1
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Walker TE, Shirzadeh M, Sun HM, McCabe JW, Roth A, Moghadamchargari Z, Clemmer DE, Laganowsky A, Rye H, Russell DH. Temperature Regulates Stability, Ligand Binding (Mg 2+ and ATP), and Stoichiometry of GroEL-GroES Complexes. J Am Chem Soc 2022; 144:2667-2678. [PMID: 35107280 PMCID: PMC8939001 DOI: 10.1021/jacs.1c11341] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chaperonins are nanomachines that harness ATP hydrolysis to power and catalyze protein folding, a chemical action that is directly linked to the maintenance of cell function through protein folding/refolding and assembly. GroEL and the GroEL-GroES complex are archetypal examples of such protein folding machines. Here, variable-temperature electrospray ionization (vT-ESI) native mass spectrometry is used to delineate the effects of solution temperature and ATP concentrations on the stabilities of GroEL and GroEL-GroES complexes. The results show clear evidence for destabilization of both GroEL14 and GroES7 at temperatures of 50 and 45 °C, respectively, substantially below the previously reported melting temperature (Tm ∼ 70 °C). This destabilization is accompanied by temperature-dependent reaction products that have previously unreported stoichiometries, viz. GroEL14-GroESy-ATPn, where y = 1, 2, 8 and n = 0, 1, 2, 8, that are also dependent on Mg2+ and ATP concentrations. Variable-temperature native mass spectrometry reveals new insights about the stability of GroEL in response to temperature effects: (i) temperature-dependent ATP binding to GroEL; (ii) effects of temperature as well as Mg2+ and ATP concentrations on the stoichiometry of the GroEL-GroES complex, with Mg2+ showing greater effects compared to ATP; and (iii) a change in the temperature-dependent stoichiometries of the GroEL-GroES complex (GroEL14-GroES7 vs GroEL14-GroES8) between 24 and 40 °C. The similarities between results obtained by using native MS and cryo-EM [Clare et al. An expanded protein folding cage in the GroEL-gp31 complex. J. Mol. Biol. 2006, 358, 905-911; Ranson et al. Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes.Nat. Struct. Mol. Biol. 2006, 13, 147-152] underscore the utility of native MS for investigations of molecular machines as well as identification of key intermediates involved in the chaperonin-assisted protein folding cycle.
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Affiliation(s)
- Thomas E. Walker
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - He Mirabel Sun
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jacob W. McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Andrew Roth
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Zahra Moghadamchargari
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hays Rye
- Department of Biochemistry and Biophysics, 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
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2
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Jaswal SS. Lessons from a quarter century of being human in protein science. Protein Sci 2022; 31:768-783. [PMID: 35048424 PMCID: PMC8927861 DOI: 10.1002/pro.4278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 11/05/2022]
Abstract
Over the past quarter century, my engagement with the protein society has allowed me to witness first-hand the evolution of our deepening understanding of the complexity of protein folding landscapes. During my own evolution as a protein scientist, my passion for protein folding has deepened into an obsession with mapping and decoding the thermodynamic and kinetic secrets of protein landscapes - especially those of rebel proteins, whose "non-traditional" behavior has challenged our paradigms and inspired the expansion of our models and methods. It is perhaps not surprising that I see parallels in the evolution of the landscape framework and in the development of our own trajectories as humans in STEM. Just as with proteins however, we need to recognize that our individual human landscapes are not isolated from our local departmental and institutional communities, and are integrated into the larger networks of our STEM disciplines, academia, industry and/or government, not to mention society. My experience with hundreds of participants in the Being Human in STEM initiative that Amherst College undergraduates and I co-founded in 2016 has helped me find hope for STEM and humanity. If we commit to reconciling our identities as scientists with our responsibilities as human beings, together we can accelerate the evolution of individual, community and societal landscapes to contribute to addressing the dire challenges facing our planet. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sheila S Jaswal
- Department of Chemistry, and Program in Biochemistry & Biophysics Amherst College
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3
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Abstract
Molecular chaperones are the guardians of the proteome inside the cell. Chaperones recognize and bind unfolded or misfolded substrates, thereby preventing further aggregation; promoting correct protein folding; and, in some instances, even disaggregating already formed aggregates. Chaperones perform their function by means of an array of weak protein-protein interactions that take place over a wide range of timescales and are therefore invisible to structural techniques dependent upon the availability of highly homogeneous samples. Nuclear magnetic resonance (NMR) spectroscopy, however, is ideally suited to study dynamic, rapidly interconverting conformational states and protein-protein interactions in solution, even if these involve a high-molecular-weight component. In this review, we give a brief overview of the principles used by chaperones to bind their client proteins and describe NMR methods that have emerged as valuable tools to probe chaperone-substrate and chaperone-chaperone interactions. We then focus on a few systems for which the application of these methods has greatly increased our understanding of the mechanisms underlying chaperone functions. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom;
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA;
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4
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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5
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Ando T, Jongruja N, Okumura N, Morikawa K, Kanaya S, Takao T. Identification of the ternary complex of ribonuclease HI:RNA/DNA hybrid:metal ions by ESI mass spectrometry. J Biol Chem 2021; 296:100462. [PMID: 33639158 PMCID: PMC8042393 DOI: 10.1016/j.jbc.2021.100462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/14/2021] [Accepted: 02/23/2021] [Indexed: 12/17/2022] Open
Abstract
Ribonuclease HI, an endoribonuclease, catalyzes the hydrolysis of the RNA strand of an RNA/DNA hybrid and requires divalent metal ions for its enzymatic activity. However, the mechanistic details of the activity of ribonuclease HI and its interaction with divalent metal ions remain unclear. In this study, we performed real-time monitoring of the enzyme–substrate complex in the presence of divalent metal ions (Mn2+ or Zn2+) using electrospray ionization–mass spectrometry (ESI-MS). The findings provide clear evidence that the enzymatic activity of the ternary complex requires the binding of two divalent metal ions. The Zn2+ ions bind to both the enzyme itself and the enzyme:substrate complex more strongly than Mn2+ ions, and gives, in part, the ternary complex, [RNase HI:nicked RNA/DNA hybrid:2Zn2+], suggesting that the ternary complex is retained, even after the hydrolysis of the substrate. The collective results presented herein shed new light on the essential role of divalent metal ions in the activity of ribonuclease HI and demonstrate how Zn2+ ions confer inhibitory properties on the activity of this enzyme by forming a highly stable complex with the substrate.
