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Jethva PN, Gross ML. Hydrogen Deuterium Exchange and other Mass Spectrometry-based Approaches for Epitope Mapping. FRONTIERS IN ANALYTICAL SCIENCE 2023; 3:1118749. [PMID: 37746528 PMCID: PMC10512744 DOI: 10.3389/frans.2023.1118749] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Antigen-antibody interactions are a fundamental subset of protein-protein interactions responsible for the "survival of the fittest". Determining the interacting interface of the antigen, called an epitope, and that on the antibody, called a paratope, is crucial to antibody development. Because each antigen presents multiple epitopes (unique footprints), sophisticated approaches are required to determine the target region for a given antibody. Although X-ray crystallography, Cryo-EM, and nuclear magnetic resonance can provide atomic details of an epitope, they are often laborious, poor in throughput, and insensitive. Mass spectrometry-based approaches offer rapid turnaround, intermediate structural resolution, and virtually no size limit for the antigen, making them a vital approach for epitope mapping. In this review, we describe in detail the principles of hydrogen deuterium exchange mass spectrometry in application to epitope mapping. We also show that a combination of MS-based approaches can assist or complement epitope mapping and push the limit of structural resolution to the residue level. We describe in detail the MS methods used in epitope mapping, provide our perspective about the approaches, and focus on elucidating the role that HDX-MS is playing now and in the future by organizing a discussion centered around several improvements in prototype instrument/applications used for epitope mapping. At the end, we provide a tabular summary of the current literature on HDX-MS-based epitope mapping.
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Affiliation(s)
- Prashant N. Jethva
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
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2
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Gordon BH, Liu P, Whittington AC, Silvers R, Miller BG. Biochemical methods to map and quantify allosteric motions in human glucokinase. Methods Enzymol 2023; 685:433-459. [PMID: 37245911 PMCID: PMC10308428 DOI: 10.1016/bs.mie.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Allosteric regulation of protein function is ubiquitous in biology. Allostery originates from ligand-mediated alterations in polypeptide structure and/or dynamics, which produce a cooperative kinetic or thermodynamic response to changing ligand concentrations. Establishing a mechanistic description of individual allosteric events requires both mapping the relevant changes in protein structure and quantifying the rates of differential conformational dynamics in the absence and presence of effectors. In this chapter, we describe three biochemical approaches to understand the dynamic and structural signatures of protein allostery using the well-established cooperative enzyme glucokinase as a case study. The combined application of pulsed proteolysis, biomolecular nuclear magnetic resonance spectroscopy and hydrogen-deuterium exchange mass spectrometry offers complementary information that can used to establish molecular models for allosteric proteins, especially when differential protein dynamics are involved.
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Affiliation(s)
- Blaine H Gordon
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
| | - Peilu Liu
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, United States
| | - A Carl Whittington
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Robert Silvers
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States.
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3
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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] [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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4
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Eggertson MJ, Fadgen K, Engen JR, Wales TE. Considerations in the Analysis of Hydrogen Exchange Mass Spectrometry Data. Methods Mol Biol 2020; 2051:407-435. [PMID: 31552640 DOI: 10.1007/978-1-4939-9744-2_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A major component of a hydrogen exchange mass spectrometry experiment is the analysis of protein and peptide mass spectra to yield information about deuterium incorporation. The processing of data that are produced includes the identification of each peptic peptide to create a master table/array of peptide identity that typically includes sequence, retention time and retention time range, mass range, and undeuterated mass. The amount of deuterium incorporated into each of the peptides in this array must then be determined. Various software platforms have been developed in order to perform this specific type of data analysis. We describe the fundamental parameters to be considered at each step along the way and how data processing, either by an individual or by software, must approach the analysis.
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Affiliation(s)
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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5
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Benhaim M, Lee KK, Guttman M. Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry. Protein Pept Lett 2019; 26:16-26. [PMID: 30543159 PMCID: PMC6386625 DOI: 10.2174/0929866526666181212165037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 11/17/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Structural biology has provided a fundamental understanding of protein structure and mechanistic insight into their function. However, high-resolution structures alone are insufficient for a complete understanding of protein behavior. Higher energy conformations, conformational changes, and subtle structural fluctuations that underlie the proper function of proteins are often difficult to probe using traditional structural approaches. Hydrogen/Deuterium Exchange with Mass Spectrometry (HDX-MS) provides a way to probe the accessibility of backbone amide protons under native conditions, which reports on local structural dynamics of solution protein structure that can be used to track complex structural rearrangements that occur in the course of a protein's function. CONCLUSION In the last 20 years the advances in labeling techniques, sample preparation, instrumentation, and data analysis have enabled HDX to gain insights into very complex biological systems. Analysis of challenging targets such as membrane protein complexes is now feasible and the field is paving the way to the analysis of more and more complex systems.
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Affiliation(s)
- Mark Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
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6
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Davila S, Liu P, Smith A, Marshall AG, Pedigo S. Spontaneous Calcium-Independent Dimerization of the Isolated First Domain of Neural Cadherin. Biochemistry 2018; 57:6404-6415. [PMID: 30387993 DOI: 10.1021/acs.biochem.8b00733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cadherins are calcium-dependent, transmembrane adhesion molecules that assemble through direct noncovalent association of their N-terminal extracellular modular domains. As the transmembrane component of adherens junctions, they indirectly link adherent cells' actin cytoskeletons. Here, we investigate the most distal extracellular domain of neural cadherin (N-cadherin), a protein required at excitatory synapses, the site of long-term potentiation. This domain is the site of the adhesive interface, and it forms a dimer spontaneously without binding calcium, a surprising finding given that calcium binding is required for proper physiological function. A critical tryptophan at position 2, W2, provides a spectroscopic probe for the "closed" monomer and strand-swapped dimer. Spectroscopic studies show that W2 remains docked in the two forms but has a different apparent interaction with the hydrophobic pocket. Size-exclusion chromatography was used to measure the levels of the monomer and dimer over time to study the kinetics and equilibria of the unexpected spontaneous dimer formation ( Kd = 130 μM; τ = 2 days at 4 °C). Our results support the idea that NCAD1 is missing critical contacts that facilitate the rapid exchange of the βA-strand. Furthermore, the monomer and dimer have equivalent and exceptionally high intrinsic stability for a 99-residue Ig-like domain with no internal disulfides ( Tm = 77 °C; Δ H = 85 kcal/mol). Ultimately, a complete analysis of synapse dynamics requires characterization of the kinetics and equilibria of N-cadherin. The studies reported here take a reductionist approach to understanding the essential biophysics of an atypical Ig-like domain that is the site of the adhesive interface of N-cadherin.
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Affiliation(s)
- Samantha Davila
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677 , United States
| | - Peilu Liu
- Department of Chemistry & Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States.,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Alexis Smith
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677 , United States
| | - Alan G Marshall
- Department of Chemistry & Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States.,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Susan Pedigo
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677 , United States
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7
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Xiao K, Zhao Y, Choi M, Liu H, Blanc A, Qian J, Cahill TJ, Li X, Xiao Y, Clark LJ, Li S. Revealing the architecture of protein complexes by an orthogonal approach combining HDXMS, CXMS, and disulfide trapping. Nat Protoc 2018; 13:1403-1428. [PMID: 29844522 DOI: 10.1038/nprot.2018.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many cellular functions necessitate structural assemblies of two or more associated proteins. The structural characterization of protein complexes using standard methods, such as X-ray crystallography, is challenging. Herein, we describe an orthogonal approach using hydrogen-deuterium-exchange mass spectrometry (HDXMS), cross-linking mass spectrometry (CXMS), and disulfide trapping to map interactions within protein complexes. HDXMS measures changes in solvent accessibility and hydrogen bonding upon complex formation; a decrease in HDX rate could account for newly formed intermolecular or intramolecular interactions. To distinguish between inter- and intramolecular interactions, we use a CXMS method to determine the position of direct interface regions by trapping intermolecular residues in close proximity to various cross-linkers (e.g., disuccinimidyl adipate (DSA)) of different lengths and reactive groups. Both MS-based experiments are performed on high-resolution mass spectrometers (e.g., an Orbitrap Elite hybrid mass spectrometer). The physiological relevance of the interactions identified through HDXMS and CXMS is investigated by transiently co-expressing cysteine mutant pairs, one mutant on each protein at the discovered interfaces, in an appropriate cell line, such as HEK293. Disulfide-trapped protein complexes are formed within cells spontaneously or are facilitated by addition of oxidation reagents such as H2O2 or diamide. Western blotting analysis, in the presence and absence of reducing reagents, is used to determine whether the disulfide bonds are formed in the proposed complex interface in physiologically relevant milieus. The procedure described here requires 1-2 months. We demonstrate this approach using the β2-adrenergic receptor-β-arrestin1 complex as the model system.
