous conditions were covalently modified preferentially at the lysine 29 and arginine 54 positions, indicating that elements of three-dimensional structure were maintained in the gas phase. On the other hand, most ubiquitin ions produced in denaturing conditions were labeled at various other lysine residues, likely due to the availability of additional sites following methanol- and low-pH-induced unfolding. These data support the conservation of ubiquitin structural elements in the gas phase. The research presented here provides the basis for residue-specific characterization of biomolecules in the gas phase.
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Affiliation(s)
| | | | - Ian K. Webb
- Indiana University Purdue University Indianapolis, Indianapolis, IN, USA 46202
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7
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El-Baba TJ, Fuller DR, Woodall DW, Raab SA, Conant CR, Dilger JM, Toker Y, Williams ER, Russell DH, Clemmer DE. Melting proteins confined in nanodroplets with 10.6 μm light provides clues about early steps of denaturation. Chem Commun (Camb) 2018; 54:3270-3273. [PMID: 29536995 PMCID: PMC5871606 DOI: 10.1039/c7cc09829d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Ubiquitin confined within nanodroplets was irradiated with a variable-power CO2 laser. Mass spectrometry analysis shows evidence for a protein "melting"-like transition within droplets prior to solvent evaporation and ion formation. Ion mobility spectrometry reveals that structures associated with early steps of denaturation are trapped because of short droplet lifetimes.
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Affiliation(s)
- Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana, 47401, USA.
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8
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El-Baba TJ, Woodall DW, Raab SA, Fuller DR, Laganowsky A, Russell DH, Clemmer DE. Melting Proteins: Evidence for Multiple Stable Structures upon Thermal Denaturation of Native Ubiquitin from Ion Mobility Spectrometry-Mass Spectrometry Measurements. J Am Chem Soc 2017; 139:6306-6309. [DOI: 10.1021/jacs.7b02774] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tarick J. El-Baba
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel W. Woodall
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Shannon A. Raab
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel R. Fuller
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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9
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Ujma J, Giles K, Morris M, Barran PE. New High Resolution Ion Mobility Mass Spectrometer Capable of Measurements of Collision Cross Sections from 150 to 520 K. Anal Chem 2016; 88:9469-9478. [DOI: 10.1021/acs.analchem.6b01812] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jakub Ujma
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
for Biotechnology, University of Manchester, Manchester M1 7DN, U.K
| | | | | | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
for Biotechnology, University of Manchester, Manchester M1 7DN, U.K
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10
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Aznauryan M, Delgado L, Soranno A, Nettels D, Huang JR, Labhardt AM, Grzesiek S, Schuler B. Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS. Proc Natl Acad Sci U S A 2016; 113:E5389-98. [PMID: 27566405 PMCID: PMC5027429 DOI: 10.1073/pnas.1607193113] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The properties of unfolded proteins are essential both for the mechanisms of protein folding and for the function of the large group of intrinsically disordered proteins. However, the detailed structural and dynamical characterization of these highly dynamic and conformationally heterogeneous ensembles has remained challenging. Here we combine and compare three of the leading techniques for the investigation of unfolded proteins, NMR spectroscopy (NMR), small-angle X-ray scattering (SAXS), and single-molecule Förster resonance energy transfer (FRET), with the goal of quantitatively testing their consistency and complementarity and for obtaining a comprehensive view of the unfolded-state ensemble. Using unfolded ubiquitin as a test case, we find that its average dimensions derived from FRET and from structural ensembles calculated using the program X-PLOR-NIH based on NMR and SAXS restraints agree remarkably well; even the shapes of the underlying intramolecular distance distributions are in good agreement, attesting to the reliability of the approaches. The NMR-based results provide a highly sensitive way of quantifying residual structure in the unfolded state. FRET-based nanosecond fluorescence correlation spectroscopy allows long-range distances and chain dynamics to be probed in a time range inaccessible by NMR. The combined techniques thus provide a way of optimally using the complementarity of the available methods for a quantitative structural and dynamical description of unfolded proteins both at the global and the local level.
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Affiliation(s)
- Mikayel Aznauryan
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | | | - Andrea Soranno
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Jie-Rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming University, Taipei City 112, Taiwan
| | | | | | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland; Department of Physics, University of Zurich, 8057 Zurich, Switzerland
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11
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Surana P, Das R. Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR. Protein Sci 2016; 25:1438-50. [PMID: 27111887 DOI: 10.1002/pro.2940] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 04/20/2016] [Indexed: 01/29/2023]
Abstract
The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly-Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process.
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Affiliation(s)
- Parag Surana
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, Karnataka, India
| | - Ranabir Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, Karnataka, India
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12
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Bychkova VE, Basova LV, Balobanov VA. How membrane surface affects protein structure. BIOCHEMISTRY (MOSCOW) 2015; 79:1483-514. [DOI: 10.1134/s0006297914130045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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13
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Shi H, Atlasevich N, Merenbloom SI, Clemmer DE. Solution dependence of the collisional activation of ubiquitin [M + 7H](7+) ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2000-8. [PMID: 24658799 PMCID: PMC4171273 DOI: 10.1007/s13361-014-0834-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/31/2013] [Accepted: 01/10/2014] [Indexed: 05/12/2023]
Abstract
The solution dependence of gas-phase unfolding for ubiquitin [M + 7H](7+) ions has been studied by ion mobility spectrometry-mass spectrometry (IMS-MS). Different acidic water:methanol solutions are used to favor the native (N), more helical (A), or unfolded (U) solution states of ubiquitin. Unfolding of gas-phase ubiquitin ions is achieved by collisional heating and newly formed structures are examined by IMS. With an activation voltage of 100 V, a selected distribution of compact structures unfolds, forming three resolvable elongated states (E1-E3). The relative populations of these elongated structures depend strongly on the solution composition. Activation of compact ions from aqueous solutions known to favor N-state ubiquitin produces mostly the E1 type elongated state, whereas activation of compact ions from methanol containing solutions that populate A-state ubiquitin favors the E3 elongated state. Presumably, this difference arises because of differences in precursor ion structures emerging from solution. Thus, it appears that information about solution populations can be retained after ionization, selection, and activation to produce the elongated states. These data as well as others are discussed.