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Affiliation(s)
- Tomoshige Ando
- Institute for Protein Research, Osaka University, Osaka, Japan
| | | | - Nobuaki Okumura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kosuke Morikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | - Toshifumi Takao
- Institute for Protein Research, Osaka University, Osaka, Japan.
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Robinson CV. Christopher Dobson, 1949-2019: Mentor, Friend, Scientist Extraordinaire. Annu Rev Biochem 2020; 89:1-19. [PMID: 32343910 DOI: 10.1146/annurev-biochem-011520-105226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is impossible to do justice in one review article to a researcher of the stature of Christopher Dobson. His career spanned almost five decades, resulting in more than 870 publications and a legacy that will continue to influence the lives of many for decades to come. In this review, I have attempted to capture Chris's major contributions: his early work, dedicated to understanding protein-folding mechanisms; his collaborative work with physicists to understand the process of protein aggregation; and finally, his later career in which he developed strategies to prevent misfolding. However, it is not only this body of work but also the man himself who inspired an entire generation of scientists through his patience, ability to mentor, and innate generosity. These qualities remain a hallmark of the way in which he conducted his research-research that will leave a lasting imprint on science.
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Affiliation(s)
- Carol V Robinson
- Department of Physical and Theoretical Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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7
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Singh AK, Balchin D, Imamoglu R, Hayer-Hartl M, Hartl FU. Efficient Catalysis of Protein Folding by GroEL/ES of the Obligate Chaperonin Substrate MetF. J Mol Biol 2020; 432:2304-2318. [PMID: 32135190 DOI: 10.1016/j.jmb.2020.02.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 11/16/2022]
Abstract
The cylindrical chaperonin GroEL and its cofactor GroES mediate ATP-dependent protein folding in Escherichia coli by transiently encapsulating non-native substrate in a nano-cage formed by the GroEL ring cavity and the lid-shaped GroES. Mechanistic studies of GroEL/ES with heterologous protein substrates suggested that the chaperonin is inefficient, typically requiring multiple ATP-dependent encapsulation cycles with only a few percent of protein folded per cycle. Here we analyzed the spontaneous and chaperonin-assisted folding of the essential enzyme 5,10-methylenetetrahydrofolate reductase (MetF) of E. coli, an obligate GroEL/ES substrate. We found that MetF, a homotetramer of 33-kDa subunits with (β/α)8 TIM-barrel fold, populates a kinetically trapped folding intermediate(s) (MetF-I) upon dilution from denaturant that fails to convert to the native state, even in the absence of aggregation. GroEL/ES recognizes MetF-I and catalyzes rapid folding, with ~50% of protein folded in a single round of encapsulation. Analysis by hydrogen/deuterium exchange at peptide resolution showed that the MetF subunit folds to completion in the GroEL/ES nano-cage and binds its cofactor flavin adenine dinucleotide. Rapid folding required the net negative charge character of the wall of the chaperonin cavity. These findings reveal a remarkable capacity of GroEL/ES to catalyze folding of an endogenous substrate protein that would have coevolved with the chaperonin system.
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Affiliation(s)
- Amit K Singh
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany
| | - David Balchin
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany
| | - Rahmi Imamoglu
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany.
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8
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Abstract
This chronologue seeks to document the discovery and development of an understanding of oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell. It provides detail regarding genetic, physiologic, biochemical, and biophysical studies of these ATP-utilizing machines from both in vivo and in vitro observations. The chronologue is organized into various topics of physiology and mechanism, for each of which a chronologic order is generally followed. The text is liberally illustrated to provide firsthand inspection of the key pieces of experimental data that propelled this field. Because of the length and depth of this piece, the use of the outline as a guide for selected reading is encouraged, but it should also be of help in pursuing the text in direct order.
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9
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Georgescauld F, Wales TE, Engen JR. Hydrogen deuterium exchange mass spectrometry applied to chaperones and chaperone-assisted protein folding. Expert Rev Proteomics 2019; 16:613-625. [DOI: 10.1080/14789450.2019.1633920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Florian Georgescauld
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Institut de Biologie Physico-Chimique, Paris, France
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
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10
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Viegas J. Profile of Dame Carol Robinson. Proc Natl Acad Sci U S A 2019; 116:7608-7610. [DOI: 10.1073/pnas.1903862116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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11
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Rath P, Sharpe T, Kohl B, Hiller S. Two‐State Folding of the Outer Membrane Protein X into a Lipid Bilayer Membrane. Angew Chem Int Ed Engl 2019; 58:2665-2669. [DOI: 10.1002/anie.201812321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/17/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Parthasarathi Rath
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Timothy Sharpe
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Bastian Kohl
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Sebastian Hiller
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
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12
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Affiliation(s)
- Parthasarathi Rath
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Timothy Sharpe
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Bastian Kohl
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
| | - Sebastian Hiller
- BiozentrumUniversity of Basel Klingenbergstrasse 70 4056 Basel Switzerland
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13
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Abstract
Following initial discoveries of noncovalent associations surviving in the gas phase, only a few practitioners pursued this research area. Today scientists around the world are using these approaches to ascertain the heterogeneity and stoichiometry of proteins within complexes. Recent developments further highlight opportunities for studying the effects of protein glycosylation on antibody–antigen interactions and drug binding, as well as site-directed mutagenesis and posttranslational modification on membrane protein interfaces. As a result of many developments over the last two decades, mass spectrometry of protein complexes has exploded and is now undertaken not just in dedicated research laboratories in academia, but also in pharmaceutical and biotechnology companies. It is therefore timely to trace the history of these developments in this personal perspective. In this Inaugural Article, I trace some key steps that have enabled the development of mass spectrometry for the study of intact protein complexes from a variety of cellular environments. Beginning with the preservation of the first soluble complexes from plasma, I describe our early experiments that capitalize on the heterogeneity of subunit composition during assembly and exchange reactions. During these investigations, we observed many assemblies and intermediates with different subunit stoichiometries, and were keen to ascertain whether or not their overall topology was preserved in the mass spectrometer. Adapting ion mobility and soft-landing methodologies, we showed how ring-shaped complexes could survive the phase transition. The next logical progression from soluble complexes was to membrane protein assemblies but this was not straightforward. We encountered many pitfalls along the way, largely due to the use of detergent micelles to protect and stabilize complexes. Further obstacles presented when we attempted to distinguish lipids that copurify from those that are important for function. Developing new experimental protocols, we have subsequently defined lipids that change protein conformation, mediate oligomeric states, and facilitate downstream coupling of G protein-coupled receptors. Very recently, using a radical method—ejecting protein complexes directly from native membranes into mass spectrometers—we provided insights into associations within membranes and mitochondria. Together, these developments suggest the beginnings of mass spectrometry meeting with cell biology.
