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Neamtu A, Serban DN, Barritt GJ, Isac DL, Vasiliu T, Laaksonen A, Serban IL. Molecular dynamics simulations reveal the hidden EF-hand of EF-SAM as a possible key thermal sensor for STIM1 activation by temperature. J Biol Chem 2023; 299:104970. [PMID: 37380078 PMCID: PMC10400917 DOI: 10.1016/j.jbc.2023.104970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/07/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
Intracellular calcium signaling is essential for many cellular processes, including store-operated Ca2+ entry (SOCE), which is initiated by stromal interaction molecule 1 (STIM1) detecting endoplasmic reticulum (ER) Ca2+ depletion. STIM1 is also activated by temperature independent of ER Ca2+ depletion. Here we provide evidence, from advanced molecular dynamics simulations, that EF-SAM may act as a true temperature sensor for STIM1, with the prompt and extended unfolding of the hidden EF-hand subdomain (hEF) even at slightly elevated temperatures, exposing a highly conserved hydrophobic Phe108. Our study also suggests an interplay between Ca2+ and temperature sensing, as both, the canonical EF-hand subdomain (cEF) and the hidden EF-hand subdomain (hEF), exhibit much higher thermal stability in the Ca2+-loaded form compared to the Ca2+-free form. The SAM domain, surprisingly, displays high thermal stability compared to the EF-hands and may act as a stabilizer for the latter. We propose a modular architecture for the EF-hand-SAM domain of STIM1 composed of a thermal sensor (hEF), a Ca2+ sensor (cEF), and a stabilizing domain (SAM). Our findings provide important insights into the mechanism of temperature-dependent regulation of STIM1, which has broad implications for understanding the role of temperature in cellular physiology.
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Affiliation(s)
- Andrei Neamtu
- Department of Physiology, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania; Center of Advanced Research in Bionanocojugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry Iasi, Iasi, Romania
| | - Dragomir N Serban
- Department of Physiology, "Grigore T. Popa" University of Medicine and Pharmacy, Iasi, Romania.
| | - Greg J Barritt
- Discipline of Medical Biochemistry, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Dragos Lucian Isac
- Center of Advanced Research in Bionanocojugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry Iasi, Iasi, Romania
| | - Tudor Vasiliu
- Center of Advanced Research in Bionanocojugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry Iasi, Iasi, Romania
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden; Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania; State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, P. R. China
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2
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The native state conformational heterogeneity in the energy landscape of protein folding. Biophys Chem 2022; 283:106761. [DOI: 10.1016/j.bpc.2022.106761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/18/2022]
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3
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Bhattacharjee R, Udgaonkar JB. Structural Characterization of the Cooperativity of Unfolding of a Heterodimeric Protein using Hydrogen Exchange-Mass Spectrometry. J Mol Biol 2021; 433:167268. [PMID: 34563547 DOI: 10.1016/j.jmb.2021.167268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
Little is known about how the sequence of structural changes in one chain of a heterodimeric protein is coupled to those in the other chain during protein folding and unfolding reactions, and whether individual secondary structural changes in the two chains occur in one or many coordinated steps. Here, the unfolding mechanism of a small heterodimeric protein, double chain monellin, has been characterized using hydrogen exchange-mass spectrometry. Transient structure opening, which enables HX, was found to be describable by a five state N ↔ I1 ↔ I2 ↔ I3 ↔ U mechanism. Structural changes occur gradually in the first three steps, and cooperatively in the last step. β strands 2, 4 and 5, as well as the α-helix undergo transient unfolding during all three non-cooperative steps, while β1 and the two loops on both sides of the helix undergo transient unfolding during the first two steps. In the absence of GdnHCl, only β3 in chain A of the protein unfolds during the last cooperative step, while in the presence of 1 M GdnHCl, not only β3, but also β2 in chain B unfolds cooperatively. Hence, the extent of cooperative structural change and size of the cooperative unfolding unit increase when the protein is destabilized by denaturant. The naturally evolved two-chain variant of monellin folds and unfolds in a more cooperative manner than does a single chain variant created artificially, suggesting that increasing folding cooperativity, even at the cost of decreasing stability, may be a driving force in the evolution of proteins.
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Affiliation(s)
- Rupam Bhattacharjee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India; Indian Institute of Science Education and Research, Pune, India. https://twitter.com/Rupam_B01
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India; Indian Institute of Science Education and Research, Pune, India.
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4
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Lento C, Wilson DJ. Subsecond Time-Resolved Mass Spectrometry in Dynamic Structural Biology. Chem Rev 2021; 122:7624-7646. [PMID: 34324314 DOI: 10.1021/acs.chemrev.1c00222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Life at the molecular level is a dynamic world, where the key players-proteins, oligonucleotides, lipids, and carbohydrates-are in a perpetual state of structural flux, shifting rapidly between local minima on their conformational free energy landscapes. The techniques of classical structural biology, X-ray crystallography, structural NMR, and cryo-electron microscopy (cryo-EM), while capable of extraordinary structural resolution, are innately ill-suited to characterize biomolecules in their dynamically active states. Subsecond time-resolved mass spectrometry (MS) provides a unique window into the dynamic world of biological macromolecules, offering the capacity to directly monitor biochemical processes and conformational shifts with a structural dimension provided by the electrospray charge-state distribution, ion mobility, covalent labeling, or hydrogen-deuterium exchange. Over the past two decades, this suite of techniques has provided important insights into the inherently dynamic processes that drive function and pathogenesis in biological macromolecules, including (mis)folding, complexation, aggregation, ligand binding, and enzyme catalysis, among others. This Review provides a comprehensive account of subsecond time-resolved MS and the advances it has enabled in dynamic structural biology, with an emphasis on insights into the dynamic drivers of protein function.
