1
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Lu H, Zhu Z, Fields L, Zhang H, Li L. Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross-Linking. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39300771 DOI: 10.1002/mas.21908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/31/2024] [Accepted: 09/02/2024] [Indexed: 09/22/2024]
Abstract
The exploration of protein structure and function stands at the forefront of life science and represents an ever-expanding focus in the development of proteomics. As mass spectrometry (MS) offers readout of protein conformational changes at both the protein and peptide levels, MS-based structural proteomics is making significant strides in the realms of structural and molecular biology, complementing traditional structural biology techniques. This review focuses on two powerful MS-based techniques for peptide-level readout, namely limited proteolysis-mass spectrometry (LiP-MS) and cross-linking mass spectrometry (XL-MS). First, we discuss the principles, features, and different workflows of these two methods. Subsequently, we delve into the bioinformatics strategies and software tools used for interpreting data associated with these protein conformation readouts and how the data can be integrated with other computational tools. Furthermore, we provide a comprehensive summary of the noteworthy applications of LiP-MS and XL-MS in diverse areas including neurodegenerative diseases, interactome studies, membrane proteins, and artificial intelligence-based structural analysis. Finally, we discuss the factors that modulate protein conformational changes. We also highlight the remaining challenges in understanding the intricacies of protein conformational changes by LiP-MS and XL-MS technologies.
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Affiliation(s)
- Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zexin Zhu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
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2
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Martina M, Banderali U, Yogi A, Arbabi Ghahroudi M, Liu H, Sulea T, Durocher Y, Hussack G, van Faassen H, Chakravarty B, Liu QY, Iqbal U, Ling B, Lessard E, Sheff J, Robotham A, Callaghan D, Moreno M, Comas T, Ly D, Stanimirovic D. A Novel Antigen Design Strategy to Isolate Single-Domain Antibodies that Target Human Nav1.7 and Reduce Pain in Animal Models. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405432. [PMID: 39206821 DOI: 10.1002/advs.202405432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/01/2024] [Indexed: 09/04/2024]
Abstract
Genetic studies have identified the voltage-gated sodium channel 1.7 (Nav1.7) as pain target. Due to the ineffectiveness of small molecules and monoclonal antibodies as therapeutics for pain, single-domain antibodies (VHHs) are developed against the human Nav1.7 (hNav1.7) using a novel antigen presentation strategy. A 70 amino-acid peptide from the hNav1.7 protein is identified as a target antigen. A recombinant version of this peptide is grafted into the complementarity determining region 3 (CDR3) loop of an inert VHH in order to maintain the native 3D conformation of the peptide. This antigen is used to isolate one VHH able to i) bind hNav1.7, ii) slow the deactivation of hNav1.7, iii) reduce the ability of eliciting action potentials in nociceptors, and iv) reverse hyperalgesia in in vivo rat and mouse models. This VHH exhibits the potential to be developed as a therapeutic capable of suppressing pain. This novel antigen presentation strategy can be applied to develop biologics against other difficult targets such as ion channels, transporters and GPCRs.
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Affiliation(s)
- Marzia Martina
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Umberto Banderali
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Alvaro Yogi
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Mehdi Arbabi Ghahroudi
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1N 5A2, Canada
| | - Hong Liu
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue Montréal, Quebec, H4P 2R2, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue Montréal, Quebec, H4P 2R2, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1N 5A2, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1N 5A2, Canada
| | - Balu Chakravarty
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Qing Yan Liu
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Umar Iqbal
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Binbing Ling
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Etienne Lessard
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue Montréal, Quebec, H4P 2R2, Canada
| | - Joey Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1N 5A2, Canada
| | - Anna Robotham
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1N 5A2, Canada
| | - Debbie Callaghan
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1N 5A2, Canada
| | - Maria Moreno
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Tanya Comas
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Dao Ly
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
| | - Danica Stanimirovic
- Human Health Therapeutics Research Center, National Research Council Canada, 1200 Montreal Road, Building M54, Ottawa, ON, K1A 0R6, Canada
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3
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Filandr F, Sarpe V, Raval S, Crowder DA, Khan MF, Douglas P, Coales S, Viner R, Syed A, Tainer JA, Lees-Miller SP, Schriemer DC. Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology. Nat Commun 2024; 15:2200. [PMID: 38467655 PMCID: PMC10928179 DOI: 10.1038/s41467-024-46610-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
We present a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS2) that supports the acquisition of peptide fragment ions alongside their peptide precursors. The approach enables true auto-curation of HX data by mining a rich set of deuterated fragments, generated by collisional-induced dissociation (CID), to simultaneously confirm the peptide ID and authenticate MS1-based deuteration calculations. The high redundancy provided by the fragments supports a confidence assessment of deuterium calculations using a combinatorial strategy. The approach requires data-independent acquisition (DIA) methods that are available on most MS platforms, making the switch to HX-MS2 straightforward. Importantly, we find that HX-DIA enables a proteomics-grade approach and wide-spread applications. Considerable time is saved through auto-curation and complex samples can now be characterized and at higher throughput. We illustrate these advantages in a drug binding analysis of the ultra-large protein kinase DNA-PKcs, isolated directly from mammalian cells.
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Affiliation(s)
- Frantisek Filandr
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Shaunak Raval
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
- Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Morgan F Khan
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Pauline Douglas
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Stephen Coales
- Trajan Scientific & Medical - Raleigh, Morrisville, NC, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, USA
| | - Aleem Syed
- Division of Radiation and Genome Instability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada.
- Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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4
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Nouchikian L, Fernandez-Martinez D, Renard PY, Sabot C, Duménil G, Rey M, Chamot-Rooke J. Do Not Waste Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin. Anal Chem 2024; 96:2506-2513. [PMID: 38294351 PMCID: PMC10867798 DOI: 10.1021/acs.analchem.3c04682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) has become a very useful tool for studying protein complexes and interactions in living systems. It enables the investigation of many large and dynamic assemblies in their native state, providing an unbiased view of their protein interactions and restraints for integrative modeling. More researchers are turning toward trying XL-MS to probe their complexes of interest, especially in their native environments. However, due to the presence of other potentially higher abundant proteins, sufficient cross-links on a system of interest may not be reached to achieve satisfactory structural and interaction information. There are currently no rules for predicting whether XL-MS experiments are likely to work or not; in other words, if a protein complex of interest will lead to useful XL-MS data. Here, we show that a simple iBAQ (intensity-based absolute quantification) analysis performed from trypsin digest data can provide a good understanding of whether proteins of interest are abundant enough to achieve successful cross-linking data. Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein. We foresee that this guideline is a good starting point for researchers who would like to use XL-MS to study their protein of interest and help ensure a successful cross-linking experiment from the beginning. Data are available via ProteomeXchange with identifier PXD045792.
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Affiliation(s)
- Lucienne Nouchikian
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
| | - David Fernandez-Martinez
- Institut
Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis
of Vascular Infections Unit, Paris 75015, France
| | - Pierre-Yves Renard
- Univ
Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA
UMR 6014, INC3M FR 3038, Rouen F-76000, France
| | - Cyrille Sabot
- Univ
Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA
UMR 6014, INC3M FR 3038, Rouen F-76000, France
| | - Guillaume Duménil
- Institut
Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis
of Vascular Infections Unit, Paris 75015, France
| | - Martial Rey
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
| | - Julia Chamot-Rooke
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
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5
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Brodie NI, Sarpe V, Crowder DA, Schriemer D. All-in-One Pseudo-MS 3 Method for the Analysis of Gas-Phase Cleavable Protein Crosslinking Reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2146-2155. [PMID: 37590165 PMCID: PMC11250984 DOI: 10.1021/jasms.3c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Crosslinking mass spectrometry (XL-MS) supports structure analysis of individual proteins and highly complex whole-cell interactomes. The identification of crosslinked peptides from enzymatic digests remains challenging, especially at the cell level. Empirical methods that use gas-phase cleavable crosslinkers can simplify the identification process by enabling an MS3-based strategy that turns crosslink identification into a simpler problem of detecting two separable peptides. However, the method is limited to select instrument platforms and is challenged by duty cycle constraints. Here, we revisit a pseudo-MS3 concept that incorporates in-source fragmentation, where a fast switch between gentle high-transmission source conditions and harsher in-source fragmentation settings liberates peptides for standard MS2-based peptide identification. We present an all-in-one method where retention time matches between the crosslink precursor and the liberated peptides establish linkage, and MS2 sequencing identifies the source-liberated peptides. We demonstrate that DC4, a very labile cleavable crosslinker, generates high-intensity peptides in-source. Crosslinks can be identified from these liberated peptides, as they are chromatographically well-resolved from monolinks. Using bovine serum albumin (BSA) as a crosslinking test case, we detect 27% more crosslinks with pseudo-MS3 over a best-in-class MS3 method. While performance is slightly lower for whole-cell lysates (generating two-thirds of the identifications of a standard method), we find that 60% of these hits are unique, highlighting the complementarity of the method.
