1
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Hamuro Y. Interpretation of Hydrogen/Deuterium Exchange Mass Spectrometry. J Am Soc Mass Spectrom 2024; 35:819-828. [PMID: 38639434 PMCID: PMC11067899 DOI: 10.1021/jasms.4c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024]
Abstract
This paper sheds light on the meaning of hydrogen/deuterium exchange-mass spectrometry (HDX-MS) data. HDX-MS data provide not structural information but dynamic information on an analyte protein. First, the reaction mechanism of backbone amide HDX reaction is considered and the correlation between the parameters from an X-ray crystal structure and the protection factors of HDX reactions of cytochrome c is evaluated. The presence of H-bonds in a protein structure has a strong influence on HDX rates which represent protein dynamics, while the solvent accessibility only weakly affects the HDX rates. Second, the energy diagrams of the HDX reaction at each residue in the presence and absence of perturbation are described. Whereas the free energy change upon mutation can be directly measured by the HDX rates, the free energy change upon ligand binding may be complicated due to the presence of unbound analyte protein in the protein-ligand mixture. Third, the meanings of HDX and other biophysical techniques are explained using a hypothetical protein folding well. The shape of the protein folding well describes the protein dynamics and provides Boltzmann distribution of open and closed states which yield HDX protection factors, while a protein's crystal structure represents a snapshot near the bottom of the well. All biophysical data should be consistent yet provide different information because they monitor different parts of the same protein folding well.
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2
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Baxa MC, Lin X, Mukinay CD, Chakravarthy S, Sachleben JR, Antilla S, Hartrampf N, Riback JA, Gagnon IA, Pentelute BL, Clark PL, Sosnick TR. How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins. Protein Sci 2024; 33:e4986. [PMID: 38607226 PMCID: PMC11010952 DOI: 10.1002/pro.4986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024]
Abstract
Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti-freeze protein (red-sfAFP) is unaffected by temperature and ionic strength and persists as a near-SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red-sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red-sfAFP had minimal effect on ν. Water remained a good solvent even with 21 consecutive glycine residues (ν > 0.5), and red-sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine-rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.
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Affiliation(s)
- Michael C. Baxa
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Xiaoxuan Lin
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Cedrick D. Mukinay
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team (BioCAT), Center for Synchrotron Radiation Research and Instrumentation and Department of Biological and Chemical SciencesIllinois Institute of TechnologyChicagoIllinoisUSA
- Present address:
Cytiva, Fast TrakMarlboroughMAUSA
| | | | - Sarah Antilla
- Department of Materials Science and EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Nina Hartrampf
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Present address:
Department of ChemistryUniversity of ZurichSwitzerland
| | - Joshua A. Riback
- Graduate Program in Biophysical ScienceUniversity of ChicagoChicagoIllinoisUSA
- Present address:
Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTXUSA
| | - Isabelle A. Gagnon
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Bradley L. Pentelute
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Patricia L. Clark
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Tobin R. Sosnick
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
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3
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Cockram PE, Walters BT, Lictao A, Shanahan F, Wertz IE, Foster SA, Rudolph J. Allosteric Inhibitors of the SARS-COV-2 Papain-like Protease Domain Induce Proteasomal Degradation of Its Parent Protein NSP3. ACS Chem Biol 2024; 19:22-36. [PMID: 38150587 DOI: 10.1021/acschembio.3c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The papain-like protease of SARS-COV-2 is essential for viral replication and pathogenesis. Its location within a much larger multifunctional protein, NSP3, makes it an ideal candidate for a targeted degradation approach capable of eliminating multiple functions with a single-molecule treatment. In this work, we have developed a HiBiT-based cellular model to study NSP3 degradation and used this platform for the discovery of monovalent NSP3 degraders. We present previously unreported degradation activity of published papain-like protease inhibitors. Follow-up exploration of structure-activity relationships and mechanism-of-action studies points to the recruitment of the ubiquitin-proteasome machinery that is solely driven by site occupancy, regardless of molecular features of the ligand. Supported by HDX data, we hypothesize that binding-induced structural changes in NSP3 trigger the recruitment of an E3 ligase and lead to proteasomal degradation.
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Affiliation(s)
- Peter E Cockram
- Discovery Chemistry, Genentech, South San Francisco, California 94080, United States
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Benjamin T Walters
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California 94080, United States
| | - Aaron Lictao
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California 94080, United States
| | - Frances Shanahan
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Ingrid E Wertz
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Scott A Foster
- Discovery Oncology, Genentech, South San Francisco, California 94080, United States
| | - Joachim Rudolph
- Discovery Chemistry, Genentech, South San Francisco, California 94080, United States
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4
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Abstract
Prestin responds to transmembrane voltage fluctuations by changing its cross-sectional area, a process underlying the electromotility of outer hair cells and cochlear amplification. Prestin belongs to the SLC26 family of anion transporters yet is the only member capable of displaying electromotility. Prestin's voltage-dependent conformational changes are driven by the putative displacement of residue R399 and a set of sparse charged residues within the transmembrane domain, following the binding of a Cl- anion at a conserved binding site formed by the amino termini of the TM3 and TM10 helices. However, a major conundrum arises as to how an anion that binds in proximity to a positive charge (R399), can promote the voltage sensitivity of prestin. Using hydrogen-deuterium exchange mass spectrometry, we find that prestin displays an unstable anion-binding site, where folding of the amino termini of TM3 and TM10 is coupled to Cl- binding. This event shortens the TM3-TM10 electrostatic gap, thereby connecting the two helices, resulting in reduced cross-sectional area. These folding events upon anion binding are absent in SLC26A9, a non-electromotile transporter closely related to prestin. Dynamics of prestin embedded in a lipid bilayer closely match that in detergent micelle, except for a destabilized lipid-facing helix TM6 that is critical to prestin's mechanical expansion. We observe helix fraying at prestin's anion-binding site but cooperative unfolding of multiple lipid-facing helices, features that may promote prestin's fast electromechanical rearrangements. These results highlight a novel role of the folding equilibrium of the anion-binding site, and help define prestin's unique voltage-sensing mechanism and electromotility.
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Affiliation(s)
- Xiaoxuan Lin
- Center for Mechanical Excitability, The University of ChicagoChicagoUnited States
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Patrick R Haller
- Center for Mechanical Excitability, The University of ChicagoChicagoUnited States
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Navid Bavi
- Center for Mechanical Excitability, The University of ChicagoChicagoUnited States
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Nabil Faruk
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
| | - Eduardo Perozo
- Center for Mechanical Excitability, The University of ChicagoChicagoUnited States
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
- Institute for Neuroscience, The University of ChicagoChicagoUnited States
- Institute for Biophysical Dynamics, The University of ChicagoChicagoUnited States
| | - Tobin R Sosnick
- Center for Mechanical Excitability, The University of ChicagoChicagoUnited States
- Department of Biochemistry and Molecular Biology, The University of ChicagoChicagoUnited States
- Institute for Biophysical Dynamics, The University of ChicagoChicagoUnited States
- Prizker School for Molecular Engineering, The University of ChicagoChicagoUnited States
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5
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Anderson KW, Hudgens JW. Hydrophilic Interaction Liquid Chromatography at Subzero Temperature for Hydrogen-Deuterium Exchange Mass Spectrometry. J Am Soc Mass Spectrom 2023; 34:2672-2679. [PMID: 37930109 PMCID: PMC10704588 DOI: 10.1021/jasms.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Chromatographic separations at subzero temperature significantly improve the precision of back-exchange-corrected hydrogen-deuterium exchange mass spectrometry (HDX-MS) determinations. Our previously reported dual-enzyme HDX-MS analysis instrument used reversed phase liquid chromatography (RPLC) at -30 °C, but high backpressures limited flow rates and required materials and equipment rated for very high pressures. Here, we report the design and performance of a dual-enzyme HDX-MS analysis instrument comprising a RPLC trap column and a hydrophilic interaction liquid chromatography (HILIC) analytical column in a two-dimensional RPLC-HILIC configuration at subzero temperature. During operation at -30 °C, the HILIC column manifests greatly reduced backpressure, which enables faster analytical flow rates and the use of materials rated for lower maximum pressures. The average peptide eluted from a HILIC column during a 40 min gradient at -30 °C contained ≈13% more deuterium than peptides eluted from a tandem RPLC-RPLC apparatus using a conventional 8 min gradient at 0 °C. A subset of peptides eluted from the HILIC apparatus contained ≈24% more deuterium.
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Affiliation(s)
- Kyle W. Anderson
- Bioprocess
Measurements Group, Biomolecular Measurement Division, National Institute of Standards and Technology, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Jeffrey W. Hudgens
- Bioprocess
Measurements Group, Biomolecular Measurement Division, National Institute of Standards and Technology, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
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6
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Pal S, Udgaonkar JB. Mutations of evolutionarily conserved aromatic residues suggest that misfolding of the mouse prion protein may commence in multiple ways. J Neurochem 2023; 167:696-710. [PMID: 37941487 DOI: 10.1111/jnc.16007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
The misfolding of the mammalian prion protein from its α-helix rich cellular isoform to its β-sheet rich infectious isoform is associated with several neurodegenerative diseases. The determination of the structural mechanism by which misfolding commences, still remains an unsolved problem. In the current study, native-state hydrogen exchange coupled with mass spectrometry has revealed that the N state of the mouse prion protein (moPrP) at pH 4 is in dynamic equilibrium with multiple partially unfolded forms (PUFs) capable of initiating misfolding. Mutation of three evolutionarily conserved aromatic residues, Tyr168, Phe174, and Tyr217 present at the interface of the β2-α2 loop and the C-terminal end of α3 in the structured C-terminal domain of moPrP significantly destabilize the native state (N) of the protein. They also reduce the free energy differences between the N state and two PUFs identified as PUF1 and PUF2**. It is shown that PUF2** in which the β2-α2 loop and the C-terminal end of α3 are disordered, has the same stability as the previously identified PUF2*, but to have a very different structure. Misfolding can commence from both PUF1 and PUF2**, as it can from PUF2*. Hence, misfolding can commence and proceed in multiple ways from structurally distinct precursor conformations. The increased extents to which PUF1 and PUF2** are populated at equilibrium in the case of the mutant variants, greatly accelerate their misfolding. The results suggest that the three aromatic residues may have been evolutionarily selected to impede the misfolding of moPrP.