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Affiliation(s)
- Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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5
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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6
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Genereux JC. Mass spectrometric approaches for profiling protein folding and stability. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 118:111-144. [PMID: 31928723 DOI: 10.1016/bs.apcsb.2019.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein stability reports on protein homeostasis, function, and binding interactions, such as to other proteins, metabolites and drugs. As such, there is a pressing need for technologies that can report on protein stability. The ideal technique could be applied in vitro or in vivo systems, proteome-wide, independently of matrix, under native conditions, with residue-level resolution, and on protein at endogenous levels. Mass spectrometry has rapidly become a preferred technology for identifying and quantifying proteins. As such, it has been increasingly incorporated into methodologies for interrogating protein stability and folding. Although no single technology can satisfy all desired applications, several emerging approaches have shown outstanding success at providing biological insight into the stability of the proteome. This chapter outlines some of these recent emerging technologies.
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Affiliation(s)
- Joseph C Genereux
- Department of Chemistry, University of California, Riverside, CA, United States
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7
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Mishra P, Jha SK. Slow Motion Protein Dance Visualized Using Red-Edge Excitation Shift of a Buried Fluorophore. J Phys Chem B 2019; 123:1256-1264. [PMID: 30640479 DOI: 10.1021/acs.jpcb.8b11151] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It has been extremely challenging to detect protein structures with a dynamic core, such as dry molten globules, that remain in equilibrium with the tightly packed native (N) state and that are important for a myriad of entropy-driven protein functions. Here, we detect the higher entropy conformations of a human serum protein, using red-edge excitation shift experiments. We covalently introduced a fluorophore inside the protein core and observed that in a subset of native population, the side chains of the polar and buried residues have different spatial arrangements than the mean population and that they solvate the fluorophore on a timescale much slower than the nanosecond timescale of fluorescence. Our results provide direct evidence for the dense fluidity of protein core and show that alternate side-chain packing arrangements exist in the core that might be important for multiple binding functions of this protein.
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Affiliation(s)
- Prajna Mishra
- Physical and Materials Chemistry Division, Academy of Scientific and Innovative Research (AcSIR) , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411008 , Maharashtra , India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, Academy of Scientific and Innovative Research (AcSIR) , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411008 , Maharashtra , India
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8
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Mishra P, Jha SK. An Alternatively Packed Dry Molten Globule-like Intermediate in the Native State Ensemble of a Multidomain Protein. J Phys Chem B 2017; 121:9336-9347. [DOI: 10.1021/acs.jpcb.7b07032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Prajna Mishra
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
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9
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Irvine GW, Stillman MJ. Residue Modification and Mass Spectrometry for the Investigation of Structural and Metalation Properties of Metallothionein and Cysteine-Rich Proteins. Int J Mol Sci 2017; 18:ijms18050913. [PMID: 28445428 PMCID: PMC5454826 DOI: 10.3390/ijms18050913] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 12/23/2022] Open
Abstract
Structural information regarding metallothioneins (MTs) has been hard to come by due to its highly dynamic nature in the absence of metal-thiolate cluster formation and crystallization difficulties. Thus, typical spectroscopic methods for structural determination are limited in their usefulness when applied to MTs. Mass spectrometric methods have revolutionized our understanding of protein dynamics, structure, and folding. Recently, advances have been made in residue modification mass spectrometry in order to probe the hard-to-characterize structure of apo- and partially metalated MTs. By using different cysteine specific alkylation reagents, time dependent electrospray ionization mass spectrometry (ESI-MS), and step-wise “snapshot” ESI-MS, we are beginning to understand the dynamics of the conformers of apo-MT and related species. In this review we highlight recent papers that use these and similar techniques for structure elucidation and attempt to explain in a concise manner the data interpretations of these complex methods. We expect increasing resolution in our picture of the structural conformations of metal-free MTs as these techniques are more widely adopted and combined with other promising tools for structural elucidation.
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Affiliation(s)
- Gordon W Irvine
- Department of Chemistry, The University of Western Ontario, London, ON N6A 3K7, Canada.
| | - Martin J Stillman
- Department of Chemistry, The University of Western Ontario, London, ON N6A 3K7, Canada.
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10
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Acharya N, Mishra P, Jha SK. A dry molten globule-like intermediate during the base-induced unfolding of a multidomain protein. Phys Chem Chem Phys 2017; 19:30207-30216. [DOI: 10.1039/c7cp06614g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An early intermediate during the base-induced unfolding of a multidomain protein resembles a dry molten globule state in which the structure is expanded without core hydration.