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Affiliation(s)
- Nicholas I Brodie
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
| | - David Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N-4N1
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6
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Wolf E, Lento C, Pu J, Dickinson BC, Wilson DJ. Innate Conformational Dynamics Drive Binding Specificity in Anti-Apoptotic Proteins Mcl-1 and Bcl-2. Biochemistry 2023; 62:1619-1630. [PMID: 37192192 PMCID: PMC10249625 DOI: 10.1021/acs.biochem.2c00709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/02/2023] [Indexed: 05/18/2023]
Abstract
The structurally conserved B-cell lymphoma 2 (Bcl-2) family of protein function to promote or inhibit apoptosis through an exceedingly complex web of specific, intrafamilial protein-protein interactions. The critical role of these proteins in lymphomas and other cancers has motivated a widespread interest in understanding the molecular mechanisms that drive specificity in Bcl-2 family interactions. However, the high degree of structural similarity among Bcl-2 homologues has made it difficult to rationalize the highly specific (and often divergent) binding behavior exhibited by these proteins using conventional structural arguments. In this work, we use time-resolved hydrogen deuterium exchange mass spectrometry to explore shifts in conformational dynamics associated with binding partner engagement in the Bcl-2 family proteins Bcl-2 and Mcl-1. Using this approach combined with homology modeling, we reveal that Mcl-1 binding is driven by a large-scale shift in conformational dynamics, while Bcl-2 complexation occurs primarily through a classical charge compensation mechanism. This work has implications for understanding the evolution of internally regulated biological systems composed of structurally similar proteins and for the development of drugs targeting Bcl-2 family proteins for promotion of apoptosis in cancer.
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Affiliation(s)
- Esther Wolf
- Department
of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Cristina Lento
- Department
of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jinyue Pu
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Derek J. Wilson
- Department
of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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7
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Unterhauser J, Ahammer L, Rainer T, Eidelpes R, Führer S, Nothegger B, Covaciu CE, Cova V, Kamenik AS, Liedl KR, Müller T, Breuker K, Eisendle K, Reider N, Letschka T, Tollinger M. Covalent polyphenol modification of a reactive cysteine in the major apple allergen Mal d 1. Food Chem 2023; 410:135374. [PMID: 36608553 DOI: 10.1016/j.foodchem.2022.135374] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023]
Abstract
Naturally occurring polyphenols can modify the molecular properties of food allergens. For the major apple allergen Mal d 1 it has been postulated that chemical reactions with polyphenols cause permanent changes in the tertiary structure, causing a loss of conformational IgE epitopes and reducing allergenicity. In our study, we investigated the effect that reactions with oxidized polyphenols have on the structure of Mal d 1 by mass spectrometry and NMR spectroscopy. We showed that a surface-exposed cysteine residue in this allergen spontaneously reacts with oxidized polyphenols under formation of a defined covalent adduct. Chemical modification of Mal d 1 did not destabilize or perturb the three-dimensional fold, nor did it interfere with ligand binding to its internal pocket. A structural model of the chemically modified apple allergen is presented, which reveals that the bound polyphenol partially covers a conformational IgE epitope on the protein surface.
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Affiliation(s)
- Jana Unterhauser
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Linda Ahammer
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Tobias Rainer
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Reiner Eidelpes
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Sebastian Führer
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Bettina Nothegger
- Department of Dermatology, Venerology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudia E Covaciu
- Department of Dermatology, Venerology and Allergology, Central Teaching Hospital, Bolzano/Bozen, Italy
| | - Valentina Cova
- Department of Molecular Biology and Microbiology, Laimburg Research Centre, Ora/Auer, Italy
| | - Anna S Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Thomas Müller
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus Eisendle
- Department of Dermatology, Venerology and Allergology, Central Teaching Hospital, Bolzano/Bozen, Italy
| | - Norbert Reider
- Department of Dermatology, Venerology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Thomas Letschka
- Department of Molecular Biology and Microbiology, Laimburg Research Centre, Ora/Auer, Italy.
| | - Martin Tollinger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria.
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8
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Gelinas AD, Tan TK, Liu S, Jaramillo JG, Chadwick J, Harding AC, Zhang C, Ream BE, Chase CN, Otis MR, Lee T, Schneider DJ, James WS, Janjic N. Broadly neutralizing aptamers to SARS-CoV-2: A diverse panel of modified DNA antiviral agents. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:370-382. [PMID: 36714461 PMCID: PMC9859636 DOI: 10.1016/j.omtn.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Since its discovery, COVID-19 has rapidly spread across the globe and has had a massive toll on human health, with infection mortality rates as high as 10%, and a crippling impact on the world economy. Despite numerous advances, there remains an urgent need for accurate and rapid point-of-care diagnostic tests and better therapeutic treatment options. To contribute chemically distinct, non-protein-based affinity reagents, we report here the identification of modified DNA-based aptamers that selectively bind to the S1, S2, or receptor-binding domain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Several aptamers inhibit the binding of the spike protein to its cell-surface receptor angiotensin-converting enzyme 2 (ACE2) and neutralize authentic SARS-CoV-2 virus in vitro, including all variants of concern. With a high degree of nuclease resistance imparted by the base modifications, these reagents represent a new class of molecules with potential for further development as diagnostics or therapeutics.
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Affiliation(s)
- Amy D. Gelinas
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Tiong Kit Tan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sai Liu
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Javier G. Jaramillo
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - James Chadwick
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Adam C. Harding
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Chi Zhang
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Brian E. Ream
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | | | - Matthew R. Otis
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Thomas Lee
- Department of Biochemistry, University of Colorado, Boulder, JSCBB, C1B90, 3415 Colorado Avenue, Boulder, CO 80303, USA
| | | | - William S. James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Corresponding author William S. James, James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Nebojsa Janjic
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
- Corresponding author Nebojsa Janjic, SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA.
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9
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Anacleto J, Lento C, Sarpe V, Maqsood A, Mehrazma B, Schriemer D, Wilson DJ. Apparatus for Automated Continuous Hydrogen Deuterium Exchange Mass Spectrometry Measurements from Milliseconds to Hours. Anal Chem 2023; 95:4421-4428. [PMID: 36880265 PMCID: PMC9996604 DOI: 10.1021/acs.analchem.2c05003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a rapidly growing technique for protein characterization in industry and academia, complementing the "static" picture provided by classical structural biology with information about the dynamic structural changes that accompany biological function. Conventional hydrogen deuterium exchange experiments, carried out on commercially available systems, typically collect 4-5 exchange timepoints on a timescale ranging from tens of seconds to hours using a workflow that can require 24 h or more of continuous data collection for triplicate measurements. A small number of groups have developed setups for millisecond timescale HDX, allowing for the characterization of dynamic shifts in weakly structured or disordered regions of proteins. This capability is particularly important given the central role that weakly ordered protein regions often play in protein function and pathogenesis. In this work, we introduce a new continuous flow injection setup for time-resolved HDX-MS (CFI-TRESI-HDX) that allows automated, continuous or discrete labeling time measurements from milliseconds to hours. The device is composed almost entirely of "off-the-shelf" LC components and can acquire an essentially unlimited number of timepoints with substantially reduced runtimes compared to conventional systems.
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Affiliation(s)
- Joseph Anacleto
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology, Calgary, Alberta T2N 4N1, Canada
| | - Ayesha Maqsood
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Banafsheh Mehrazma
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - David Schriemer
- Department of Biochemistry and Molecular Biology, Calgary, Alberta T2N 4N1, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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10
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Sheff J, Kelly J, Foss M, Brunette E, Kemmerich K, van Faassen H, Raphael S, Hussack G, Comamala G, Rand K, Stanimirovic DB. Epitope mapping of a blood-brain barrier crossing antibody targeting the cysteine-rich region of IGF1R using hydrogen-exchange mass spectrometry enabled by electrochemical reduction. J Biochem 2023; 173:95-105. [PMID: 36346120 DOI: 10.1093/jb/mvac088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/04/2022] [Accepted: 10/23/2022] [Indexed: 11/11/2022] Open
Abstract
Pathologies of the central nervous system impact a significant portion of our population, and the delivery of therapeutics for effective treatment is challenging. The insulin-like growth factor-1 receptor (IGF1R) has emerged as a target for receptor-mediated transcytosis, a process by which antibodies are shuttled across the blood-brain barrier (BBB). Here, we describe the biophysical characterization of VHH-IR4, a BBB-crossing single-domain antibody (sdAb). Binding was confirmed by isothermal titration calorimetry and an epitope was highlighted by surface plasmon resonance that does not overlap with the IGF-1 binding site or other known BBB-crossing sdAbs. The epitope was mapped with a combination of linear peptide scanning and hydrogen-deuterium exchange mass spectrometry (HDX-MS). IGF1R is large and heavily disulphide bonded, and comprehensive HDX analysis was achieved only through the use of online electrochemical reduction coupled with a multiprotease approach, which identified an epitope for VHH-IR4 within the cysteine-rich region (CRR) of IGF1R spanning residues W244-G265. This is the first report of an sdAb binding the CRR. We show that VHH-IR4 inhibits ligand induced auto-phosphorylation of IGF1R and that this effect is mediated by downstream conformational effects. Our results will guide the selection of antibodies with improved trafficking and optimized IGF1R binding characteristics.