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14
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Harris MJ, Raghavan D, Borysik AJ. Quantitative Evaluation of Native Protein Folds and Assemblies by Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS). J Am Soc Mass Spectrom 2019; 30:58-66. [PMID: 30280315 PMCID: PMC6318237 DOI: 10.1007/s13361-018-2070-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) has significant potential for protein structure initiatives but its relationship with protein conformations is unclear. We report on the efficacy of HDX-MS to distinguish between native and non-native proteins using a popular approach to calculate HDX protection factors (PFs) from protein structures. The ability of HDX-MS to identify native protein conformations is quantified by binary structural classification such that merits of the approach for protein modelling can be quantified and better understood. We show that highly accurate PF calculations are not a prerequisite for HDX-MS simulations that are capable of effectively discriminating between native and non-native protein folds. The simulations can also be performed directly on unique structures facilitating high-throughput evaluation of many alternate conformations. The ability of HDX-MS to classify the conformations of homo-protein assemblies is also investigated. In contrast to protein monomers, we show a significant lack of correspondence between the simulated and experimental HDX-MS data for these systems with a subsequent decrease in the ability of HDX-MS to identify native states. However, we demonstrate surprisingly high diagnostic ability of the simulated data for assemblies in which a significant proportion of the individual chains occupy protein-protein interfaces. We relate this to the number of peptides that can sample alternate subunit orientations and discuss these observations within the larger context of applying HDX-MS to evaluate protein structures. Graphical Abstract.
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Affiliation(s)
- Matthew J Harris
- Department of Chemistry, King's College London, Britannia House, London, SE1 1DB, UK
| | - Deepika Raghavan
- Department of Chemistry, King's College London, Britannia House, London, SE1 1DB, UK
| | - Antoni J Borysik
- Department of Chemistry, King's College London, Britannia House, London, SE1 1DB, UK.
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15
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Riccardi Sirtori F, Altomare A, Carini M, Aldini G, Regazzoni L. MS methods to study macromolecule-ligand interaction: Applications in drug discovery. Methods 2018; 144:152-74. [PMID: 29890284 DOI: 10.1016/j.ymeth.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022] Open
Abstract
The interaction of small compounds (i.e. ligands) with macromolecules or macromolecule assemblies (i.e. targets) is the mechanism of action of most of the drugs available today. Mass spectrometry is a popular technique for the interrogation of macromolecule-ligand interactions and therefore is also widely used in drug discovery and development. Thanks to its versatility, mass spectrometry is used for multiple purposes such as biomarker screening, identification of the mechanism of action, ligand structure optimization or toxicity assessment. The evolution and automation of the instruments now allows the development of high throughput methods with high sensitivity and a minimized false discovery rate. Herein, all these approaches are described with a focus on the methods for studying macromolecule-ligand interaction aimed at defining the structure-activity relationships of drug candidates, along with their mechanism of action, metabolism and toxicity.
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16
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Abstract
Chaperonins are a subclass of molecular chaperones that assist cellular proteins to fold and assemble into their native shape. Much work has been done on Type I chaperonins, which has elucidated their elegant mechanism. Some debate remains about the details in these mechanisms, but nonetheless the roles of these in helping protein folding have been understood in great depth. In this review we discuss the known functions of atypical Type I chaperonins, highlighting evolutionary aspects that might lead chaperonins to perform alternate functions.
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17
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Robinson CV. From molecular chaperones to membrane motors: through the lens of a mass spectrometrist. Biochem Soc Trans 2017; 45:251-60. [PMID: 28202679 DOI: 10.1042/BST20160395] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/07/2016] [Accepted: 12/12/2016] [Indexed: 12/25/2022]
Abstract
Twenty-five years ago, we obtained our first mass spectra of molecular chaperones in complex with protein ligands and entered a new field of gas-phase structural biology. It is perhaps now time to pause and reflect, and to ask how many of our initial structure predictions and models derived from mass spectrometry (MS) datasets were correct. With recent advances in structure determination, many of the most challenging complexes that we studied over the years have become tractable by other structural biology approaches enabling such comparisons to be made. Moreover, in the light of powerful new electron microscopy methods, what role is there now for MS? In considering these questions, I will give my personal view on progress and problems as well as my predictions for future directions.
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18
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Haverland NA, Skinner OS, Fellers RT, Tariq AA, Early BP, LeDuc RD, Fornelli L, Compton PD, Kelleher NL. Defining Gas-Phase Fragmentation Propensities of Intact Proteins During Native Top-Down Mass Spectrometry. J Am Soc Mass Spectrom 2017; 28:1203-1215. [PMID: 28374312 PMCID: PMC5452613 DOI: 10.1007/s13361-017-1635-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 05/03/2023]
Abstract
Fragmentation of intact proteins in the gas phase is influenced by amino acid composition, the mass and charge of precursor ions, higher order structure, and the dissociation technique used. The likelihood of fragmentation occurring between a pair of residues is referred to as the fragmentation propensity and is calculated by dividing the total number of assigned fragmentation events by the total number of possible fragmentation events for each residue pair. Here, we describe general fragmentation propensities when performing top-down mass spectrometry (TDMS) using denaturing or native electrospray ionization. A total of 5311 matched fragmentation sites were collected for 131 proteoforms that were analyzed over 165 experiments using native top-down mass spectrometry (nTDMS). These data were used to determine the fragmentation propensities for 399 residue pairs. In comparison to denatured top-down mass spectrometry (dTDMS), the fragmentation pathways occurring either N-terminal to proline or C-terminal to aspartic acid were even more enhanced in nTDMS compared with other residues. More generally, 257/399 (64%) of the fragmentation propensities were significantly altered (P ≤ 0.05) when using nTDMS compared with dTDMS, and of these, 123 were altered by 2-fold or greater. The most notable enhancements of fragmentation propensities for TDMS in native versus denatured mode occurred (1) C-terminal to aspartic acid, (2) between phenylalanine and tryptophan (F|W), and (3) between tryptophan and alanine (W|A). The fragmentation propensities presented here will be of high value in the development of tailored scoring systems used in nTDMS of both intact proteins and protein complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Nicole A Haverland
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Owen S Skinner
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Ryan T Fellers
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Areeba A Tariq
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Bryan P Early
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Richard D LeDuc
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Luca Fornelli
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Philip D Compton
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Neil L Kelleher
- Department of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA.