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Affiliation(s)
- Kunhong Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Vascular Medicine Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Biomedical Mass Spectrometry Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yang Zhao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Minjung Choi
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Hongda Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adi Blanc
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Jiang Qian
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Thomas J Cahill
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Xue Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Yunfang Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lisa J Clark
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sheng Li
- Department of Chemistry, University of California at San Diego, La Jolla, California, USA
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8
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MS-based conformation analysis of recombinant proteins in design, optimization and development of biopharmaceuticals. Methods 2018; 144:134-151. [PMID: 29678586 DOI: 10.1016/j.ymeth.2018.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/10/2018] [Accepted: 04/12/2018] [Indexed: 01/18/2023] Open
Abstract
Mass spectrometry (MS)-based methods for analyzing protein higher order structures have gained increasing application in the field of biopharmaceutical development. The predominant methods used in this area include native MS, hydrogen deuterium exchange-MS, covalent labeling, cross-linking and limited proteolysis. These MS-based methods will be briefly described in this article, followed by a discussion on how these methods contribute at different stages of discovery and development of protein therapeutics.
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9
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Sternisha SM, Liu P, Marshall AG, Miller BG. Mechanistic Origins of Enzyme Activation in Human Glucokinase Variants Associated with Congenital Hyperinsulinism. Biochemistry 2018; 57:1632-1639. [PMID: 29425029 DOI: 10.1021/acs.biochem.8b00022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human glucokinase (GCK) acts as the body's primary glucose sensor and plays a critical role in glucose homeostatic maintenance. Gain-of-function mutations in gck produce hyperactive enzyme variants that cause congenital hyperinsulinism. Prior biochemical and biophysical studies suggest that activated disease variants can be segregated into two mechanistically distinct classes, termed α-type and β-type. Steady-state viscosity variation studies indicate that the kcat values of wild-type GCK and an α-type variant are partially diffusion-limited, whereas the kcat value of a β-type variant is viscosity-independent. Transient-state chemical quench-flow analyses demonstrate that wild-type GCK and the α-type variant display burst kinetics, whereas the β-type variant lacks a burst phase. Comparative hydrogen-deuterium exchange mass spectrometry of unliganded enzymes demonstrates that a disordered active site loop, which folds upon binding of glucose, is protected from exchange in the α-type variant. The α-type variant also displays an increased level of exchange within a β-strand located near the enzyme's hinge region, which becomes more solvent-exposed upon glucose binding. In contrast, β-type activation causes no substantial difference in global or local exchange relative to that of unliganded, wild-type GCK. Together, these results demonstrate that α-type activation results from a shift in the conformational ensemble of unliganded GCK toward a state resembling the glucose-bound conformation, whereas β-type activation is attributable to an accelerated rate of product release. This work elucidates the molecular basis of naturally occurring, activated GCK disease variants and provides insight into the structural and dynamic origins of GCK's unique kinetic cooperativity.
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Affiliation(s)
- Shawn M Sternisha
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
| | - Peilu Liu
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
| | - Alan G Marshall
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States.,Ion Cyclotron Resonance Program , The National High Magnetic Field Laboratory , Tallahassee , Florida 32310 , United States
| | - Brian G Miller
- Department of Chemistry and Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States
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10
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Tian S, Yu G, He H, Zhao Y, Liu P, Marshall AG, Demeler B, Stagg SM, Li H. Pih1p-Tah1p Puts a Lid on Hexameric AAA+ ATPases Rvb1/2p. Structure 2017; 25:1519-1529.e4. [PMID: 28919439 PMCID: PMC6625358 DOI: 10.1016/j.str.2017.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/11/2017] [Accepted: 08/07/2017] [Indexed: 11/21/2022]
Abstract
The Saccharomyces cerevisiae (Sc) R2TP complex affords an Hsp90-mediated and nucleotide-driven chaperone activity to proteins of small ribonucleoprotein particles (snoRNPs). The current lack of structural information on the ScR2TP complex, however, prevents a mechanistic understanding of this biological process. We characterized the structure of the ScR2TP complex made up of two AAA+ ATPases, Rvb1/2p, and two Hsp90 binding proteins, Tah1p and Pih1p, and its interaction with the snoRNP protein Nop58p by a combination of analytical ultracentrifugation, isothermal titration calorimetry, chemical crosslinking, hydrogen-deuterium exchange, and cryoelectron microscopy methods. We find that Pih1p-Tah1p interacts with Rvb1/2p cooperatively through the nucleotide-sensitive domain of Rvb1/2p. Nop58p further binds Pih1p-Tahp1 on top of the dome-shaped R2TP. Consequently, nucleotide binding releases Pih1p-Tah1p from Rvb1/2p, which offers a mechanism for nucleotide-driven binding and release of snoRNP intermediates.
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Affiliation(s)
- Shaoxiong Tian
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Ge Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Huan He
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Peilu Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Ion Cyclotron Resonance Program, The National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Scott M Stagg
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hong Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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11
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Claesen J, Burzykowski T. Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry. MASS SPECTROMETRY REVIEWS 2017; 36:649-667. [PMID: 27602546 DOI: 10.1002/mas.21519] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 05/08/2016] [Accepted: 08/18/2016] [Indexed: 06/06/2023]
Abstract
Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvements and the increased use of protein-HDXMS, large amounts of complex data are generated, which require appropriate analysis. Computational analysis of HDXMS requires several steps. A typical workflow for proteins consists of identification of (non-)deuterated peptides or fragments of the protein under study (local analysis), or identification of the deuterated protein as a whole (global analysis); determination of the deuteration level; estimation of the protection extent or exchange rates of the labile backbone amide hydrogen atoms; and a statistically sound interpretation of the estimated protection extent or exchange rates. Several algorithms, specifically designed for HDX analysis, have been proposed. They range from procedures that focus on one specific step in the analysis of HDX data to complete HDX workflow analysis tools. In this review, we provide an overview of the computational methods and discuss outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:649-667, 2017.
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Affiliation(s)
- Jürgen Claesen
- I-BioStat, Hasselt University, Campus Diepenbeek, Agoralaan Gebouw D, Diepenbeek 3590, Belgium
| | - Tomasz Burzykowski
- I-BioStat, Hasselt University, Campus Diepenbeek, Agoralaan Gebouw D, Diepenbeek 3590, Belgium
- Statistics and Medical informatics Unit, Medical University of Bialystok, Białystok, Poland
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12
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Tao Y, Fang P, Kim S, Guo M, Young NL, Marshall AG. Mapping the contact surfaces in the Lamin A:AIMP3 complex by hydrogen/deuterium exchange FT-ICR mass spectrometry. PLoS One 2017; 12:e0181869. [PMID: 28797100 PMCID: PMC5552228 DOI: 10.1371/journal.pone.0181869] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3 interacts with LmnA is unclear. Here we report solution-phase hydrogen/deuterium exchange (HDX) for AIMP3, LmnA, and AIMP3 in association with the LmnA C-terminus. Reversed-phase LC coupled with LTQ 14.5 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) results in high mass accuracy and resolving power for comparing the D-uptake profiles for AIMP3, LmnA, and their complex. The results show that the AIMP3-LmnA interaction involves one of the two putative binding sites and an adjacent novel interface on AIMP3. LmnA binds AIMP3 via its extreme C-terminus. Together these findings provide a structural insight for understanding the interaction between AIMP3 and LmnA in AIMP3 degradation.
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Affiliation(s)
- Yeqing Tao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
| | - Pengfei Fang
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, United States of America
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, United States of America
| | - Nicolas L. Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, United States of America
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13
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Chen J, Zhang Q, Ren W, Li W. Piecing Together the Allosteric Patterns of Chaperonin GroEL. J Phys Chem B 2017; 121:4987-4996. [PMID: 28430446 DOI: 10.1021/acs.jpcb.7b01992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite considerable efforts, elucidating the allostery of large macromolecular assemblies at a molecular level in solution remains technically challenging due to its structural complexity. Here we have employed an approach combining amide backbone hydrogen/deuterium exchange coupled with mass spectrometry, fluorescence spectroscopy, and molecular simulations to characterize allosteric patterns of chaperonin GroEL, an ∼800 kDa tetradecamer from E. coli. Using available crystal structures of GroEL, we quantitatively map out GroEL allosteric changes in solution by resolving exchange behaviors of 133 overlapping proteolytic peptides with more than 95% sequence coverage. This comprehensive analysis gives a refined resolution down to five residues to pilot the GroEL allosteric determinants, of which the localized dynamics is monitored by tryptophan-mutated GroEL. Furthermore, the GroEL conformational transition is evaluated by molecular dynamics simulations with an atomic-interaction-based coarse-grained model. Collectively, we provide a practical methodology to analyze GroEL allostery in solution.