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Affiliation(s)
- Joey Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - John Kelly
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Mary Foss
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Eric Brunette
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Kristin Kemmerich
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Shalini Raphael
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Gerard Comamala
- Department of Pharmacy, University of Copenhagen, 2100, Copenhagen, Denmark.2100
| | - Kasper Rand
- Department of Pharmacy, University of Copenhagen, 2100, Copenhagen, Denmark.2100
| | - Danica B Stanimirovic
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
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11
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Cupp-Sutton KA, Welborn T, Fang M, Langford JB, Wang Z, Smith K, Wu S. The Deuterium Calculator: An Open-Source Tool for Hydrogen-Deuterium Exchange Mass Spectrometry Analysis. J Proteome Res 2023; 22:532-538. [PMID: 36695755 DOI: 10.1021/acs.jproteome.2c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful protein footprinting technique to study protein dynamics and binding; however, HDX-MS data analysis is often challenging and time-consuming. Moreover, the HDX community is expanding to investigate multiprotein and highly complex protein systems which further complicates data analysis. Thus, a simple, open-source software package designed to analyze large and highly complex protein systems is needed. In this vein, we have developed "The Deuterium Calculator", a Python-based software package for HDX-MS data analysis. The Deuterium Calculator is capable of differential and nondifferential HDX-MS analysis, produces standardized data files according to recommendations from the International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX) to increase transparency in data analysis, and generates Woods' plots for statistical analysis and data visualization. This standard output can be used to perform time dependent deuteration studies and for the study of protein folding kinetics or differential uptake. Moreover, The Deuterium Calculator is capable of performing these analyses on large HDX-MS data sets (e.g., LC-HDX-MS from cell lysate digest). The Deuterium Calculator is freely available for download at https://github.com/OUWuLab/TheDeuteriumCalculator.git. Data are available via ProteomeXchange with identifier PXD036813.
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Affiliation(s)
- Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma73012, United States
| | - Thomas Welborn
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma73012, United States
| | - Mulin Fang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma73012, United States
| | - Joel B Langford
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma73012, United States
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma73012, United States
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma73104, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma73012, United States
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12
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Aerts J, Andrén PE, Jansson ET. Zero-Degree Celsius Capillary Electrophoresis Electrospray Ionization for Hydrogen Exchange Mass Spectrometry. Anal Chem 2022; 95:1149-1158. [PMID: 36546842 PMCID: PMC9850406 DOI: 10.1021/acs.analchem.2c03893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Currently, fast liquid chromatographic separations at low temperatures are exclusively used for the separation of peptides generated in hydrogen deuterium exchange (HDX) workflows. However, it has been suggested that capillary electrophoresis may be a better option for use with HDX. We performed in solution HDX on peptides and bovine hemoglobin (Hb) followed by quenching, pepsin digestion, and cold capillary electrophoretic separation coupled with mass spectrometry (MS) detection for benchmarking a laboratory-built HDX-MS platform. We found that capillaries with a neutral coating to eliminate electroosmotic flow and adsorptive processes provided fast separations with upper limit peak capacities surpassing 170. In contrast, uncoated capillaries achieved 30% higher deuterium retention for an angiotensin II peptide standard owing to faster separations but with only half the peak capacity of coated capillaries. Data obtained using two different separation conditions on peptic digests of Hb showed strong agreement of the relative deuterium uptake between methods. Processed data for denatured versus native Hb after deuterium labeling for the longest timepoint in this study (50,000 s) also showed agreement with subunit interaction sites determined by crystallographic methods. All proteomic data are available under DOI: 10.6019/PXD034245.
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Affiliation(s)
- Jordan
T. Aerts
- Department
of Pharmaceutical Biosciences, Uppsala University, Uppsala751 24, Sweden
| | - Per E. Andrén
- Department
of Pharmaceutical Biosciences, Uppsala University, Uppsala751 24, Sweden,Science
for Life Laboratory, Spatial Mass Spectrometry, Uppsala University, Uppsala751 24, Sweden
| | - Erik T. Jansson
- Department
of Pharmaceutical Biosciences, Uppsala University, Uppsala751 24, Sweden,
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13
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Hassell D, Denney A, Singer E, Benson A, Roth A, Ceglowski J, Steingesser M, McMurray M. Chaperone requirements for de novo folding of Saccharomyces cerevisiae septins. Mol Biol Cell 2022; 33:ar111. [PMID: 35947497 PMCID: PMC9635297 DOI: 10.1091/mbc.e22-07-0262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/02/2022] [Indexed: 11/11/2022] Open
Abstract
Polymers of septin protein complexes play cytoskeletal roles in eukaryotic cells. The specific subunit composition within complexes controls functions and higher-order structural properties. All septins have globular GTPase domains. The other eukaryotic cytoskeletal NTPases strictly require assistance from molecular chaperones of the cytosol, particularly the cage-like chaperonins, to fold into oligomerization-competent conformations. We previously identified cytosolic chaperones that bind septins and influence the oligomerization ability of septins carrying mutations linked to human disease, but it was unknown to what extent wild-type septins require chaperone assistance for their native folding. Here we use a combination of in vivo and in vitro approaches to demonstrate chaperone requirements for de novo folding and complex assembly by budding yeast septins. Individually purified septins adopted nonnative conformations and formed nonnative homodimers. In chaperonin- or Hsp70-deficient cells, septins folded slower and were unable to assemble posttranslationally into native complexes. One septin, Cdc12, was so dependent on cotranslational chaperonin assistance that translation failed without it. Our findings point to distinct translation elongation rates for different septins as a possible mechanism to direct a stepwise, cotranslational assembly pathway in which general cytosolic chaperones act as key intermediaries.
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Affiliation(s)
- Daniel Hassell
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Ashley Denney
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Emily Singer
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Aleyna Benson
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Andrew Roth
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Julia Ceglowski
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Marc Steingesser
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Michael McMurray
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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14
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Rossotti MA, van Faassen H, Tran AT, Sheff J, Sandhu JK, Duque D, Hewitt M, Wen X, Bavananthasivam J, Beitari S, Matte K, Laroche G, Giguère PM, Gervais C, Stuible M, Guimond J, Perret S, Hussack G, Langlois MA, Durocher Y, Tanha J. Arsenal of nanobodies shows broad-spectrum neutralization against SARS-CoV-2 variants of concern in vitro and in vivo in hamster models. Commun Biol 2022; 5:933. [PMID: 36085335 PMCID: PMC9461429 DOI: 10.1038/s42003-022-03866-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Nanobodies offer several potential advantages over mAbs for the control of SARS-CoV-2. Their ability to access cryptic epitopes conserved across SARS-CoV-2 variants of concern (VoCs) and feasibility to engineer modular, multimeric designs, make these antibody fragments ideal candidates for developing broad-spectrum therapeutics against current and continually emerging SARS-CoV-2 VoCs. Here we describe a diverse collection of 37 anti-SARS-CoV-2 spike glycoprotein nanobodies extensively characterized as both monovalent and IgG Fc-fused bivalent modalities. The nanobodies were collectively shown to have high intrinsic affinity; high thermal, thermodynamic and aerosolization stability; broad subunit/domain specificity and cross-reactivity across existing VoCs; wide-ranging epitopic and mechanistic diversity and high and broad in vitro neutralization potencies. A select set of Fc-fused nanobodies showed high neutralization efficacies in hamster models of SARS-CoV-2 infection, reducing viral burden by up to six orders of magnitude to below detectable levels. In vivo protection was demonstrated with anti-RBD and previously unreported anti-NTD and anti-S2 nanobodies. This collection of nanobodies provides a potential therapeutic toolbox from which various cocktails or multi-paratopic formats could be built to combat multiple SARS-CoV-2 variants.
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Affiliation(s)
- Martin A Rossotti
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Anh T Tran
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Joey Sheff
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Jagdeep K Sandhu
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Diana Duque
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Melissa Hewitt
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Xiaoxue Wen
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Jegarubee Bavananthasivam
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Saina Beitari
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Kevin Matte
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Geneviève Laroche
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Patrick M Giguère
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- University of Ottawa Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Christian Gervais
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Montréal, QC, Canada
| | - Matthew Stuible
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Montréal, QC, Canada
| | - Julie Guimond
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Montréal, QC, Canada
| | - Sylvie Perret
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Montréal, QC, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Montréal, QC, Canada
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, Ottawa, ON, Canada.
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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15
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Rainer T, Egger AS, Zeindl R, Tollinger M, Kwiatkowski M, Müller T. 3D-Printed High-Pressure-Resistant Immobilized Enzyme Microreactor (μIMER) for Protein Analysis. Anal Chem 2022; 94:8580-8587. [PMID: 35678765 PMCID: PMC9218953 DOI: 10.1021/acs.analchem.1c05232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Additive manufacturing
(3D printing) has greatly revolutionized
the way researchers approach certain technical challenges. Despite
its outstanding print quality and resolution, stereolithography (SLA)
printing is cost-effective and relatively accessible. However, applications
involving mass spectrometry (MS) are few due to residual oligomers
and additives leaching from SLA-printed devices that interfere with
MS analyses. We identified the crosslinking agent urethane dimethacrylate
as the main contaminant derived from SLA prints. A stringent washing
and post-curing protocol mitigated sample contamination and rendered
SLA prints suitable for MS hyphenation. Thereafter, SLA printing was
used to produce 360 μm I.D. microcolumn chips with excellent
structural properties. By packing the column with polystyrene microspheres
and covalently immobilizing pepsin, an exceptionally effective microscale
immobilized enzyme reactor (μIMER) was created. Implemented
in an online liquid chromatography-MS/MS setup, the protease microcolumn
enabled reproducible protein digestion and peptide mapping with 100%
sequence coverage obtained for three different recombinant proteins.