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14
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Abstract
![]()
Ion mobility spectrometry coupled
with mass spectrometry (IMS–MS)
is used to investigate the populations of different states for ubiquitin
in water:methanol solutions. In these experiments, ubiquitin is electrosprayed
from 20 water:methanol (100:0 to 5:95, pH = 2) solutions, ranging
from native to denaturing conditions. With an increased percentage
of methanol in solution, ubiquitin ions ([M + 7H]7+ to
[M + 12H]12+) show substantial variations in both charge
state distributions and ion mobility distributions. Analysis of these
data provides evidence for the existence of five ubiquitin states
in solution: the native N state, favored in solutions of 100:0 to
70:30 water:methanol for the +7 and +8 charge states; the more helical
A state and a new closely related A′ state, favored in solutions
of 70:30 to 5:95 water:methanol for the +9 to +12 charge states; the
unfolded U state, populated in 40:60 to 5:95 water:methanol solutions
for the +8 to +10 and +12 charge states; and a new low-abundance state
termed the B state, observed for 100:0 to 70:30 water:methanol solutions
in the +8 to +10 and +12 charge states. The relative abundances for
different states in different solutions are determined. The analysis
presented here provides insight into how solution structures evolve
into anhydrous conformations and demonstrates the utility of IMS–MS
methods as a means of characterizing populations of conformers for
proteins in solution.
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Affiliation(s)
- Huilin Shi
- Department of Chemistry, Indiana University , 800 Kirkwood Avenue, Bloomington, Indiana 47405, United States
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15
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Mandal M, Mukhopadhyay C. Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin. Phys Chem Chem Phys 2014; 16:21706-16. [DOI: 10.1039/c4cp01657b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
All atom molecular dynamics simulations have been used to explore the atomic detail mechanism of guanidinium induced unfolding of the protein ubiquitin.
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Affiliation(s)
- Manoj Mandal
- Department of Chemistry
- University of Calcutta
- Kolkata – 700 009, India
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16
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Conformer-specific characterization of nonnative protein states using hydrogen exchange and top-down mass spectrometry. Proc Natl Acad Sci U S A 2013; 110:20087-92. [PMID: 24277803 DOI: 10.1073/pnas.1315029110] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Characterization of structure and dynamics of nonnative protein states is important for understanding molecular mechanisms of processes as diverse as folding, binding, aggregation, and enzyme catalysis to name just a few; however, selectively probing local minima within rugged energy landscapes remains a problem. Mass spectrometry (MS) coupled with hydrogen/deuterium exchange (HDX) offers a unique advantage of being able to make a distinction among multiple protein conformers that coexist in solution; however, detailed structural interrogation of such states previously remained out of reach of HDX MS. In this work, we exploited the aforementioned unique feature of HDX MS in combination with the ability of MS to isolate narrow populations of protein ions to characterize individual protein conformers coexisting in solution in equilibrium. Subsequent fragmentation of the protein ions using electron-capture dissociation allowed us to allocate the deuterium distribution along the protein backbone, yielding a backbone-amide protection map for the selected conformer unaffected by contributions from other protein states present in solution. The method was tested with the small regulatory protein ubiquitin (Ub), which is known to form nonnative intermediate states under a variety of mildly denaturing conditions. Protection maps of these intermediate states obtained at residue-level resolution provide clear evidence that they are very similar to the so-called A-state of Ub that is formed in solutions with low pH and high alcohol. Method validation was carried out by comparing the backbone-amide protection map of native Ub with those deduced from high-resolution NMR measurements.
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Kumar TKS, Sivaraman T, Samuel D, Srisailam S, Ganesh G, Hsieh HC, Hung KW, Peng HJ, Ho MC, Arunkumar AI, Yu C. Protein Folding and β-Sheet Proteins. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200000141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Webb IK, Mentinova M, McGee WM, McLuckey SA. Gas-phase intramolecular protein crosslinking via ion/ion reactions: ubiquitin and a homobifunctional sulfo-NHS ester. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:733-43. [PMID: 23463545 PMCID: PMC3644013 DOI: 10.1007/s13361-013-0590-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/18/2012] [Accepted: 01/18/2013] [Indexed: 05/11/2023]
Abstract
Gas-phase intra-molecular crosslinking of protein ubiquitin cations has been demonstrated via ion/ion reactions with anions of a homobifunctional N-hydroxysulfosuccinimide (sulfo-NHS) ester reagent. The ion/ion reaction between multiply-protonated ubiquitin and crosslinker monoanions produces a stable, charge-reduced complex. Covalent crosslinking is indicated by the consecutive loss of 2 molecules of sulfo-NHS under ion trap collisional activation conditions. Covalent modification is verified by the presence of covalently crosslinked sequence ions produced by ion-trap collision-induced dissociation of the ion generated from the losses of sulfo-NHS. Analysis of the crosslinked sequence fragments allows for the localization of crosslinked primary amines, enabling proximity mapping of the gas-phase 3-D structures. The presence of two unprotonated reactive sites within the distance constraint of the crosslinker is required for successful crosslinking. The ability to covalently crosslink is, therefore, sensitive to protein charge state. As the charge state increases, fewer reactive sites are available and protein structure is more likely to become extended because of intramolecular electrostatic repulsion. At high charge states, the reagent shows little evidence for covalent crosslinking but does show evidence for 'electrostatic crosslinking' in that the binding of the sulfonate groups to the protein is sufficiently strong that backbone cleavages are favored over reagent detachment under ion trap collisional activation conditions.
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Shi H, Gu L, Clemmer DE, Robinson RAS. Effects of Fe(II)/H2O2 oxidation on ubiquitin conformers measured by ion mobility-mass spectrometry. J Phys Chem B 2013; 117:164-73. [PMID: 23211023 PMCID: PMC3552375 DOI: 10.1021/jp3099544] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxidative modifications can have significant effects on protein structure in solution. Here, the structures and stabilities of oxidized ubiquitin ions electrosprayed from an aqueous solution (pH 2) are studied by ion mobility spectrometry-mass spectrometry (IMS-MS). IMS-MS has proven to be a valuable technique to assess gas phase and in many cases, solution structures. Herein, in vitro oxidation is performed by Fenton chemistry with Fe(II)/hydrogen peroxide. Most molecules in solution remain unmodified, whereas ∼20% of the population belongs to an M+16 Da oxidized species. Ions of low charge states (+7 and +8) show substantial variance in collision cross section distributions between unmodified and oxidized species. Novel and previously reported gaussian conformers are used to model cross section distributions for +7 and +8 oxidized ubiquitin ions, respectively, in order to correlate variances in observed gas-phase distributions to changes in populations of solution states. Based on gaussian modeling, oxidized ions of charge state +7 have an A-state conformation which is more populated for oxidized relative to unmodified ions. Oxidized ubiquitin ions of charge state +8 have a distribution of conformers arising from native-state ubiquitin and higher intensities of A- and U-state conformers relative to unmodified ions. This work provides evidence that incorporation of a single oxygen atom to ubiquitin leads to destabilization of the native state in an acidic solution (pH ∼2) and to unfolding of gas-phase compact structures.