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Affiliation(s)
- Jin Chen
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences , Okazaki 444-8787, Japan
| | - Qian Zhang
- Department of Chemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Weitong Ren
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University , Nanjing 210093, China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University , Nanjing 210093, China
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14
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Structural characterization of human aminoacyl-tRNA synthetases for translational and nontranslational functions. Methods 2017; 113:83-90. [DOI: 10.1016/j.ymeth.2016.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/14/2016] [Accepted: 11/21/2016] [Indexed: 11/18/2022] Open
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15
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Graham BW, Tao Y, Dodge KL, Thaxton CT, Olaso D, Young NL, Marshall AG, Trakselis MA. DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase. J Biol Chem 2016; 291:12467-12480. [PMID: 27044751 DOI: 10.1074/jbc.m116.719591] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 11/06/2022] Open
Abstract
The archaeal minichromosomal maintenance (MCM) helicase from Sulfolobus solfataricus (SsoMCM) is a model for understanding structural and mechanistic aspects of DNA unwinding. Although interactions of the encircled DNA strand within the central channel provide an accepted mode for translocation, interactions with the excluded strand on the exterior surface have mostly been ignored with regard to DNA unwinding. We have previously proposed an extension of the traditional steric exclusion model of unwinding to also include significant contributions with the excluded strand during unwinding, termed steric exclusion and wrapping (SEW). The SEW model hypothesizes that the displaced single strand tracks along paths on the exterior surface of hexameric helicases to protect single-stranded DNA (ssDNA) and stabilize the complex in a forward unwinding mode. Using hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance MS, we have probed the binding sites for ssDNA, using multiple substrates targeting both the encircled and excluded strand interactions. In each experiment, we have obtained >98.7% sequence coverage of SsoMCM from >650 peptides (5-30 residues in length) and are able to identify interacting residues on both the interior and exterior of SsoMCM. Based on identified contacts, positively charged residues within the external waist region were mutated and shown to generally lower DNA unwinding without negatively affecting the ATP hydrolysis. The combined data globally identify binding sites for ssDNA during SsoMCM unwinding as well as validating the importance of the SEW model for hexameric helicase unwinding.
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Affiliation(s)
- Brian W Graham
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Yeqing Tao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Katie L Dodge
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Carly T Thaxton
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Danae Olaso
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798
| | - Nicolas L Young
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310
| | - Alan G Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306; National High Magnetic Field Laboratory, Tallahassee, Florida 32310
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798.
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16
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Jiang J, Gao L, Bie X, Lu Z, Liu H, Zhang C, Lu F, Zhao H. Identification of novel surfactin derivatives from NRPS modification of Bacillus subtilis and its antifungal activity against Fusarium moniliforme. BMC Microbiol 2016; 16:31. [PMID: 26957318 PMCID: PMC4784341 DOI: 10.1186/s12866-016-0645-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 02/25/2016] [Indexed: 12/03/2022] Open
Abstract
Background Bacillus subtilis strain PB2-L1 produces the lipopeptide surfactin, a highly potent biosurfactant synthesized by a large multimodular nonribosomal peptide synthetase (NRPS). In the present study, the modules SrfA-A-Leu, SrfA-B-Asp, and SrfA-B-Leu from surfactin NRPS in B. subtilis BP2-L1 were successfully knocked-out using a temperature-sensitive plasmid, pKS2-mediated-based, homologous, recombination method. Results Three novel surfactin products were produced, individually lacking amino acid Leu-3, Asp-5, or Leu-6. These surfactins were detected, isolated, and characterized by HPLC and LC-FTICR-MS/MS. In comparison with native surfactin, [∆Leu3]surfactin and [∆Leu6]surfactin showed evidence of reduced toxicity, while [∆Asp5]surfactin showed stronger inhibition than native surfactin against B. pumilus and Micrococcus luteus. These results showed that the minimum inhibitory concentration of [∆Leu6]surfactin for Fusarium moniliforme was 50 μg/mL, such that [∆Leu6]surfactin could lead to mycelium projection, cell damage, and leakage of nucleic acids and protein. These factors all contributed to stimulating apoptosis in F. moniliforme. Conclusions The present results revealed that [∆Leu6]surfactin showed a significant antifungal activity against F. moniliforme and might successfully be employed to control fungal food contamination and improve food safety.
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Affiliation(s)
- Jian Jiang
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing, 210095, P.R. China
| | - Ling Gao
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing, 210095, P.R. China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing, 210095, P.R. China.
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing, 210095, P.R. China
| | - Hongxia Liu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing, 210095, P.R. China
| | - Chong Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing, 210095, P.R. China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing, 210095, P.R. China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing, 210095, P.R. China
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17
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Kazazić S, Bertoša B, Luić M, Mikleušević G, Tarnowski K, Dadlez M, Narczyk M, Bzowska A. New Insights into Active Site Conformation Dynamics of E. coli PNP Revealed by Combined H/D Exchange Approach and Molecular Dynamics Simulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:73-82. [PMID: 26337516 DOI: 10.1007/s13361-015-1239-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 07/24/2015] [Accepted: 07/26/2015] [Indexed: 06/05/2023]
Abstract
The biologically active form of purine nucleoside phosphorylase (PNP) from Escherichia coli (EC 2.4.2.1) is a homohexamer unit, assembled as a trimer of dimers. Upon binding of phosphate, neighboring monomers adopt different active site conformations, described as open and closed. To get insight into the functions of the two distinctive active site conformations, virtually inactive Arg24Ala mutant is complexed with phosphate; all active sites are found to be in the open conformation. To understand how the sites of neighboring monomers communicate with each other, we have combined H/D exchange (H/DX) experiments with molecular dynamics (MD) simulations. Both methods point to the mobility of the enzyme, associated with a few flexible regions situated at the surface and within the dimer interface. Although H/DX provides an average extent of deuterium uptake for all six hexamer active sites, it was able to indicate the dynamic mechanism of cross-talk between monomers, allostery. Using this technique, it was found that phosphate binding to the wild type (WT) causes arrest of the molecular motion in backbone fragments that are flexible in a ligand-free state. This was not the case for the Arg24Ala mutant. Upon nucleoside substrate/inhibitor binding, some release of the phosphate-induced arrest is observed for the WT, whereas the opposite effects occur for the Arg24Ala mutant. MD simulations confirmed that phosphate is bound tightly in the closed active sites of the WT; conversely, in the open conformation of the active site of the WT phosphate is bound loosely moving towards the exit of the active site. In Arg24Ala mutant binary complex Pi is bound loosely, too.
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Affiliation(s)
- Saša Kazazić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Branimir Bertoša
- Division of Physical Chemistry, Faculty of Science at University of Zagreb, Zagreb, Croatia.
| | - Marija Luić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Goran Mikleušević
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Krzysztof Tarnowski
- Institute of Biochemistry and Biophysics Department, Polish Academy of Science, Warsaw, Poland
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics Department, Polish Academy of Science, Warsaw, Poland
| | - Marta Narczyk
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
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18
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Guan X, Noble KA, Tao Y, Roux KH, Sathe SK, Young NL, Marshall AG. Epitope mapping of 7S cashew antigen in complex with antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:812-819. [PMID: 26169135 DOI: 10.1002/jms.3589] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 06/04/2023]
Abstract
The potential epitope of a recombinant food allergen protein, cashew Ana o 1, reactive to monoclonal antibody, mAb 2G4, has been mapped by solution-phase amide backbone H/D exchange (HDX) monitored by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Purified mAb 2G4 was incubated with recombinant Ana o 1 (rAna o 1) to form antigen:monoclonal antibody (Ag:mAb) complexes. Complexed and uncomplexed (free) rAna o 1 were then subjected to HDX-MS analysis. Five regions protected from H/D exchange upon mAb binding are identified as potential conformational epitope-contributing segments.