Additionally, when assessing the μIMER digestion efficiency
for complex proteome samples, it delivered a 144-fold faster and significantly
more efficient protein digestion compared to 24 h for bulk digestion.
The 3D-printed μIMER withstands remarkably high pressures above
130 bar and retains its activity for several weeks. This versatile
platform will enable researchers to produce tailored polymer-based
enzyme reactors for various applications in analytical chemistry and
beyond.
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Affiliation(s)
- Tobias Rainer
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Anna-Sophia Egger
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Ricarda Zeindl
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
| | - Thomas Müller
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University Innsbruck, 6020 Innsbruck, Austria
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16
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Crook OM, Chung CW, Deane CM. Empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry. Commun Biol 2022; 5:588. [PMID: 35705679 PMCID: PMC9200815 DOI: 10.1038/s42003-022-03517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a technique to explore differential protein structure by examining the rate of deuterium incorporation for specific peptides. This rate will be altered upon structural perturbation and detecting significant changes to this rate requires a statistical test. To determine rates of incorporation, HDX-MS measurements are frequently made over a time course. However, current statistical testing procedures ignore the correlations in the temporal dimension of the data. Using tools from functional data analysis, we develop a testing procedure that explicitly incorporates a model of hydrogen deuterium exchange. To further improve statistical power, we develop an empirical Bayes version of our method, allowing us to borrow information across peptides and stabilise variance estimates for low sample sizes. Our approach has increased power, reduces false positives and improves interpretation over linear model-based approaches. Due to the improved flexibility of our method, we can apply it to a multi-antibody epitope-mapping experiment where current approaches are inapplicable due insufficient flexibility. Hence, our approach allows HDX-MS to be applied in more experimental scenarios and reduces the burden on experimentalists to produce excessive replicates. Our approach is implemented in the R-package “hdxstats”: https://github.com/ococrook/hdxstats. A statistical analysis approach for HDX-MS time series data incorporates correlations in time, reducing false positives and improving statistical power and data interpretation.
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Affiliation(s)
- Oliver M Crook
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK.
| | - Chun-Wa Chung
- Structural and Biophysical Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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17
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Advances in Mass Spectrometry-based Epitope Mapping of Protein Therapeutics. J Pharm Biomed Anal 2022; 215:114754. [DOI: 10.1016/j.jpba.2022.114754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/16/2022] [Accepted: 04/03/2022] [Indexed: 11/21/2022]
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18
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Morris J, Takahashi-Ruiz L, Persi LN, Summers JC, McCauley EP, Chan PYW, Amberchan G, Lizama-Chamu I, Coppage DA, Crews P, Risinger AL, Johnson TA. Re-evaluation of the Fijianolide/Laulimalide Chemotype Suggests an Alternate Mechanism of Action for C-15/C-20 Analogs. ACS OMEGA 2022; 7:8824-8832. [PMID: 35309480 PMCID: PMC8928504 DOI: 10.1021/acsomega.1c07146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Herein, we report on naturally derived microtubule stabilizers with activity against triple negative breast cancer (TNBC) cell lines, including paclitaxel, fijianolide B/laulimalide (3), fijianolide B di-acetate (4), and two new semisynthetic analogs of 3, which include fijianolide J (5) and fijianolide L (6). Similar to paclitaxel, compound 3 demonstrated classic microtubule stabilizing activity with potent (GI50 = 0.7-17 nM) antiproliferative efficacy among the five molecularly distinct TNBC cell lines. Alternatively, compounds 5 or 6, generated from oxidation of C-20 or C-15 and C-20 respectively, resulted in a unique profile with reduced potency (GI50 = 4-9 μM), but improved efficacy in some lines, suggesting a distinct mechanism of action. The C-15, C-20 di-acetate, and dioxo modifications on 4 and 6 resulted in compounds devoid of classic microtubule stabilizing activity in biochemical assays. While 4 also had no detectable effect on cellular microtubules, 6 promoted a reorganization of the cytoskeleton resulting in an accumulation of microtubules at the cell periphery. Compound 5, with a single C-20 oxo substitution, displayed a mixed phenotype, sharing properties of 3 and 6. These results demonstrate the importance of the C-15/C-20 chiral centers, which appear to be required for the potent microtubule stabilizing activity of this chemotype and that oxidation of these sites promotes unanticipated cytoskeletal alterations that are distinct from classic microtubule stabilization, likely through a distinct mechanism of action.
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Affiliation(s)
- Joseph
D. Morris
- Department
of Natural Sciences, Dominican University
of California, San Rafael, California 94901, United States
| | - Leila Takahashi-Ruiz
- Department
of Pharmacology, University of Texas Health
Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Lauren N. Persi
- Department
of Natural Sciences, Dominican University
of California, San Rafael, California 94901, United States
| | - Jonathan C. Summers
- Department
of Natural Sciences, Dominican University
of California, San Rafael, California 94901, United States
| | - Erin P. McCauley
- Department
of Chemistry & Biochemistry, University
of California, Santa Cruz, California 95064, United States
| | - Peter Y. W. Chan
- Department
of Pharmacology, University of Texas Health
Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Gabriella Amberchan
- Department
of Chemistry & Biochemistry, University
of California, Santa Cruz, California 95064, United States
| | - Itzel Lizama-Chamu
- Department
of Chemistry & Biochemistry, University
of California, Santa Cruz, California 95064, United States
| | - David A. Coppage
- Department
of Chemistry & Biochemistry, University
of California, Santa Cruz, California 95064, United States
| | - Phillip Crews
- Department
of Chemistry & Biochemistry, University
of California, Santa Cruz, California 95064, United States
| | - April L. Risinger
- Department
of Pharmacology, University of Texas Health
Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Tyler A. Johnson
- Department
of Natural Sciences, Dominican University
of California, San Rafael, California 94901, United States
- Department
of Chemistry & Biochemistry, University
of California, Santa Cruz, California 95064, United States
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19
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Karaca E, Prévost C, Sacquin-Mora S. Modeling the Dynamics of Protein-Protein Interfaces, How and Why? Molecules 2022; 27:1841. [PMID: 35335203 PMCID: PMC8950966 DOI: 10.3390/molecules27061841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 12/07/2022] Open
Abstract
Protein-protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein-protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein-protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein-protein interface.
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Affiliation(s)
- Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey;
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Chantal Prévost
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| | - Sophie Sacquin-Mora
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
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20
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Devaurs D, Antunes DA, Borysik AJ. Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 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] [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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21
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Canul‐Tec JC, Kumar A, Dhenin J, Assal R, Legrand P, Rey M, Chamot‐Rooke J, Reyes N. The ion-coupling mechanism of human excitatory amino acid transporters. EMBO J 2022; 41:e108341. [PMID: 34747040 PMCID: PMC8724772 DOI: 10.15252/embj.2021108341] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 01/07/2023] Open
Abstract
Excitatory amino acid transporters (EAATs) maintain glutamate gradients in the brain essential for neurotransmission and to prevent neuronal death. They use ionic gradients as energy source and co-transport transmitter into the cytoplasm with Na+ and H+ , while counter-transporting K+ to re-initiate the transport cycle. However, the molecular mechanisms underlying ion-coupled transport remain incompletely understood. Here, we present 3D X-ray crystallographic and cryo-EM structures, as well as thermodynamic analysis of human EAAT1 in different ion bound conformations, including elusive counter-transport ion bound states. Binding energies of Na+ and H+ , and unexpectedly Ca2+ , are coupled to neurotransmitter binding. Ca2+ competes for a conserved Na+ site, suggesting a regulatory role for Ca2+ in glutamate transport at the synapse, while H+ binds to a conserved glutamate residue stabilizing substrate occlusion. The counter-transported ion binding site overlaps with that of glutamate, revealing the K+ -based mechanism to exclude the transmitter during the transport cycle and to prevent its neurotoxic release on the extracellular side.