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Affiliation(s)
- Suman Pal
- Indian Institute of Science Education and Research Pune, Pune, India
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7
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Lin X, Haller P, Bavi N, Faruk N, Perozo E, Sosnick TR. Folding of Prestin's Anion-Binding Site and the Mechanism of Outer Hair Cell Electromotility. bioRxiv 2023:2023.02.27.530320. [PMID: 36909622 PMCID: PMC10002659 DOI: 10.1101/2023.02.27.530320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Prestin responds to transmembrane voltage fluctuations by changing its cross-sectional area, a process underlying the electromotility of outer hair cells and cochlear amplification. Prestin belongs to the SLC26 family of anion transporters yet is the only member capable of displaying electromotility. Prestin's voltage-dependent conformational changes are driven by the putative displacement of residue R399 and a set of sparse charged residues within the transmembrane domain, following the binding of a Cl - anion at a conserved binding site formed by amino termini of the TM3 and TM10 helices. However, a major conundrum arises as to how an anion that binds in proximity to a positive charge (R399), can promote the voltage sensitivity of prestin. Using hydrogen-deuterium exchange mass spectrometry, we find that prestin displays an unstable anion-binding site, where folding of the amino termini of TM3 and TM10 is coupled to Cl - binding. This event shortens the TM3-TM10 electrostatic gap, thereby connecting the two helices, resulting in reduced cross-sectional area. These folding events upon anion-binding are absent in SLC26A9, a non-electromotile transporter closely related to prestin. Dynamics of prestin embedded in a lipid bilayer closely match that in detergent micelle, except for a destabilized lipid-facing helix TM6 that is critical to prestin's mechanical expansion. We observe helix fraying at prestin's anion-binding site but cooperative unfolding of multiple lipid-facing helices, features that may promote prestin's fast electromechanical rearrangements. These results highlight a novel role of the folding equilibrium of the anion-binding site, and helps define prestin's unique voltage-sensing mechanism and electromotility.
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8
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Goldman N, Chandra A, Johnson I, Sullivan MA, Patil AR, Vanderbeck A, Jay A, Zhou Y, Ferrari EK, Mayne L, Aguilan J, Xue HH, Faryabi RB, John Wherry E, Sidoli S, Maillard I, Vahedi G. Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity. Nat Immunol 2023; 24:1698-1710. [PMID: 37592014 PMCID: PMC10919931 DOI: 10.1038/s41590-023-01599-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/20/2023] [Indexed: 08/19/2023]
Abstract
In development, pioneer transcription factors access silent chromatin to reveal lineage-specific gene programs. The structured DNA-binding domains of pioneer factors have been well characterized, but whether and how intrinsically disordered regions affect chromatin and control cell fate is unclear. Here, we report that deletion of an intrinsically disordered region of the pioneer factor TCF-1 (termed L1) leads to an early developmental block in T cells. The few T cells that develop from progenitors expressing TCF-1 lacking L1 exhibit lineage infidelity distinct from the lineage diversion of TCF-1-deficient cells. Mechanistically, L1 is required for activation of T cell genes and repression of GATA2-driven genes, normally reserved to the mast cell and dendritic cell lineages. Underlying this lineage diversion, L1 mediates binding of TCF-1 to its earliest target genes, which are subject to repression as T cells develop. These data suggest that the intrinsically disordered N terminus of TCF-1 maintains T cell lineage fidelity.
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Affiliation(s)
- Naomi Goldman
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Aditi Chandra
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Isabelle Johnson
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Matthew A Sullivan
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Abhijeet R Patil
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Ashley Vanderbeck
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Atishay Jay
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Yeqiao Zhou
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Emily K Ferrari
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Leland Mayne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Jennifer Aguilan
- Department of Biochemistry, Albert Einstein School of Medicine, New York City, NY, USA
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
- New Jersey Veterans Affairs Health Care System, East Orange, NJ, USA
| | - Robert B Faryabi
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein School of Medicine, New York City, NY, USA
| | - Ivan Maillard
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
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9
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Kaur U, Kihn KC, Ke H, Kuo W, Gierasch LM, Hebert DN, Wintrode PL, Deredge D, Gershenson A. The conformational landscape of a serpin N-terminal subdomain facilitates folding and in-cell quality control. bioRxiv 2023:2023.04.24.537978. [PMID: 37163105 PMCID: PMC10168285 DOI: 10.1101/2023.04.24.537978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many multi-domain proteins including the serpin family of serine protease inhibitors contain non-sequential domains composed of regions that are far apart in sequence. Because proteins are translated vectorially from N- to C-terminus, such domains pose a particular challenge: how to balance the conformational lability necessary to form productive interactions between early and late translated regions while avoiding aggregation. This balance is mediated by the protein sequence properties and the interactions of the folding protein with the cellular quality control machinery. For serpins, particularly α 1 -antitrypsin (AAT), mutations often lead to polymer accumulation in cells and consequent disease suggesting that the lability/aggregation balance is especially precarious. Therefore, we investigated the properties of progressively longer AAT N-terminal fragments in solution and in cells. The N-terminal subdomain, residues 1-190 (AAT190), is monomeric in solution and efficiently degraded in cells. More β -rich fragments, 1-290 and 1-323, form small oligomers in solution, but are still efficiently degraded, and even the polymerization promoting Siiyama (S53F) mutation did not significantly affect fragment degradation. In vitro, the AAT190 region is among the last regions incorporated into the final structure. Hydrogen-deuterium exchange mass spectrometry and enhanced sampling molecular dynamics simulations show that AAT190 has a broad, dynamic conformational ensemble that helps protect one particularly aggregation prone β -strand from solvent. These AAT190 dynamics result in transient exposure of sequences that are buried in folded, full-length AAT, which may provide important recognition sites for the cellular quality control machinery and facilitate degradation and, under favorable conditions, reduce the likelihood of polymerization.
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Affiliation(s)
- Upneet Kaur
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Kyle C. Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Haiping Ke
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Weiwei Kuo
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
| | - Lila M. Gierasch
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003
| | - Daniel N. Hebert
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Anne Gershenson
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
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10
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Christofi E, Barran P. Ion Mobility Mass Spectrometry (IM-MS) for Structural Biology: Insights Gained by Measuring Mass, Charge, and Collision Cross Section. Chem Rev 2023; 123:2902-2949. [PMID: 36827511 PMCID: PMC10037255 DOI: 10.1021/acs.chemrev.2c00600] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
The investigation of macromolecular biomolecules with ion mobility mass spectrometry (IM-MS) techniques has provided substantial insights into the field of structural biology over the past two decades. An IM-MS workflow applied to a given target analyte provides mass, charge, and conformation, and all three of these can be used to discern structural information. While mass and charge are determined in mass spectrometry (MS), it is the addition of ion mobility that enables the separation of isomeric and isobaric ions and the direct elucidation of conformation, which has reaped huge benefits for structural biology. In this review, where we focus on the analysis of proteins and their complexes, we outline the typical features of an IM-MS experiment from the preparation of samples, the creation of ions, and their separation in different mobility and mass spectrometers. We describe the interpretation of ion mobility data in terms of protein conformation and how the data can be compared with data from other sources with the use of computational tools. The benefit of coupling mobility analysis to activation via collisions with gas or surfaces or photons photoactivation is detailed with reference to recent examples. And finally, we focus on insights afforded by IM-MS experiments when applied to the study of conformationally dynamic and intrinsically disordered proteins.
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Affiliation(s)
- Emilia Christofi
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, United Kingdom
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11
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Kish M, Smith V, Lethbridge N, Cole L, Bond NJ, Phillips JJ. Online Fully Automated System for Hydrogen/Deuterium-Exchange Mass Spectrometry with Millisecond Time Resolution. Anal Chem 2023; 95:5000-5008. [PMID: 36896500 PMCID: PMC10034745 DOI: 10.1021/acs.analchem.2c05310] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Amide hydrogen/deuterium-exchange mass spectrometry (HDX-MS) is a powerful tool for analyzing the conformational dynamics of proteins in a solution. Current conventional methods have a measurement limit starting from several seconds and are solely reliant on the speed of manual pipetting or a liquid handling robot. Weakly protected regions of polypeptides, such as in short peptides, exposed loops and intrinsically disordered the protein exchange on the millisecond timescale. Typical HDX methods often cannot resolve the structural dynamics and stability in these cases. Numerous academic laboratories have demonstrated the considerable utility of acquiring HDX-MS data in the sub-second regimes. Here, we describe the development of a fully automated HDX-MS apparatus to resolve amide exchange on the millisecond timescale. Like conventional systems, this instrument boasts automated sample injection with software selection of labeling times, online flow mixing and quenching, while being fully integrated with a liquid chromatography-MS system for existing standard "bottom-up" workflows. HDX-MS's rapid exchange kinetics of several peptides demonstrate the repeatability, reproducibility, back-exchange, and mixing kinetics achieved with the system. Comparably, peptide coverage of 96.4% with 273 peptides was achieved, supporting the equivalence of the system to standard robotics. Additionally, time windows of 50 ms-300 s allowed full kinetic transitions to be observed for many amide groups; especially important are short time points (50-150 ms) for regions that are likely highly dynamic and solvent- exposed. We demonstrate that information on structural dynamics and stability can be measured for stretches of weakly stable polypeptides in small peptides and in local regions of a large enzyme, glycogen phosphorylase.