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Affiliation(s)
- Huilin Shi
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Liqing Gu
- Department of Chemistry, University of Pittsburgh, 200 University Drive, Pittsburgh, PA 15260
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Renã A. S. Robinson
- Department of Chemistry, University of Pittsburgh, 200 University Drive, Pittsburgh, PA 15260
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20
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Abstract
Protein domains are conspicuous structural units in globular proteins, and their identification has been a topic of intense biochemical interest dating back to the earliest crystal structures. Numerous disparate domain identification algorithms have been proposed, all involving some combination of visual intuition and/or structure-based decomposition. Instead, we present a rigorous, thermodynamically-based approach that redefines domains as cooperative chain segments. In greater detail, most small proteins fold with high cooperativity, meaning that the equilibrium population is dominated by completely folded and completely unfolded molecules, with a negligible subpopulation of partially folded intermediates. Here, we redefine structural domains in thermodynamic terms as cooperative folding units, based on m-values, which measure the cooperativity of a protein or its substructures. In our analysis, a domain is equated to a contiguous segment of the folded protein whose m-value is largely unaffected when that segment is excised from its parent structure. Defined in this way, a domain is a self-contained cooperative unit; i.e., its cooperativity depends primarily upon intrasegment interactions, not intersegment interactions. Implementing this concept computationally, the domains in a large representative set of proteins were identified; all exhibit consistency with experimental findings. Specifically, our domain divisions correspond to the experimentally determined equilibrium folding intermediates in a set of nine proteins. The approach was also proofed against a representative set of 71 additional proteins, again with confirmatory results. Our reframed interpretation of a protein domain transforms an indeterminate structural phenomenon into a quantifiable molecular property grounded in solution thermodynamics.
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Shi H, Pierson NA, Valentine SJ, Clemmer DE. Conformation types of ubiquitin [M+8H]8+ Ions from water:methanol solutions: evidence for the N and A States in aqueous solution. J Phys Chem B 2012; 116:3344-52. [PMID: 22315998 PMCID: PMC3351143 DOI: 10.1021/jp210797x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ion mobility and mass spectrometry measurements are used to examine the gas-phase populations of [M+8H](8+) ubiquitin ions formed upon electrospraying 20 different solutions from 100:0 to 5:95 water:methanol that are maintained at pH = 2.0. Over this range of solution conditions, mobility distributions for the +8 charge state show substantial variations. Here we develop a model that treats the combined measurements as one data set. By varying the relative abundances of a discrete set of conformation types, it is possible to represent distributions obtained from any solution. For solutions that favor the well-known A-state ubiquitin, it is possible to represent the gas-phase distributions with seven conformation types. Aqueous conditions that favor the native structure require four more structural types to represent the distribution. This analysis provides the first direct evidence for trace amounts of the A state under native conditions. The method of analysis presented here should help illuminate how solution populations evolve into new gas-phase structures as solvent is removed. Evidence for trace quantities of previously unknown states under native solution conditions may provide insight about the relationship of dynamics to protein function as well as misfolding and aggregation phenomena.
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Affiliation(s)
- Huilin Shi
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Nicholas A. Pierson
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - Stephen J. Valentine
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Ave. Bloomington, IN 47405
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22
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Wyttenbach T, Bowers MT. Structural Stability from Solution to the Gas Phase: Native Solution Structure of Ubiquitin Survives Analysis in a Solvent-Free Ion Mobility–Mass Spectrometry Environment. J Phys Chem B 2011; 115:12266-75. [DOI: 10.1021/jp206867a] [Citation(s) in RCA: 258] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Thomas Wyttenbach
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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23
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Miura Y. NMR studies on thermal stability of α-helix conformation of melittin in pure ethanol and ethanol-water mixture solvents. J Pept Sci 2011; 17:798-804. [DOI: 10.1002/psc.1405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 06/30/2011] [Accepted: 07/14/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Yoshinori Miura
- Center for Advanced Instrumental Analysis; Kyushu University; Kasuga; Japan
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24
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Pasikowski P, Cydzik M, Kluczyk A, Stefanowicz P, Szewczuk Z. Ubiquitin fragments: their known biological activities and putative roles. Biomol Concepts 2010; 1:67-83. [PMID: 25961987 DOI: 10.1515/bmc.2010.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ubiquitin (Ub) is involved in many key processes of cell biology. Identification of compounds that could interfere in the ubiquitination process is of importance. It could be expected that peptides derived from the Ub-binding regions might be able to interact with Ub receptors themselves and modify an ability of the Ub receptors interactions. This review summarizes current knowledge about known Ub-derived peptides and discusses putative activity of unexplored Ub fragments. Among identified biologically active Ub-derived peptides, its decapeptide fragment of the LEDGRTLSDY sequence was found to exhibit strong immunosuppressive effects on the cellular and humoral immune responses, comparable to that of cyclosporine. Some of the Ub fragments possess strong antibacterial and antifungal potency. In the search for new peptides that could interfere in the interaction of Ub with other proteins, we investigated the pentapeptide Ub sequences present in non-ubiquitin proteins. Based on examination of the Swiss-Prot database, we postulated that sequences of some Ub fragments often exist in other protein molecules. However, some of those motives are represented more frequently than others and could be involved in regulation of cellular processes related to Ub.