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Affiliation(s)
- Juan C Canul‐Tec
- Membrane Protein Mechanisms UnitInstitut PasteurParisFrance
- Membrane Protein Mechanisms GroupEuropean Institute of Chemistry and BiologyUniversity of BordeauxPessacFrance
- CNRS UMR 5234 Fundamental Microbiology and PathogenicityBordeauxFrance
| | - Anand Kumar
- Membrane Protein Mechanisms UnitInstitut PasteurParisFrance
- Membrane Protein Mechanisms GroupEuropean Institute of Chemistry and BiologyUniversity of BordeauxPessacFrance
- CNRS UMR 5234 Fundamental Microbiology and PathogenicityBordeauxFrance
| | - Jonathan Dhenin
- Mass Spectrometry for Biology Unit, CNRS USR 2000Institut PasteurParisFrance
| | - Reda Assal
- Membrane Protein Mechanisms UnitInstitut PasteurParisFrance
| | - Pierre Legrand
- Synchrotron SOLEILL'Orme des MerisiersGif‐sur‐YvetteFrance
| | - Martial Rey
- Mass Spectrometry for Biology Unit, CNRS USR 2000Institut PasteurParisFrance
| | - Julia Chamot‐Rooke
- Mass Spectrometry for Biology Unit, CNRS USR 2000Institut PasteurParisFrance
| | - Nicolas Reyes
- Membrane Protein Mechanisms UnitInstitut PasteurParisFrance
- Membrane Protein Mechanisms GroupEuropean Institute of Chemistry and BiologyUniversity of BordeauxPessacFrance
- CNRS UMR 5234 Fundamental Microbiology and PathogenicityBordeauxFrance
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22
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Sheff JG, Kelly JF, Robotham A, Sulea T, Malenfant F, L'Abbé D, Duchesne M, Pelletier A, Lefebvre J, Acel A, Parat M, Gosselin M, Wu C, Fortin Y, Baardsnes J, Van Faassen H, Awrey S, Chafe SC, McDonald PC, Dedhar S, Lenferink AEG. Hydrogen-deuterium exchange mass spectrometry reveals three unique binding responses of mAbs directed to the catalytic domain of hCAIX. MAbs 2021; 13:1997072. [PMID: 34812124 PMCID: PMC8632303 DOI: 10.1080/19420862.2021.1997072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human carbonic anhydrase (hCAIX), an extracellular enzyme that catalyzes the reversible hydration of CO2, is often overexpressed in solid tumors. This enzyme is instrumental in maintaining the survival of cancer cells in a hypoxic and acidic tumor microenvironment. Absent in most normal tissues, hCAIX is a promising therapeutic target for detection and treatment of solid tumors. Screening of a library of anti-hCAIX monoclonal antibodies (mAbs) previously identified three therapeutic candidates (mAb c2C7, m4A2 and m9B6) with distinct biophysical and functional characteristics. Selective binding to the catalytic domain was confirmed by yeast surface display and isothermal calorimetry, and deeper insight into the dynamic binding profiles of these mAbs upon binding were highlighted by bottom-up hydrogen-deuterium exchange mass spectrometry (HDX-MS). Here, a conformational and allosterically silent epitope was identified for the antibody-drug conjugate candidate c2C7. Unique binding profiles are described for both inhibitory antibodies, m4A2 and m9B6. M4A2 reduces the ability of the enzyme to hydrate CO2 by steric gating at the entrance of the catalytic cavity. Conversely, m9B6 disrupts the secondary structure that is necessary for substrate binding and hydration. The synergy of these two inhibitory mechanisms is demonstrated in in vitro activity assays and HDX-MS. Finally, the ability of m4A2 to modulate extracellular pH and intracellular metabolism is reported. By highlighting three unique modes by which hCAIX can be targeted, this study demonstrates both the utility of HDX-MS as an important tool in the characterization of anti-cancer biotherapeutics, and the underlying value of CAIX as a therapeutic target.
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Affiliation(s)
- Joey G Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - John F Kelly
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anna Robotham
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Félix Malenfant
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Denis L'Abbé
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mélanie Duchesne
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Alex Pelletier
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jean Lefebvre
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Andrea Acel
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Marie Parat
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mylene Gosselin
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Cunle Wu
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yves Fortin
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Henk Van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Shannon Awrey
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada
| | - Shawn C Chafe
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada
| | - Paul C McDonald
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada
| | - Shoukat Dedhar
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Anne E G Lenferink
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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23
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Ziemianowicz DS, Saltzberg D, Pells T, Crowder DA, Schräder C, Hepburn M, Sali A, Schriemer DC. IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics. Mol Cell Proteomics 2021; 20:100139. [PMID: 34418567 PMCID: PMC8452774 DOI: 10.1016/j.mcpro.2021.100139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/27/2021] [Accepted: 08/11/2021] [Indexed: 11/01/2022] Open
Abstract
Proteomics methodology has expanded to include protein structural analysis, primarily through cross-linking mass spectrometry (XL-MS) and hydrogen-deuterium exchange mass spectrometry (HX-MS). However, while the structural proteomics community has effective tools for primary data analysis, there is a need for structure modeling pipelines that are accessible to the proteomics specialist. Integrative structural biology requires the aggregation of multiple distinct types of data to generate models that satisfy all inputs. Here, we describe IMProv, an app in the Mass Spec Studio that combines XL-MS data with other structural data, such as cryo-EM densities and crystallographic structures, for integrative structure modeling on high-performance computing platforms. The resource provides an easily deployed bundle that includes the open-source Integrative Modeling Platform program (IMP) and its dependencies. IMProv also provides functionality to adjust cross-link distance restraints according to the underlying dynamics of cross-linked sites, as characterized by HX-MS. A dynamics-driven conditioning of restraint values can improve structure modeling precision, as illustrated by an integrative structure of the five-membered Polycomb Repressive Complex 2. IMProv is extensible to additional types of data.
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Affiliation(s)
- Daniel S Ziemianowicz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Daniel Saltzberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, California, USA
| | - Troy Pells
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Christoph Schräder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Morgan Hepburn
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, California, USA
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada; Department of Chemistry, University of Calgary, Calgary, Alberta, Canada.
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24
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Oganesyan I, Lento C, Tandon A, Wilson DJ. Conformational Dynamics of α-Synuclein during the Interaction with Phospholipid Nanodiscs by Millisecond Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1169-1179. [PMID: 33784451 DOI: 10.1021/jasms.0c00463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Both normal and pathological functions of α-synuclein (αSN), an abundant protein in the central and peripheral nervous system, have been linked to its interaction with membrane lipid bilayers. The ability to characterize structural transitions of αSN upon membrane complexation will clarify molecular mechanisms associated with αSN-linked pathologies, including Parkinson's disease (PD), multiple systems atrophy, and other synucleinopathies. In this work, time-resolved electrospray ionization hydrogen/deuterium exchange mass spectrometry (TRESI-HDX-MS) was employed to acquire a detailed picture of αSN's conformational transitions as it undergoes complexation with nanodisc membrane mimics with different headgroup charges (zwitterionic DMPC and negative POPG). Using this approach, αSN interactions with DMPC nanodiscs were shown to be rapid exchanging and to have little impact on the αSN conformational ensemble. Interactions with nanodiscs containing lipids known to promote amyloidogenesis (e.g., POPG), on the other hand, were observed to induce substantial and specific changes in the αSN conformational ensemble. Ultimately, we identify a region corresponding residues 19-28 and 45-57 of the αSN sequence that is uniquely impacted by interactions with "amyloidogenic" lipid membranes, supporting the existing "broken-helix" model for α-synuclein/membrane interactions, but do not detect a "helical extension" that is also thought to play a role in αSN aggregation.
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Affiliation(s)
- Irina Oganesyan
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Anurag Tandon
- Department of Medicine, University of Toronto, Toronto M5S 1A1, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University, Toronto M3J 1P3, Canada
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25
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Raval S, Sarpe V, Hepburn M, Crowder DA, Zhang T, Viner R, Schriemer DC. Improving Spectral Validation Rates in Hydrogen-Deuterium Exchange Data Analysis. Anal Chem 2021; 93:4246-4254. [PMID: 33592142 DOI: 10.1021/acs.analchem.0c05045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The data analysis practices associated with hydrogen-deuterium exchange mass spectrometry (HX-MS) lag far behind that of most other MS-based protein analysis tools. A reliance on external tools from other fields and a persistent need for manual data validation restrict this powerful technology to the expert user. Here, we provide an extensive upgrade to the HX data analysis suite available in the Mass Spec Studio in the form of two new apps (HX-PIPE and HX-DEAL), completing a workflow that provides an HX-tailored peptide identification capability, accelerated validation routines, automated spectral deconvolution strategies, and a rich set of exportable graphics and statistical reports. With these new tools, we demonstrate that the peptide identifications obtained from undeuterated samples generated at the start of a project contain information that helps predict and control the extent of manual validation required. We also uncover a large fraction of HX-usable peptides that remains unidentified in most experiments. We show that automated spectral deconvolution routines can identify exchange regimes in a project-wide manner, although they remain difficult to accurately assign in all scenarios. Taken together, these new tools provide a robust and complete solution suitable for the analysis of high-complexity HX-MS data.