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Affiliation(s)
- Monika Kish
- Living Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, U.K
| | | | | | - Lindsay Cole
- Applied Photophysics Ltd, Leatherhead KT227BA, U.K
| | - Nicholas J Bond
- Analytical Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Milstein Building, Granta Park, Cambridge CB21 6GH, U.K
| | - Jonathan J Phillips
- Living Systems Institute, Department of Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, U.K
- Alan Turing Institute, British Library, London NW1 2DB, U.K
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12
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Calvaresi V, Wrobel AG, Toporowska J, Hammerschmid D, Doores KJ, Bradshaw RT, Parsons RB, Benton DJ, Roustan C, Reading E, Malim MH, Gamblin SJ, Politis A. Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein. Nat Commun 2023; 14:1421. [PMID: 36918534 PMCID: PMC10013288 DOI: 10.1038/s41467-023-36745-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/15/2023] [Indexed: 03/15/2023] Open
Abstract
SARS-CoV-2 spike glycoprotein mediates receptor binding and subsequent membrane fusion. It exists in a range of conformations, including a closed state unable to bind the ACE2 receptor, and an open state that does so but displays more exposed antigenic surface. Spikes of variants of concern (VOCs) acquired amino acid changes linked to increased virulence and immune evasion. Here, using HDX-MS, we identified changes in spike dynamics that we associate with the transition from closed to open conformations, to ACE2 binding, and to specific mutations in VOCs. We show that the RBD-associated subdomain plays a role in spike opening, whereas the NTD acts as a hotspot of conformational divergence of VOC spikes driving immune evasion. Alpha, beta and delta spikes assume predominantly open conformations and ACE2 binding increases the dynamics of their core helices, priming spikes for fusion. Conversely, substitutions in omicron spike lead to predominantly closed conformations, presumably enabling it to escape antibodies. At the same time, its core helices show characteristics of being pre-primed for fusion even in the absence of ACE2. These data inform on SARS-CoV-2 evolution and omicron variant emergence.
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Affiliation(s)
- Valeria Calvaresi
- Department of Chemistry, King's College London, SE1 1DB, London, UK.
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.
| | | | | | - Katie J Doores
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, SE1 9RT, London, UK
| | | | | | - Donald J Benton
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Chloë Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT, London, UK
| | - Eamonn Reading
- Department of Chemistry, King's College London, SE1 1DB, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, SE1 9RT, London, UK
| | - Steve J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, SE1 1DB, London, UK.
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, M13 9PT, Manchester, UK.
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN, Manchester, UK.
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13
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Yanaka S, Yagi-Utsumi M, Kato K, Kuwajima K. The B domain of protein A retains residual structures in 6 M guanidinium chloride as revealed by hydrogen/deuterium-exchange NMR spectroscopy. Protein Sci 2023; 32:e4569. [PMID: 36659853 PMCID: PMC9926473 DOI: 10.1002/pro.4569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
The characterization of residual structures persistent in unfolded proteins is an important issue in studies of protein folding, because the residual structures present, if any, may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the residual structures of the isolated B domain (BDPA) of staphylococcal protein A in 6 M guanidinium chloride. BDPA is a small three-helix-bundle protein, and until recently its folding/unfolding reaction has been treated as a simple two-state process between the native and the fully unfolded states. We employed a dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange 2D NMR techniques with the use of spin desalting columns, which allowed us to investigate the H/D-exchange behavior of individually identified peptide amide (NH) protons. We obtained H/D-exchange protection factors of the 21 NH protons that form an α-helical hydrogen bond in the native structure, and the majority of these NH protons were significantly protected with a protection factor of 2.0-5.2 in 6 M guanidinium chloride, strongly suggesting that these weakly protected NH protons form much stronger hydrogen bonds under native folding conditions. The results can be used to deduce the structure of an early folding intermediate, when such an intermediate is shown by other methods. Among three native helical regions, the third helix in the C-terminal side was highly protected and stabilized by side-chain salt bridges, probably acting as the folding initiation site of BDPA. The present results are discussed in relation to previous experimental and computational findings on the folding mechanisms of BDPA.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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14
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Stankov S, Vitali C, Park J, Nguyen D, Mayne L, Englander SW, Levin MG, Vujkovic M, Hand NJ, Phillips MC, Rader DJ. Comparison of the structure-function properties of wild-type human apoA-V and a C-terminal truncation associated with elevated plasma triglycerides. medRxiv 2023:2023.02.21.23286268. [PMID: 36865344 PMCID: PMC9980232 DOI: 10.1101/2023.02.21.23286268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Background Plasma triglycerides (TGs) are causally associated with coronary artery disease and acute pancreatitis. Apolipoprotein A-V (apoA-V, gene APOA5) is a liver-secreted protein that is carried on triglyceride-rich lipoproteins and promotes the enzymatic activity of lipoprotein lipase (LPL), thereby reducing TG levels. Little is known about apoA-V structure-function; naturally occurring human APOA5 variants can provide novel insights. Methods We used hydrogen-deuterium exchange mass spectrometry to determine the secondary structure of human apoA-V in lipid-free and lipid-associated conditions and identified a C-terminal hydrophobic face. Then, we used genomic data in the Penn Medicine Biobank to identify a rare variant, Q252X, predicted to specifically eliminate this region. We interrogated the function of apoA-V Q252X using recombinant protein in vitro and in vivo in apoa5 knockout mice. Results Human apoA-V Q252X carriers exhibited elevated plasma TG levels consistent with loss of function. Apoa5 knockout mice injected with AAV vectors expressing wildtype and variant APOA5-AAV recapitulated this phenotype. Part of the loss of function is due to reduced mRNA expression. Functionally, recombinant apoA-V Q252X was more readily soluble in aqueous solutions and more exchangeable with lipoproteins than WT apoA-V. Despite lacking the C-terminal hydrophobic region (a putative lipid binding domain) this protein also decreased plasma TG in vivo. Conclusions Deletion of apoA-V's C-terminus leads to reduced apoA-V bioavailability in vivo and higher TG levels. However, the C-terminus is not required for lipoprotein binding or enhancement of intravascular lipolytic activity. WT apoA-V is highly prone to aggregation, and this property is markedly reduced in recombinant apoA-V lacking the C-terminus.
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Affiliation(s)
- Sylvia Stankov
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cecilia Vitali
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Park
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Nguyen
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leland Mayne
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - S. Walter Englander
- Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Michael G. Levin
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
| | - Marijana Vujkovic
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA
| | - Nicholas J. Hand
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael C. Phillips
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J. Rader
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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15
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Mi T, Nguyen D, Burgess K. Bicyclic Schellman Loop Mimics (BSMs): Rigid Synthetic C-Caps for Enforcing Peptide Helicity. ACS Cent Sci 2023; 9:300-306. [PMID: 36844493 PMCID: PMC9951308 DOI: 10.1021/acscentsci.2c01265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Indexed: 06/18/2023]
Abstract
Macrocyclic peptides are the prevalent way to mimic interface helices for disruption of protein interactions, but current strategies to do this via synthetic C-cap mimics are underdeveloped and suboptimal. Bioinformatic studies described here were undertaken to better understand Schellman loops, the most common C-caps in proteins, to design superior synthetic mimics. An algorithm (Schellman Loop Finder) was developed, and data mining with this led to the discovery that these secondary structures are often stabilized by combinations of three hydrophobic side chains, most frequently from Leu, to form hydrophobic triangles. That insight facilitated design of synthetic mimics, bicyclic Schellman loop mimics (BSMs), where the hydrophobic triumvirate was replaced by 1,3,5-trimethylbenzene. We demonstrate that BSMs can be made quickly and efficiently, and are more rigid and helix-inducing than the best current C-cap mimics, which are rare and all monocycles.
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16
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Palhano Zanela TM, Woudenberg A, Romero Bello KG, Underbakke ES. Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation. Structure 2023; 31:447-454.e5. [PMID: 36870334 DOI: 10.1016/j.str.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/11/2023] [Accepted: 02/07/2023] [Indexed: 03/06/2023]
Abstract
Pyk2 is a multidomain non-receptor tyrosine kinase that undergoes a multistage activation mechanism. Activation is instigated by conformational rearrangements relieving autoinhibitory FERM domain interactions. The kinase autophosphorylates a central linker residue to recruit Src kinase. Pyk2 and Src mutually phosphorylate activation loops to confer full activation. While the mechanisms of autoinhibition are established, the conformational dynamics associated with autophosphorylation and Src recruitment remain unclear. We employ hydrogen/deuterium exchange mass spectrometry and kinase activity profiling to map the conformational dynamics associated with substrate binding and Src-mediated activation loop phosphorylation. Nucleotide engagement stabilizes the autoinhibitory interface, while phosphorylation deprotects both FERM and kinase regulatory surfaces. Phosphorylation organizes active site motifs linking catalytic loop with activation segment. Dynamics of the activation segment anchor propagate to EF/G helices to prevent reversion of the autoinhibitory FERM interaction. We employ targeted mutagenesis to dissect how phosphorylation-induced conformational rearrangements elevate kinase activity above the basal autophosphorylation rate.