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Affiliation(s)
- Nirbhik Acharya
- Physical and Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Prajna Mishra
- Physical and Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
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11
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Malhotra P, Udgaonkar JB. How cooperative are protein folding and unfolding transitions? Protein Sci 2016; 25:1924-1941. [PMID: 27522064 PMCID: PMC5079258 DOI: 10.1002/pro.3015] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 11/12/2022]
Abstract
A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two-state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non-cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier-less "downhill" folding, as well as for continuous "uphill" unfolding transitions, indicate that gradual non-cooperative processes may be ubiquitous features on the free energy landscape of protein folding.
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Affiliation(s)
- Pooja Malhotra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
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12
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Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation. Sci Rep 2016; 6:32277. [PMID: 27573790 PMCID: PMC5004150 DOI: 10.1038/srep32277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 08/05/2016] [Indexed: 01/10/2023] Open
Abstract
Temporal binding of urea to lysozyme was examined using X-ray diffraction of single crystals of urea/lysozyme complexes prepared by soaking native lysozyme crystals in solutions containing 9 M urea. Four different soak times of 2, 4, 7 and 10 hours were used. The five crystal structures (including the native lysozyme), refined to 1.6 Å resolution, reveal that as the soaking time increased, more and more first-shell water molecules are replaced by urea. The number of hydrogen bonds between urea and the protein is similar to that between protein and water molecules replaced by urea. However, the number of van der Waals contacts to protein from urea is almost double that between the protein and the replaced water. The hydrogen bonding and van der Waals interactions are initially greater with the backbone and later with side chains of charged residues. Urea altered the water-water hydrogen bond network both by replacing water solvating hydrophobic residues and by shortening the first-shell intra-water hydrogen bonds by 0.2 Å. These interaction data suggest that urea uses both 'direct' and 'indirect' mechanisms to unfold lysozyme. Specific structural changes constitute the first steps in lysozyme unfolding by urea.
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13
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Acharya N, Mishra P, Jha SK. Evidence for Dry Molten Globule-Like Domains in the pH-Induced Equilibrium Folding Intermediate of a Multidomain Protein. J Phys Chem Lett 2016; 7:173-179. [PMID: 26700266 DOI: 10.1021/acs.jpclett.5b02545] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The role of van der Waals (vdW) packing interactions compared to the hydrophobic effect in stabilizing the functional structure of proteins is poorly understood. Here we show, using fluorescence resonance energy transfer, dynamic fluorescence quenching, red-edge excitation shift, and near- and far-UV circular dichroism, that the pH-induced structural perturbation of a multidomain protein leads to the formation of a state in which two out of the three domains have characteristics of dry molten globules, that is, the domains are expanded compared to the native protein with disrupted packing interactions but have dry cores. We quantitatively estimate the energetic contribution of vdW interactions and show that they play an important role in the stability of the native state and cooperativity of its structural transition, in addition to the hydrophobic effect. Our results also indicate that during the pH-induced unfolding, side-chain unlocking and hydrophobic solvation occur in two distinct steps and not in a concerted manner, as commonly believed.
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Affiliation(s)
- Nirbhik Acharya
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Prajna Mishra
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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14
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Malhotra P, Udgaonkar JB. High-Energy Intermediates in Protein Unfolding Characterized by Thiol Labeling under Nativelike Conditions. Biochemistry 2014; 53:3608-20. [DOI: 10.1021/bi401493t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pooja Malhotra
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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15
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Jha SK, Marqusee S. Kinetic evidence for a two-stage mechanism of protein denaturation by guanidinium chloride. Proc Natl Acad Sci U S A 2014; 111:4856-61. [PMID: 24639503 PMCID: PMC3977270 DOI: 10.1073/pnas.1315453111] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dry molten globular (DMG) intermediates, an expanded form of the native protein with a dry core, have been observed during denaturant-induced unfolding of many proteins. These observations are counterintuitive because traditional models of chemical denaturation rely on changes in solvent-accessible surface area, and there is no notable change in solvent-accessible surface area during the formation of the DMG. Here we show, using multisite fluorescence resonance energy transfer, far-UV CD, and kinetic thiol-labeling experiments, that the guanidinium chloride (GdmCl)-induced unfolding of RNase H also begins with the formation of the DMG. Population of the DMG occurs within the 5-ms dead time of our measurements. We observe that the size and/or population of the DMG is linearly dependent on [GdmCl], although not as strongly as the second and major step of unfolding, which is accompanied by core solvation and global unfolding. This rapid GdmCl-dependent population of the DMG indicates that GdmCl can interact with the protein before disrupting the hydrophobic core. These results imply that the effect of chemical denaturants cannot be interpreted solely as a disruption of the hydrophobic effect and strongly support recent computational studies, which hypothesize that chemical denaturants first interact directly with the protein surface before completely unfolding the protein in the second step (direct interaction mechanism).