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Affiliation(s)
- Xiaoyan Guan
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Kyle A Noble
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Yeqing Tao
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
| | - Kenneth H Roux
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Shridhar K Sathe
- Department of Nutrition, Food and Exercise Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Nicolas L Young
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
| | - Alan G Marshall
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL, 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL, 32306, USA
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19
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Engen JR, Wales TE. Analytical Aspects of Hydrogen Exchange Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:127-48. [PMID: 26048552 PMCID: PMC4989240 DOI: 10.1146/annurev-anchem-062011-143113] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This article reviews the analytical aspects of measuring hydrogen exchange by mass spectrometry (HX MS). We describe the nature of analytical selectivity in hydrogen exchange, then review the analytical tools required to accomplish fragmentation, separation, and the mass spectrometry measurements under restrictive exchange quench conditions. In contrast to analytical quantitation that relies on measurements of peak intensity or area, quantitation in HX MS depends on measuring a mass change with respect to an undeuterated or deuterated control, resulting in a value between zero and the maximum amount of deuterium that can be incorporated. Reliable quantitation is a function of experimental fidelity and to achieve high measurement reproducibility, a large number of experimental variables must be controlled during sample preparation and analysis. The method also reports on important qualitative aspects of the sample, including conformational heterogeneity and population dynamics.
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Affiliation(s)
- John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115;
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20
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Salisbury JP, Liu Q, Agar JN. QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure. BMC Bioinformatics 2014; 15:403. [PMID: 25495703 PMCID: PMC4274694 DOI: 10.1186/s12859-014-0403-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/01/2014] [Indexed: 12/25/2022] Open
Abstract
Background Hydrogen/deuterium exchange (HDX) coupled to mass spectrometry permits analysis of structure, dynamics, and molecular interactions of proteins. HDX mass spectrometry is confounded by deuterium exchange-associated peaks overlapping with peaks of heavy, natural abundance isotopes, such as carbon-13. Recent studies demonstrated that high-performance mass spectrometers could resolve isotopic fine structure and eliminate this peak overlap, allowing direct detection and quantification of deuterium incorporation. Results Here, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure. Given a peptide sequence (or elemental formula) and charge state, the mass-to-charge ratios of deuterium-associated peaks of the specified ion is determined. Intensities of peaks in an experimental mass spectrum within bins corresponding to these values are used to determine the distribution of deuterium incorporated. A theoretical spectrum can then be calculated based on the estimated distribution of deuterium exchange to confirm interpretation of the spectrum. Deuterium incorporation can also be detected for ion signals without a priori specification of an elemental formula, permitting detection of exchange in complex samples of unidentified material such as natural organic matter. A tool is also incorporated into QUDeX-MS to help in assigning ion signals from peptides arising from enzymatic digestion of proteins. MATLAB-deployable and standalone versions are available for academic use at qudex-ms.sourceforge.net and agarlabs.com. Conclusion Isotopic fine structure HDX-MS offers the potential to increase sequence coverage of proteins being analyzed through mass accuracy and deconvolution of overlapping ion signals. As previously demonstrated, however, the data analysis workflow for HDX-MS data with resolved isotopic fine structure is distinct. QUDeX-MS we hope will aid in the adoption of isotopic fine structure HDX-MS by providing an intuitive workflow and interface for data analysis.
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Affiliation(s)
- Joseph P Salisbury
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences and Barnett Institute of Chemical and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.
| | - Qian Liu
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences and Barnett Institute of Chemical and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.
| | - Jeffrey N Agar
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences and Barnett Institute of Chemical and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.
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21
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Lindner R, Lou X, Reinstein J, Shoeman RL, Hamprecht FA, Winkler A. Hexicon 2: automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1018-28. [PMID: 24676893 PMCID: PMC4018513 DOI: 10.1007/s13361-014-0850-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 05/12/2023]
Abstract
Hydrogen-deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.
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Affiliation(s)
- Robert Lindner
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Xinghua Lou
- Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg, Heidelberg, Germany
| | - Jochen Reinstein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Robert L Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Fred A Hamprecht
- Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg, Heidelberg, Germany
| | - Andreas Winkler
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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22
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Thalassinos K, Pandurangan AP, Xu M, Alber F, Topf M. Conformational States of macromolecular assemblies explored by integrative structure calculation. Structure 2014; 21:1500-8. [PMID: 24010709 PMCID: PMC3988990 DOI: 10.1016/j.str.2013.08.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 08/10/2013] [Accepted: 08/12/2013] [Indexed: 12/22/2022]
Abstract
A detailed description of macromolecular assemblies in multiple conformational states can be very valuable for understanding cellular processes. At present, structural determination of most assemblies in different biologically relevant conformations cannot be achieved by a single technique and thus requires an integrative approach that combines information from multiple sources. Different techniques require different computational methods to allow efficient and accurate data processing and analysis. Here, we summarize the latest advances and future challenges in computational methods that help the interpretation of data from two techniques—mass spectrometry and three-dimensional cryo-electron microscopy (with focus on alignment and classification of heterogeneous subtomograms from cryo-electron tomography). We evaluate how new developments in these two broad fields will lead to further integration with atomic structures to broaden our picture of the dynamic behavior of assemblies in their native environment.
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Affiliation(s)
- Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
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23
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Liu Q, Easterling ML, Agar JN. Resolving isotopic fine structure to detect and quantify natural abundance- and hydrogen/deuterium exchange-derived isotopomers. Anal Chem 2013; 86:820-5. [PMID: 24328359 DOI: 10.1021/ac403365g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) is used for analyzing protein dynamics, protein folding/unfolding, and molecular interactions. Until this study, HDX MS experiments employed mass spectral resolving powers that afforded only one peak per nominal mass in a given peptide's isotope distribution, and HDX MS data analysis methods were developed accordingly. A level of complexity that is inherent to HDX MS remained unaddressed, namely, various combinations of natural abundance heavy isotopes and exchanged deuterium shared the same nominal mass and overlapped at previous resolving powers. For example, an A + 2 peak is comprised of (among other isotopomers) a two-(2)H-exchanged/zero-(13)C isotopomer, a one-(2)H-exchanged/one-(13)C isotopomer, and a zero-(2)H-exchanged/two-(13)C isotopomer. Notably, such isotopomers differ slightly in mass as a result of the ∼3 mDa mass defect between (2)H and (13)C atoms. Previous HDX MS methods did not resolve these isotopomers, requiring a natural-abundance-only (before HDX or "time zero") spectrum and data processing to remove its contribution. It is demonstrated here that high-resolution mass spectrometry can be used to detect isotopic fine structure, such as in the A + 2 profile example above, deconvolving the isotopomer species resulting from deuterium incorporation. Resolving isotopic fine structure during HDX MS therefore permits direct monitoring of HDX, which can be calculated as the sum of the fractional peak magnitudes of the deuterium-exchanged isotopomers. This obviates both the need for a time zero spectrum as well as data processing to account for natural abundance heavy isotopes, saving instrument and analysis time.
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Affiliation(s)
- Qian Liu
- Department of Chemistry, Brandeis University , Waltham, Massachusetts 02453, United States
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24
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Guttman M, Weis DD, Engen JR, Lee KK. Analysis of overlapped and noisy hydrogen/deuterium exchange mass spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1906-12. [PMID: 24018862 PMCID: PMC3855366 DOI: 10.1007/s13361-013-0727-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 07/29/2013] [Accepted: 08/02/2013] [Indexed: 05/05/2023]
Abstract
Noisy and overlapped mass spectrometry data hinder the sequence coverage that can be obtained from hydrogen deuterium exchange analysis, and places a limit on the complexity of the samples that can be studied by this technique. Advances in instrumentation have addressed these limits, but as the complexity of the biological samples under investigation increases, these problems are re-encountered. Here we describe the use of binomial distribution fitting with asymmetric linear squares regression for calculating the accurate deuterium content for mass envelopes of low signal or that contain significant overlap. The approach is demonstrated with a test data set of HIV Env gp140 wherein inclusion of the new analysis regime resulted in obtaining exchange data for 42 additional peptides, improving the sequence coverage by 11%. At the same time, the precision of deuterium uptake measurements was improved for nearly every peptide examined. The improved processing algorithms also provide an efficient method for deconvolution of bimodal mass envelopes and EX1 kinetic signatures. All these functions and visualization tools have been implemented in the new version of the freely available software, HX-Express v2.