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Affiliation(s)
- Tania M Palhano Zanela
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Alexzandrea Woudenberg
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Karen G Romero Bello
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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17
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Pal S, Udgaonkar JB. Evolutionarily Conserved Proline Residues Impede the Misfolding of the Mouse Prion Protein by Destabilizing an Aggregation-competent Partially Unfolded Form. J Mol Biol 2022; 434:167854. [PMID: 36228749 DOI: 10.1016/j.jmb.2022.167854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/04/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022]
Abstract
The misfolding of the prion protein has been linked to several neurodegenerative diseases. Despite extensive studies, the mechanism of the misfolding process remains poorly understood. The present study structurally delineates the role of the conserved proline residues present in the structured C-terminal domain of the mouse prion protein (moPrP) in the misfolding process. It is shown that mutation of these Pro residues to Ala leads to destabilization of the native (N) state, and also to rapid misfolding. Using hydrogen-deuterium exchange (HDX) studies coupled with mass spectrometry (MS), it has been shown that the N state of moPrP is in rapid equilibrium with a partially unfolded form (PUF2*) at pH 4. It has been shown that the Pro to Ala mutations make PUF2* energetically more accessible from the N state by stabilizing it relative to the unfolded (U) state. The apparent rate constant of misfolding is found to be linearly proportional to the extent to which PUF2* is populated in equilibrium with the N state, strongly indicating that misfolding commences from PUF2*. It has also been shown that the Pro residues restrict the boundary of the structural core of the misfolded oligomers. Overall, this study highlights how the conserved proline residues control misfolding of the prion protein by modulating the stability of the partially unfolded form from which misfolding commences.
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Affiliation(s)
- Suman Pal
- Indian Institute of Science Education and Research, Pune, India
| | - Jayant B Udgaonkar
- Indian Institute of Science Education and Research, Pune, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
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18
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Parson MA, Jenkins ML, Burke JE. Investigating how intrinsically disordered regions contribute to protein function using HDX-MS. Biochem Soc Trans 2022. [DOI: 10.1042/bst20220206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022]
Abstract
A large amount of the human proteome is composed of highly dynamic regions that do not adopt a single static conformation. These regions are defined as intrinsically disordered, and they are found in a third of all eukaryotic proteins. They play instrumental roles in many aspects of protein signaling, but can be challenging to characterize by biophysical methods. Intriguingly, many of these regions can adopt stable secondary structure upon interaction with a variety of binding partners, including proteins, lipids, and ligands. This review will discuss the application of Hydrogen-deuterium exchange mass spectrometry (HDX-MS) as a powerful biophysical tool that is particularly well suited for structural and functional characterization of intrinsically disordered regions in proteins. A focus will be on the theory of hydrogen exchange, and its practical application to identify disordered regions, as well as characterize how they participate in protein–protein and protein–membrane interfaces. A particular emphasis will be on how HDX-MS data can be presented specifically tailored for analysis of intrinsically disordered regions, as well as the technical aspects that are critical to consider when designing HDX-MS experiments for proteins containing intrinsically disordered regions.
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19
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Tajoddin NN, Konermann L. Structural Dynamics of a Thermally Stressed Monoclonal Antibody Characterized by Temperature-Dependent H/D Exchange Mass Spectrometry. Anal Chem 2022; 94:15499-15509. [DOI: 10.1021/acs.analchem.2c03931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nastaran N. Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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20
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Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is becoming part of the standard repertoire of techniques used by molecular biologists to investigate protein structure and dynamics. This is partly due to the increased use of automation in all stages of the technique and its versatility of application-many proteins that present challenges with techniques such as X-ray crystallography and cryoelectron microscopy are amenable to investigation with HDX-MS. The present review is aimed at scientists who are curious about the technique, and how it may aid their research. It describes the fundamental basis of solvent exchange, the basics of a standard HDX-MS experiment, as well as highlighting emerging novel experimental advances, which point to where the field is heading.
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21
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Peterle D, Wales TE, Engen JR. Simple and Fast Maximally Deuterated Control (maxD) Preparation for Hydrogen-Deuterium Exchange Mass Spectrometry Experiments. Anal Chem 2022; 94:10142-10150. [PMID: 35796687 DOI: 10.1021/acs.analchem.2c01446] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During the analysis steps of hydrogen-deuterium exchange (HDX) mass spectrometry (MS), there is an unavoidable loss of deuterons, or back-exchange. Understanding back-exchange is necessary to correct for loss during analysis, to calculate the absolute amount of exchange, and to ensure that deuterium recovery is as high as possible during liquid chromatography (LC)-MS. Back-exchange can be measured and corrected for using a maximally deuterated species (here called maxD), in which the protein is deuterated at positions and analyzed with the same buffer components, %D2O, quenching conditions, and LC-MS parameters used during the analysis of other labeled samples. Here, we describe a robust and broadly applicable protocol, using denaturation followed by deuteration, to prepare a maxD control sample in ∼40 min for nonmembrane proteins. The protocol was evaluated with a number of proteins that varied in both size and folded structure. The relative fractional uptake and level of back-exchange with this protocol were both equivalent to those obtained with earlier protocols that either require much more time or require isolation of peptic peptides prior to deuteration. Placing strong denaturation first in the protocol allowed for maximum deuteration in a short time (∼10 min) with equal or more deuteration found in other methods. The absence of high temperatures and low pH during the deuteration step limited protein aggregation. This high-performance, fast, and easy-to-perform protocol should enhance routine preparation of maxD controls.
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Affiliation(s)
- Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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22
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Anderson KW, Hudgens JW. Chromatography at -30 °C for Reduced Back-Exchange, Reduced Carryover, and Improved Dynamic Range for Hydrogen-Deuterium Exchange Mass Spectrometry. J Am Soc Mass Spectrom 2022; 33:1282-1292. [PMID: 35732031 PMCID: PMC9264389 DOI: 10.1021/jasms.2c00096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
For hydrogen-deuterium exchange mass spectrometry (HDX-MS) to have an increased role in quality control of biopharmaceuticals, H for D back-exchange occurring during protein analyses should be minimized to promote greater reproducibility. Standard HDX-MS analysis systems that digest proteins and separate peptides at pH 2.7 and 0 °C can lose >30% of the deuterium marker within 15 min of sample injection. This report describes the architecture and performance of a dual-enzyme, HDX-MS instrument that conducts liquid chromatography (LC) separations at subzero temperature, thereby reducing back-exchange and supporting longer LC separations with improved chromatographic resolution. LC separations of perdeuterated, fully reduced, iodoacetamide-treated BSA protein digest standard peptides were performed at 0, -10, -20, and -30 °C in ethylene glycol (EG)/H2O mixtures. Analyses conducted at -20 and -30 °C produced similar results. After subtracting for deuterium retained in arginine side chains, the average peptide eluted during a 40 min gradient contained ≈16% more deuterium than peptides eluted with a conventional 8 min gradient at 0 °C. A subset of peptides exhibited ≈26% more deuterium. Although chromatographic peaks shift with EG concentration and temperature, the apparatus elutes unbroadened LC peaks. Electrospray ion intensity does not decline with increasing EG fraction. To minimize bias from sample carryover, the fluidic circuits allow flush and backflush cleaning of all enzyme and LC columns. The system can perform LC separations and clean enzyme columns simultaneously. Temperature zones are controlled ±0.058 °C. The potential of increased sensitivity by mixing acetonitrile with the analytical column effluent was also examined.
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Affiliation(s)
- Kyle W. Anderson
- National
Institute of Standards and Technology, Bioprocess
Measurement Group, Biomolecular Measurements Division, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Jeffrey W. Hudgens
- National
Institute of Standards and Technology, Bioprocess
Measurement Group, Biomolecular Measurements Division, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
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23
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Kuwajima K, Yagi-Utsumi M, Yanaka S, Kato K. DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science. Molecules 2022; 27:molecules27123748. [PMID: 35744871 PMCID: PMC9230524 DOI: 10.3390/molecules27123748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
Hydrogen/deuterium (H/D) exchange combined with two-dimensional (2D) NMR spectroscopy has been widely used for studying the structure, stability, and dynamics of proteins. When we apply the H/D-exchange method to investigate non-native states of proteins such as equilibrium and kinetic folding intermediates, H/D-exchange quenching techniques are indispensable, because the exchange reaction is usually too fast to follow by 2D NMR. In this article, we will describe the dimethylsulfoxide (DMSO)-quenched H/D-exchange method and its applications in protein science. In this method, the H/D-exchange buffer is replaced by an aprotic DMSO solution, which quenches the exchange reaction. We have improved the DMSO-quenched method by using spin desalting columns, which are used for medium exchange from the H/D-exchange buffer to the DMSO solution. This improvement has allowed us to monitor the H/D exchange of proteins at a high concentration of salts or denaturants. We describe methodological details of the improved DMSO-quenched method and present a case study using the improved method on the H/D-exchange behavior of unfolded human ubiquitin in 6 M guanidinium chloride.
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Affiliation(s)
- Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Correspondence: (K.K.); (K.K.)
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
- Correspondence: (K.K.); (K.K.)
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24
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Tran MH, Schoeder CT, Schey KL, Meiler J. Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook. Front Immunol 2022; 13:859964. [PMID: 35720345 PMCID: PMC9204306 DOI: 10.3389/fimmu.2022.859964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022] Open
Abstract
Although computational structure prediction has had great successes in recent years, it regularly fails to predict the interactions of large protein complexes with residue-level accuracy, or even the correct orientation of the protein partners. The performance of computational docking can be notably enhanced by incorporating experimental data from structural biology techniques. A rapid method to probe protein-protein interactions is hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS has been increasingly used for epitope-mapping of antibodies (Abs) to their respective antigens (Ags) in the past few years. In this paper, we review the current state of HDX-MS in studying protein interactions, specifically Ab-Ag interactions, and how it has been used to inform computational structure prediction calculations. Particularly, we address the limitations of HDX-MS in epitope mapping and techniques and protocols applied to overcome these barriers. Furthermore, we explore computational methods that leverage HDX-MS to aid structure prediction, including the computational simulation of HDX-MS data and the combination of HDX-MS and protein docking. We point out challenges in interpreting and incorporating HDX-MS data into Ab-Ag complex docking and highlight the opportunities they provide to build towards a more optimized hybrid method, allowing for more reliable, high throughput epitope identification.