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Affiliation(s)
| | - Susan Marqusee
- California Institute for Quantitative Biosciences and
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220
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Vahidi S, Stocks BB, Liaghati-Mobarhan Y, Konermann L. Submillisecond protein folding events monitored by rapid mixing and mass spectrometry-based oxidative labeling. Anal Chem 2013; 85:8618-25. [PMID: 23841479 DOI: 10.1021/ac401148z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Kinetic measurements can provide insights into protein folding mechanisms. However, the initial (submillisecond) stages of folding still represent a formidable analytical challenge. A number of ultrarapid triggering techniques have been available for some time, but coupling of these techniques with detection methods that are capable of providing detailed structural information has proven to be difficult. The current work addresses this issue by combining submillisecond mixing with laser-induced oxidative labeling. Apomyoglobin (aMb) serves as a model system for our measurements. Exposure of the protein to a brief pulse of hydroxyl radical (·OH) at different time points during folding introduces covalent modifications at solvent accessible side chains. The extent of labeling is monitored using mass spectrometry-based peptide mapping, providing spatially resolved measurements of changes in solvent accessibility. The submillisecond mixer used here improves the time resolution by a factor of 50 compared to earlier ·OH labeling experiments from our laboratory. Data obtained in this way indicate that early aMb folding events are driven by both local and sequence-remote docking of hydrophobic side chains. Assembly of a partially formed A(E)G(H) scaffold after 0.2 ms is followed by stepwise consolidation that ultimately yields the native state. Major conformational changes go to completion within 0.1 s. The technique introduced here is capable of providing in-depth structural information on very short time scales that have thus far been dominated by low resolution (global) spectroscopic probes. By employing submillisecond mixing in conjunction with slower mixing techniques, it is possible to observe complete folding pathways, from fractions of a millisecond all the way to minutes.
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Affiliation(s)
- Siavash Vahidi
- Departments of Chemistry and Biochemistry, The University of Western Ontario , London, Ontario, N6A 5B7, Canada
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17
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Pečová M, Šebela M, Marková Z, Poláková K, Čuda J, Šafářová K, Zbořil R. Thermostable trypsin conjugates immobilized to biogenic magnetite show a high operational stability and remarkable reusability for protein digestion. NANOTECHNOLOGY 2013; 24:125102. [PMID: 23466477 DOI: 10.1088/0957-4484/24/12/125102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this work, magnetosomes produced by microorganisms were chosen as a suitable magnetic carrier for covalent immobilization of thermostable trypsin conjugates with an expected applicability for efficient and rapid digestion of proteins at elevated temperatures. First, a biogenic magnetite was isolated from Magnetospirillum gryphiswaldense and its free surface was coated with the natural polysaccharide chitosan containing free amino and hydroxy groups. Prior to covalent immobilization, bovine trypsin was modified by conjugating with α-, β- and γ-cyclodextrin. Modified trypsin was bound to the magnetic carriers via amino groups using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysulfosuccinimide as coupling reagents. The magnetic biomaterial was characterized by magnetometric analysis and electron microscopy. With regard to their biochemical properties, the immobilized trypsin conjugates showed an increased resistance to elevated temperatures, eliminated autolysis, had an unchanged pH optimum and a significant storage stability and reusability. Considering these parameters, the presented enzymatic system exhibits properties that are superior to those of trypsin forms obtained by other frequently used approaches. The proteolytic performance was demonstrated during in-solution digestion of model proteins (horseradish peroxidase, bovine serum albumin and hen egg white lysozyme) followed by mass spectrometry. It is shown that both magnetic immobilization and chemical modification enhance the characteristics of trypsin making it a promising tool for protein digestion.
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Affiliation(s)
- M Pečová
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
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18
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Khanal A, Pan Y, Brown LS, Konermann L. Pulsed hydrogen/deuterium exchange mass spectrometry for time-resolved membrane protein folding studies. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1620-6. [PMID: 23280751 DOI: 10.1002/jms.3127] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/16/2012] [Accepted: 10/17/2012] [Indexed: 05/10/2023]
Abstract
Kinetic folding experiments by pulsed hydrogen/deuterium exchange (HDX) mass spectrometry (MS) are a well-established tool for water-soluble proteins. To the best of our knowledge, the current study is the first that applies this approach to an integral membrane protein. The native state of bacteriorhodopsin (BR) comprises seven transmembrane helices and a covalently bound retinal cofactor. BR exposure to sodium dodecyl sulfate (SDS) induces partial unfolding and retinal loss. We employ a custom-built three-stage mixing device for pulsed-HDX/MS investigations of BR refolding. The reaction is triggered by mixing SDS-denatured protein with bicelles. After a variable folding time (10 ms to 24 h), the protein is exposed to excess D(2) O buffer under rapid exchange conditions. The HDX pulse is terminated by acid quenching after 24 ms. Subsequent off-line analysis is performed by size exclusion chromatography and electrospray MS. These measurements yield the number of protected backbone N-H sites as a function of folding time, reflecting the recovery of secondary structure. Our results indicate that much of the BR secondary structure is formed quite late during the reaction, on a time scale of 10 s and beyond. It is hoped that in the future it will be possible to extend the pulsed-HDX/MS approach employed here to membrane proteins other than BR.