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Affiliation(s)
- Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA,
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25
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Kim DG, Lee JY, Kwon NH, Fang P, Zhang Q, Wang J, Young NL, Guo M, Cho HY, Mushtaq AU, Jeon YH, Choi JW, Han JM, Kang HW, Joo JE, Hur Y, Kang W, Yang H, Nam DH, Lee MS, Lee JW, Kim ES, Moon A, Kim K, Kim D, Kang EJ, Moon Y, Rhee KH, Han BW, Yang JS, Han G, Yang WS, Lee C, Wang MW, Kim S. Chemical inhibition of prometastatic lysyl-tRNA synthetase-laminin receptor interaction. Nat Chem Biol 2013; 10:29-34. [PMID: 24212136 DOI: 10.1038/nchembio.1381] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/18/2013] [Indexed: 01/11/2023]
Abstract
Lysyl-tRNA synthetase (KRS), a protein synthesis enzyme in the cytosol, relocates to the plasma membrane after a laminin signal and stabilizes a 67-kDa laminin receptor (67LR) that is implicated in cancer metastasis; however, its potential as an antimetastatic therapeutic target has not been explored. We found that the small compound BC-K-YH16899, which binds KRS, impinged on the interaction of KRS with 67LR and suppressed metastasis in three different mouse models. The compound inhibited the KRS-67LR interaction in two ways. First, it directly blocked the association between KRS and 67LR. Second, it suppressed the dynamic movement of the N-terminal extension of KRS and reduced membrane localization of KRS. However, it did not affect the catalytic activity of KRS. Our results suggest that specific modulation of a cancer-related KRS-67LR interaction may offer a way to control metastasis while avoiding the toxicities associated with inhibition of the normal functions of KRS.
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Affiliation(s)
- Dae Gyu Kim
- 1] Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea. [2] Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea. [3]
| | - Jin Young Lee
- 1] Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea. [2] Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea. [3]
| | - Nam Hoon Kwon
- 1] Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea. [2] Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Pengfei Fang
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, USA
| | - Qian Zhang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, USA
| | - Jing Wang
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, USA
| | - Nicolas L Young
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
| | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, USA
| | - Hye Young Cho
- College of Pharmacy, Korea University, Sejong, Korea
| | | | - Young Ho Jeon
- College of Pharmacy, Korea University, Sejong, Korea
| | - Jin Woo Choi
- 1] Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea. [2] Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jung Min Han
- 1] Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea. [2] Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | | | | | - Youn Hur
- Yuhan Research Institute, Yongin, Korea
| | - Wonyoung Kang
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Heekyoung Yang
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Do-Hyun Nam
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Mi-Sook Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Jung Weon Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Eun-Sook Kim
- College of Pharmacy, Duksung Women's University, Seoul, Korea
| | - Aree Moon
- College of Pharmacy, Duksung Women's University, Seoul, Korea
| | - Kibom Kim
- 1] Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea. [2] Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Doyeun Kim
- 1] Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea. [2] Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Eun Joo Kang
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea
| | - Youngji Moon
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea
| | - Kyung Hee Rhee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Jee Sun Yang
- Translational Research Center for Protein Function Control, Department of Biotechnology and WCU Department of Biomedical Sciences, Yonsei University, Seoul, Korea
| | - Gyoonhee Han
- Translational Research Center for Protein Function Control, Department of Biotechnology and WCU Department of Biomedical Sciences, Yonsei University, Seoul, Korea
| | - Won Suk Yang
- 1] Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea. [2] Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Cheolju Lee
- BRI, Korea Institute of Science and Technology, Seoul, Korea
| | - Ming-Wei Wang
- The National Center for Drug Screening, Zhangjiang High-Tech Park, Shanghai, China
| | - Sunghoon Kim
- 1] Medicinal Bioconvergence Research Center, Seoul National University, Seoul, Korea. [2] Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea. [3] World Class University Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul, Korea
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26
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Zhang Q, Noble KA, Mao Y, Young NL, Sathe SK, Roux KH, Marshall AG. Rapid screening for potential epitopes reactive with a polycolonal antibody by solution-phase H/D exchange monitored by FT-ICR mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1016-1025. [PMID: 23681851 DOI: 10.1007/s13361-013-0644-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 04/03/2013] [Accepted: 04/03/2013] [Indexed: 06/02/2023]
Abstract
The potential epitopes of a recombinant food allergen protein, cashew Ana o 2, reactive to polyclonal antibodies, were mapped by solution-phase amide backbone H/D exchange (HDX) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Ana o 2 polyclonal antibodies were purified in the serum from a goat immunized with cashew nut extract. Antibodies were incubated with recombinant Ana o 2 (rAna o 2) to form antigen:polyclonal antibody (Ag:pAb) complexes. Complexed and uncomplexed (free) rAna o 2 were then subjected to HDX-MS analysis. Four regions protected from H/D exchange upon pAb binding are identified as potential epitopes and mapped onto a homologous model.
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Affiliation(s)
- Qian Zhang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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27
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Willison LN, Zhang Q, Su M, Teuber SS, Sathe SK, Roux KH. Conformational epitope mapping of Pru du 6, a major allergen from almond nut. Mol Immunol 2013; 55:253-63. [PMID: 23498967 DOI: 10.1016/j.molimm.2013.02.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/13/2013] [Accepted: 02/16/2013] [Indexed: 10/27/2022]
Abstract
Tree nuts are a widely consumed food. Although enjoyed safely by most individuals, allergic reactions to tree nuts, including almond, are not uncommon. Almond prunin (Pru du 6), an 11S globulin (legumin), is an abundant nut seed protein and a major allergen. Conformational epitope mapping studies of prunin have been performed with a murine monoclonal antibody (mAb) 4C10. This mAb reacts with non-reduced but not reduced prunin in immunoblotting assays, indicating the recognition of a conformational epitope. 4C10 competes with patient IgE, as assessed by ELISA, indicating clinical significance of the epitope. To characterize the 4C10 epitope, hydrogen/deuterium exchange (HDX) monitored by 14.5 T Fourier transform ion cyclotron resonance mass spectrometry (MS) was performed on the native prunin-4C10 complex and on uncomplexed native prunin. Several epitope candidate peptides that differ in deuterium uptake between the complexed and uncomplexed forms were identified. The epitope was further mapped by analyzing chimeric molecules incorporating segments of the homologous soybean allergen, Gly m 6, in immunoassays. These data indicate that the 4C10 epitope overlaps with a subset of patient IgE binding epitopes on almond prunin and further supports HDX-MS as a valid technique for mapping conformational epitopes.
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Affiliation(s)
- LeAnna N Willison
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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28
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Zhang Q, Chen J, Kuwajima K, Zhang HM, Xian F, Young NL, Marshall AG. Nucleotide-induced conformational changes of tetradecameric GroEL mapped by H/D exchange monitored by FT-ICR mass spectrometry. Sci Rep 2013; 3:1247. [PMID: 23409238 PMCID: PMC3570780 DOI: 10.1038/srep01247] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/06/2012] [Indexed: 11/29/2022] Open
Abstract
Here we employ hydrogen/deuterium exchange mass spectrometry (HDX-MS) to access E. coli chaperonin GroEL conformation. The ~800 kDa tetradecameric GroEL plays an essential role in the proper folding of many proteins. Previous studies of the structural dynamics of GroEL upon ATP binding have been inconsistent, showing either minimal or major allosteric changes. Our results, based on the native, non-mutated, protein under physiological conditions in solution demonstrate substantial changes in conformation and/or flexibility upon ATP binding. We capture the pivotal step in its functional cycle by use of a non-hydrolyzable ATP analog, ATPγS, to mimic the ATP-bound GroEL state. Comparison of HDX-MS results for apo GroEL and GroEL-ATPγS enables the characterization of the nucleotide-regulated conformational changes throughout the entire protein with high sequence resolution. The 14-mer GroEL complex is the largest protein assembly yet accessed by HDX-MS, with sequence resolution of segments of as few as five amino acids.
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Affiliation(s)
- Qian Zhang
- Florida State University, Department of Chemistry, Tallahassee, FL 32306, USA
- These authors contributed equally to this work
| | - Jin Chen
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- These authors contributed equally to this work
| | - Kunihiro Kuwajima
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Department of Functional Molecular Science, School of Physical Sciences, Graduate University for Advanced Studies (Sokendai), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
| | - Hui-Min Zhang
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Feng Xian
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Nicolas L. Young
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Alan G. Marshall
- Florida State University, Department of Chemistry, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
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29
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Noble AJ, Zhang Q, O'Donnell J, Hariri H, Bhattacharya N, Marshall AG, Stagg SM. A pseudoatomic model of the COPII cage obtained from cryo-electron microscopy and mass spectrometry. Nat Struct Mol Biol 2013; 20:167-73. [PMID: 23262493 PMCID: PMC3565055 DOI: 10.1038/nsmb.2467] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/09/2012] [Indexed: 12/23/2022]
Abstract
COPII vesicles transport proteins from the endoplasmic reticulum to the Golgi apparatus. Previous COPII-cage cryo-EM structures lacked the resolution necessary to determine the residues of Sec13 and Sec31 that mediate assembly and flexibility of the COPII cage. Here we present a 12-Å structure of the human COPII cage, where the tertiary structure of Sec13 and Sec31 is clearly identifiable. We employ this structure and a homology model of the Sec13-Sec31 complex to create a reliable pseudoatomic model of the COPII cage. We combined this model with hydrogen/deuterium-exchange MS analysis to characterize four distinct contact regions at the vertices of the COPII cage. Furthermore, we found that the two-fold symmetry of the Sec31 dimeric region in Sec13-Sec31 is broken upon cage formation and that the resulting hinge is essential to form the proper edge geometry in COPII cages.