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Affiliation(s)
- Shaunak Raval
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N-4N1
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
| | - Morgan Hepburn
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
| | - Terry Zhang
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Rosa Viner
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - David C Schriemer
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada T2N-4N1.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N-4N1
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26
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Sheff J, Wang P, Xu P, Arbour M, Masson L, van Faassen H, Hussack G, Kemmerich K, Brunette E, Stanimirovic D, Hill JJ, Kelly J, Ni F. Defining the epitope of a blood-brain barrier crossing single domain antibody specific for the type 1 insulin-like growth factor receptor. Sci Rep 2021; 11:4284. [PMID: 33608571 PMCID: PMC7896052 DOI: 10.1038/s41598-021-83198-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
Ligand-activated signaling through the type 1 insulin-like growth factor receptor (IGF1R) is implicated in many physiological processes ranging from normal human growth to cancer proliferation and metastasis. IGF1R has also emerged as a target for receptor-mediated transcytosis, a transport phenomenon that can be exploited to shuttle biotherapeutics across the blood–brain barrier (BBB). We employed differential hydrogen–deuterium exchange mass spectrometry (HDX-MS) and nuclear magnetic resonance (NMR) to characterize the interactions of the IGF1R ectodomain with a recently discovered BBB-crossing single-domain antibody (sdAb), VHH-IR5, in comparison with IGF-1 binding. HDX-MS confirmed that IGF-1 induced global conformational shifts in the L1/FnIII-1/-2 domains and α-CT helix of IGF1R. In contrast, the VHH-IR5 sdAb-mediated changes in conformational dynamics were limited to the α-CT helix and its immediate vicinity (L1 domain). High-resolution NMR spectroscopy titration data and linear peptide scanning demonstrated that VHH-IR5 has high-affinity binding interactions with a peptide sequence around the C-terminal region of the α-CT helix. Taken together, these results define a core linear epitope for VHH-IR5 within the α-CT helix, overlapping the IGF-1 binding site, and suggest a potential role for the α-CT helix in sdAb-mediated transcytosis.
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Affiliation(s)
- Joey Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Ping Wang
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Ping Xu
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Melanie Arbour
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Luke Masson
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Henk van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Greg Hussack
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Kristin Kemmerich
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Eric Brunette
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Danica Stanimirovic
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Jennifer J Hill
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - John Kelly
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Feng Ni
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada.
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27
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Filandrova R, Kavan D, Kadek A, Novak P, Man P. Studying Protein-DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry. Methods Mol Biol 2021; 2247:193-219. [PMID: 33301119 DOI: 10.1007/978-1-0716-1126-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Protein hydrogen/deuterium exchange (HDX) coupled to mass spectrometry (MS) can be used to study interactions of proteins with various ligands, to describe the effects of mutations, or to reveal structural responses of proteins to different experimental conditions. It is often described as a method with virtually no limitations in terms of protein size or sample composition. While this is generally true, there are, however, ligands or buffer components that can significantly complicate the analysis. One such compound, that can make HDX-MS troublesome, is DNA. In this chapter, we will focus on the analysis of protein-DNA interactions, describe the detailed protocol, and point out ways to overcome the complications arising from the presence of DNA.
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Affiliation(s)
- Ruzena Filandrova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alan Kadek
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Petr Novak
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Man
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
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28
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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: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [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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29
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Cárdenas R, Martínez-Seoane J, Amero C. Combining Experimental Data and Computational Methods for the Non-Computer Specialist. Molecules 2020; 25:E4783. [PMID: 33081072 PMCID: PMC7594097 DOI: 10.3390/molecules25204783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 01/01/2023] Open
Abstract
Experimental methods are indispensable for the study of the function of biological macromolecules, not just as static structures, but as dynamic systems that change conformation, bind partners, perform reactions, and respond to different stimulus. However, providing a detailed structural interpretation of the results is often a very challenging task. While experimental and computational methods are often considered as two different and separate approaches, the power and utility of combining both is undeniable. The integration of the experimental data with computational techniques can assist and enrich the interpretation, providing new detailed molecular understanding of the systems. Here, we briefly describe the basic principles of how experimental data can be combined with computational methods to obtain insights into the molecular mechanism and expand the interpretation through the generation of detailed models.
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Affiliation(s)
| | | | - Carlos Amero
- Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico; (R.C.); (J.M.-S.)
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30
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Medits I, Vaney M, Rouvinski A, Rey M, Chamot‐Rooke J, Rey FA, Heinz FX, Stiasny K. Extensive flavivirus E trimer breathing accompanies stem zippering of the post-fusion hairpin. EMBO Rep 2020; 21:e50069. [PMID: 32484292 PMCID: PMC7403712 DOI: 10.15252/embr.202050069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/23/2022] Open
Abstract
Flaviviruses enter cells by fusion with endosomal membranes through a rearrangement of the envelope protein E, a class II membrane fusion protein, into fusogenic trimers. The rod-like E subunits bend into "hairpins" to bring the fusion loops next to the C-terminal transmembrane (TM) anchors, with the TM-proximal "stem" element zippering the E trimer to force apposition of the membranes. The structure of the complete class II trimeric hairpin is known for phleboviruses but not for flaviviruses, for which the stem is only partially resolved. Here, we performed comparative analyses of E-protein trimers from the tick-borne encephalitis flavivirus with sequential stem truncations. Our thermostability and antibody-binding data suggest that the stem "zipper" ends at a characteristic flavivirus conserved sequence (CS) that cloaks the fusion loops, with the downstream segment not contributing to trimer stability. We further identified a highly dynamic behavior of E trimers C-terminally truncated upstream the CS, which, unlike fully stem-zippered trimers, undergo rapid deuterium exchange at the trimer interface. These results thus identify important "breathing" intermediates in the E-protein-driven membrane fusion process.
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Affiliation(s)
- Iris Medits
- Center for VirologyMedical University of ViennaViennaAustria
| | | | - Alexander Rouvinski
- Unité de Virologie StructuraleInstitut PasteurCNRS UMR 3569 VirologieParisFrance
- Present address:
Department of Microbiology and Molecular GeneticsInstitute for Medical Research Israel‐CanadaThe Kuvin Center for the Study of Infectious and Tropical DiseasesThe Hebrew University of JerusalemJerusalemIsrael
| | - Martial Rey
- Unité de Spectrométrie de Masse pour la BiologieInstitut PasteurCNRS USR 2000ParisFrance
| | - Julia Chamot‐Rooke
- Unité de Spectrométrie de Masse pour la BiologieInstitut PasteurCNRS USR 2000ParisFrance
| | - Felix A Rey
- Unité de Virologie StructuraleInstitut PasteurCNRS UMR 3569 VirologieParisFrance
| | - Franz X Heinz
- Center for VirologyMedical University of ViennaViennaAustria
| | - Karin Stiasny
- Center for VirologyMedical University of ViennaViennaAustria
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31
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Ziemianowicz DS, Sarpe V, Crowder D, Pells TJ, Raval S, Hepburn M, Rafiei A, Schriemer DC. Harmonizing structural mass spectrometry analyses in the mass spec studio. J Proteomics 2020; 225:103844. [DOI: 10.1016/j.jprot.2020.103844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/23/2020] [Accepted: 05/24/2020] [Indexed: 01/06/2023]
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32
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Bouyssié D, Lesne J, Locard-Paulet M, Albigot R, Burlet-Schiltz O, Marcoux J. HDX-Viewer: interactive 3D visualization of hydrogen-deuterium exchange data. Bioinformatics 2020; 35:5331-5333. [PMID: 31287496 PMCID: PMC6954641 DOI: 10.1093/bioinformatics/btz550] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/04/2019] [Accepted: 07/08/2019] [Indexed: 11/26/2022] Open
Abstract
Summary With the advent of fully automated sample preparation robots for Hydrogen–Deuterium eXchange coupled to Mass Spectrometry (HDX-MS), this method has become paramount for ligand binding or epitope mapping screening, both in academic research and biopharmaceutical industries. However, bridging the gap between commercial HDX-MS software (for raw data interpretation) and molecular viewers (to map experiment results onto a 3D structure for biological interpretation) remains laborious and requires simple but sometimes limiting coding skills. We solved this bottleneck by developing HDX-Viewer, an open-source web-based application that facilitates and quickens HDX-MS data analysis. This user-friendly application automatically incorporates HDX-MS data from a custom template or commercial HDX-MS software in PDB files, and uploads them to an online 3D molecular viewer, thereby facilitating their visualization and biological interpretation. Availability and implementation The HDX-Viewer web application is released under the CeCILL (http://www.cecill.info) and GNU LGPL licenses and can be found at https://masstools.ipbs.fr/hdx-viewer. The source code is available at https://github.com/david-bouyssie/hdx-viewer.
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Affiliation(s)
- David Bouyssié
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jean Lesne
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie Locard-Paulet
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Renaud Albigot
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
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33
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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34
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Koukos P, Bonvin A. Integrative Modelling of Biomolecular Complexes. J Mol Biol 2020; 432:2861-2881. [DOI: 10.1016/j.jmb.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
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35
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Huang X, Slavkovic S, Song E, Botta A, Mehrazma B, Lento C, Johnson PE, Sweeney G, Wilson DJ. A Unique Conformational Distortion Mechanism Drives Lipocalin 2 Binding to Bacterial Siderophores. ACS Chem Biol 2020; 15:234-242. [PMID: 31613081 DOI: 10.1021/acschembio.9b00820] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Lcn2 is a host defense protein induced via the innate immune response to sequester iron-loaded bacterial siderophores. However, excess or prolonged elevation of Lcn2 levels can induce adverse cellular effects, including oxidative stress and inflammation. In this work, we use Hydrogen-Deuterium eXchange (HDX) and Isothermal Titration Calorimetry (ITC) to characterize the binding interaction between Lcn2 and siderophores enterobactin and 2,3-DHBA, in the presence and absence of iron. Our results indicate a rare "Type II" interaction in which binding of siderophores drives the protein conformational equilibrium toward an unfolded state. Linking our molecular model to cellular assays, we demonstrate that this "distorted binding mode" facilitates a deleterious cellular accumulation of reactive oxygen species that could represent the molecular origin of Lcn2 pathology. These results add important insights into mechanisms of Lcn2 action and have implications in Lcn2-mediated effects including inflammation.