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Affiliation(s)
- Anil Khanal
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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19
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Dasgupta A, Udgaonkar JB. Transient Non-Native Burial of a Trp Residue Occurs Initially during the Unfolding of a SH3 Domain. Biochemistry 2012; 51:8226-34. [DOI: 10.1021/bi3008627] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Amrita Dasgupta
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
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20
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Chen J, Cui W, Giblin D, Gross ML. New protein footprinting: fast photochemical iodination combined with top-down and bottom-up mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1306-18. [PMID: 22669760 PMCID: PMC3630512 DOI: 10.1007/s13361-012-0403-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 04/25/2012] [Accepted: 04/25/2012] [Indexed: 05/02/2023]
Abstract
We report a new approach for the fast photochemical oxidation of proteins (FPOP) whereby iodine species are used as the modifying reagent. We generate the radicals by photolysis of iodobenzoic acid at 248 nm; the putative iodine radical then rapidly modifies the target protein. This iodine-radical labeling is sensitive, tunable, and site-specific, modifying only histidine and tyrosine residues in contrast to OH radicals that modify 14 amino-acid side chains. We iodinated myoglobin (Mb) and apomyoglobin (aMb) in their native states and analyzed the outcome by both top-down and bottom-up proteomic strategies. Top-down sequencing selects a certain level (addition of one I, two I's) of modification and determines the major components produced in the modification reaction, whereas bottom-up reveals details for each modification site. Tyr146 is found to be modified for aMb but less so for Mb. His82, His93, and His97 are at least 10 times more modified for aMb than for Mb, in agreement with NMR studies. For carbonic anhydrase and its apo form, there are no significant differences of the modification extents, indicating their similarity in conformation and providing a control for this approach. For lispro insulin, insulin-EDTA, and insulin complexed with zinc, iodination yields are sensitive to differences in insulin oligomerization state. The iodine radical labeling is a promising addition to protein footprinting methods, offering higher specificity and lower reactivity than ∙OH and SO(4)(-∙), two other radicals already employed in FPOP.
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Affiliation(s)
- Jiawei Chen
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130, USA
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21
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Dasgupta A, Udgaonkar JB. Four-State Folding of a SH3 Domain: Salt-Induced Modulation of the Stabilities of the Intermediates and Native State. Biochemistry 2012; 51:4723-34. [DOI: 10.1021/bi300223b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amrita Dasgupta
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
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22
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Jha SK, Deepalakshmi PD, Udgaonkar JB. Characterization of deamidation of barstar using electrospray ionization quadrupole time-of-flight mass spectrometry, which stabilizes an equilibrium unfolding intermediate. Protein Sci 2012; 21:633-46. [PMID: 22431291 DOI: 10.1002/pro.2047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 02/01/2012] [Accepted: 02/13/2012] [Indexed: 11/09/2022]
Abstract
Deamidation of asparaginyl residues is a common posttranslational modification in proteins and has been studied extensively because of its important biological effects, such as those on enzymatic activity, protein folding, and proteolytic degradation. However, characterization of the sites of deamidation of a protein has been a difficult analytical problem. In this study, mass spectrometry has been used as an analytical tool to characterize the deamidation of barstar, an RNAse inhibitor. Upon incubation of the protein at alkaline pH for 5 h, intact mass analysis of barstar, using electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QToF MS), indicated an increase in the mass of +2 Da, suggesting possible deamidation of the protein. The sites of deamidation have been identified using the conventional bottom-up approach using a capillary liquid chromatography connected on line to an ESI QToF mass spectrometer and top down approach by direct infusion of the intact protein and fragmenting inside MS. These chemical modifications are shown to lead to stabilization of an unfolding intermediate, which can be observed in equilibrium unfolding studies.
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Affiliation(s)
- Santosh Kumar Jha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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23
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Zhang Y, Zhang H, Cui W, Chen H. Tandem MS analysis of selenamide-derivatized peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1610-1621. [PMID: 21953264 PMCID: PMC3731447 DOI: 10.1007/s13361-011-0170-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/15/2011] [Accepted: 05/15/2011] [Indexed: 05/27/2023]
Abstract
Our previous study showed that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used for selective and rapid derivatization of protein/peptide thiols in high conversion yield. This paper reports the systematic investigation of MS/MS dissociation behaviors of selenamide-derivatized peptide ions upon collision induced dissociation (CID) and electron transfer dissociation (ETD). In the positive ion mode, derivatized peptide ions exhibit tag-dependent CID dissociation pathways. For instance, ebselen-derivatized peptide ions preferentially undergo Se-S bond cleavage upon CID to produce a characteristic fragment ion, the protonated ebselen (m/z 276), which allows selective identification of thiol peptides from protein digest as well as selective detection of thiol proteins from protein mixture using precursor ion scan (PIS). In contrast, NPSP-derivatized peptide ions retain their phenylselenenyl tags during CID, which is useful in sequencing peptides and locating cysteine residues. In the negative ion CID mode, both types of tags are preferentially lost via the Se-S cleavage, analogous to the S-S bond cleavage during CID of disulfide-containing peptide anions. In consideration of the convenience in preparing selenamide-derivatized peptides and the similarity of Se-S of the tag to the S-S bond, we also examined ETD of the derivatized peptide ions to probe the mechanism for electron-based ion dissociation. Interestingly, facile cleavage of Se-S bond occurs to the peptide ions carrying either protons or alkali metal ions, while backbone cleavage to form c/z ions is severely inhibited. These results are in agreement with the Utah-Washington mechanism proposed for depicting electron-based ion dissociation processes.