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Affiliation(s)
- Minh H. Tran
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, United States
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Clara T. Schoeder
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
| | - Kevin L. Schey
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Jens Meiler
- Center of Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
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25
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Stofella M, Skinner SP, Sobott F, Houwing-Duistermaat J, Paci E. High-Resolution Hydrogen-Deuterium Protection Factors from Sparse Mass Spectrometry Data Validated by Nuclear Magnetic Resonance Measurements. J Am Soc Mass Spectrom 2022; 33:813-822. [PMID: 35385652 PMCID: PMC9074100 DOI: 10.1021/jasms.2c00005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Experimental measurement of time-dependent spontaneous exchange of amide protons with deuterium of the solvent provides information on the structure and dynamical structural variation in proteins. Two experimental techniques are used to probe the exchange: NMR, which relies on different magnetic properties of hydrogen and deuterium, and MS, which exploits the change in mass due to deuteration. NMR provides residue-specific information, that is, the rate of exchange or, analogously, the protection factor (i.e., the unitless ratio between the rate of exchange for a completely unstructured state and the observed rate). MS provides information that is specific to peptides obtained by proteolytic digestion. The spatial resolution of HDX-MS measurements depends on the proteolytic pattern of the protein, the fragmentation method used, and the overlap between peptides. Different computational approaches have been proposed to extract residue-specific information from peptide-level HDX-MS measurements. Here, we demonstrate the advantages of a method recently proposed that exploits self-consistency and classifies the possible sets of protection factors into a finite number of alternative solutions compatible with experimental data. The degeneracy of the solutions can be reduced (or completely removed) by exploiting the additional information encoded in the shape of the isotopic envelopes. We show how sparse and noisy MS data can provide high-resolution protection factors that correlate with NMR measurements probing the same protein under the same conditions.
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Affiliation(s)
- Michele Stofella
- School
of Molecular and Cellular Biology, University
of Leeds, LS2 9JT Leeds, United Kingdom
- Dipartimento
di Fisica e Astronomia, Università
di Bologna, 40127 Bologna, Italy
| | - Simon P. Skinner
- School
of Molecular and Cellular Biology, University
of Leeds, LS2 9JT Leeds, United Kingdom
| | - Frank Sobott
- School
of Molecular and Cellular Biology, University
of Leeds, LS2 9JT Leeds, United Kingdom
| | | | - Emanuele Paci
- School
of Molecular and Cellular Biology, University
of Leeds, LS2 9JT Leeds, United Kingdom
- Dipartimento
di Fisica e Astronomia, Università
di Bologna, 40127 Bologna, Italy
- (E.P.)
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26
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Devaurs D, Antunes DA, Borysik AJ. Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data. J Am Soc Mass Spectrom 2022; 33:215-237. [PMID: 35077179 DOI: 10.1021/jasms.1c00328] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Data produced by hydrogen-exchange monitoring experiments have been used in structural studies of molecules for several decades. Despite uncertainties about the structural determinants of hydrogen exchange itself, such data have successfully helped guide the structural modeling of challenging molecular systems, such as membrane proteins or large macromolecular complexes. As hydrogen-exchange monitoring provides information on the dynamics of molecules in solution, it can complement other experimental techniques in so-called integrative modeling approaches. However, hydrogen-exchange data have often only been used to qualitatively assess molecular structures produced by computational modeling tools. In this paper, we look beyond qualitative approaches and survey the various paradigms under which hydrogen-exchange data have been used to quantitatively guide the computational modeling of molecular structures. Although numerous prediction models have been proposed to link molecular structure and hydrogen exchange, none of them has been widely accepted by the structural biology community. Here, we present as many hydrogen-exchange prediction models as we could find in the literature, with the aim of providing the first exhaustive list of its kind. From purely structure-based models to so-called fractional-population models or knowledge-based models, the field is quite vast. We aspire for this paper to become a resource for practitioners to gain a broader perspective on the field and guide research toward the definition of better prediction models. This will eventually improve synergies between hydrogen-exchange monitoring and molecular modeling.
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Affiliation(s)
- Didier Devaurs
- MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, U.K
| | - Dinler A Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77005, United States
| | - Antoni J Borysik
- Department of Chemistry, King's College London, London SE1 1DB, U.K
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27
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Fields JK, Kihn K, Birkedal GS, Klontz EH, Sjöström K, Günther S, Beadenkopf R, Forsberg G, Liberg D, Snyder GA, Deredge D, Sundberg EJ. Molecular Basis of Selective Cytokine Signaling Inhibition by Antibodies Targeting a Shared Receptor. Front Immunol 2022; 12:779100. [PMID: 35003094 PMCID: PMC8740070 DOI: 10.3389/fimmu.2021.779100] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022] Open
Abstract
Interleukin-1 (IL-1) family cytokines are potent mediators of inflammation, acting to coordinate local and systemic immune responses to a wide range of stimuli. Aberrant signaling by IL-1 family cytokine members, however, is linked to myriad inflammatory syndromes, autoimmune conditions and cancers. As such, blocking the inflammatory signals inherent to IL-1 family signaling is an established and expanding therapeutic strategy. While several FDA-approved IL-1 inhibitors exist, including an Fc fusion protein, a neutralizing antibody, and an antagonist cytokine, none specifically targets the co-receptor IL-1 receptor accessory protein (IL-1RAcP). Most IL-1 family cytokines form productive signaling complexes by binding first to their cognate receptors – IL-1RI for IL-1α and IL-1β; ST2 for IL-33; and IL-36R for IL-36α, IL-36β and IL-36γ – after which they recruit the shared secondary receptor IL-1RAcP to form a ternary cytokine/receptor/co-receptor complex. Recently, IL-1RAcP was identified as a biomarker for both AML and CML. IL-1RAcP has also been implicated in tumor progression in solid tumors and an anti-IL1RAP antibody (nadunolimab, CAN04) is in phase II clinical studies in pancreatic cancer and non-small cell lung cancer (NCT03267316). As IL-1RAcP is common to all of the abovementioned IL-1 family cytokines, targeting this co-receptor raises the possibility of selective signaling inhibition for different IL-1 family cytokines. Indeed, previous studies of IL-1β and IL-33 signaling complexes have revealed that these cytokines employ distinct mechanisms of IL-1RAcP recruitment even though their overall cytokine/receptor/co-receptor complexes are structurally similar. Here, using functional, biophysical, and structural analyses, we show that antibodies specific for IL-1RAcP can differentially block signaling by IL-1 family cytokines depending on the distinct IL-1RAcP epitopes that they engage. Our results indicate that targeting a shared cytokine receptor is a viable therapeutic strategy for selective cytokine signaling inhibition.
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Affiliation(s)
- James K Fields
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States.,Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, United States.,Program in Molecular Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Kyle Kihn
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | | | - Erik H Klontz
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States.,Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, United States.,Program in Molecular Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | - Sebastian Günther
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Robert Beadenkopf
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | | | - Greg A Snyder
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States.,Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Daniel Deredge
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - Eric J Sundberg
- Department of Biochemistry, Emory School of Medicine, Atlanta, GA, United States
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28
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Kihn KC, Wilson T, Smith AK, Bradshaw RT, Wintrode PL, Forrest LR, Wilks A, Deredge DJ. Modeling the native ensemble of PhuS using enhanced sampling MD and HDX-ensemble reweighting. Biophys J 2021; 120:5141-5157. [PMID: 34767787 PMCID: PMC8715216 DOI: 10.1016/j.bpj.2021.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/13/2021] [Accepted: 11/04/2021] [Indexed: 11/25/2022] Open
Abstract
The cytoplasmic heme binding protein from Pseudomonas aeruginosa, PhuS, plays two essential roles in regulating heme uptake and iron homeostasis. First, PhuS shuttles exogenous heme to heme oxygenase (HemO) for degradation and iron release. Second, PhuS binds DNA and modulates the transcription of the prrF/H small RNAs (sRNAs) involved in the iron-sparing response. Heme binding to PhuS regulates this dual function, as the unliganded form binds DNA, whereas the heme-bound form binds HemO. Crystallographic studies revealed nearly identical structures for apo- and holo-PhuS, and yet numerous solution-based measurements indicate that heme binding is accompanied by large conformational rearrangements. In particular, hydrogen-deuterium exchange mass spectrometry (HDX-MS) of apo- versus holo-PhuS revealed large differences in deuterium uptake, notably in α-helices 6, 7, and 8 (α6,7,8), which contribute to the heme binding pocket. These helices were mostly labile in apo-PhuS but largely protected in holo-PhuS. In contrast, in silico-predicted deuterium uptake levels of α6,7,8 from molecular dynamics (MD) simulations of the apo- and holo-PhuS structures are highly similar, consistent only with the holo-PhuS HDX-MS data. To rationalize this discrepancy between crystal structures, simulations, and observed HDX-MS, we exploit a recently developed computational approach (HDXer) that fits the relative weights of conformational populations within an ensemble of structures to conform to a target set of HDX-MS data. Here, a combination of enhanced sampling MD, HDXer, and dimensionality reduction analysis reveals an apo-PhuS conformational landscape in which α6, 7, and 8 are significantly rearranged compared to the crystal structure, including a loss of secondary structure in α6 and the displacement of α7 toward the HemO binding interface. Circular dichroism analysis confirms the loss of secondary structure, and the extracted ensembles of apo-PhuS and of heme-transfer-impaired H212R mutant, are consistent with known heme binding and transfer properties. The proposed conformational landscape provides structural insights into the modulation by heme of the dual function of PhuS.