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25
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Mishra P, Volety S, Rao CM, Prabha CR. Glutamate64 to Glycine Substitution in G1 -bulge of Ubiquitin Impairs Function and Stabilizes Structure of the Protein. J Biochem 2009; 146:563-9. [DOI: 10.1093/jb/mvp106] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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Das A, Mukhopadhyay C. Mechanical unfolding pathway and origin of mechanical stability of proteins of ubiquitin family: An investigation by steered molecular dynamics simulation. Proteins 2009; 75:1024-34. [DOI: 10.1002/prot.22314] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Chung HS, Shandiz A, Sosnick TR, Tokmakoff A. Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding. Biochemistry 2009; 47:13870-7. [PMID: 19053229 DOI: 10.1021/bi801603e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Crucial to revealing mechanistic details of protein folding is a characterization of the transition state ensemble and its structural dynamics. To probe the transition state of ubiquitin thermal unfolding, we examine unfolding dynamics and kinetics of wild-type and mutant ubiquitin using time-resolved nonlinear infrared spectroscopy after a nanosecond temperature jump. We observe spectral changes on two different time scales. A fast nonexponential microsecond phase is attributed to downhill unfolding from the transition state region, which is induced by a shift of the barrier due to the rapid temperature change. Slow millisecond changes arise from thermally activated folding and unfolding kinetics. Mutants that stabilize or destabilize beta strands III-V lead to a decreased or increased amplitude of the microsecond phase, indicating that the disruption or weakening of these strands occurs in the transition state. Unfolding features from microseconds to milliseconds can be explained by temperature-dependent changes of a two-dimensional free energy surface constructed by the native contacts between beta strands of the protein. In addition, the results support the possibility of an intermediate state in thermal unfolding.
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Affiliation(s)
- Hoi Sung Chung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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28
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Kumar D, Chugh J, Sharma S, Hosur RV. Conserved structural and dynamics features in the denatured states of drosophila SUMO, human SUMO and ubiquitin proteins: Implications to sequence-folding paradigm. Proteins 2008; 76:387-402. [DOI: 10.1002/prot.22354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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29
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Chung HS, Tokmakoff A. Temperature-dependent downhill unfolding of ubiquitin. I. Nanosecond-to-millisecond resolved nonlinear infrared spectroscopy. Proteins 2008; 72:474-87. [PMID: 18384151 DOI: 10.1002/prot.22043] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Transient thermal unfolding of ubiquitin is investigated using nonlinear infrared spectroscopy after a nanosecond laser temperature jump (T-jump). The abrupt change in the unfolding free energy surface and the ns time resolution allow us to observe a fast response on ns to micros time-scales, which we attribute to downhill unfolding, before a cross-over to ms kinetics. The downhill unfolding by a sub-population of folded proteins is induced through a shift of the barrier toward the native state. By adjusting the T-jump width, the effect of the initial (T(i)) and final (T(f)) temperature on the unfolding dynamics can be separated. From the amplitude of the fast downhill unfolding, the fractional population prepared at the unfolding transition state is obtained. This population increases with both T(i) and with T(f). A two-state kinetic analysis of the ms refolding provides thermodynamic information about the barrier height. By a combination of the fast and slow unfolding and folding parameters, a quasi-two-state kinetic analysis is performed to calculate the time-dependent population changes of the folded state. This calculation coincides with the experimentally obtained population changes at low temperature but deviations are found in the T-jump from 67 to 78 degrees C. Using temperature-dependent barrier height changes, a temperature Phi value analysis is performed. The result shows a decreasing trend of Phi(T) with temperature, which indicates an increase of the heterogeneity of the transition state. We conclude that ubiquitin unfolds along a well-defined pathway at low temperature which expands with increasing temperature to include multiple routes.
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Affiliation(s)
- Hoi Sung Chung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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30
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Chung HS, Tokmakoff A. Temperature-dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface. Proteins 2008; 72:488-97. [PMID: 18384149 DOI: 10.1002/prot.22042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
To provide evidence for the interpretation of temperature-dependent unfolding kinetics and the downhill unfolding scenario presented in the accompanying experimental article (Part I), the free energy surface of ubiquitin unfolding is calculated using statistical mechanical models of the Muñoz-Eaton (ME) form. The models allow only two states for each amino acid residue, folded or unfolded, and permutations of these states generate an ensemble of microstates. One-dimensional free energy curves are calculated using the number of folded residues as a reaction coordinate. The proposed sequential unfolding of ubiquitin's beta-sheet is tested by mapping the free energy onto two reaction coordinates inspired by the experiment as follows: the number of folded residues in ubiquitin's stable beta-strands I and II and those of the less stable strands III-V. Although the original ME model successfully captures folding features of zipper-like one-dimensional folders, it misses important tertiary interactions between residues that are far from each other in primary sequence. To take tertiary contacts into account, partially folded microstates based on a spherical growth model are included in the calculation and compared with the original model. By calculating the folding probability of each residue for a given point on the free energy surface, the unfolding pathway of ubiquitin is visualized. At low temperature, thermal unfolding occurs along a sequential unfolding pathway as follows: disruption of the beta-strands III-V followed by unfolding of the strands I and II. At high temperature, multiple unfolding routes are formed. The heterogeneity of the transition state explains the global nonexponential unfolding observed in the T-jump experiment at high temperature. The calculation also reports a high stability for the alpha-helix of ubiquitin.
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Affiliation(s)
- Hoi Sung Chung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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31
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Chung HS, Ganim Z, Jones KC, Tokmakoff A. Transient 2D IR spectroscopy of ubiquitin unfolding dynamics. Proc Natl Acad Sci U S A 2007; 104:14237-42. [PMID: 17551015 PMCID: PMC1964855 DOI: 10.1073/pnas.0700959104] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Indexed: 11/18/2022] Open
Abstract
Transient two-dimensional infrared (2D IR) spectroscopy is used as a probe of protein unfolding dynamics in a direct comparison of fast unfolding experiments with molecular dynamics simulations. In the experiments, the unfolding of ubiquitin is initiated by a laser temperature jump, and protein structural evolution from nanoseconds to milliseconds is probed using amide I 2D IR spectroscopy. The temperature jump prepares a subensemble near the unfolding transition state, leading to quasi-barrierless unfolding (the "burst phase") before the millisecond activated unfolding kinetics. The burst phase unfolding of ubiquitin is characterized by a loss of the coupling between vibrations of the beta-sheet, a process that manifests itself in the 2D IR spectrum as a frequency blue-shift and intensity decrease of the diagonal and cross-peaks of the sheet's two IR active modes. As the sheet unfolds, increased fluctuations and solvent exposure of the beta-sheet amide groups are also characterized by increases in homogeneous linewidth. Experimental spectra are compared with 2D IR spectra calculated from the time-evolving structures in a molecular dynamics simulation of ubiquitin unfolding. Unfolding is described as a sequential unfolding of strands in ubiquitin's beta-sheet, using two collective coordinates of the sheet: (i) the native interstrand contacts between adjacent beta-strands I and II and (ii) the remaining beta-strand contacts within the sheet. The methods used illustrate the general principles by which 2D IR spectroscopy can be used for detailed dynamical comparisons of experiment and simulation.