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Libich DS, Tugarinov V, Ghirlando R, Clore GM. Confinement and Stabilization of Fyn SH3 Folding Intermediate Mimetics within the Cavity of the Chaperonin GroEL Demonstrated by Relaxation-Based NMR. Biochemistry 2017; 56:903-906. [PMID: 28156097 DOI: 10.1021/acs.biochem.6b01237] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of two folding intermediate mimetics of the model protein substrate Fyn SH3 with the chaperonin GroEL, a supramolecular foldase/unfoldase machine, has been investigated by 15N relaxation-based nuclear magnetic resonance spectroscopy (lifetime line broadening, dark state exchange saturation transfer, and relaxation dispersion). The two mimetics comprise C-terminal truncations of wild-type and triple-mutant (A39V/N53P/V55L) Fyn SH3 in which the C-terminal strand of the SH3 domain is unfolded, while preserving the remaining domain structure. Quantitative analysis of the data reveals that a mobile state of the SH3 domain confined and tethered within the cavity of GroEL, possibly through interactions with the disordered, methionine-rich C-terminal tail(s), can be detected, and that the native state of the folding intermediate mimetics is stabilized by both confinement within and binding to apo GroEL. These data provide a basis for understanding the passive activity of GroEL as a foldase/unfoldase: the unfolded state, in the absence of hydrophobic GroEL-binding consensus sequences, is destabilized within the cavity because of its larger radius of gyration compared to that of the folding intermediate, while the folding intermediate is stabilized relative to the native state because of exposure of a hydrophobic patch that favors GroEL binding.
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Affiliation(s)
- David S Libich
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Vitali Tugarinov
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - Rodolfo Ghirlando
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
| | - G Marius Clore
- Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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Libich DS, Tugarinov V, Clore GM. Intrinsic unfoldase/foldase activity of the chaperonin GroEL directly demonstrated using multinuclear relaxation-based NMR. Proc Natl Acad Sci U S A 2015; 112:8817-23. [PMID: 26124125 DOI: 10.1073/pnas.1510083112] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The prototypical chaperonin GroEL assists protein folding through an ATP-dependent encapsulation mechanism. The details of how GroEL folds proteins remain elusive, particularly because encapsulation is not an absolute requirement for successful re/folding. Here we make use of a metastable model protein substrate, comprising a triple mutant of Fyn SH3, to directly demonstrate, by simultaneous analysis of three complementary NMR-based relaxation experiments (lifetime line broadening, dark state exchange saturation transfer, and Carr-Purcell-Meinboom-Gill relaxation dispersion), that apo GroEL accelerates the overall interconversion rate between the native state and a well-defined folding intermediate by about 20-fold, under conditions where the "invisible" GroEL-bound states have occupancies below 1%. This is largely achieved through a 500-fold acceleration in the folded-to-intermediate transition of the protein substrate. Catalysis is modulated by a kinetic deuterium isotope effect that reduces the overall interconversion rate between the GroEL-bound species by about 3-fold, indicative of a significant hydrophobic contribution. The location of the GroEL binding site on the folding intermediate, mapped from (15)N, (1)HN, and (13)Cmethyl relaxation dispersion experiments, is composed of a prominent, surface-exposed hydrophobic patch.
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Jiang J, Zhang H, Orf GS, Lu Y, Xu W, Harrington LB, Liu H, Lo CS, Blankenship RE. Evidence of functional trimeric chlorophyll a/c-peridinin proteins in the dinoflagellate Symbiodinium. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2014; 1837:1904-12. [DOI: 10.1016/j.bbabio.2014.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/07/2014] [Accepted: 07/24/2014] [Indexed: 12/17/2022]
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Abstract
Sparsely populated transient states of proteins and their complexes play an important role in many biological processes including protein-protein and protein-DNA recognition, allostery, conformational selection, induced fit and self-assembly. These states are difficult to study as their low population and transient nature makes them effectively invisible to conventional structural and biophysical techniques. In the present article, I summarize recent NMR developments in our laboratory, including the use of paramagnetic relaxation enhancement, lifetime line broadening and dark-state exchange saturation transfer spectroscopy, that have permitted such sparsely populated states to be detected, characterized and, in some instances, visualized. I illustrate the application of these methods to the elucidation of mechanisms whereby transcription factors locate their specific target sites within an overwhelming sea of non-specific DNA, to the characterization of encounter complexes in protein-protein recognition, to large-scale interdomain motions involved in ligand binding, and to the interaction of monomeric amyloid β-peptide with the surface of amyloid protofibrils and the internal cavity surface of the chaperonin GroEL.
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Georgescauld F, Popova K, Gupta AJ, Bracher A, Engen JR, Hayer-Hartl M, Hartl FU. GroEL/ES chaperonin modulates the mechanism and accelerates the rate of TIM-barrel domain folding. Cell 2014; 157:922-34. [PMID: 24813614 DOI: 10.1016/j.cell.2014.03.038] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 02/04/2014] [Accepted: 03/14/2014] [Indexed: 11/23/2022]
Abstract
The GroEL/ES chaperonin system functions as a protein folding cage. Many obligate substrates of GroEL share the (βα)8 TIM-barrel fold, but how the chaperonin promotes folding of these proteins is not known. Here, we analyzed the folding of DapA at peptide resolution using hydrogen/deuterium exchange and mass spectrometry. During spontaneous folding, all elements of the DapA TIM barrel acquire structure simultaneously in a process associated with a long search time. In contrast, GroEL/ES accelerates folding more than 30-fold by catalyzing segmental structure formation in the TIM barrel. Segmental structure formation is also observed during the fast spontaneous folding of a structural homolog of DapA from a bacterium that lacks GroEL/ES. Thus, chaperonin independence correlates with folding properties otherwise enforced by protein confinement in the GroEL/ES cage. We suggest that folding catalysis by GroEL/ES is required by a set of proteins to reach native state at a biologically relevant timescale, avoiding aggregation or degradation.