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Affiliation(s)
- Yun Zhang
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
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24
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Structural and kinetic mapping of side-chain exposure onto the protein energy landscape. Proc Natl Acad Sci U S A 2011; 108:10532-7. [PMID: 21670244 DOI: 10.1073/pnas.1103629108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated.
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25
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Jha SK, Dasgupta A, Malhotra P, Udgaonkar JB. Identification of Multiple Folding Pathways of Monellin Using Pulsed Thiol Labeling and Mass Spectrometry. Biochemistry 2011; 50:3062-74. [DOI: 10.1021/bi1006332] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Santosh Kumar Jha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Amrita Dasgupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Pooja Malhotra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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26
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Chen J, Rempel DL, Gross ML. Temperature jump and fast photochemical oxidation probe submillisecond protein folding. J Am Chem Soc 2011; 132:15502-4. [PMID: 20958033 DOI: 10.1021/ja106518d] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new mass-spectrometry-based approach for studying protein-folding dynamics on the submillisecond time scale. The strategy couples a temperature jump with fast photochemical oxidation of proteins (FPOP), whereby folding/unfolding is followed by changes in oxidative modifications by OH radical reactions. Using a flow system containing the protein barstar as a model, we altered the protein's equilibrium conformation by applying the temperature jump and demonstrated that its reactivity with OH free radicals serves as a reporter of the conformational change. Furthermore, we found that the time-dependent increase in mass resulting from free-radical oxidation is a measure of the rate constant for the transition from the unfolded to the first intermediate state. This advance offers the promise that, when extended with mass-spectrometry-based proteomic analysis, the sites and kinetics of folding/unfolding can also be followed on the submillisecond time scale.
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Affiliation(s)
- Jiawei Chen
- Department of Chemistry, Washington University, One Brookings Drive, Saint Louis, Missouri 63130, United States
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27
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Isom DG, Marguet PR, Oas TG, Hellinga HW. A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity. Proteins 2011; 79:1034-47. [PMID: 21387407 DOI: 10.1002/prot.22932] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 10/08/2010] [Accepted: 10/26/2010] [Indexed: 01/02/2023]
Abstract
Protein thermodynamic stability is a fundamental physical characteristic that determines biological function. Furthermore, alteration of thermodynamic stability by macromolecular interactions or biochemical modifications is a powerful tool for assessing the relationship between protein structure, stability, and biological function. High-throughput approaches for quantifying protein stability are beginning to emerge that enable thermodynamic measurements on small amounts of material, in short periods of time, and using readily accessible instrumentation. Here we present such a method, fast quantitative cysteine reactivity, which exploits the linkage between protein stability, sidechain protection by protein structure, and structural dynamics to characterize the thermodynamic and kinetic properties of proteins. In this approach, the reaction of a protected cysteine and thiol-reactive fluorogenic indicator is monitored over a gradient of temperatures after a short incubation time. These labeling data can be used to determine the midpoint of thermal unfolding, measure the temperature dependence of protein stability, quantify ligand-binding affinity, and, under certain conditions, estimate folding rate constants. Here, we demonstrate the fQCR method by characterizing these thermodynamic and kinetic properties for variants of Staphylococcal nuclease and E. coli ribose-binding protein engineered to contain single, protected cysteines. These straightforward, information-rich experiments are likely to find applications in protein engineering and functional genomics.
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Affiliation(s)
- Daniel G Isom
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.
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28
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Jha A, Ishii K, Udgaonkar JB, Tahara T, Krishnamoorthy G. Exploration of the Correlation between Solvation Dynamics and Internal Dynamics of a Protein. Biochemistry 2010; 50:397-408. [DOI: 10.1021/bi101440c] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Anjali Jha
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Wako, Saitama 351-0198, Japan
| | - Jayant B. Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Wako, Saitama 351-0198, Japan
| | - G. Krishnamoorthy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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29
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Xu K, Zhang Y, Tang B, Laskin J, Roach PJ, Chen H. Study of Highly Selective and Efficient Thiol Derivatization Using Selenium Reagents by Mass Spectrometry. Anal Chem 2010; 82:6926-32. [DOI: 10.1021/ac1011602] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kehua Xu
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, China, 250014, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, Washington 99352
| | - Yun Zhang
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, China, 250014, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, Washington 99352
| | - Bo Tang
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, China, 250014, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, Washington 99352
| | - Julia Laskin
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, China, 250014, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, Washington 99352
| | - Patrick J. Roach
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, China, 250014, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, Washington 99352
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, China, 250014, and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, Washington 99352
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30
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Konermann L, Stocks BB, Pan Y, Tong X. Mass spectrometry combined with oxidative labeling for exploring protein structure and folding. MASS SPECTROMETRY REVIEWS 2010; 29:651-667. [PMID: 19672951 DOI: 10.1002/mas.20256] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This review discusses various mass spectrometry (MS)-based approaches for exploring structural aspects of proteins in solution. Electrospray ionization (ESI)-MS, in particular, has found fascinating applications in this area. For example, when used in conjunction with solution-phase hydrogen/deuterium exchange (HDX), ESI-MS is a highly sensitive tool for probing conformational dynamics. The main focus of this article is a technique that is complementary to HDX, that is, the covalent labeling of proteins by hydroxyl radicals. The reactivity of individual amino acid side chains with *OH is strongly affected by their degree of solvent exposure. Thus, analysis of the oxidative labeling pattern by peptide mapping and tandem mass spectrometry provides detailed structural information. A convenient method for *OH production is the photolysis of H(2)O(2) by a pulsed UV laser, resulting in oxidative labeling on the microsecond time scale. Selected examples demonstrate the use of this technique for structural studies on membrane proteins, and the combination with rapid mixing devices for characterizing the properties of short-lived protein (un)folding intermediates.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada N6A 5B7.