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Affiliation(s)
- Alex J Noble
- Department of Physics, Florida State University, Tallahassee, Florida, USA
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30
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Abstract
A major component of a hydrogen exchange mass spectrometry experiment is the analysis of protein and peptide mass spectra to yield information about deuterium incorporation. The processing of data that are produced includes the identification of each peptic peptide to create a master table/array of peptide sequence, retention time and retention time range, mass range, and undeuterated mass. The amount of deuterium incorporated into each of the peptides in this array must then be determined. Various software platforms have been developed in order to perform this specific type of data analysis. We describe the fundamental parameters to be considered at each step along the way and how data processing, either by an individual or by software, must approach the analysis.
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31
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Mo J, Tymiak AA, Chen G. Structural mass spectrometry in biologics discovery: advances and future trends. Drug Discov Today 2012; 17:1323-30. [DOI: 10.1016/j.drudis.2012.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/11/2012] [Accepted: 07/13/2012] [Indexed: 11/16/2022]
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32
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Burns KM, Rey M, Baker CAH, Schriemer DC. Platform dependencies in bottom-up hydrogen/deuterium exchange mass spectrometry. Mol Cell Proteomics 2012. [PMID: 23197788 DOI: 10.1074/mcp.m112.023770] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hydrogen-deuterium exchange mass spectrometry is an important method for protein structure-function analysis. The bottom-up approach uses protein digestion to localize deuteration to higher resolution, and the essential measurement involves centroid mass determinations on a very large set of peptides. In the course of evaluating systems for various projects, we established two (HDX-MS) platforms that consisted of a FT-MS and a high-resolution QTOF mass spectrometer, each with matched front-end fluidic systems. Digests of proteins spanning a 20-110 kDa range were deuterated to equilibrium, and figures-of-merit for a typical bottom-up (HDX-MS) experiment were compared for each platform. The Orbitrap Velos identified 64% more peptides than the 5600 QTOF, with a 42% overlap between the two systems, independent of protein size. Precision in deuterium measurements using the Orbitrap marginally exceeded that of the QTOF, depending on the Orbitrap resolution setting. However, the unique nature of FT-MS data generates situations where deuteration measurements can be inaccurate, because of destructive interference arising from mismatches in elemental mass defects. This is shown through the analysis of the peptides common to both platforms, where deuteration values can be as low as 35% of the expected values, depending on FT-MS resolution, peptide length and charge state. These findings are supported by simulations of Orbitrap transients, and highlight that caution should be exercised in deriving centroid mass values from FT transients that do not support baseline separation of the full isotopic composition.
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Affiliation(s)
- Kyle M Burns
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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33
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Fajer PG, Bou-Assaf GM, Marshall AG. Improved sequence resolution by global analysis of overlapped peptides in hydrogen/deuterium exchange mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1202-8. [PMID: 22528203 DOI: 10.1007/s13361-012-0373-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 05/12/2023]
Abstract
Management of the enormous amount of data produced during solution-phase hydrogen/deuterium exchange monitored by mass spectrometry has stimulated software analysis development. The proteolysis step of the experiment generates multiple peptide fragments, most of which overlap. Prior automated data reduction algorithms extract the deuteration level for individual peptides, but do not exploit the additional information arising from fragment overlap. Here, we describe an algorithm that determines discrete rate constant values to each of the amide hydrogens in overlapped fragments. By considering all of the overlapped peptide segments simultaneously, sequence resolution can be improved significantly, sometimes to the individual amino acid level. We have validated the method with simulated deuterium uptake data for seven overlapped fragments of a poly-Ala nonapeptide, and then applied it to extract rate constant values for the first 29 N-terminal amino acids of C22A FK506-binding protein.
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Affiliation(s)
- Piotr G Fajer
- Institute of Molecular Biophysics, Biological Sciences Department, Florida State University, Tallahassee, FL 32306, USA.
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34
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Lee PS, Zhang HM, Marshall AG, Yang XL, Schimmel P. Uncovering of a short internal peptide activates a tRNA synthetase procytokine. J Biol Chem 2012; 287:20504-8. [PMID: 22549774 PMCID: PMC3370235 DOI: 10.1074/jbc.c112.369439] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 04/28/2012] [Indexed: 11/06/2022] Open
Abstract
In higher organisms, aminoacyl-tRNA synthetases developed receptor-mediated ex-translational functions that are activated by various natural mechanisms. Hydrogen-deuterium exchange combined with mass spectrometry and small-angle x-ray scattering showed that activation of the cytokine function of the 528-amino acid human tyrosyl-tRNA synthetase was associated with pinpointed uncovering of a miniature internal ELR tripeptide that triggers receptor signaling. The results reveal the structural simplicity of how the ex-translational function is implemented.
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Affiliation(s)
| | - Hui-Min Zhang
- the National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Alan G. Marshall
- the National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Xiang-Lei Yang
- From the Departments of Molecular Biology and
- Chemical Physiology and
| | - Paul Schimmel
- From the Departments of Molecular Biology and
- The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La, Jolla, California 92037 and
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35
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Valeja SG, Emmett MR, Marshall AG. Polar aprotic modifiers for chromatographic separation and back-exchange reduction for protein hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:699-707. [PMID: 22298288 PMCID: PMC3835171 DOI: 10.1007/s13361-011-0329-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 12/08/2011] [Accepted: 12/24/2011] [Indexed: 05/20/2023]
Abstract
Hydrogen/deuterium exchange monitored by mass spectrometry is an important non-perturbing tool to study protein structure and protein–protein interactions. However, water in the reversed-phase liquid chromatography mobile phase leads to back-exchange of D for H during chromatographic separation of proteolytic peptides following H/D exchange, resulting in incorrect identification of fast-exchanging hydrogens as unexchanged hydrogens. Previously, fast high-performance liquid chromatography (HPLC) and supercritical fluid chromatography have been shown to decrease back-exchange. Here, we show that replacement of up to 40% of the water in the LC mobile phase by the modifiers, dimethylformamide (DMF) and N-methylpyrrolidone (NMP) (i.e., polar organic modifiers that lack rapid exchanging hydrogens), significantly reduces back-exchange. On-line LC micro-ESI FT-ICR MS resolves overlapped proteolytic peptide isotopic distributions, allowing for quantitative determination of the extent of back-exchange. The DMF modified solvent composition also improves chromatographic separation while reducing back-exchange relative to conventional solvent.
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Affiliation(s)
- Santosh G. Valeja
- Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306, USA
| | - Mark R. Emmett
- Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306, USA
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310-4005, USA
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306, USA
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310-4005, USA
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36
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Unique domain appended to vertebrate tRNA synthetase is essential for vascular development. Nat Commun 2012; 3:681. [PMID: 22353712 PMCID: PMC3293412 DOI: 10.1038/ncomms1686] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 01/16/2012] [Indexed: 11/08/2022] Open
Abstract
New domains were progressively added to cytoplasmic aminoacyl transfer RNA (tRNA) synthetases during evolution. One example is the UNE-S domain, appended to seryl-tRNA synthetase (SerRS) in species that developed closed circulatory systems. Here we show using solution and crystal structure analyses and in vitro and in vivo functional studies that UNE-S harbours a robust nuclear localization signal (NLS) directing SerRS to the nucleus where it attenuates vascular endothelial growth factor A expression. We also show that SerRS mutants previously linked to vasculature abnormalities either deleted the NLS or have the NLS sequestered in an alternative conformation. A structure-based second-site mutation, designed to release the sequestered NLS, restored normal vasculature. Thus, the essential function of SerRS in vascular development depends on UNE-S. These results are the first to show an essential role for a tRNA synthetase-associated appended domain at the organism level, and suggest that acquisition of UNE-S has a role in the establishment of the closed circulatory systems of vertebrates.
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37
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Miller DE, Prasannan CB, Villar MT, Fenton AW, Artigues A. HDXFinder: automated analysis and data reporting of deuterium/hydrogen exchange mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:425-9. [PMID: 22083588 PMCID: PMC3839233 DOI: 10.1007/s13361-011-0234-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 08/03/2011] [Accepted: 08/12/2011] [Indexed: 05/12/2023]
Abstract
Hydrogen/deuterium exchange in combination with mass spectrometry (H/D MS) is a sensitive technique for detection of changes in protein conformation and dynamics. However, wide application of H/D MS has been hindered, in part, by the lack of computational tools necessary for efficient analysis of the large data sets associated with this technique. We report a novel web-based application for automatic analysis of H/D MS experimental data. This application relies on the high resolution of mass spectrometers to extract all isotopic envelopes before correlating these envelopes with individual peptides. Although a fully automatic analysis is possible, a variety of graphical tools are included to aid in the verification of correlations and rankings of the isotopic peptide envelopes. As a demonstration, the rate constants for H/D exchange of peptides from rabbit muscle pyruvate kinase are mapped onto the structure of this protein.