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Affiliation(s)
- Kyle C Kihn
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Tyree Wilson
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Ally K Smith
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | | | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Angela Wilks
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
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29
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Abstract
This Account describes considerations for the data generation, data analysis, and data interpretation of a hydrogen/deuterium exchange-mass spectrometry (HDX-MS) experiment to have a quantitative argument. Although HDX-MS has gained its popularity as a biophysical tool, the argument from its data often remains qualitative. To generate HDX-MS data that are more suitable for a quantitative argument, the sequence coverage and sequence resolution should be optimized during the feasibility stage, and the time window coverage and time window resolution should be improved during the HDX stage. To extract biophysically meaningful values for a certain perturbation from medium-resolution HDX-MS data, there are two major ways: (i) estimating the area between the two deuterium buildup curves using centroid values with and without the perturbation when plotted against log time scale and (ii) dissecting into multiple single-exponential curves using the isotope envelopes. To have more accurate arguments for an HDX-MS perturbation study, (i) false negatives due to sequence coverage, (ii) false negatives due to time window coverage, (iii) false positives due to sequence resolution, and (iv) false positives due to allosteric effects should be carefully examined.
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Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, United States
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30
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Carvajal MFCA, Preston JM, Jamhawi NM, Sabo TM, Bhattacharya S, Aramini JM, Wittebort RJ, Koder RL. Dynamics in natural and designed elastins and their relation to elastic fiber structure and recoil. Biophys J 2021; 120:4623-4634. [PMID: 34339635 PMCID: PMC8553601 DOI: 10.1016/j.bpj.2021.06.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 05/06/2021] [Accepted: 06/16/2021] [Indexed: 11/25/2022] Open
Abstract
Elastin fibers assemble in the extracellular matrix from the precursor protein tropoelastin and provide the flexibility and spontaneous recoil required for arterial function. Unlike many proteins, a structure-function mechanism for elastin has been elusive. We have performed detailed NMR relaxation studies of the dynamics of the minielastins 24x' and 20x' using solution NMR, and of purified bovine elastin fibers in the presence and absence of mechanical stress using solid state NMR. The low sequence complexity of the minielastins enables us to determine average dynamical timescales and degrees of local ordering in the cross-link and hydrophobic modules separately using NMR relaxation by taking advantage of their residue-specific resolution. We find an extremely high degree of disorder, with order parameters for the entirety of the hydrophobic domains near zero, resembling that of simple chemical polymers and less than the order parameters that have been observed in other intrinsically disordered proteins. We find that average backbone order parameters in natural, purified elastin fibers are comparable to those found in 24x' and 20x' in solution. The difference in dynamics, compared with the minielastins, is that backbone correlation times are significantly slowed in purified elastin. Moreover, when elastin is mechanically stretched, the high chain disorder in purified elastin is retained, showing that any change in local ordering is below that detectable in our experiment. Combined with our previous finding of a 10-fold increase in the ordering of water when fully hydrated elastin fibers are stretched by 50%, these results support the hypothesis that stretch induced solvent ordering, i.e., the hydrophobic effect, is a key player in the elastic recoil of elastin as opposed to configurational entropy loss.
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Affiliation(s)
| | | | - Nour M Jamhawi
- Department of Chemistry, University of Louisville, Louisville, Kentucky
| | - T Michael Sabo
- Department of Medicine and the James Brown Cancer Center, University of Louisville School of Medicine, Louisville, Kentucky
| | | | - James M Aramini
- Advanced Science Research Center, The City University of New York, New York, New York
| | | | - Ronald L Koder
- Department of Physics, The City College of New York, New York, New York; Graduate Programs of Physics, Chemistry, Biochemistry and Biology, The Graduate Center of CUNY, New York, New York.
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31
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Smit JH, Krishnamurthy S, Srinivasu BY, Parakra R, Karamanou S, Economou A. Probing Universal Protein Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy. Anal Chem 2021; 93:12840-12847. [PMID: 34523340 DOI: 10.1021/acs.analchem.1c02155] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to monitor protein intrinsic dynamics. The technique provides high-resolution information on how protein intrinsic dynamics are altered in response to biological signals, such as ligand binding, oligomerization, or allosteric networks. However, identification, interpretation, and visualization of such events from HDX-MS data sets is challenging as these data sets consist of many individual data points collected across peptides, time points, and experimental conditions. Here, we present PyHDX, an open-source Python package and webserver, that allows the user to batch extract the universal quantity Gibbs free energy at residue levels over multiple protein conditions and homologues. The output is directly visualized on a linear map or 3D structures or is exported as .csv files or PyMOL scripts.
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Affiliation(s)
- Jochem H Smit
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Srinath Krishnamurthy
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Bindu Y Srinivasu
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Rinky Parakra
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
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32
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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33
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Cornwell O, Ault JR, Bond NJ, Radford SE, Ashcroft AE. Investigation of D76N β 2-Microglobulin Using Protein Footprinting and Structural Mass Spectrometry. J Am Soc Mass Spectrom 2021; 32:1583-1592. [PMID: 33586970 PMCID: PMC9282677 DOI: 10.1021/jasms.0c00438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
NMR studies and X-ray crystallography have shown that the structures of the 99-residue amyloidogenic protein β2-microglobulin (β2m) and its more aggregation-prone variant, D76N, are indistinguishable, and hence, the reason for the striking difference in their aggregation propensities remains elusive. Here, we have employed two protein footprinting methods, hydrogen-deuterium exchange (HDX) and fast photochemical oxidation of proteins (FPOP), in conjunction with ion mobility-mass spectrometry, to probe the differences in conformational dynamics of the two proteins. Using HDX-MS, a clear difference in HDX protection is observed between these two proteins in the E-F loop (residues 70-77) which contains the D76N substitution, with a significantly higher deuterium uptake being observed in the variant protein. Conversely, following FPOP-MS only minimal differences in the level of oxidation between the two proteins are observed in the E-F loop region, suggesting only modest side-chain movements in that area. Together the HDX-MS and FPOP-MS data suggest that a tangible perturbation to the hydrogen-bonding network in the E-F loop has taken place in the D76N variant and furthermore illustrate the benefit of using multiple complementary footprinting methods to address subtle, but possibly biologically important, differences between highly similar proteins.
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Affiliation(s)
- Owen Cornwell
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - James R. Ault
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Nicholas J. Bond
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Alison E. Ashcroft
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
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34
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Song X, An L, Wang M, Chen J, Liu Z, Yao L. Osmolytes Can Destabilize Proteins in Cells by Modulating Electrostatics and Quinary Interactions. ACS Chem Biol 2021; 16:864-871. [PMID: 33843182 DOI: 10.1021/acschembio.1c00024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although numerous in vitro studies have shown that osmolytes are capable of stabilizing proteins, their effect on protein folding in vivo has been less understood. In this work, we investigated the effect of osmolytes, including glycerol, sorbitol, betaine, and taurine, on the folding of a protein GB3 variant in E. coli cells using NMR spectroscopy. 400 mM osmolytes were added to E. coli cells; only glycerol stabilizes the folded protein, whereas betaine and taurine considerably destabilize the protein through modulating folding and unfolding rates. Further investigation indicates that betaine and taurine can enhance the quinary interaction between the protein and cellular environment and manifestly weaken the electrostatic attraction in protein salt bridges. The combination of the two factors causes destabilization of the protein in E. coli cells. These factors counteract the preferential exclusion mechanism that is adopted by osmolytes to stabilize proteins.
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Affiliation(s)
- Xiangfei Song
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liaoyuan An
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengting Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Zhijun Liu
- National Facility for Protein Science, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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35
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Abstract
Amide hydrogen-deuterium exchange (HDX) has long been used to determine regional flexibility and binding sites in proteins; however, the data are too sparse for full structural characterization. Experiments that measure HDX rates, such as HDX-NMR, have far higher throughput compared to structure determination via X-ray crystallography, cryo-EM, or a full suite of NMR experiments. Data from HDX-NMR experiments encode information on the protein structure, making HDX a prime candidate to be supplemented by computational algorithms for protein structure prediction. We have developed a methodology to incorporate HDX-NMR data into ab initio protein structure prediction using the Rosetta software framework to predict structures based on experimental agreement. To demonstrate the efficacy of our algorithm, we examined 38 proteins with HDX-NMR data available, comparing the predicted model with and without the incorporation of HDX data into scoring. The root-mean-square deviation (rmsd, a measure of the average atomic distance between superimposed models) of the predicted model improved by 1.42 Å on average after incorporating the HDX-NMR data into scoring. The average rmsd improvement for the proteins where the selected model rmsd changed after incorporating HDX data was 3.63 Å, including one improvement of more than 11 Å and seven proteins improving by greater than 4 Å, with 12/15 proteins improving overall. Additionally, for independent verification, two proteins that were not part of the original benchmark were scored including HDX data, with a dramatic improvement of the selected model rmsd of nearly 9 Å for one of the proteins. Moreover, we have developed a confidence metric allowing us to successfully identify near-native models in the absence of a native structure. Improvement in model selection with a strong confidence measure demonstrates that protein structure prediction with HDX-NMR is a powerful tool which can be performed with minimal additional computational strain and expense.