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Affiliation(s)
- Hoi Sung Chung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ziad Ganim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kevin C. Jones
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Andrei Tokmakoff
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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32
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Kony DB, Hünenberger PH, van Gunsteren WF. Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics. Protein Sci 2007; 16:1101-18. [PMID: 17525462 PMCID: PMC2206653 DOI: 10.1110/ps.062323407] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A series of explicit-solvent molecular dynamics simulations of the protein ubiquitin are reported, which investigate the effect of environmental factors (presence of methanol cosolvent in the aqueous solution, neutral or low pH value, room or elevated temperature) on the structure, stability, and dynamics of the protein. The simulations are initiated either from the native structure of the protein or from a model of a partially folded state (A-state) that is known to exist at low pH in methanol-water mixtures. The main results of the simulations are: (1) The ubiquitin native structure is remarkably stable at neutral pH in water; (2) the addition of the methanol cosolvent enhances the stability of the secondary structure but weakens tertiary interactions within the protein; (3) this influence of methanol on the protein structure is enhanced at low pH, while the effect of lowering the pH in pure water is limited; and (4) the A-state of ubiquitin can be described as a set of relatively rigid secondary structure elements (a native-like beta-sheet and native-like alpha-helix plus two nonnative alpha-helices) connected by flexible linkers.
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Affiliation(s)
- David B Kony
- Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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33
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Collins ES, Wirmer J, Hirai K, Tachibana H, Segawa SI, Dobson CM, Schwalbe H. Characterisation of disulfide-bond dynamics in non-native states of lysozyme and its disulfide deletion mutants by NMR. Chembiochem 2006; 6:1619-27. [PMID: 16138305 DOI: 10.1002/cbic.200500196] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This report describes NMR-spectroscopic investigations of the conformational dynamics of disulfide bonds in hen-egg-white lysozyme substitution mutants. The following four systems have been investigated: 2SS(alpha), a lysozyme variant that contains C64A, C76A, C80A and C94A substitutions, was studied in water at pH 2 and 3.8 and in urea (8 M, pH 2); 2SS(beta) lysozyme, which has C6S, C30A, C115A and C127A substitutions, was studied in water (pH 2) and urea (8 M, pH 2). The NMR analysis of heteronuclear 15N-relaxation rates shows that the barrier to disulfide-bond isomerisation can vary substantially in different lysozyme mutants and depends on the residual structure present in these states. The investigations reveal cooperativity in the modulation of micro- to millisecond dynamics that is due to the presence of multiple disulfide bridges in lysozyme. Mutation of cysteines in one of the two structural domains substantially diminishes the barrier to rotational isomerisation in the other domain. However, the interactions between hydrophobic clusters within and across the domains remains intact.
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Affiliation(s)
- Emily S Collins
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
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34
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Dastidar SG, Mukhopadhyay C. Unfolding dynamics of the protein ubiquitin: insight from simulation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2005; 72:051928. [PMID: 16383666 DOI: 10.1103/physreve.72.051928] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Indexed: 05/05/2023]
Abstract
The temperature-induced unfolding pathway of ubiquitin has been investigated by molecular dynamics simulation at four different temperatures. It has been observed that the sequences of the unfolding events are same at all the temperatures. However, the time scale of the dynamics at different temperatures are different. The transition states at various temperatures also possess similar secondary structural elements. The intermediate conformations visited by the protein at different temperatures can help determination of the transition states. The well known " state" of ubiquitin, hitherto found to be stable only in methanol water mixture, have been observed to be a common transient intermediate conformation in the unfolding path of the protein in water. Our observation about the similarities of the unfolding process at different temperatures strongly recommend for a defined pathway for the unfolding process.
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Affiliation(s)
- Shubhra Ghosh Dastidar
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata-700 009, India
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35
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Kumar Y, Muzammil S, Tayyab S. Influence of Fluoro, Chloro and Alkyl Alcohols on the Folding Pathway of Human Serum Albumin. ACTA ACUST UNITED AC 2005; 138:335-41. [PMID: 16272127 DOI: 10.1093/jb/mvi131] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Urea-induced equilibrium unfolding of human serum albumin (HSA) when studied by mean residue ellipticity at 222 nm (MRE(222)) or intrinsic fluorescence measurements showed a two-step, three-state transition with a stable intermediate around 4.6-5.2 M urea. The presence of 2,2,2-trifluoroethanol (TFE) resulted in a single-step, two-state transition with a significant shift towards higher urea concentration, suggesting the stabilizing effect of TFE. The free energy of stabilization (DeltaDeltaG(D)(H(2)O)) in the presence of 3.0 M TFE was determined to be 2.68 and 2.72 kcal/mol by MRE(222) and fluorescence measurements, respectively. The stabilizing potential of other alcohols on the refolding behavior of HSA at 5.0 M urea (where the intermediate exists) as studied by MRE(222) and intrinsic fluorescence measurements showed the following order: 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) > TFE > 2-chloroethanol > tert-butanol > iso-propanol > ethanol > methanol. Further, the extent of refolding at the highest concentration of alcohol was similar in all cases. The stabilizing effect of TFE on guanidine hydrochloride (GdnHCl)-induced unfolding of HSA was nearly equal to that found for urea denaturation, as reflected in the DeltaDeltaG(D)(H(2)O) value (2.38 kcal/mol). Taken together, these results suggest that the stabilizing effect of TFE and other alcohols on urea/GdnHCl-induced unfolding of HSA is higher for alcohols that contain bulky groups or fluorine atoms.