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Affiliation(s)
| | | | | | - Aron W. Fenton
- Corresponding authors, Antonio Artigues, The University of Kansas Medical Center, Biochemistry and Molecular Biology, MS 3030, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, Phone: (913) 588-7487, Fax: (913) 588-7440, , Aron W. Fenton, The University of Kansas Medical Center, Biochemistry and Molecular Biology, MS 3030, 3901Rainbow Boulevard, Kansas City, Kansas 66160, Phone: (913) 588-7033, Fax: (913) 588-7440,
| | - Antonio Artigues
- Corresponding authors, Antonio Artigues, The University of Kansas Medical Center, Biochemistry and Molecular Biology, MS 3030, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, Phone: (913) 588-7487, Fax: (913) 588-7440, , Aron W. Fenton, The University of Kansas Medical Center, Biochemistry and Molecular Biology, MS 3030, 3901Rainbow Boulevard, Kansas City, Kansas 66160, Phone: (913) 588-7033, Fax: (913) 588-7440,
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38
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Zhang Q, Willison LN, Tripathi P, Sathe SK, Roux KH, Emmett MR, Blakney GT, Zhang HM, Marshall AG. Epitope mapping of a 95 kDa antigen in complex with antibody by solution-phase amide backbone hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 2011; 83:7129-36. [PMID: 21861454 PMCID: PMC3173601 DOI: 10.1021/ac201501z] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The epitopes of a homohexameric food allergen protein, cashew Ana o 2, identified by two monoclonal antibodies, 2B5 and 1F5, were mapped by solution-phase amide backbone H/D exchange (HDX) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and the results were compared to previous mapping by immunological and mutational analyses. Antibody 2B5 defines a conformational epitope, and 1F5 defines a linear epitope. Intact murine IgG antibodies were incubated with recombinant Ana o 2 (rAna o 2) to form antigen-monoclonal antibody (Ag-mAb) complexes. mAb-complexed and uncomplexed (free) rAna o 2 were then subjected to HDX. HDX instrumentation and automation were optimized to achieve high sequence coverage by protease XIII digestion. The regions protected from H/D exchange upon antibody binding overlap and thus confirm the previously identified epitope-bearing segments: the first extension of HDX monitored by mass spectrometry to a full-length antigen-antibody complex in solution.
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Affiliation(s)
- Qian Zhang
- Department Chemistry & Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL 32306
| | - LeAnna N. Willison
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Pallavi Tripathi
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Shridhar K. Sathe
- Department of Nutrition, Food and Exercise Sciences, Florida State University, Tallahassee, FL 32306
| | - Kenneth H. Roux
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Mark R. Emmett
- Department Chemistry & Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL 32306
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State Universitiy, 1800 E. Paul Dirac Drive, Tallahassee, FL 323010-4005
| | - Greg T. Blakney
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State Universitiy, 1800 E. Paul Dirac Drive, Tallahassee, FL 323010-4005
| | - Hui-Min Zhang
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State Universitiy, 1800 E. Paul Dirac Drive, Tallahassee, FL 323010-4005
| | - Alan G. Marshall
- Department Chemistry & Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL 32306
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State Universitiy, 1800 E. Paul Dirac Drive, Tallahassee, FL 323010-4005
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39
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Chalmers MJ, Busby SA, Pascal BD, West GM, Griffin PR. Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions. Expert Rev Proteomics 2011; 8:43-59. [PMID: 21329427 DOI: 10.1586/epr.10.109] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Functional regulation of ligand-activated receptors is driven by alterations in the conformational dynamics of the protein upon ligand binding. Differential hydrogen/deuterium exchange (HDX) coupled with mass spectrometry has emerged as a rapid and sensitive approach for characterization of perturbations in conformational dynamics of proteins following ligand binding. While this technique is sensitive to detecting ligand interactions and alterations in receptor dynamics, it also can provide important mechanistic insights into ligand regulation. For example, HDX has been used to determine a novel mechanism of ligand activation of the nuclear receptor peroxisome proliferator activated receptor-γ, perform detailed analyses of binding modes of ligands within the ligand-binding pocket of two estrogen receptor isoforms, providing insight into selectivity, and helped classify different types of estrogen receptor-α ligands by correlating their pharmacology with the way they interact with the receptor based solely on hierarchical clustering of receptor HDX signatures. Beyond small-molecule-receptor interactions, this technique has also been applied to study protein-protein complexes, such as mapping antibody-antigen interactions. In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein-ligand interactions has had an impact on biology and drug discovery.
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Affiliation(s)
- Michael J Chalmers
- The Scripps Research Molecular Screening Center, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
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40
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Structural context for mobilization of a human tRNA synthetase from its cytoplasmic complex. Proc Natl Acad Sci U S A 2011; 108:8239-44. [PMID: 21536907 DOI: 10.1073/pnas.1100224108] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human lysyl-tRNA synthetase is bound to the multi-tRNA synthetase complex (MSC) that maintains and regulates the aminoacylation and nuclear functions of LysRS. The p38 scaffold protein binds LysRS to the MSC and, only with the appropriate cue, mobilizes LysRS for redirection to the nucleus to interact with the microphthalmia associated transcription factor (MITF). In recent work, an (α(2))(2) LysRS tetramer crystallized to yield a high-resolution structure and raised the question of how LysRS is arranged (dimer or tetramer) in the MSC to interact with p38. To understand the structural organization of the LysRS-p38 complex that regulates LysRS mobilization, we investigated the complex by use of small angle X-ray scattering and hydrogen-deuterium exchange with mass spectrometry in solution. The structure revealed a surprising α(2)β(1):β(1)α(2) organization in which a dimeric p38 scaffold holds two LysRS α(2) dimers in a parallel configuration. Each of the N-terminal 48 residues of p38 binds one LysRS dimer and, in so doing, brings two copies of the LysRS dimer into the MSC. The results suggest that this unique geometry, which reconfigures the LysRS tetramer from α(2):α(2) to α(2)β(1):β(1)α(2), is designed to control both retention and mobilization of LysRS from the MSC.
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41
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Bou-Assaf GM, Chamoun JE, Emmett MR, Fajer PG, Marshall AG. Complexation and Calcium-Induced Conformational Changes in the Cardiac Troponin Complex Monitored by Hydrogen/Deuterium Exchange and FT-ICR Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 302:116-124. [PMID: 21765647 PMCID: PMC3134279 DOI: 10.1016/j.ijms.2010.08.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cardiac muscle contraction is regulated by the heterotrimeric complex: troponin. We apply solution-phase hydrogen/deuterium exchange monitored by FT-ICR mass spectrometry to study the structural dynamics and the Ca-induced conformational changes of the cardiac isoform of troponin, by comparing H/D exchange rate constants for TnC alone, the binary TnC:TnI complex, and the ternary TnC:TnI:TnT complex for Ca-free and Ca-saturated states. The wide range of exchange rate constants indicates that the complexes possess both highly flexible and very rigid domains. Fast exchange rates were observed for the N-terminal extension of TnI (specific to the cardiac isoform), the DE linker in TnC alone, and the mobile domain of TnI. The slowest rates were for the IT coiled-coil that grants stability and stiffness to the complex. Ca(2+) binding to site II of the N-lobe of TnC induces short-range allosteric effects, mainly protection for the C-lobe of TnC that transmits long-range conformational changes that reach the IT coiled-coil and even TnT1. The present results corroborate prior X-ray crystallography and NMR interpretations and also illuminate domains that were not resolved or truncated in those experiments.