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36
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Hamilton GL, Alper J, Sanabria H. Reporting on the future of integrative structural biology ORAU workshop. FRONT BIOSCI-LANDMRK 2020; 25:43-68. [PMID: 31585877 PMCID: PMC7323472 DOI: 10.2741/4794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Integrative and hybrid methods have the potential to bridge long-standing knowledge gaps in structural biology. These methods will have a prominent role in the future of the field as we make advances toward a complete, unified representation of biology that spans the molecular and cellular scales. The Department of Physics and Astronomy at Clemson University hosted The Future of Integrative Structural Biology workshop on April 29, 2017 and partially sponsored by partially sponsored by a program of the Oak Ridge Associated Universities (ORAU). The workshop brought experts from multiple structural biology disciplines together to discuss near-term steps toward the goal of a molecular atlas of the cell. The discussion focused on the types of structural data that should be represented, how this data should be represented, and how the time domain might be incorporated into such an atlas. The consensus was that an explorable, map-like Virtual Cell, containing both spatial and temporal data bridging the atomic and cellular length scales obtained by multiple experimental methods, represents the best path toward a complete atlas of the cell.
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Affiliation(s)
- George L Hamilton
- Physics and Astronomy, Clemson University, 216 Kinard Lab, Clemson, S.C. USA
| | - Joshua Alper
- Physics and Astronomy, Clemson University, 302B Kinard Lab, Clemson, S.C. 29634-0978. USA
| | - Hugo Sanabria
- Physics and Astronomy, Clemson University, 214 Kinard Lab, Clemson, S.C. 29634-0978. USA,
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37
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Lumpkin RJ, Komives EA. DECA, A Comprehensive, Automatic Post-processing Program for HDX-MS Data. Mol Cell Proteomics 2019; 18:2516-2523. [PMID: 31594786 PMCID: PMC6885705 DOI: 10.1074/mcp.tir119.001731] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/17/2019] [Indexed: 11/06/2022] Open
Abstract
Amide hydrogen-deuterium exchange mass spectrometry (HDX-MS) has become widely popular for mapping protein-ligand interfaces, for understanding protein-protein interactions, and for discovering dynamic allostery. Several platforms are now available which provide large data sets of amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data. Although many of these platforms provide some down-stream processing, a comprehensive software that provides the most commonly used down-stream processing tools such as automatic back-exchange correction options, analysis of overlapping peptides, calculations of relative deuterium uptake into regions of the protein after such corrections, rigorous statistical analysis of the significance of uptake differences, and generation of high quality figures for data presentation is not yet available. Here we describe the Deuterium Exchange Correction and Analysis (DECA) software package, which provides all these downstream processing options for data from the most popular mass spectrometry platforms. The major functions of the software are demonstrated on sample data.
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Affiliation(s)
- Ryan J Lumpkin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378.
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38
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Zhang MM, Beno BR, Huang RYC, Adhikari J, Deyanova EG, Li J, Chen G, Gross ML. An Integrated Approach for Determining a Protein-Protein Binding Interface in Solution and an Evaluation of Hydrogen-Deuterium Exchange Kinetics for Adjudicating Candidate Docking Models. Anal Chem 2019; 91:15709-15717. [PMID: 31710208 DOI: 10.1021/acs.analchem.9b03879] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We describe an integrated approach of using hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (XL-MS), and molecular docking to characterize the binding interface and to predict the three-dimensional quaternary structure of a protein-protein complex in solution. Interleukin 7 (IL-7) and its α-receptor, IL-7Rα, serving as essential mediators in the immune system, are the model system. HDX kinetics reports widespread protection on IL-7Rα but shows no differential evidence of binding-induced protection or remote conformational change. Cross-linking with reagents that differ in spacer lengths and targeting residues increases the spatial resolution. Using five cross-links as distance restraints for protein-protein docking, we generated a high-confidence model of the IL-7/IL-7Rα complex. Both the predicted binding interface and regions with direct contacts agree well with those in the solid-state structure, as confirmed by previous X-ray crystallography. An additional binding region was revealed to be the C-terminus of helix B of IL-7, highlighting the value of solution-based characterization. To generalize the integrated approach, protein-protein docking was executed with a different number of cross-links. Combining cluster analysis and HDX kinetics adjudication, we found that two intermolecular cross-link-derived restraints are sufficient to generate a high-confidence model with root-mean-square distance (rmsd) value of all alpha carbons below 2.0 Å relative to the crystal structure. The remarkable results of binding-interface determination and quaternary structure prediction highlight the effectiveness and capability of the integrated approach, which will allow more efficient and comprehensive analysis of interprotein interactions with broad applications in the multiple stages of design, implementation, and evaluation for protein therapeutics.
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Affiliation(s)
- Mengru Mira Zhang
- Department of Chemistry , Washington University , St. Louis , Missouri 63130 , United States
| | - Brett R Beno
- Molecular Structure & Design, Molecular Discovery Technologies, Research and Development , Bristol-Myers Squibb , Princeton , New Jersey 08540 , United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - Jagat Adhikari
- Department of Chemistry , Washington University , St. Louis , Missouri 63130 , United States
| | - Ekaterina G Deyanova
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - Jing Li
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - Michael L Gross
- Department of Chemistry , Washington University , St. Louis , Missouri 63130 , United States
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39
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Zheng J, Strutzenberg T, Pascal BD, Griffin PR. Protein dynamics and conformational changes explored by hydrogen/deuterium exchange mass spectrometry. Curr Opin Struct Biol 2019; 58:305-313. [DOI: 10.1016/j.sbi.2019.06.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 06/15/2019] [Accepted: 06/25/2019] [Indexed: 12/31/2022]
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40
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Szymkowicz L, Lento C, Wilson DJ. Impact of Cardiolipin and Phosphatidylcholine Interactions on the Conformational Ensemble of Cytochrome c. Biochemistry 2019; 58:3617-3626. [DOI: 10.1021/acs.biochem.9b00495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Lisa Szymkowicz
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Derek J. Wilson
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
- Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada M3J 1P3
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41
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Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods 2019; 16:595-602. [PMID: 31249422 PMCID: PMC6614034 DOI: 10.1038/s41592-019-0459-y] [Citation(s) in RCA: 396] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.
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Affiliation(s)
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ganesh S Anand
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Christoph Borchers
- Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Sébastien Brier
- Institut Pasteur, Chemistry and Structural Biology Department, Paris, France
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - S Walter Englander
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Yoshitomo Hamuro
- Johnson & Johnson Pharmaeutical Research and Development, Jersey City, NJ, USA
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | | | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, Odense, Denmark
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Leland Mayne
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Dana Reichmann
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Joost Snijder
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Timothy S Strutzenberg
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | | | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Benjamin T Walters
- Department of Early Stage Pharmaceutical Development, Genentech, Inc., South San Francisco, CA, USA
| | - David D Weis
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, ON, Canada
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | | | - Jie Zheng
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB, Canada.
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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42
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Ziemianowicz DS, Sarpe V, Schriemer DC. Quantitative Analysis of Protein Covalent Labeling Mass Spectrometry Data in the Mass Spec Studio. Anal Chem 2019; 91:8492-8499. [PMID: 31198032 DOI: 10.1021/acs.analchem.9b01625] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Covalent labeling with mass spectrometry (CL-MS) provides a direct measure of the chemical and structural features of proteins with the potential for resolution at the amino-acid level. Unfortunately, most applications of CL-MS are limited to narrowly defined differential analyses, where small numbers of residues are compared between two or more protein states. Extending the utility of high-resolution CL-MS for structure-based applications requires more robust computational routines and the development of methodology capable of reporting of labeling yield accurately. Here, we provide a substantial improvement in the analysis of CL-MS data with the development of an extended plug-in built within the Mass Spec Studio development framework (MSS-CLEAN). All elements of data analysis-from database search to site-resolved and normalized labeling output-are accommodated, as illustrated through the nonselective labeling of the human kinesin Eg5 with photoconverted 3,3'-azibutan-1-ol. In developing the new features within the CL-MS plug-in, we identified additional complexities associated with the application of CL reagents, arising primarily from digestion-induced bias in yield measurements and ambiguities in site localization. A strategy is presented involving the use of redundant site labeling data from overlapping peptides, the imputation of missing data, and a normalization routine to determine relative protection factors. These elements together provide for a robust structural interpretation of CL-MS/MS data while minimizing the over-reporting of labeling site resolution. Finally, to minimize bias, we recommend that digestion strategies for the generation of useful overlapping peptides involve the application of complementary enzymes that drive digestion to completion.