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Affiliation(s)
- Daniel R Marzolf
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
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Kaur K, Xiong J, Sawant N, Agarwal S, Hickey JM, Holland DA, Mukhopadhyay TK, Brady JR, Dalvie NC, Tracey MK, Love KR, Love JC, Weis DD, Joshi SB, Volkin DB. Mechanism of Thimerosal-Induced Structural Destabilization of a Recombinant Rotavirus P[4] Protein Antigen Formulated as a Multi-Dose Vaccine. J Pharm Sci 2021; 110:1054-1066. [PMID: 33278412 PMCID: PMC7884053 DOI: 10.1016/j.xphs.2020.11.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 12/23/2022]
Abstract
In a companion paper, a two-step developability assessment is presented to rapidly evaluate low-cost formulations (multi-dose, aluminum-adjuvanted) for new subunit vaccine candidates. As a case study, a non-replicating rotavirus (NRRV) recombinant protein antigen P[4] was found to be destabilized by the vaccine preservative thimerosal, and this effect was mitigated by modification of the free cysteine (C173S). In this work, the mechanism(s) of thimerosal-P[4] protein interactions, along with subsequent effects on the P[4] protein's structural integrity, are determined. Reversible complexation of ethylmercury, a thimerosal degradation byproduct, with the single cysteine residue of P[4] protein is demonstrated by intact protein mass analysis and biophysical studies. A working mechanism involving a reversible S-Hg coordinate bond is presented based on the literature. This reaction increased the local backbone flexibility of P[4] within the helical region surrounding the cysteine residue and then caused more global destabilization, both as detected by HX-MS. These effects correlate with changes in antibody-P[4] binding parameters and alterations in P[4] conformational stability due to C173S modification. Epitope mapping by HX-MS demonstrated involvement of the same cysteine-containing helical region of P[4] in antibody-antigen binding. Future formulation challenges to develop low-cost, multi-dose formulations for new recombinant protein vaccine candidates are discussed.
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Affiliation(s)
- Kawaljit Kaur
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Jian Xiong
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Nishant Sawant
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Sanjeev Agarwal
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - John M Hickey
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - David A Holland
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - Tarit K Mukhopadhyay
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London WC1E 6BT, UK
| | - Joseph R Brady
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Neil C Dalvie
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mary Kate Tracey
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kerry R Love
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - J Christopher Love
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David D Weis
- Department of Chemistry and R.N. Adams Institute of Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045
| | - Sangeeta B Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047.
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37
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Salmas RE, Borysik AJ. HDXmodeller: an online webserver for high-resolution HDX-MS with auto-validation. Commun Biol 2021; 4:199. [PMID: 33589746 DOI: 10.1038/s42003-021-01709-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022] Open
Abstract
The extent to which proteins are protected from hydrogen deuterium exchange (HDX) provides valuable insight into their folding, dynamics and interactions. Characterised by mass spectrometry (MS), HDX benefits from negligible mass restrictions and exceptional throughput and sensitivity but at the expense of resolution. Exchange mechanisms which naturally transpire for individual residues cannot be accurately located or understood because amino acids are characterised in differently sized groups depending on the extent of proteolytic digestion. Here we report HDXmodeller, the world's first online webserver for high-resolution HDX-MS. HDXmodeller accepts low-resolution HDX-MS input data and returns high-resolution exchange rates quantified for each residue. Crucially, HDXmodeller also returns a set of unique statistics that can correctly validate exchange rate models to an accuracy of 99%. Remarkably, these statistics are derived without any prior knowledge of the individual exchange rates and facilitate unparallel user confidence and the capacity to evaluate different data optimisation strategies.
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Abstract
Chemistry related to hydrogen/deuterium exchange-mass spectrometry (HDX-MS) for the analysis of proteins is described. First, the HDX rates of various functional groups in proteins are explained by reviewing the observed rates described in the literature, followed by estimating rates of all types of heteroatom hydrogens in proteins using proton transfer theory and the pKa values. The estimated HDX rates match well with the respective observed rates for most functional groups, with the exception of indole and amide groups. The discrepancies between the observed and estimated HDX rates for these groups are explained by the reaction mechanisms. Second, the factors that affect the HDX rates of backbone amide hydrogen, including side chain, N- and C-terminals, pH, temperature, organic solvent, and isotopes, are discussed. These factors are important for the proper design of exchange reactions and downstream process as well as the analysis and interpretation of HDX-MS data.
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Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, United States
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39
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Lee PS, Bradshaw RT, Marinelli F, Kihn K, Smith A, Wintrode PL, Deredge DJ, Faraldo-Gómez JD, Forrest LR. Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]. Living J Comput Mol Sci 2021; 3:1521. [PMID: 36644498 PMCID: PMC9835200 DOI: 10.33011/livecoms.3.1.1521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Hydrogen-deuterium exchange (HDX) is a comprehensive yet detailed probe of protein structure and dynamics and, coupled to mass spectrometry, has become a powerful tool for investigating an increasingly large array of systems. Computer simulations are often used to help rationalize experimental observations of exchange, but interpretations have frequently been limited to simple, subjective correlations between microscopic dynamical fluctuations and the observed macroscopic exchange behavior. With this in mind, we previously developed the HDX ensemble reweighting approach and associated software, HDXer, to aid the objective interpretation of HDX data using molecular simulations. HDXer has two main functions; first, to compute H-D exchange rates that describe each structure in a candidate ensemble of protein structures, for example from molecular simulations, and second, to objectively reweight the conformational populations present in a candidate ensemble to conform to experimental exchange data. In this article, we first describe the HDXer approach, theory, and implementation. We then guide users through a suite of tutorials that demonstrate the practical aspects of preparing experimental data, computing HDX levels from molecular simulations, and performing ensemble reweighting analyses. Finally we provide a practical discussion of the capabilities and limitations of the HDXer methods including recommendations for a user's own analyses. Overall, this article is intended to provide an up-to-date, pedagogical counterpart to the software, which is freely available at https://github.com/Lucy-Forrest-Lab/HDXer.
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Affiliation(s)
- Paul Suhwan Lee
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Richard T. Bradshaw
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA,For correspondence: (RTB); (LRF)
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kyle Kihn
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Ally Smith
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Patrick L. Wintrode
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Daniel J. Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - José D. Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucy R. Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA,For correspondence: (RTB); (LRF)
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40
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Anderson KW, Scott K, Karageorgos IL, Gallagher ES, Tayi VS, Butler M, Hudgens JW. Dataset from HDX-MS Studies of IgG1 Glycoforms and Their Interactions with the FcγRIa (CD64) Receptor. J Res Natl Inst Stand Technol 2021; vol:126010. [PMID: 36474595 PMCID: PMC9681196 DOI: 10.6028/jres.126.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 05/17/2023]
Abstract
This document presents hydrogen-deuterium exchange mass spectrometry (HDX-MS) data from measurements of three purified IgG1 glycoform samples, predominantly G0F, G2F, and SAF, in isolation and in complexation with the high-affinity receptor, FcγRIa (CD64). The IgG1 antibody used in this study, aIL8hFc, is a murine-human chimeric IgG1, which inhibits IL-8 binding to human neutrophils.
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Affiliation(s)
- Kyle W. Anderson
- National Institute of Standards and Technology, Gaithersburg, MD 20899,
USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850,
USA
| | - Kerry Scott
- National Institute of Standards and Technology, Gaithersburg, MD 20899,
USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850,
USA
| | - Ioannis L. Karageorgos
- National Institute of Standards and Technology, Gaithersburg, MD 20899,
USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850,
USA
| | - Elyssia S. Gallagher
- National Institute of Standards and Technology, Gaithersburg, MD 20899,
USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850,
USA
| | - Venkata S. Tayi
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2,
Canada
| | - Michael Butler
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2,
Canada
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin,
Ireland
| | - Jeffrey W. Hudgens
- National Institute of Standards and Technology, Gaithersburg, MD 20899,
USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850,
USA
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41
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Ozohanics O, Ambrus A. Hydrogen-Deuterium Exchange Mass Spectrometry: A Novel Structural Biology Approach to Structure, Dynamics and Interactions of Proteins and Their Complexes. Life (Basel) 2020; 10:E286. [PMID: 33203161 PMCID: PMC7696067 DOI: 10.3390/life10110286] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022] Open
Abstract
Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) is a rapidly evolving technique for analyzing structural features and dynamic properties of proteins. It may stand alone or serve as a complementary method to cryo-electron-microscopy (EM) or other structural biology approaches. HDX-MS is capable of providing information on individual proteins as well as large protein complexes. Owing to recent methodological advancements and improving availability of instrumentation, HDX-MS is becoming a routine technique for some applications. When dealing with samples of low to medium complexity and sizes of less than 150 kDa, conformation and ligand interaction analyses by HDX-MS are already almost routine applications. This is also well supported by the rapid evolution of the computational (software) background that facilitates the analysis of the obtained experimental data. HDX-MS can cope at times with analytes that are difficult to tackle by any other approach. Large complexes like viral capsids as well as disordered proteins can also be analyzed by this method. HDX-MS has recently become an established tool in the drug discovery process and biopharmaceutical development, as it is now also capable of dissecting post-translational modifications and membrane proteins. This mini review provides the reader with an introduction to the technique and a brief overview of the most common applications. Furthermore, the most challenging likely applications, the analyses of glycosylated and membrane proteins, are also highlighted.