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Affiliation(s)
- Yogesh Kumar
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India
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36
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Chung HS, Khalil M, Smith AW, Ganim Z, Tokmakoff A. Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin. Proc Natl Acad Sci U S A 2005; 102:612-7. [PMID: 15630083 PMCID: PMC545570 DOI: 10.1073/pnas.0408646102] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Steady-state and transient conformational changes upon the thermal unfolding of ubiquitin were investigated with nonlinear IR spectroscopy of the amide I vibrations. Equilibrium temperature-dependent 2D IR spectroscopy reveals the unfolding of the beta-sheet of ubiquitin through the loss of cross peaks formed between transitions arising from delocalized vibrations of the beta-sheet. Transient unfolding after a nanosecond temperature jump is monitored with dispersed vibrational echo spectroscopy, a projection of the 2D IR spectrum. Whereas the equilibrium study follows a simple two-state unfolding, the transient experiments observe complex relaxation behavior that differs for various spectral components and spans 6 decades in time. The transient behavior can be separated into fast and slow time scales. From 100 ns to 0.5 ms, the spectral features associated with beta-sheet unfolding relax in a sequential, nonexponential manner, with time constants of 3 micros and 80 micros. By modeling the amide I vibrations of ubiquitin, this observation is explained as unfolding of the less stable strands III-V of the beta-sheet before unfolding of the hairpin that forms part of the hydrophobic core. This downhill unfolding is followed by exponential barrier-crossing kinetics on a 3-ms time scale.
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Affiliation(s)
- Hoi Sung Chung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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37
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Affiliation(s)
- H Jane Dyson
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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38
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Brüschweiler R. Efficient RMSD measures for the comparison of two molecular ensembles. Root-mean-square deviation. Proteins 2003; 50:26-34. [PMID: 12471596 DOI: 10.1002/prot.10250] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Quantitative measures are presented for comparing the conformations of two molecular ensembles. The measures are based on Kabsch's formula for the root-mean-square deviation (RMSD) and the covariance matrix of atomic positions of isotropically distributed ensembles (IDE). By using a Taylor series expansion, it is shown that the RMSD can be expressed solely in terms of the IDE matrices. A fast approximate method is introduced for the pairwise RMSD determination whose computational cost scales linearly with the number of structures. A similarity measure for two structural ensembles that is based on the trace metric of the differences of powers of the IDE matrices is presented. The measures are illustrated for conformational ensembles generated by a molecular dynamics computer simulation of a partially folded A-state analog of ubiquitin.
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Affiliation(s)
- Rafael Brüschweiler
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610-1477, USA.
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39
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Sorenson JM, Head-Gordon T. Toward minimalist models of larger proteins: A ubiquitin-like protein. Proteins 2002. [DOI: 10.1002/prot.1174] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Prompers JJ, Brüschweiler R. Dynamic and structural analysis of isotropically distributed molecular ensembles. Proteins 2002; 46:177-89. [PMID: 11807946 DOI: 10.1002/prot.10025] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An efficient new method is presented for the characterization of motional correlations derived from a set of protein structures without requiring the separation of overall and internal motion. In this method, termed isotropically distributed ensemble (IDE) analysis, each structure is represented by an ensemble of isotropically distributed replicas corresponding to the situation found in an isotropic protein solution. This leads to a covariance matrix of the cartesian atomic positions with elements proportional to the ensemble average of scalar products of the position vectors with respect to the center of mass. Diagonalization of the covariance matrix yields eigenmodes and amplitudes that describe concerted motions of atoms, including overall rotational and intramolecular dynamics. It is demonstrated that this covariance matrix naturally distinguishes between "rigid" and "mobile" parts without necessitating a priori selection of a reference structure and an atom set for the orientational alignment process. The method was applied to the analysis of a 5-ns molecular dynamics trajectory of native ubiquitin and a 40-ns trajectory of a partially folded state of ubiquitin. The results were compared with essential dynamics analysis. By taking advantage of the spherical symmetry of the IDE covariance matrix, more than a 10-fold speed up is achieved for the computation of eigenmodes and mode amplitudes. IDE analysis is particularly suitable for studying the correlated dynamics of flexible and large molecules.
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Affiliation(s)
- Jeanine J Prompers
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610-1477, USA
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41
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Bolton D, Evans PA, Stott K, Broadhurst RW. Structure and properties of a dimeric N-terminal fragment of human ubiquitin. J Mol Biol 2001; 314:773-87. [PMID: 11733996 DOI: 10.1006/jmbi.2001.5181] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Previous peptide dissection and kinetic experiments have indicated that in vitro folding of ubiquitin may proceed via transient species in which native-like structure has been acquired in the first 45 residues. A peptide fragment, UQ(1-51), encompassing residues 1 to 51 of ubiquitin was produced in order to test whether this portion has propensity for independent self-assembly. Surprisingly, the construct formed a folded symmetrical dimer that was stabilised by 0.8 M sodium sulphate at 298 K (the S state). The solution structure of the UQ(1-51) dimer was determined by multinuclear NMR spectroscopy. Each subunit of UQ(1-51) consists of an N-terminal beta-hairpin followed by an alpha-helix and a final beta-strand, with orientations similar to intact ubiquitin. The dimer is formed by the third beta-strand of one subunit interleaving between the hairpin and third strand of the other to give a six-stranded beta-sheet, with the two alpha-helices sitting on top. The helix-helix and strand portions of the dimer interface also mimic related features in the structure of ubiquitin. The structural specificity of the UQ(1-51) peptide is tuneable: as the concentration of sodium sulphate is decreased, near-native alternative conformations are populated in slow chemical exchange. Magnetization transfer experiments were performed to characterize the various species present in 0.35 M sodium sulphate, namely the S state and two minor forms. Chemical shift differences suggest that one minor form is very similar to the S state, while the other experiences a significant conformational change in the third strand. A segmental rearrangement of the third strand in one subunit of the S state would render the dimer asymmetric, accounting for most of our results. Similar small-scale transitions in proteins are often invoked to explain solvent exchange at backbone amide proton sites that have an intermediate level of protection.