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31
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Stocks BB, Konermann L. Time-dependent changes in side-chain solvent accessibility during cytochrome c folding probed by pulsed oxidative labeling and mass spectrometry. J Mol Biol 2010; 398:362-73. [PMID: 20230834 DOI: 10.1016/j.jmb.2010.03.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 03/08/2010] [Accepted: 03/08/2010] [Indexed: 11/28/2022]
Abstract
The current work employs a novel approach for characterizing structural changes during the refolding of acid-denatured cytochrome c (cyt c). At various time points (ranging from 10 ms to 5 min) after a pH jump from 2 to 7, the protein is exposed to a microsecond hydroxyl radical (.OH) pulse that induces oxidative labeling of solvent-exposed side chains. Most of the covalent modifications appear as +16-Da adducts that are readily detectable by mass spectrometry. The overall extent of labeling decreases as folding proceeds, reflecting dramatic changes in the accessibility of numerous residues. Peptide mapping and tandem mass spectrometry reveal that the side chains of C14, C17, H33, F46, Y48, W59, M65, Y67, Y74, M80, I81, and Y97 are among the dominant sites of oxidation. Temporal changes in the accessibility of these residues are consistent with docking of the N- and C-terminal helices as early as 10 ms. However, structural reorganization at the helix interface takes place up to at least 1 s. Initial misligation of the heme iron by H33 leads to distal crowding, giving rise to low solvent accessibility of the displaced (native) M80 ligand and the adjacent I81. W59 retains a surprisingly high level of accessibility long into the folding process, indicating the presence of packing defects in the hydrophobically collapsed core. Overall, the results of this work are consistent with previous hydrogen/deuterium exchange studies that proposed a foldon-mediated mechanism. The structural data obtained by .OH labeling monitor the packing and burial of side chains, whereas hydrogen/deuterium exchange primarily monitors the formation of secondary structure elements. Hence, the two approaches yield complementary information. Considering the very short time scale of pulsed oxidative labeling, an extension of the approach used here to sub-millisecond folding studies should be feasible.
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Affiliation(s)
- Bradley B Stocks
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
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32
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Picomole-scale characterization of protein stability and function by quantitative cysteine reactivity. Proc Natl Acad Sci U S A 2010; 107:4908-13. [PMID: 20194783 DOI: 10.1073/pnas.0910421107] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Gibbs free energy difference between native and unfolded states ("stability") is one of the fundamental characteristics of a protein. By exploiting the thermodynamic linkage between ligand binding and stability, interactions of a protein with small molecules, nucleic acids, or other proteins can be detected and quantified. Determination of protein stability can therefore provide a universal monitor of biochemical function. Yet, the use of stability measurements as a functional probe is underutilized, because such experiments traditionally require large amounts of protein and special instrumentation. Here we present the quantitative cysteine reactivity (QCR) technique to determine protein stabilities rapidly and accurately using only picomole quantities of material and readily accessible laboratory equipment. We demonstrate that QCR-derived stabilities can be used to measure ligand binding over a wide range of ligand concentrations and affinities. We anticipate that this technique will have broad applications in high-throughput protein engineering experiments and functional genomics.
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33
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Jha A, Udgaonkar JB, Krishnamoorthy G. Characterization of the Heterogeneity and Specificity of Interpolypeptide Interactions in Amyloid Protofibrils by Measurement of Site-Specific Fluorescence Anisotropy Decay Kinetics. J Mol Biol 2009; 393:735-52. [DOI: 10.1016/j.jmb.2009.08.053] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 07/24/2009] [Accepted: 08/17/2009] [Indexed: 10/20/2022]
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34
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Stocks BB, Konermann L. Structural Characterization of Short-Lived Protein Unfolding Intermediates by Laser-Induced Oxidative Labeling and Mass Spectrometry. Anal Chem 2008; 81:20-7. [DOI: 10.1021/ac801888h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bradley B. Stocks
- Departments of Biochemistry and Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Lars Konermann
- Departments of Biochemistry and Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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35
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Pan Y, Stocks BB, Brown L, Konermann L. Structural Characterization of an Integral Membrane Protein in Its Natural Lipid Environment by Oxidative Methionine Labeling and Mass Spectrometry. Anal Chem 2008; 81:28-35. [DOI: 10.1021/ac8020449] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan Pan
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Bradley B. Stocks
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Leonid Brown
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Lars Konermann
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada, and Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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36
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Kumar S, Udgaonkar JB. Conformational conversion may precede or follow aggregate elongation on alternative pathways of amyloid protofibril formation. J Mol Biol 2008; 385:1266-76. [PMID: 19063899 DOI: 10.1016/j.jmb.2008.11.033] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 11/14/2008] [Accepted: 11/15/2008] [Indexed: 11/30/2022]
Abstract