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Affiliation(s)
- George M. Bou-Assaf
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
| | - Jean E. Chamoun
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Mark R. Emmett
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
| | - Piotr G. Fajer
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Alan G. Marshall
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
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Chalmers MJ, Pascal BD, Willis S, Zhang J, Iturria SJ, Dodge JA, Griffin PR. Methods for the Analysis of High Precision Differential Hydrogen Deuterium Exchange Data. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2011; 302:59-68. [PMID: 21528013 PMCID: PMC3081588 DOI: 10.1016/j.ijms.2010.08.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Hydrogen/deuterium exchange (HDX) mass spectrometry has been widely applied to the characterization of protein dynamics. More recently, differential HDX has been shown to be effective for the characterization of ligand binding. Previously we have described a fully automated HDX system for use as a ligand screening platform. Here we describe and validate the required data analysis workflow to facilitate the use of HDX as a robust approach for ligand screening. Following acquisition of HDX data at a single on-exchange time point (n ≥ 3), one way analysis of variance in conjunction with the Tukey multiple comparison procedure is used to establish the significance of any measured difference. Analysis results are graphed with respect to a single peptide, ligand or group of ligands, or displayed as an overview within a heat map. For the heat map display, only Δ%D values with a Tukey-adjusted P value less than 0.05 are colored. Hierarchical clustering is used to bin compounds with highly similar HDX signatures. The workflow is evaluated with a small data set showing the ligand binding domain (LDB) of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) screened against 10 functionally selective ligands. More significantly, data for the vitamin D receptor (VDR) in complex with 87 ligands are presented. To highlight the robustness and precision of our automated HDX platform we analyzed the data from 4191 replicate HDX measurements acquired over an eight month timeframe. Ninety six percent of these measurements were within 10 percent of the mean value. Work has begun to integrate these analysis and graphing components within our HDX software suite.
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Affiliation(s)
- Michael J. Chalmers
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida, 33458
- The Scripps Research Molecular Screening Center, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida, 33458
| | - Bruce D. Pascal
- Translational Research Institute, Informatics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida, 33458
| | - Scooter Willis
- Translational Research Institute, Informatics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida, 33458
| | - Jun Zhang
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida, 33458
| | - Stephen J. Iturria
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, 46285
| | - Jeffery A. Dodge
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, 46285
| | - Patrick R. Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida, 33458
- The Scripps Research Molecular Screening Center, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida, 33458
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Zhang HM, Yu X, Greig MJ, Gajiwala KS, Wu JC, Diehl W, Lunney EA, Emmett MR, Marshall AG. Drug binding and resistance mechanism of KIT tyrosine kinase revealed by hydrogen/deuterium exchange FTICR mass spectrometry. Protein Sci 2010; 19:703-15. [PMID: 20095048 DOI: 10.1002/pro.347] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mutations of the receptor tyrosine kinase KIT are linked to certain cancers such as gastrointestinal stromal tumors (GISTs). Biophysical, biochemical, and structural studies have provided insight into the molecular basis of resistance to the KIT inhibitors, imatinib and sunitinib. Here, solution-phase hydrogen/deuterium exchange (HDX) and direct binding mass spectrometry experiments provide a link between static structure models and the dynamic equilibrium of the multiple states of KIT, supporting that sunitinib targets the autoinhibited conformation of WT-KIT. The D816H mutation shifts the KIT conformational equilibrium toward the activated state. The V560D mutant exhibits two low energy conformations: one is more flexible and resembles the D816H mutant shifted toward the activated conformation, and the other is less flexible and resembles the wild-type KIT in the autoinhibited conformation. This result correlates with the V560D mutant exhibiting a sensitivity to sunitinib that is less than for WT KIT but greater than for KIT D816H. These findings support the elucidation of the resistance mechanism for the KIT mutants.
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Affiliation(s)
- Hui-Min Zhang
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310-4005, USA
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Althaus E, Canzar S, Ehrler C, Emmett MR, Karrenbauer A, Marshall AG, Meyer-Bäse A, Tipton JD, Zhang HM. Computing H/D-exchange rates of single residues from data of proteolytic fragments. BMC Bioinformatics 2010; 11:424. [PMID: 20701784 PMCID: PMC2936929 DOI: 10.1186/1471-2105-11-424] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 08/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex. In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides generated from the protease digest of the protein is related to the solvent accessibility of amide protons within the original protein construct. RESULTS In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue resolution. CONCLUSIONS With our new method it is possible to automatically determine deuterium exchange with higher spatial resolution than the level of digested fragments.
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Affiliation(s)
- Ernst Althaus
- Institut für Informatik, Fachbereich 08, Staudingerweg 9, 55099 Mainz, Germany.
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45
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Bou-Assaf GM, Chamoun JE, Emmett MR, Fajer PG, Marshall AG. Advantages of isotopic depletion of proteins for hydrogen/deuterium exchange experiments monitored by mass spectrometry. Anal Chem 2010; 82:3293-9. [PMID: 20337424 DOI: 10.1021/ac100079z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solution-phase hydrogen/deuterium exchange (HDX) monitored by mass spectrometry is an excellent tool to study protein-protein interactions and conformational changes in biological systems, especially when traditional methods such as X-ray crystallography or nuclear magnetic resonance are not feasible. Peak overlap among the dozens of proteolytic fragments (including those from autolysis of the protease) can be severe, due to high protein molecular weight(s) and the broad isotopic distributions due to multiple deuterations of many peptides. In addition, different subunits of a protein complex can yield isomeric proteolytic fragments. Here, we show that depletion of (13)C and/or (15)N for one or more protein subunits of a complex can greatly simplify the mass spectra, increase the signal-to-noise ratio of the depleted fragment ions, and remove ambiguity in assignment of the m/z values to the correct isomeric peptides. Specifically, it becomes possible to monitor the exchange progress for two isobaric fragments originating from two or more different subunits within the complex, without having to resort to tandem mass spectrometry techniques that can lead to deuterium scrambling in the gas phase. Finally, because the isotopic distribution for a small to medium-size peptide is essentially just the monoisotopic species ((12)C(c)(1)H(h)(14)N(n)(16)O(o)(32)S(s)), it is not necessary to deconvolve the natural abundance distribution for each partially deuterated peptide during HDX data reduction.
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Affiliation(s)
- George M Bou-Assaf
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
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46
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Rey M, Mrázek H, Pompach P, Novák P, Pelosi L, Brandolin G, Forest E, Havlíček V, Man P. Effective Removal of Nonionic Detergents in Protein Mass Spectrometry, Hydrogen/Deuterium Exchange, and Proteomics. Anal Chem 2010; 82:5107-16. [DOI: 10.1021/ac100171m] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Martial Rey
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (BBSI), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), UMR 5092 CNRS-CEA-UJF, Grenoble, F-38054, France, Laboratory of Molecular Structure Characterization, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, CZ-142 20, Czech Republic, Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, CZ-12840, Czech Republic, Laboratoire de
| | - Hynek Mrázek
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (BBSI), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), UMR 5092 CNRS-CEA-UJF, Grenoble, F-38054, France, Laboratory of Molecular Structure Characterization, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, CZ-142 20, Czech Republic, Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, CZ-12840, Czech Republic, Laboratoire de
| | - Petr Pompach
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (BBSI), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), UMR 5092 CNRS-CEA-UJF, Grenoble, F-38054, France, Laboratory of Molecular Structure Characterization, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, CZ-142 20, Czech Republic, Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, CZ-12840, Czech Republic, Laboratoire de
| | - Petr Novák
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (BBSI), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), UMR 5092 CNRS-CEA-UJF, Grenoble, F-38054, France, Laboratory of Molecular Structure Characterization, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, CZ-142 20, Czech Republic, Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, CZ-12840, Czech Republic, Laboratoire de
| | - Ludovic Pelosi
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (BBSI), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), UMR 5092 CNRS-CEA-UJF, Grenoble, F-38054, France, Laboratory of Molecular Structure Characterization, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, CZ-142 20, Czech Republic, Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, CZ-12840, Czech Republic, Laboratoire de
| | - Gérard Brandolin
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (BBSI), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), UMR 5092 CNRS-CEA-UJF, Grenoble, F-38054, France, Laboratory of Molecular Structure Characterization, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, CZ-142 20, Czech Republic, Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, CZ-12840, Czech Republic, Laboratoire de
| | - Eric Forest
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (BBSI), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), UMR 5092 CNRS-CEA-UJF, Grenoble, F-38054, France, Laboratory of Molecular Structure Characterization, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, CZ-142 20, Czech Republic, Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, CZ-12840, Czech Republic, Laboratoire de
| | - Vladimír Havlíček
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (BBSI), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), UMR 5092 CNRS-CEA-UJF, Grenoble, F-38054, France, Laboratory of Molecular Structure Characterization, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, CZ-142 20, Czech Republic, Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, CZ-12840, Czech Republic, Laboratoire de
| | - Petr Man
- Laboratoire de Biochimie et Biophysique des Systèmes Intégrés (BBSI), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), UMR 5092 CNRS-CEA-UJF, Grenoble, F-38054, France, Laboratory of Molecular Structure Characterization, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4, CZ-142 20, Czech Republic, Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, CZ-12840, Czech Republic, Laboratoire de
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