1
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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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2
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Meng Q, Song YL, Zhou C, He H, Zhang N, Zhou H. A hydrogen-deuterium exchange mass spectrometry-based protocol for protein-small molecule interaction analysis. BIOPHYSICS REPORTS 2023; 9:99-111. [PMID: 37753061 PMCID: PMC10518522 DOI: 10.52601/bpr.2023.230006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/17/2023] [Indexed: 09/28/2023] Open
Abstract
Protein-small molecule interaction is vital in regulating protein functions and controlling various cellular processes. Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful methodology to study protein-small molecule interactions, however, to accurately probe the conformational dynamics of the protein upon small molecule binding, the HDX-MS experimental conditions should be carefully controlled and optimized. Here, we present the detailed continuous-labeling, bottom-up HDX-MS protocol for studying protein-small molecule interactions. We took a side-by-side HDX kinetics comparison of the Hsp90N protein with or without the treatment of small molecules (i.e., Radicicol, Geldanamycin) for displaying conformational changes induced by molecular interactions between Hsp90N and small molecules. Our sensitive and robust experimental protocol can facilitate the novice to quickly carry out the structural characterization of protein-small molecule interactions.
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Affiliation(s)
- Qian Meng
- Analytical Research Center for Organic and Biological Molecules, State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Department of Pharmacology, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yuan-Li Song
- Analytical Research Center for Organic and Biological Molecules, State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Zhou
- Analytical Research Center for Organic and Biological Molecules, State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Han He
- Analytical Research Center for Organic and Biological Molecules, State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Naixia Zhang
- Analytical Research Center for Organic and Biological Molecules, State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Zhou
- Analytical Research Center for Organic and Biological Molecules, State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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3
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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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4
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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5
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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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6
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Narang D, Lento C, J. Wilson D. HDX-MS: An Analytical Tool to Capture Protein Motion in Action. Biomedicines 2020; 8:biomedicines8070224. [PMID: 32709043 PMCID: PMC7399943 DOI: 10.3390/biomedicines8070224] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/07/2023] Open
Abstract
Virtually all protein functions in the cell, including pathogenic processes, require coordinated motion of atoms or domains, i.e., conformational dynamics. Understanding protein dynamics is therefore critical both for drug development and to learn about the underlying molecular causes of many diseases. Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) provides valuable information about protein dynamics, which is highly complementary to the static picture provided by conventional high-resolution structural tools (i.e., X-ray crystallography and structural NMR). The amount of protein required to carry out HDX-MS experiments is a fraction of the amount required by alternative biophysical techniques, which are also usually lower resolution. Use of HDX-MS is growing quickly both in industry and academia, and it has been successfully used in numerous drug and vaccine development efforts, with important roles in understanding allosteric effects and mapping binding sites.
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Affiliation(s)
- Dominic Narang
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
| | - Derek J. Wilson
- Department of Chemistry, York University, Toronto, ON M3J 1P3, Canada; (D.N.); (C.L.)
- Centre for Research of Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University, Toronto, ON M3J 1P3, Canada
- Correspondence:
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7
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Lugo MR, Lyons B, Lento C, Wilson DJ, Merrill AR. Dynamics of Scabin toxin. A proposal for the binding mode of the DNA substrate. PLoS One 2018; 13:e0194425. [PMID: 29543870 PMCID: PMC5854381 DOI: 10.1371/journal.pone.0194425] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/04/2018] [Indexed: 12/29/2022] Open
Abstract
Scabin is a mono-ADP-ribosyltransferase enzyme and is a putative virulence factor produced by the plant pathogen, Streptomyces scabies. Previously, crystal structures of Scabin were solved in the presence and absence of substrate analogues and inhibitors. Herein, experimental (hydrogen-deuterium exchange), simulated (molecular dynamics), and theoretical (Gaussian Network Modeling) approaches were systematically applied to study the dynamics of apo-Scabin in the context of a Scabin·NAD+·DNA model. MD simulations revealed that the apo-Scabin solution conformation correlates well with the X-ray crystal structure, beyond the conformation of the exposed, mobile regions. In turn, the MD fluctuations correspond with the crystallographic B-factors, with the fluctuations derived from a Gaussian network model, and with the experimental H/D exchange rates. An Essential Dynamics Analysis identified the dynamic aspects of the toxin as a crab-claw-like mechanism of two topological domains, along with coupled deformations of exposed motifs. The “crab-claw” movement resembles the motion of C3-like toxins and emerges as a property of the central β scaffold of catalytic single domain toxins. The exposure and high mobility of the cis side motifs in the Scabin β-core suggest involvement in DNA substrate binding. A ternary Scabin·NAD+·DNA model was produced via an independent docking methodology, where the intermolecular interactions correspond to the region of high mobility identified by dynamics analyses and agree with binding and kinetic data reported for wild-type and Scabin variants. Based on data for the Pierisin-like toxin group, the sequence motif Rβ1–RLa–NLc–STTβ2–WPN–WARTT–(QxE)ARTT emerges as a catalytic signature involved in the enzymatic activity of these DNA-acting toxins. However, these results also show that Scabin possesses a unique DNA-binding motif within the Pierisin-like toxin group.
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Affiliation(s)
- Miguel R Lugo
- Department of Molecular and Cell Biology, University of Guelph, Guelph, Ontario, Canada
| | - Bronwyn Lyons
- Department of Molecular and Cell Biology, University of Guelph, Guelph, Ontario, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cristina Lento
- Chemistry Department, York University, Toronto, Ontario, Canada.,The Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
| | - Derek J Wilson
- Chemistry Department, York University, Toronto, Ontario, Canada.,The Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
| | - A Rod Merrill
- Department of Molecular and Cell Biology, University of Guelph, Guelph, Ontario, Canada
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