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Affiliation(s)
- Oliver Ozohanics
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, 37–47 Tuzolto Street, 1094 Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Institute of Biochemistry and Molecular Biology, Semmelweis University, 37–47 Tuzolto Street, 1094 Budapest, Hungary
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42
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Affiliation(s)
- John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas Botzanowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Florian Georgescauld
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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43
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Yagi-Utsumi M, Chandak MS, Yanaka S, Hiranyakorn M, Nakamura T, Kato K, Kuwajima K. Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR. Biophys J 2020; 119:2029-2038. [PMID: 33142107 DOI: 10.1016/j.bpj.2020.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/10/2020] [Accepted: 10/07/2020] [Indexed: 12/01/2022] Open
Abstract
The characterization of residual structures persistent in unfolded proteins in concentrated denaturant solution is currently an important issue in studies of protein folding because the residual structure present, if any, in the unfolded state may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the hydrogen/deuterium (H/D)-exchange behavior of unfolded human ubiquitin in 6 M guanidinium chloride. We employed a dimethylsulfoxide (DMSO)-quenched H/D-exchange NMR technique with the use of spin desalting columns, which allowed us to perform a quick medium exchange from 6 M guanidinium chloride to a quenching DMSO solution. Based on the backbone resonance assignment of ubiquitin in the DMSO solution, we successfully investigated the H/D-exchange kinetics of 60 identified peptide amide groups in the ubiquitin sequence. Although a majority of these amide groups were not protected, certain amide groups involved in a middle helix (residues 23-34) and an N-terminal β-hairpin (residues 2-16) were significantly protected with a protection factor of 2.1-4.2, indicating that there were residual structures in unfolded ubiquitin and that these amide groups were more than 52% hydrogen bonded in the residual structures. We show that the hydrogen-bonded residual structures in the α-helix and the β-hairpin are formed even in 6 M guanidinium chloride, suggesting that these residual structures may function as a folding initiation site to guide the subsequent folding reactions of ubiquitin.
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Affiliation(s)
- Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Mahesh S Chandak
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Methanee Hiranyakorn
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Takashi Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan.
| | - Kunihiro Kuwajima
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan; Department of Physics, Graduate School of Science, the University of Tokyo, Tokyo, Japan; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
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44
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Narang D, Lento C, J. Wilson D. HDX-MS: An Analytical Tool to Capture Protein Motion in Action. Biomedicines 2020; 8:biomedicines8070224. [PMID: 32709043 PMCID: PMC7399943 DOI: 10.3390/biomedicines8070224] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/07/2023] Open
Abstract
Virtually all protein functions in the cell, including pathogenic processes, require coordinated motion of atoms or domains, i.e., conformational dynamics. Understanding protein dynamics is therefore critical both for drug development and to learn about the underlying molecular causes of many diseases. Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) provides valuable information about protein dynamics, which is highly complementary to the static picture provided by conventional high-resolution structural tools (i.e., X-ray crystallography and structural NMR). The amount of protein required to carry out HDX-MS experiments is a fraction of the amount required by alternative biophysical techniques, which are also usually lower resolution. Use of HDX-MS is growing quickly both in industry and academia, and it has been successfully used in numerous drug and vaccine development efforts, with important roles in understanding allosteric effects and mapping binding sites.
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Affiliation(s)
- Dominic Narang
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
| | - Derek J. Wilson
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
- Centre for Research of Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University, Toronto, ON M3J 1P3, Canada
- Correspondence:
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45
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Affiliation(s)
- Nastaran N. Tajoddin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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46
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Ye X, Lin J, Mayne L, Shorter J, Englander SW. Structural and kinetic basis for the regulation and potentiation of Hsp104 function. Proc Natl Acad Sci U S A 2020; 117:9384-92. [PMID: 32277033 DOI: 10.1073/pnas.1921968117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Hsp104 provides a valuable model for the many essential proteostatic functions performed by the AAA+ superfamily of protein molecular machines. We developed and used a powerful hydrogen exchange mass spectrometry (HX MS) analysis that can provide positionally resolved information on structure, dynamics, and energetics of the Hsp104 molecular machinery, even during functional cycling. HX MS reveals that the ATPase cycle is rate-limited by ADP release from nucleotide-binding domain 1 (NBD1). The middle domain (MD) serves to regulate Hsp104 activity by slowing ADP release. Mutational potentiation accelerates ADP release, thereby increasing ATPase activity. It reduces time in the open state, thereby decreasing substrate protein loss. During active cycling, Hsp104 transits repeatedly between whole hexamer closed and open states. Under diverse conditions, the shift of open/closed balance can lead to premature substrate loss, normal processing, or the generation of a strong pulling force. HX MS exposes the mechanisms of these functions at near-residue resolution.
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47
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Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR. Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles. Biophys J 2020; 118:1649-1664. [PMID: 32105651 PMCID: PMC7136279 DOI: 10.1016/j.bpj.2020.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 01/12/2023] Open
Abstract
Hydrogen-deuterium exchange combined with mass spectrometry (HDX-MS) is a widely applied biophysical technique that probes the structure and dynamics of biomolecules without the need for site-directed modifications or bio-orthogonal labels. The mechanistic interpretation of HDX data, however, is often qualitative and subjective, owing to a lack of quantitative methods to rigorously translate observed deuteration levels into atomistic structural information. To help address this problem, we have developed a methodology to generate structural ensembles that faithfully reproduce HDX-MS measurements. In this approach, an ensemble of protein conformations is first generated, typically using molecular dynamics simulations. A maximum-entropy bias is then applied post hoc to the resulting ensemble such that averaged peptide-deuteration levels, as predicted by an empirical model, agree with target values within a given level of uncertainty. We evaluate this approach, referred to as HDX ensemble reweighting (HDXer), for artificial target data reflecting the two major conformational states of a binding protein. We demonstrate that the information provided by HDX-MS experiments and by the model of exchange are sufficient to recover correctly weighted structural ensembles from simulations, even when the relevant conformations are rarely observed. Degrading the information content of the target data—e.g., by reducing sequence coverage, by averaging exchange levels over longer peptide segments, or by incorporating different sources of uncertainty—reduces the structural accuracy of the reweighted ensemble but still allows for useful insights into the distinctive structural features reflected by the target data. Finally, we describe a quantitative metric to rank candidate structural ensembles according to their correspondence with target data and illustrate the use of HDXer to describe changes in the conformational ensemble of the membrane protein LeuT. In summary, HDXer is designed to facilitate objective structural interpretations of HDX-MS data and to inform experimental approaches and further developments of theoretical exchange models.
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Affiliation(s)
- Richard T Bradshaw
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Unit, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland.
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48
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Pedersen MC, Wang Y, Tidemand FG, Martel A, Lindorff-Larsen K, Arleth L. PSX, Protein–Solvent Exchange: software for calculation of deuterium-exchange effects in small-angle neutron scattering measurements from protein coordinates. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719012469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Recent developments in neutron scattering instrumentation and sample handling have enabled studies of more complex biological samples and measurements at shorter exposure times. The experiments are typically conducted in D2O-based buffers to emphasize or diminish scattering from a particular component or to minimize background noise in the experiment. To extract most information from such experiments it is thus desirable to determine accurate estimates of how and when closely bound hydrogen atoms from the biomolecule exchange with the deuterium in the solvent. This article introduces and documents software, PSX, for exploring the effect of hydrogen–deuterium exchange for proteins solubilized in D2O as well as the underlying bioinformatical models. The software aims to be generally applicable for any atomistic structure of a protein and its surrounding environment, and thus captures effects of both heterogenous exchange rates throughout the protein structure and varying the experimental conditions such as pH and temperature. The paper concludes with examples of applications and estimates of the effect in typical scenarios emerging in small-angle neutron scattering on biological macromolecules in solution. The analysis presented here suggests that the common assumption of 90% exchange is in many cases an overestimate with the rapid sample handling systems currently available, which leads to fitting and calibration issues when analysing the data. Source code for the presented software is available from an online repository in which it is published under version 3 of the GNU publishing licence.
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Babić D, Kazazić S, Smith DM. Resolution of protein hydrogen/deuterium exchange by fitting amide exchange probabilities to the peptide isotopic envelopes. Rapid Commun Mass Spectrom 2019; 33:1248-1257. [PMID: 31034666 DOI: 10.1002/rcm.8460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/13/2019] [Accepted: 04/10/2019] [Indexed: 05/11/2023]
Abstract
RATIONALE Mass spectra processing in protein hydrogen/deuterium (H/D) exchange has been remarkably improved by the introduction of fitting of the amide exchange probabilities to peptide isotopic envelope intensities (Kan et al., 2013), in contrast to methods in which only the peptide deuterium uptakes (centroid shifts of isotopic envelopes) are used. However, the known implementations are based on the general fitting routines that use only the objective function values. Besides, applicability of more than one fitting method makes necessary their comparative evaluation. METHODS Two fitting methods were considered: the common least squares and the fitting of the multinomial distribution representing the number of deuterium atoms exchanged in the individual peptides. Both methods were applied either directly to the isotopic envelope data or to the deuterium distributions obtained by envelope deconvolution (i.e. de-isotoping). RESULTS An autonomous Matlab script was prepared, based on the exact expressions for the gradient and Hessian of the objective function, with the trust-region algorithm implemented in the compact analytical form recently made available. The least-squares fitting to the envelope data produced the best results, with the greatest precision and good coverage of exact values by the confidence intervals. The deuterium distributions were sensitive to the (simulated) experimental error whose progression by envelope deconvolution caused degradation in accuracy. The multinomial distribution fitting exhibited poor performance due to inadequate representation of the experimental error and missing of the appropriate weight parameters. Some specific peptide arrangement details were discussed as potential sources of ambiguity in the fitting results. CONCLUSIONS The method of fitting to peptide isotopic envelopes has been improved by using the exact gradient and Hessian of the objective function. The fitting should be repeated with different initial guesses in order to find not only the global minimum, but also the local minima with similar depths which may exist due to eventual ambiguity of the fitting results.
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Affiliation(s)
- Darko Babić
- Department of Physical Chemistry, Institute "Ruđer Bošković", HR-10002, Zagreb, Croatia
| | - Saša Kazazić
- Department of Physical Chemistry, Institute "Ruđer Bošković", HR-10002, Zagreb, Croatia
| | - David M Smith
- Department of Physical Chemistry, Institute "Ruđer Bošković", HR-10002, Zagreb, Croatia
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Affiliation(s)
- Rajashekar Kammari
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Elizabeth M. Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
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