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Nishida N, Yagi-utsumi M, Motojima F, Yoshida M, Shimada I, Kato K. Nuclear magnetic resonance approaches for characterizing interactions between the bacterial chaperonin GroEL and unstructured proteins. J Biosci Bioeng 2013; 116:160-4. [DOI: 10.1016/j.jbiosc.2013.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 02/05/2013] [Accepted: 02/19/2013] [Indexed: 12/18/2022]
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Libich DS, Fawzi NL, Ying J, Clore GM. Probing the transient dark state of substrate binding to GroEL by relaxation-based solution NMR. Proc Natl Acad Sci U S A 2013; 110:11361-6. [PMID: 23798407 DOI: 10.1073/pnas.1305715110] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanism whereby the prototypical chaperonin GroEL performs work on substrate proteins has not yet been fully elucidated, hindered by lack of detailed structural and dynamic information on the bound substrate. Previous investigations have produced conflicting reports on the state of GroEL-bound polypeptides, largely due to the transient and dynamic nature of these complexes. Here, we present a unique approach, based on combined analysis of four complementary relaxation-based NMR experiments, to probe directly the "dark" NMR-invisible state of the model, intrinsically disordered, polypeptide amyloid β (Aβ40) bound to GroEL. The four NMR experiments, lifetime line-broadening, dark-state exchange saturation transfer, relaxation dispersion, and small exchange-induced chemical shifts, are dependent in different ways on the overall exchange rates and populations of the free and bound states of the substrate, as well as on residue-specific dynamics and structure within the bound state as reported by transverse magnetization relaxation rates and backbone chemical shifts, respectively. Global fitting of all the NMR data shows that the complex is transient with a lifetime of <1 ms, that binding involves two predominantly hydrophobic segments corresponding to predicted GroEL consensus binding sequences, and that the structure of the bound polypeptide remains intrinsically and dynamically disordered with minimal changes in secondary structure propensity relative to the free state. Our results establish a unique method to observe NMR-invisible dynamic states of GroEL-bound substrates and to describe at atomic resolution the events between substrate binding and encapsulation that are crucial for understanding the normal and stress-related metabolic function of chaperonins.
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Tsytlonok M, Itzhaki LS. The how’s and why’s of protein folding intermediates. Arch Biochem Biophys 2013; 531:14-23. [DOI: 10.1016/j.abb.2012.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/05/2012] [Accepted: 10/11/2012] [Indexed: 12/13/2022]
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Jaswal SS. Biological insights from hydrogen exchange mass spectrometry. Biochim Biophys Acta 2013; 1834:1188-201. [PMID: 23117127 DOI: 10.1016/j.bbapap.2012.10.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/17/2012] [Accepted: 10/19/2012] [Indexed: 11/22/2022]
Abstract
Over the past two decades, hydrogen exchange mass spectrometry (HXMS) has achieved the status of a widespread and routine approach in the structural biology toolbox. The ability of hydrogen exchange to detect a range of protein dynamics coupled with the accessibility of mass spectrometry to mixtures and large complexes at low concentrations result in an unmatched tool for investigating proteins challenging to many other structural techniques. Recent advances in methodology and data analysis are helping HXMS deliver on its potential to uncover the connection between conformation, dynamics and the biological function of proteins and complexes. This review provides a brief overview of the HXMS method and focuses on four recent reports to highlight applications that monitor structure and dynamics of proteins and complexes, track protein folding, and map the thermodynamics and kinetics of protein unfolding at equilibrium. These case studies illustrate typical data, analysis and results for each application and demonstrate a range of biological systems for which the interpretation of HXMS in terms of structure and conformational parameters provides unique insights into function. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.
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Mapa K, Tiwari S, Kumar V, Jayaraj G, Maiti S. Information Encoded in Non-Native States Drives Substrate-Chaperone Pairing. Structure 2012; 20:1562-73. [DOI: 10.1016/j.str.2012.06.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 06/20/2012] [Accepted: 06/20/2012] [Indexed: 12/14/2022]
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Abstract
Electrospray ionization is today the most widely used ionization technique in chemical and biochemical analysis. Interfaced with a mass spectrometer it allows the investigation of the molecular composition of liquid samples. With electrospray a large variety of chemical substances can be ionized. There is no limitation in mass which thus enables even the investigation of large noncovalent protein complexes. Its high ionization efficiency profoundly changed biomolecular sciences because proteins can be identified and quantified on trace amounts in a high throughput fashion. This review article focuses mainly on the exploration of the underlying ionization mechanism. Some ionization characteristics are discussed that are related to this mechanism. Typical spectra of peptides, proteins, and noncovalent complexes are shown and the quantitative character of spectra is highlighted. Finally the possibilities and limitations in measuring the association constant of bivalent noncovalent complexes are described.
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Affiliation(s)
- Matthias Wilm
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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Abstract
The GroEL-GroES is an essential molecular chaperon system that assists protein folding in cell. Binding of various substrate proteins to GroEL is one of the key aspects in GroEL-assisted protein folding. Small peptides may mimic segments of the substrate proteins in contact with GroEL and allow detailed structural analysis of the interactions. A model peptide SBP has been shown to bind to a region in GroEL that is important for binding of substrate proteins. Here, we investigated whether the observed GroEL-SBP interaction represented those of GroEL-substrate proteins, and whether SBP was able to mimic various aspects of substrate proteins in GroE-assisted protein folding cycle. We found that SBP competed with substrate proteins, including α-lactalbumin, rhodanese, and malate dehydrogenase, in binding to GroEL. SBP stimulated GroEL ATP hydrolysis rate in a manner similar to that of α-lactalbumin. SBP did not prevent GroES from binding to GroEL, and GroES association reduced the ATPase rates of GroEL/SBP and GroEL/α-lactalbumin to a comparable extent. Binding of both SBP and α-lactalbumin to apo GroEL was dominated by hydrophobic interaction. Interestingly, association of α-lactalbumin to GroEL/GroES was thermodynamically distinct from that to GroEL with reduced affinity and decreased contribution from hydrophobic interaction. However, SBP did not display such differential binding behaviors to apo GroEL and GroEL/GroES, likely due to the lack of a contiguous polypeptide chain that links all of the bound peptide fragments. Nevertheless, studies using peptides provide valuable information on the nature of GroEL-substrate protein interaction, which is central to understand the mechanism of GroEL-assisted protein folding.