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Affiliation(s)
- D Bolton
- Cambridge Centre for Molecular Recognition Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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42
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Prompers JJ, Scheurer C, Brüschweiler R. Characterization of NMR relaxation-active motions of a partially folded A-state analogue of ubiquitin. J Mol Biol 2001; 305:1085-97. [PMID: 11162116 DOI: 10.1006/jmbi.2000.4353] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The dominant dynamics of a partially folded A-state analogue of ubiquitin that give rise to NMR 15N spin relaxation have been investigated using molecular dynamics (MD) computer simulations and reorientational quasiharmonic analysis. Starting from the X-ray structure of native ubiquitin with a protonation state corresponding to a low pH, the A-state analogue was generated by a MD simulation of a total length of 33 ns in a 60%/40% methanol/water mixture using a variable temperature scheme to control and speed up the structural transformation. The N-terminal half of the A-state analogue consists of loosely coupled native-like secondary structural elements, while the C-terminal half is mostly irregular in structure. Analysis of dipolar N-H backbone correlation functions reveals reorientational amplitudes and time-scale distributions that are comparable to those observed experimentally. Thus, the trajectory provides a realistic picture of a partially folded protein that can be used for gaining a better understanding of the various types of reorientational motions that are manifested in spin-relaxation parameters of partially folded systems. For this purpose, a reorientational quasiharmonic reorientational analysis was performed on the final 5 ns of the trajectory of the A-state analogue, and for comparison on a 5 ns trajectory of native ubiquitin. The largest amplitude reorientational modes show a markedly distinct behavior for the two states. While for native ubiquitin, such motions have a more local character involving loops and the C-terminal end of the polypeptide chain, the A-state analogue shows highly collective motions in the nanosecond time-scale range corresponding to larger-scale movements between different segments. Changes in reorientational backbone entropy between the A-state analogue and the native state of ubiquitin, which were computed from the reorientational quasiharmonic analyses, are found to depend significantly on motional correlation effects.
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Affiliation(s)
- J J Prompers
- Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA 01610, USA
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43
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Abstract
The location of protein subunits that form early during folding, constituted of consecutive secondary structure elements with some intrinsic stability and favorable tertiary interactions, is predicted using a combination of threading algorithms and local structure prediction methods. Two folding units are selected among the candidates identified in a database of known protein structures: the fragment 15-55 of 434 cro, an all-alpha protein, and the fragment 1-35 of ubiquitin, an alpha/beta protein. These units are further analyzed by means of Monte Carlo simulated annealing using several database-derived potentials describing different types of interactions. Our results suggest that the local interactions along the chain dominate in the first folding steps of both fragments, and that the formation of some of the secondary structures necessarily occurs before structure compaction. These findings led us to define a prediction protocol, which is efficient to improve the accuracy of the predicted structures. It involves a first simulation with a local interaction potential only, whose final conformation is used as a starting structure of a second simulation that uses a combination of local interaction and distance potentials. The root mean square deviations between the coordinates of predicted and native structures are as low as 2-4 A in most trials. The possibility of extending this protocol to the prediction of full proteins is discussed. Proteins 2001;42:164-176.
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Affiliation(s)
- D Gilis
- Ingénierie Biomoléculaire, Université Libre de Bruxelles, Bruxelles, Belgium.
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44
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Zerella R, Chen PY, Evans PA, Raine A, Williams DH. Structural characterization of a mutant peptide derived from ubiquitin: implications for protein folding. Protein Sci 2000; 9:2142-50. [PMID: 11152124 PMCID: PMC2144502 DOI: 10.1110/ps.9.11.2142] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The formation of the N-terminal beta-hairpin of ubiquitin is thought to be an early event in the folding of this small protein. Previously, we have shown that a peptide corresponding to residues 1-17 of ubiquitin folds autonomously and is likely to have a native-like hairpin register. To investigate the causes of the stability of this fold, we have made mutations in the amino acids at the apex of the turn. We find that in a peptide where Thr9 is replaced by Asp, U(1-17)T9D, the native conformation is stabilized with respect to the wild-type sequence, so much so that we are able to characterize the structure of the mutant peptide fully by NMR spectroscopy. The data indicate that U(1-17)T9D peptide does indeed form a hairpin with a native-like register and a type I turn with a G1 beta-bulge, as in the full-length protein. The reason for the greater stability of the U(1-17)T9D mutant remains uncertain, but there are nuclear Overhauser effects between the side chains of Asp9 and Lys 11, which may indicate that a charge-charge interaction between these residues is responsible.
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Affiliation(s)
- R Zerella
- Cambridge Centre for Molecular Recognition and University Chemical Laboratory, United Kingdom
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45
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Johnson EC, Lazar GA, Desjarlais JR, Handel TM. Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin. Structure 1999; 7:967-76. [PMID: 10467150 DOI: 10.1016/s0969-2126(99)80123-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND The recent merger of computation and protein design has resulted in a burst of success in the generation of novel proteins with native-like properties. A critical component of this coupling between theory and experiment is a detailed analysis of the structures and stabilities of designed proteins to assess and improve the accuracy of design algorithms. RESULTS Here we report the solution structure of a hydrophobic core variant of ubiquitin, referred to as 1D7, which was designed with the core-repacking algorithm ROC. As a measure of conformational specificity, we also present amide exchange protection factors and backbone and sidechain dynamics. The results indicate that 1D7 is similar to wild-type (WT) ubiquitin in backbone structure and degree of conformational specificity. We also observe a good correlation between experimentally determined sidechain structures and those predicted by ROC. However, evaluation of the core sidechain conformations indicates that, in general, 1D7 has more sidechains in less statistically favorable conformations than WT. CONCLUSIONS Our results provide an explanation for the lower stability of 1D7 compared to WT, and suggest modifications to design algorithms that may improve the accuracy with which structure and stability are predicted. The results also demonstrate that core packing can affect conformational flexibility in subtle ways that are likely to be important for the design of function and protein-ligand interactions.