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43
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Hageman TS, Weis DD. Reliable Identification of Significant Differences in Differential Hydrogen Exchange-Mass Spectrometry Measurements Using a Hybrid Significance Testing Approach. Anal Chem 2019; 91:8008-8016. [DOI: 10.1021/acs.analchem.9b01325] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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44
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Tian Y, Huang L, Ruotolo BT, Wang N. Hydrogen/deuterium exchange-mass spectrometry analysis of high concentration biotherapeutics: application to phase-separated antibody formulations. MAbs 2019; 11:779-788. [PMID: 30890021 PMCID: PMC6601547 DOI: 10.1080/19420862.2019.1589850] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High concentration biotherapeutic formulations are often required to deliver large doses of drugs to achieve a desired degree of efficacy and less frequent dose. However, highly concentrated protein-containing solutions may exhibit undesirable therapeutic properties, such as increased viscosity, aggregation, and phase separation that can affect drug efficacy and raise safety issues. The characterization of high concentration protein formulations is a critical yet challenging analytical task for therapeutic development efforts, due to the lack of technologies capable of making accurate measurements under such conditions. To address this issue, we developed a novel dilution-free hydrogen/deuterium exchange (HDX) mass spectrometry (MS) method for the direct conformational analysis of high concentration biotherapeutics. Here, we particularly focused on studying phase separation phenomenon that can occur at high protein concentrations. First, two aliquots of monoclonal antibodies (mAbs) were dialyzed in either hydrogen- or deuterium-containing buffers at low salt and pH. Phases that separated were then discretely sampled and subjected to dilution-free HDX-MS analysis through mixing the non-deuterated and deuterated protein aliquots. Our HDX-MS results analyzed at a global protein level reveal less deuterium incorporation for the protein-enriched phase compared to the protein-depleted phase present in high concentration formulations. A peptide level analysis further confirmed these observed differences, and a detailed statistical analysis provided direct information surrounding the details of the conformational changes observed. Based on our HDX-MS results, we propose possible structures for the self-associated mAbs present at high concentrations. Our new method can potentially provide useful insights into the unusual behavior of therapeutic proteins in high concentration formulations, aiding their development.
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Affiliation(s)
- Yuwei Tian
- a Bioproduct Research and Development , Lilly Research Laboratories, Eli Lilly and Company , Indianapolis , IN , USA.,b Department of Chemistry , University of Michigan , Ann Arbor , MI , USA
| | - Lihua Huang
- a Bioproduct Research and Development , Lilly Research Laboratories, Eli Lilly and Company , Indianapolis , IN , USA
| | - Brandon T Ruotolo
- b Department of Chemistry , University of Michigan , Ann Arbor , MI , USA
| | - Ning Wang
- a Bioproduct Research and Development , Lilly Research Laboratories, Eli Lilly and Company , Indianapolis , IN , USA
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45
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Garcia NK, Deperalta G, Wecksler AT. Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry. Protein Pept Lett 2019; 26:35-43. [PMID: 30484396 DOI: 10.2174/0929866526666181128141953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/01/2018] [Accepted: 10/29/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. CONCLUSION Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.
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Affiliation(s)
- Natalie K Garcia
- Department of Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA 94080, United States
| | - Galahad Deperalta
- Department of Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA 94080, United States
| | - Aaron T Wecksler
- Department of Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA 94080, United States
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46
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Marrella SA, Brown KA, Mansouri-Noori F, Porat J, Wilson DJ, Bayfield MA. An interdomain bridge influences RNA binding of the human La protein. J Biol Chem 2018; 294:1529-1540. [PMID: 30530494 DOI: 10.1074/jbc.ra118.003995] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/20/2018] [Indexed: 12/15/2022] Open
Abstract
La proteins are RNA chaperones that perform various functions depending on distinct RNA-binding modes and their subcellular localization. In the nucleus, they help process UUU-3'OH-tailed nascent RNA polymerase III transcripts, such as pre-tRNAs, whereas in the cytoplasm they contribute to translation of poly(A)-tailed mRNAs. La accumulation in the nucleus and cytoplasm is controlled by several trafficking elements, including a canonical nuclear localization signal in the extreme C terminus and a nuclear retention element (NRE) in the RNA recognition motif 2 (RRM2) domain. Previous findings indicate that cytoplasmic export of La due to mutation of the NRE can be suppressed by mutations in RRM1, but the mechanism by which the RRM1 and RRM2 domains functionally cooperate is poorly understood. In this work, we use electromobility shift assays (EMSA) to show that mutations in the NRE and RRM1 affect binding of human La to pre-tRNAs but not UUU-3'OH or poly(A) sequences, and we present compensatory mutagenesis data supporting a direct interaction between the RRM1 and RRM2 domains. Moreover, we use collision-induced unfolding and time-resolved hydrogen-deuterium exchange MS analyses to study the conformational dynamics that occur when this interaction is intact or disrupted. Our results suggest that the intracellular distribution of La may be linked to its RNA-binding modes and provide the first evidence for a direct protein-protein interdomain interaction in La proteins.
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Affiliation(s)
- Stefano A Marrella
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Kerene A Brown
- Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada; Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada; Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Farnaz Mansouri-Noori
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jennifer Porat
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Derek J Wilson
- Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada; Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada; Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada.
| | - Mark A Bayfield
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada; Centres for Research in Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada.
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47
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Oganesyan I, Lento C, Wilson DJ. Contemporary hydrogen deuterium exchange mass spectrometry. Methods 2018; 144:27-42. [DOI: 10.1016/j.ymeth.2018.04.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/16/2018] [Accepted: 04/21/2018] [Indexed: 02/07/2023] Open
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48
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Xiao K, Zhao Y, Choi M, Liu H, Blanc A, Qian J, Cahill TJ, Li X, Xiao Y, Clark LJ, Li S. Revealing the architecture of protein complexes by an orthogonal approach combining HDXMS, CXMS, and disulfide trapping. Nat Protoc 2018; 13:1403-1428. [PMID: 29844522 DOI: 10.1038/nprot.2018.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many cellular functions necessitate structural assemblies of two or more associated proteins. The structural characterization of protein complexes using standard methods, such as X-ray crystallography, is challenging. Herein, we describe an orthogonal approach using hydrogen-deuterium-exchange mass spectrometry (HDXMS), cross-linking mass spectrometry (CXMS), and disulfide trapping to map interactions within protein complexes. HDXMS measures changes in solvent accessibility and hydrogen bonding upon complex formation; a decrease in HDX rate could account for newly formed intermolecular or intramolecular interactions. To distinguish between inter- and intramolecular interactions, we use a CXMS method to determine the position of direct interface regions by trapping intermolecular residues in close proximity to various cross-linkers (e.g., disuccinimidyl adipate (DSA)) of different lengths and reactive groups. Both MS-based experiments are performed on high-resolution mass spectrometers (e.g., an Orbitrap Elite hybrid mass spectrometer). The physiological relevance of the interactions identified through HDXMS and CXMS is investigated by transiently co-expressing cysteine mutant pairs, one mutant on each protein at the discovered interfaces, in an appropriate cell line, such as HEK293. Disulfide-trapped protein complexes are formed within cells spontaneously or are facilitated by addition of oxidation reagents such as H2O2 or diamide. Western blotting analysis, in the presence and absence of reducing reagents, is used to determine whether the disulfide bonds are formed in the proposed complex interface in physiologically relevant milieus. The procedure described here requires 1-2 months. We demonstrate this approach using the β2-adrenergic receptor-β-arrestin1 complex as the model system.
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Affiliation(s)
- Kunhong Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Vascular Medicine Institute, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Biomedical Mass Spectrometry Center, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yang Zhao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Minjung Choi
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Hongda Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Adi Blanc
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Jiang Qian
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Thomas J Cahill
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Xue Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Yunfang Xiao
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lisa J Clark
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sheng Li
- Department of Chemistry, University of California at San Diego, La Jolla, California, USA
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49
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Gaalswyk K, Muniyat MI, MacCallum JL. The emerging role of physical modeling in the future of structure determination. Curr Opin Struct Biol 2018; 49:145-153. [DOI: 10.1016/j.sbi.2018.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/04/2018] [Accepted: 03/05/2018] [Indexed: 10/17/2022]
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50
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Abstract
Human deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase), essential for DNA integrity, acts as a survival factor for tumor cells and is a target for cancer chemotherapy. Here we report that the Staphylococcal repressor protein StlSaPIBov1 (Stl) forms strong complex with human dUTPase. Functional analysis reveals that this interaction results in significant reduction of both dUTPase enzymatic activity and DNA binding capability of Stl. We conducted structural studies to understand the mechanism of this mutual inhibition. Small-angle X-ray scattering (SAXS) complemented with hydrogen-deuterium exchange mass spectrometry (HDX-MS) data allowed us to obtain 3D structural models comprising a trimeric dUTPase complexed with separate Stl monomers. These models thus reveal that upon dUTPase-Stl complex formation the functional homodimer of Stl repressor dissociates, which abolishes the DNA binding ability of the protein. Active site forming dUTPase segments were directly identified to be involved in the dUTPase-Stl interaction by HDX-MS, explaining the loss of dUTPase activity upon complexation. Our results provide key novel structural insights that pave the way for further applications of the first potent proteinaceous inhibitor of human dUTPase.
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