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Affiliation(s)
- Yali Li
- Interdisciplinary Biochemistry Program, Indiana University, 212 S. Hawthorne Dr., Bloomington, IN 47405, USA
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Marklund EG, Larsson DSD, van der Spoel D, Patriksson A, Caleman C. Structural stability of electrosprayed proteins: temperature and hydration effects. Phys Chem Chem Phys 2009; 11:8069-78. [PMID: 19727514 DOI: 10.1039/b903846a] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Electrospray ionization is a gentle method for sample delivery, routinely used in gas-phase studies of proteins. It is crucial for structural investigations that the protein structure is preserved, and a good understanding of how structure is affected by the transition to the gas phase is needed for the tuning of experiments to meet that requirement. Small amounts of residual solvent have been shown to protect the protein, but temperature is important too, although it is not well understood how the latter affects structural details. Using molecular dynamics we have simulated four sparingly hydrated globular proteins (Trp-cage; Ctf, a C-terminal fragment of a bacterial ribosomal protein; ubiquitin; and lysozyme) in vacuum starting at temperatures ranging from 225 K to 425 K. For three of the proteins, our simulations show that a water layer corresponding to 3 A preserves the protein structure in vacuum, up to starting temperatures of 425 K. Only Ctf shows minor secondary structural changes at lower starting temperatures. The structural conservation stems mainly from interactions with the surrounding water. Temperature scales in simulations are not directly translatable into experiments, but the wide temperature range in which we find the proteins to be stable is reassuring for the success of future single particle imaging experiments. The water molecules aggregate in clusters and form patterns on the protein surface, maintaining a reproducible hydrogen bonding network. The simulations were performed mainly using OPLS-AA/L, with cross checks using AMBER03 and GROMOS96 53a6. Only minor differences between the results from the three different force fields were observed.
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Affiliation(s)
- Erik G Marklund
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124, Uppsala, Sweden
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Horwich AL, Fenton WA. Chaperonin-mediated protein folding: using a central cavity to kinetically assist polypeptide chain folding. Q Rev Biophys 2009; 42:83-116. [PMID: 19638247 DOI: 10.1017/S0033583509004764] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The chaperonin ring assembly GroEL provides kinetic assistance to protein folding in the cell by binding non-native protein in the hydrophobic central cavity of an open ring and subsequently, upon binding ATP and the co-chaperonin GroES to the same ring, releasing polypeptide into a now hydrophilic encapsulated cavity where productive folding occurs in isolation. The fate of polypeptide during binding, encapsulation, and folding in the chamber has been the subject of recent experimental studies and is reviewed and considered here. We conclude that GroEL, in general, behaves passively with respect to its substrate proteins during these steps. While binding appears to be able to rescue non-native polypeptides from kinetic traps, such rescue is most likely exerted at the level of maximizing hydrophobic contact, effecting alteration of the topology of weakly structured states. Encapsulation does not appear to involve 'forced unfolding', and if anything, polypeptide topology is compacted during this step. Finally, chamber-mediated folding appears to resemble folding in solution, except that major kinetic complications of multimolecular association are prevented.
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Patra AK, Udgaonkar JB. GroEL Can Unfold Late Intermediates Populated on the Folding Pathways of Monellin. J Mol Biol 2009; 389:759-75. [DOI: 10.1016/j.jmb.2009.04.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 04/10/2009] [Accepted: 04/20/2009] [Indexed: 10/20/2022]
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Meyer T, de la Cruz X, Orozco M. An Atomistic View to the Gas Phase Proteome. Structure 2009; 17:88-95. [DOI: 10.1016/j.str.2008.11.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 10/14/2008] [Accepted: 11/06/2008] [Indexed: 11/22/2022]
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Sharma S, Chakraborty K, Müller BK, Astola N, Tang YC, Lamb DC, Hayer-Hartl M, Hartl FU. Monitoring Protein Conformation along the Pathway of Chaperonin-Assisted Folding. Cell 2008; 133:142-53. [DOI: 10.1016/j.cell.2008.01.048] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 12/07/2007] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
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Abstract
This overview describes some of the new technologies that can be employed to facilitate rapid identification and characterization of proteins, including the use of correlative approaches for protein identification, rapid posttranslational modification analysis, identification of components in complex mixtures, and direct mass analysis of gel-separated proteins. The mass spectrometric methods referred to in this overview include matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS).
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Abstract
The ability to determine conformational parameters of protein-folding landscapes is critical for understanding the link between conformation, function, and disease. Monitoring hydrogen exchange (HX) of labile protons at equilibrium enables direct extraction of thermodynamic or kinetic landscape parameters in two limiting extremes. Here, we establish a quantitative framework for relating HX behavior to landscape. We use this framework to demonstrate that the range of predicted global HX behavior for the majority of a set of characterized two-state proteins under near-native conditions does not readily span between both extremes. For most, stability may be quantitatively determined under physiological conditions, with semiquantitative boundaries on kinetics additionally determined using modest experimental perturbations to shift HX behavior. The framework and relationships derived in the simple context of two-state global folding highlight the importance of understanding HX across the entire continuum of behavior, in order to apply HX to map landscapes.
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Affiliation(s)
- Sheila S Jaswal
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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Abstract
Chaperonins are large ring assemblies that assist protein folding to the native state by binding nonnative proteins in their central cavities and then, upon binding ATP, release the substrate protein into a now-encapsulated cavity to fold productively. Two families of such components have been identified: type I in mitochondria, chloroplasts, and the bacterial cytosol, which rely on a detachable "lid" structure for encapsulation, and type II in archaea and the eukaryotic cytosol, which contain a built-in protrusion structure. We discuss here a number of issues under current study. What is the range of substrates acted on by the two classes of chaperonin, in particular by GroEL in the bacterial cytoplasm and CCT in the eukaryotic cytosol, and are all these substrates subject to encapsulation? What are the determinants for substrate binding by the type II chaperonins? And is the encapsulated chaperonin cavity a passive container that prevents aggregation, or could it be playing an active role in polypeptide folding?
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Affiliation(s)
- Arthur L Horwich
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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Elad N, Farr GW, Clare DK, Orlova EV, Horwich AL, Saibil HR. Topologies of a substrate protein bound to the chaperonin GroEL. Mol Cell 2007; 26:415-26. [PMID: 17499047 PMCID: PMC1885994 DOI: 10.1016/j.molcel.2007.04.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 03/19/2007] [Accepted: 04/04/2007] [Indexed: 12/22/2022]
Abstract
The chaperonin GroEL assists polypeptide folding through sequential steps of binding nonnative protein in the central cavity of an open ring, via hydrophobic surfaces of its apical domains, followed by encapsulation in a hydrophilic cavity. To examine the binding state, we have classified a large data set of GroEL binary complexes with nonnative malate dehydrogenase (MDH), imaged by cryo-electron microscopy, to sort them into homogeneous subsets. The resulting electron density maps show MDH associated in several characteristic binding topologies either deep inside the cavity or at its inlet, contacting three to four consecutive GroEL apical domains. Consistent with visualization of bound polypeptide distributed over many parts of the central cavity, disulfide crosslinking could be carried out between a cysteine in a bound substrate protein and cysteines substituted anywhere inside GroEL. Finally, substrate binding induced adjustments in GroEL itself, observed mainly as clustering together of apical domains around sites of substrate binding.