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Affiliation(s)
- E C Johnson
- Department of Physics, University of California, Berkeley 94720, USA
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46
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Abstract
A database of hydrogen-deuterium exchange results has been compiled for proteins for which there are published rates of out-exchange in the native state, protection against exchange during folding, and out-exchange in partially folded forms. The question of whether the slow exchange core is the folding core (Woodward C, 1993, Trends Biochem Sci 18:359-360) is reexamined in a detailed comparison of the specific amide protons (NHs) and the elements of secondary structure on which they are located. For each pulsed exchange or competition experiment, probe NHs are shown explicitly; the large number and broad distribution of probe NHs support the validity of comparing out-exchange with pulsed-exchange/competition experiments. There is a strong tendency for the same elements of secondary structure to carry NHs most protected in the native state, NHs first protected during folding, and NHs most protected in partially folded species. There is not a one-to-one correspondence of individual NHs. Proteins for which there are published data for native state out-exchange and theta values are also reviewed. The elements of secondary structure containing the slowest exchanging NHs in native proteins tend to contain side chains with high theta values or be connected to a turn/loop with high theta values. A definition for a protein core is proposed, and the implications for protein folding are discussed. Apparently, during folding and in the native state, nonlocal interactions between core sequences are favored more than other possible nonlocal interactions. Other studies of partially folded bovine pancreatic trypsin inhibitor (Barbar E, Barany G, Woodward C, 1995, Biochemistry 34:11423-11434; Barber E, Hare M, Daragan V, Barany G, Woodward C, 1998, Biochemistry 37:7822-7833), suggest that developing cores have site-specific energy barriers between microstates, one disordered, and the other(s) more ordered.
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Affiliation(s)
- R Li
- Department of Biochemistry, University of Minnesota, St. Paul 55108, USA
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47
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Zerella R, Evans PA, Ionides JM, Packman LC, Trotter BW, Mackay JP, Williams DH. Autonomous folding of a peptide corresponding to the N-terminal beta-hairpin from ubiquitin. Protein Sci 1999; 8:1320-31. [PMID: 10386882 PMCID: PMC2144356 DOI: 10.1110/ps.8.6.1320] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The N-terminal 17 residues of ubiquitin have been shown by 1H NMR to fold autonomously into a beta-hairpin structure in aqueous solution. This structure has a specific, native-like register, though side-chain contacts differ in detail from those observed in the intact protein. An autonomously folding hairpin has previously been identified in the case of streptococcal protein G, which is structurally homologous with ubiquitin, but remarkably, the two are not in topologically equivalent positions in the fold. This suggests that the organization of folding may be quite different for proteins sharing similar tertiary structures. Two smaller peptides have also been studied, corresponding to the isolated arms of the N-terminal hairpin of ubiquitin, and significant differences from simple random coil predictions observed in the spectra of these subfragments, suggestive of significant limitation of the backbone conformational space sampled, presumably as a consequence of the strongly beta-structure favoring composition of the sequences. This illustrates the ability of local sequence elements to express a propensity for beta-structure even in the absence of actual sheet formation. Attempts were made to estimate the population of the folded state of the hairpin, in terms of a simple two-state folding model. Using published "random coil" values to model the unfolded state, and values derived from native ubiquitin for the putative unique, folded state, it was found that the apparent population varied widely for different residues and with different NMR parameters. Use of the spectra of the subfragment peptides to provide a more realistic model of the unfolded state led to better agreement in the estimates that could be obtained from chemical shift and coupling constant measurements, while making it clear that some other approaches to population estimation could not give meaningful results, because of the tendency to populate the beta-region of conformational space even in the absence of the hairpin structure.
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Affiliation(s)
- R Zerella
- Cambridge Centre for Molecular Recognition and University Chemical Laboratory, United Kingdom
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48
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Konermann L, Douglas DJ. Unfolding of proteins monitored by electrospray ionization mass spectrometry: a comparison of positive and negative ion modes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 1998; 9:1248-1254. [PMID: 9835071 DOI: 10.1016/s1044-0305(98)00103-2] [Citation(s) in RCA: 149] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Electrospray ionization (ESI) mass spectrometry (MS) in both the positive and negative ion mode has been used to study protein unfolding transitions of lysozyme, cytochrome c (cyt c), and ubiquitin in solution. As expected, ESI of unfolded lysozyme leads to the formation of substantially higher charge states than the tightly folded protein in both modes of operation. Surprisingly, the acid-induced unfolding of cyt c as well as the acid and the base-induced unfolding of ubiquitin show different behavior: In these three cases protein unfolding only leads to marginal changes in the negative ion charge state distributions, whereas in the positive ion mode pronounced shifts to higher charge states are observed. This shows that ESI MS in the negative ion mode as a method for probing conformational changes of proteins in solution should be treated with caution. The data presented in this work provide further evidence that the conformation of a protein in solution not its charge state is the predominant factor for determining the ESI charge state distribution in the positive ion mode. Furthermore, these data support the hypothesis of a recent study (Konermann and Douglas, Biochemistry 1997, 36, 12,296-12,302) which suggested that ESI in the positive ion mode is not sensitive to changes in the secondary structure of proteins but only to changes in the tertiary structure.
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Affiliation(s)
- L Konermann
- Department of Chemistry, University of British Columbia, Vancouver, Canada. konerman@
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49
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Michnick SW, Shakhnovich E. A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies. FOLDING & DESIGN 1998; 3:239-51. [PMID: 9710570 DOI: 10.1016/s1359-0278(98)00035-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Nucleation-growth theory predicts that fast-folding peptide sequences fold to their native structure via structures in a transition-state ensemble that share a small number of native contacts (the folding nucleus). Experimental and theoretical studies of proteins suggest that residues participating in folding nuclei are conserved among homologs. We attempted to determine if this is true in proteins with highly diverged sequences but identical folds (superfamilies). RESULTS We describe a strategy based on comparisons of residue conservation in natural superfamily sequences with simulated sequences (generated with a Monte-Carlo sequence design strategy) for the same proteins. The basic assumptions of the strategy were that natural sequences will conserve residues needed for folding and stability plus function, the simulated sequences contain no functional conservation, and nucleus residues make native contacts with each other. Based on these assumptions, we identified seven potential nucleus residues in ubiquitin superfamily members. Non-nucleus conserved residues were also identified; these are proposed to be involved in stabilizing native interactions. We found that all superfamily members conserved the same potential nucleus residue positions, except those for which the structural topology is significantly different. CONCLUSIONS Our results suggest that the conservation of the nucleus of a specific fold can be predicted by comparing designed simulated sequences with natural highly diverged sequences that fold to the same structure. We suggest that such a strategy could be used to help plan protein folding and design experiments, to identify new superfamily members, and to subdivide superfamilies further into classes having a similar folding mechanism.
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Affiliation(s)
- S W Michnick
- Département de biochime, Université de Montréal, Quebec.
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50
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