A major goal in the study of protein aggregation is to understand how the conformational heterogeneity characteristic of the process leads to structurally distinct amyloid fibrils. The small protein barstar is known to form amyloid protofibrils in multiple steps at low pH: a small oligomer, the A-form, first transforms into a larger spherical higher oligomeric intermediate (HOI), which then self-associates to form the elongated protofibril. To determine how the conformational conversion reaction during aggregation is coupled to the process of protofibril formation, cysteine-scanning mutagenesis was first used to identify specific residue positions in the protein sequence, which are important in defining the nature of the aggregation process. Two classes of mutant proteins, which are distinguished by their kinetics of aggregation at high protein concentration, have been identified: Class I mutant proteins undergo conformational conversion, as measured by an increase in thioflavin T binding ability and an increase in circular dichroism at 216 nm, significantly faster than Class II mutant proteins. At low protein concentration, the rates of conformational conversion are, however, identical for both classes of mutant proteins. At high protein concentration, the two classes of mutant proteins can be further distinguished on the basis of their rates of protofibril growth, as determined from dynamic light-scattering measurements. For Class I mutant proteins, protofibril elongation occurs at the same, or slightly faster, rate than conformational conversion. For Class II mutant proteins, protofibril elongation is significantly slower than conformational conversion. Dynamic light scattering measurements and atomic force microscopy imaging indicate that for the Class I mutant proteins, conformational conversion occurs concurrently with the self-association of prefibrillar HOIs into protofibrils. On the other hand, for the Class II mutant proteins, the prefibrillar HOI first undergoes conformational conversion, and the conformationally converted HOIs then self-associate to form protofibrils. The two classes of mutant proteins appear, therefore, to use structurally distinct pathways to form amyloid protofibrils. On one pathway, conformational conversion occurs along with, or after, elongation of the oligomers; on the other pathway, conformational conversion precedes elongation of the oligomers. Single mutations in the protein can cause aggregation to switch from one pathway to the other. Importantly, the protofibrils formed by the two classes of mutant proteins have significantly different diameters and different internal structures.
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Affiliation(s)
- Santosh Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560 065, India
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Konermann L, Tong X, Pan Y. Protein structure and dynamics studied by mass spectrometry: H/D exchange, hydroxyl radical labeling, and related approaches. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1021-1036. [PMID: 18523973 DOI: 10.1002/jms.1435] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mass spectrometry (MS) plays a central role in studies on protein structure and dynamics. This review highlights some of the recent developments in this area, with focus on applications involving the use of electrospray ionization (ESI) MS. Although this technique involves the transformation of analytes into highly nonphysiological species (desolvated gas-phase ions in the vacuum), ESI-MS can provide detailed insights into the solution-phase behavior of proteins. Notably, the ionization process itself occurs in a structurally sensitive manner. An increased degree of solution-phase unfolding is correlated with a higher level of protonation. Also, ESI allows the transfer of intact noncovalent complexes into the gas phase, thereby yielding information on binding partners, stoichiometries, and even affinities. A particular focus of this article is the use of hydrogen/deuterium exchange (HDX) methods and hydroxyl radical (.OH) labeling for monitoring dynamic and structural aspect of solution-phase proteins. Conceptual similarities and differences between the two methods are discussed. We describe a simple method for the computational simulation of protein HDX patterns, a tool that can be helpful for the interpretation of isotope exchange data recorded under mixed EX1/EX2 conditions. Important aspects of .OH labeling include a striking dependence on protein concentration, and the tendency of commonly used solvent additives to act as highly effective radical scavengers. If not properly controlled, both of these factors may lead to experimental artifacts.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada.
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Sinha KK, Udgaonkar JB. Barrierless evolution of structure during the submillisecond refolding reaction of a small protein. Proc Natl Acad Sci U S A 2008; 105:7998-8003. [PMID: 18523007 PMCID: PMC2430349 DOI: 10.1073/pnas.0803193105] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Indexed: 11/18/2022] Open
Abstract
To determine whether a protein folding reaction can occur in the absence of a dominant barrier is crucial for understanding its complexity. Here direct ultrafast kinetic measurements have been used to study the initial submillisecond (sub-ms) folding reaction of the small protein barstar. The cooperativity of the initial folding reaction has been explored by using two probes: fluorescence resonance energy transfer, through which the contraction of two intramolecular distances is measured, and the binding of 8-anilino-1-naphthalene sulfonic acid, through which the formation of hydrophobic clusters is monitored. A fast chain contraction is shown to precede the formation of hydrophobic clusters, indicating that the sub-ms folding reaction is not cooperative. The observed rate constant of the sub-ms folding reaction monitored by 8-anilino-1-naphthalene sulfonic acid fluorescence has been found to be the same in stabilizing conditions (low urea concentrations), in which specific structure is formed, and in marginally stabilizing conditions (higher urea concentrations), where virtually no structure is formed in the product of the sub-ms folding reaction. The observation that the folding rate is independent of the folding conditions suggests that the initial folding reaction occurs in the absence of a dominant free energy barrier. These results provide kinetic evidence that the formation of specific structure need not be slowed down by any significant free energy barrier during the course of a very fast protein folding reaction.
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Affiliation(s)
- Kalyan K. Sinha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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