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Affiliation(s)
- Nadav Elad
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
| | - George W. Farr
- Department of Genetics, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Daniel K. Clare
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
| | - Elena V. Orlova
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
| | - Arthur L. Horwich
- Department of Genetics, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Helen R. Saibil
- Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, UK
- Corresponding author
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Scott EA, Elbert DL. Mass spectrometric mapping of fibrinogen conformations at poly(ethylene terephthalate) interfaces. Biomaterials 2007; 28:3904-17. [PMID: 17582492 PMCID: PMC2041854 DOI: 10.1016/j.biomaterials.2007.05.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 05/21/2007] [Indexed: 12/27/2022]
Abstract
We have characterized the adsorption of bovine fibrinogen onto the biomedical polymer polyethylene terephthalate (PET) by performing mass spectrometric mapping with a lysine-reactive biotin label. After digestion with trypsin, MALDI-TOF mass spectrometry was used to detect peptides from biotinylated bovine fibrinogen, with the goal of identifying lysines that were more accessible for reaction with the chemical label after adsorption. Peptides within domains that are believed to contribute to heparin binding, leukocyte activation, and platelet adhesion were found to be biotin labeled only after bovine fibrinogen adsorbed to the PET surface. Additionally, the accessibility of lysine residues throughout the entire molecule was observed to increase as the concentration of the adsorbing bovine fibrinogen solution decreased, suggesting that the proximity of biologically active motifs to hydrophilic residues leads to their exposure. The surface area per adsorbed bovine fibrinogen molecule was quantified on PET using optical waveguide lightmode spectroscopy (OWLS), which revealed higher surface densities for bovine fibrinogen adsorbed from higher concentration solutions. By measuring changes in both the identity and conformation of proteins that adsorb from complex mixtures such as blood or plasma, this technique may have applications in fundamental studies of protein adsorption and may allow for more accurate predictions of the biocompatibility of materials.
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Affiliation(s)
| | - Donald L. Elbert
- *To whom correspondence should be addressed: Donald L. Elbert, Campus Box 1097, One Brookings Dr., St. Louis, MO 63130,
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Park ES, Fenton WA, Horwich AL. Disulfide formation as a probe of folding in GroEL-GroES reveals correct formation of long-range bonds and editing of incorrect short-range ones. Proc Natl Acad Sci U S A 2007; 104:2145-50. [PMID: 17283341 PMCID: PMC1793900 DOI: 10.1073/pnas.0610989104] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The chaperonin GroEL assists protein folding by binding nonnative forms through exposed hydrophobic surfaces in an open ring and mediating productive folding in an encapsulated hydrophilic chamber formed when it binds GroES. Little is known about the topology of nonnative proteins during folding inside the GroEL-GroES cis chamber. Here, we have monitored topology employing disulfide bond formation of a secretory protein, trypsinogen (TG), that behaves in vitro as a stringent, GroEL-GroES-requiring substrate. Inside the long-lived cis chamber formed by SR1, a single-ring version of GroEL, complexed with GroES, we observed an ordered formation of disulfide bonds. First, short-range disulfides relative to the primary structure formed, both native and nonnative. Next, the two long-range native disulfides that "pin" the two beta-barrel domains together formed. Notably, no long-range nonnative bonds were ever observed, suggesting that a native-like long-range topology is favored. At both this time and later, however, the formation of several medium-range nonnative bonds mapping to one of the beta-barrels was observed, reflecting that the population of local nonnative structure can occur even within the cis cavity. Yet both these and the short-range nonnative bonds were ultimately "edited" to native, as evidenced by the nearly complete recovery of native TG. We conclude that folding in the GroEL-GroES cavity can favor the formation of a native-like topology, here involving the proper apposition of the two domains of TG; but it also involves an ATP-independent conformational "editing" of locally incorrect structures produced during the dwell time in the cis cavity.
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Affiliation(s)
- Eun Sun Park
- *Department of Genetics and
- Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT 06510; and
| | | | - Arthur L. Horwich
- *Department of Genetics and
- Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT 06510; and
- Scripps Research Institute, La Jolla, CA 92037
- To whom correspondence should be addressed. E-mail:
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Abstract
In several experimental techniques D2O rather then H2O is often used as a solvent for proteins. Concerning the influence of the solvent on the stability of the proteins, contradicting results have been reported in literature. In this paper the influence of H2O-D2O solvent substitution on the stability of globular protein structure is determined in a systematic way. The differential scanning calorimetry technique is applied to allow for a thermodynamic analysis of two types of globular proteins: hen's egg lysozyme (LSZ) with relatively strong internal cohesion ("hard" globular protein) and bovine serum albumin (BSA), which is known for its conformational adaptability ("soft" globular protein). Both proteins tend to be more stable in D2O compared to H2O. We explain the increase of protein stability in D2O by the observation that D2O is a poorer solvent for nonpolar amino acids than H2O, implying that the hydrophobic effect is larger in D2O. In case of BSA the transitions between different isomeric forms, at low pH values the Nm and F forms, and at higher pH values Nm and B, were observed by the presence of a supplementary peak in the DSC thermogram. It appears that the pH-range for which the Nm form is the preferred one is wider in D2O than in H2O.
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Affiliation(s)
- Y M Efimova
- Department of Radiation, Radionuclides and Reactors, Faculty of Applied Sciences, Delft University of Technology, Mekelweg 15, 2629 JB Delft, The Netherlands
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46
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Abstract
Protein folding is a spontaneous process that is essential for life, yet the concentrated and complex interior of a cell is an inherently hostile environment for the efficient folding of many proteins. Some proteins-constrained by sequence, topology, size, and function-simply cannot fold by themselves and are instead prone to misfolding and aggregation. This problem is so deeply entrenched that a specialized family of proteins, known as molecular chaperones, evolved to assist in protein folding. Here we examine one essential class of molecular chaperones, the large, oligomeric, and energy utilizing chaperonins or Hsp60s. The bacterial chaperonin GroEL, along with its co-chaperonin GroES, is probably the best-studied example of this family of protein-folding machine. In this review, we examine some of the general properties of proteins that do not fold well in the absence of GroEL and then consider how folding of these proteins is enhanced by GroEL and GroES. Recent experimental and theoretical studies suggest that chaperonins like GroEL and GroES employ a combination of protein isolation, unfolding, and conformational restriction to drive protein folding under conditions where it is otherwise not possible.
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Affiliation(s)
- Zong Lin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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47
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Cliff MJ, Limpkin C, Cameron A, Burston SG, Clarke AR. Elucidation of steps in the capture of a protein substrate for efficient encapsulation by GroE. J Biol Chem 2006; 281:21266-21275. [PMID: 16684774 DOI: 10.1074/jbc.m601605200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have identified five structural rearrangements in GroEL induced by the ordered binding of ATP and GroES. The first discernable rearrangement (designated T --> R(1)) is a rapid, cooperative transition that appears not to be functionally communicated to the apical domain. In the second (R(1) --> R(2)) step, a state is formed that binds GroES weakly in a rapid, diffusion-limited process. However, a second optical signal, carried by a protein substrate bound to GroEL, responds neither to formation of the R(2) state nor to the binding of GroES. This result strongly implies that the substrate protein remains bound to the inner walls of the initially formed GroEL.GroES cavity, and is not yet displaced from its sites of interaction with GroEL. In the next rearrangement (R(2).GroES --> R(3).GroES) the strength of interaction between GroEL and GroES is greatly enhanced, and there is a large and coincident loss of fluorescence-signal intensity in the labeled protein substrate, indicating that there is either a displacement from its binding sites on GroEL or at least a significant change of environment. These results are consistent with a mechanism in which the shift in orientation of GroEL apical domains between that seen in the apo-protein and stable GroEL.GroES complexes is highly ordered, and transient conformational intermediates permit the association of GroES before the displacement of bound polypeptide. This ensures efficient encapsulation of the polypeptide within the GroEL central cavity underneath GroES.
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Affiliation(s)
- Matthew J Cliff
- Department of Biochemistry, University of Bristol, School of Medical Sciences, Bristol BS8 1TD, United Kingdom
| | - Claire Limpkin
- Department of Biochemistry, University of Bristol, School of Medical Sciences, Bristol BS8 1TD, United Kingdom
| | - Angus Cameron
- Department of Biochemistry, University of Bristol, School of Medical Sciences, Bristol BS8 1TD, United Kingdom
| | - Steven G Burston
- Department of Biochemistry, University of Bristol, School of Medical Sciences, Bristol BS8 1TD, United Kingdom.
| | - Anthony R Clarke
- Department of Biochemistry, University of Bristol, School of Medical Sciences, Bristol BS8 1TD, United Kingdom
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48
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Affiliation(s)
- Arthur L Horwich
- Department of Genetics and Howard Hughes Medical Institute, Yale School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, Connecticut 06510, USA.
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49
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Abstract
Proteins fold in a confined space not only in vivo, i.e., folding assisted by molecular chaperons and chaperonins in a crowded cellular medium, but also in vitro as in production of recombinant proteins. Despite extensive work on protein folding in bulk, little is known about how and to what extent the thermodynamics and kinetics of protein folding are altered by confinement. In this work, we use a Gō-like off-lattice model to investigate the folding and stability of an all beta-sheet protein in spherical cages of different sizes and surface hydrophobicity. We find whereas extreme confinement inhibits correct folding, a hydrophilic cage stabilizes the protein due to restriction of the unfolded configurations. In a hydrophobic cage, however, strong attraction from the cage surface destabilizes the confined protein because of competition between self-aggregation and adsorption of hydrophobic residues. We show that the kinetics of protein collapse and folding is strongly correlated with both the cage size and the surface hydrophobicity. It is demonstrated that a cage of moderate size and hydrophobicity optimizes both the folding yield and kinetics of structural transitions. To support the simulation results, we have also investigated the refolding of hen-egg lysozyme in the presence of cetyltrimethylammoniumbromide (CTAB) surfactants that provide an effective confinement of the proteins by micellization. The influence of the surfactant hydrophobicity on the structural and biological activity of the protein is determined with circular dichroism spectrum, fluorescence emission spectrum, and biological activity assay. It is shown that, as predicted by coarse-grained simulations, CTAB micelles facilitate the collapse of denatured lysozyme, whereas the addition of beta-cyclodextrin-grafted-PNIPAAm, a weakly hydrophobic stripper, dissociates CTAB micelles and promotes the conformational rearrangement and thereby gives an improved recovery of lysozyme activity.
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Affiliation(s)
- Diannan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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50
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Hagman C, Tsybin YO, Håkansson P. Solution-phase deuterium/hydrogen exchange at a specific residue using nozzle-skimmer and electron capture dissociation mass spectrometry. Rapid Commun Mass Spectrom 2006; 20:661-5. [PMID: 16447307 DOI: 10.1002/rcm.2339] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Information about protein conformation can be obtained with hydrogen/deuterium exchange (HDX) mass spectrometry. The isotopic solution-phase exchange of specific amide hydrogen atoms can be followed using low-vacuum nozzle-skimmer collision-induced dissociation (CID). In this study, the nozzle-skimmer technique was complemented by electron capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The solution-phase exchange at a specific residue is monitored by comparing isotopic distributions of two consecutive b- or c-type ions. While nozzle-skimmer fragmentation takes place in the low-vacuum region of the mass spectrometer, ECD occurs at ultra-high vacuum within the mass analyzer cell of the FTICR mass spectrometer. The dissociations take place at 10(-4) and 10(-9) mbar, respectively. Low-vacuum nozzle-skimmer fragmentation can result in intramolecular exchange between product ions and solvent molecules in the gas phase. Consequently, the solution-phase information about protein or peptide conformation is lost. It was not possible to monitor isotopic solution-phase exchange at the eighth residue in substance P, (Phe)8, with nozzle-skimmer CID. By using the in-cell ECD fragmentation method, the solution-phase exchange at the (Phe)8 residue was preserved during mass spectrometric analysis. This result shows the complementary aspects of applying fragmentation at low and at high vacuum, when studying isotopic exchange in solution at specific residues using FTICRMS.
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Affiliation(s)
- Charlotte Hagman
- Department of Engineering Sciences, Division of Ion Physics, Uppsala University, Uppsala, Box 534 S-751 21, Sweden.
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