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Jain R, Dhillon NS, Kanchustambham VL, Lodowski DT, Farquhar ER, Kiselar J, Chance MR. Evaluating Mass Spectrometry-Based Hydroxyl Radical Protein Footprinting of a Benchtop Flash Oxidation System against a Synchrotron X-ray Beamline. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:476-486. [PMID: 38335063 DOI: 10.1021/jasms.3c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Hydroxyl radical protein footprinting (HRPF) using synchrotron X-ray radiation (XFP) and mass spectrometry is a well-validated structural biology method that provides critical insights into macromolecular structural dynamics, such as determining binding sites, measuring affinity, and mapping epitopes. Numerous alternative sources for generating the hydroxyl radicals (•OH) needed for HRPF, such as laser photolysis and plasma irradiation, complement synchrotron-based HRPF, and a recently developed commercially available instrument based on flash lamp photolysis, the FOX system, enables access to laboratory benchtop HRPF. Here, we evaluate performing HRPF experiments in-house with a benchtop FOX instrument compared to synchrotron-based X-ray footprinting at the NSLS-II XFP beamline. Using lactate oxidase (LOx) as a model system, we carried out •OH labeling experiments using both instruments, followed by nanoLC-MS/MS bottom-up peptide mass mapping. Experiments were performed under high glucose concentrations to mimic the highly scavenging conditions present in biological buffers and human clinical samples, where less •OH are available for reaction with the biomolecule(s) of interest. The performance of the FOX and XFP HRPF methods was compared, and we found that tuning the •OH dosage enabled optimal labeling coverage for both setups under physiologically relevant highly scavenging conditions. Our study demonstrates the complementarity of FOX and XFP labeling approaches, demonstrating that benchtop instruments such as the FOX photolysis system can increase both the throughput and the accessibility of the HRPF technique.
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Affiliation(s)
- Rohit Jain
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nanak S Dhillon
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Vijaya Lakshmi Kanchustambham
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - David T Lodowski
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Erik R Farquhar
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Janna Kiselar
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Mark R Chance
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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2
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Farquhar ER, Vijayalakshmi K, Jain R, Wang B, Kiselar J, Chance MR. Intact mass spectrometry screening to optimize hydroxyl radical dose for protein footprinting. Biochem Biophys Res Commun 2023; 671:343-349. [PMID: 37329657 PMCID: PMC10510565 DOI: 10.1016/j.bbrc.2023.06.020] [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: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/19/2023]
Abstract
Hydroxyl radical protein footprinting (HRPF) using synchrotron radiation is a well-validated method to assess protein structure in the native solution state. In this method, X-ray radiolysis of water generates hydroxyl radicals that can react with solvent accessible side chains of proteins, with mass spectrometry used to detect the resulting labeled products. An ideal footprinting dose provides sufficient labeling to measure the structure but not so much as to influence the results. The optimization of hydroxyl radical dose is typically performed using an indirect Alexa488 fluorescence assay sensitive to hydroxyl radical concentration, but full evaluation of the experiment's outcome relies upon bottom-up liquid chromatography mass spectrometry (LC-MS) measurements to directly determine sites and extent of oxidative labeling at the peptide and protein level. A direct evaluation of the extent of labeling to provide direct and absolute measurements of dose and "safe" dose ranges in terms of, for example, average numbers of labels per protein, would provide immediate feedback on experimental outcomes prior to embarking on detailed LC-MS analyses. To this end, we describe an approach to integrate intact MS screening of labeled samples immediately following exposure, along with metrics to quantify the extent of observed labeling from the intact mass spectra. Intact MS results on the model protein lysozyme were evaluated in the context of Alexa488 assay results and a bottom-up LC-MS analysis of the same samples. This approach provides a basis for placing delivered hydroxyl radical dose metrics on firmer technical grounds for synchrotron X-ray footprinting of proteins, with explicit parameters to increase the likelihood of a productive experimental outcome. Further, the method directs approaches to provide absolute and direct dosimetry for all types of labeling for protein footprinting.
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Affiliation(s)
- Erik R Farquhar
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
| | - Kanchustambham Vijayalakshmi
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - Rohit Jain
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - Benlian Wang
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - Janna Kiselar
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - Mark R Chance
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
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3
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Wohl S, Zheng W. Interpreting Transient Interactions of Intrinsically Disordered Proteins. J Phys Chem B 2023; 127:2395-2406. [PMID: 36917561 PMCID: PMC10038935 DOI: 10.1021/acs.jpcb.3c00096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The flexible nature of intrinsically disordered proteins (IDPs) gives rise to a conformational ensemble with a diverse set of conformations. The simplest way to describe this ensemble is through a homopolymer model without any specific interactions. However, there has been growing evidence that the conformational properties of IDPs and their relevant functions can be affected by transient interactions between specific and even nonlocal pairs of amino acids. Interpreting these interactions from experimental methods, each of which is most sensitive to a different distance regime referred to as probing length, remains a challenging and unsolved problem. Here, we first show that transient interactions can be realized between short fragments of charged amino acids by generating conformational ensembles using model disordered peptides and coarse-grained simulations. Using these ensembles, we investigate how sensitive different types of experimental measurements are to the presence of transient interactions. We find methods with shorter probing lengths to be more appropriate for detecting these transient interactions, but one experimental method is not sufficient due to the existence of other weak interactions typically seen in IDPs. Finally, we develop an adjusted polymer model with an additional short-distance peak which can robustly reproduce the distance distribution function from two experimental measurements with complementary short and long probing lengths. This new model can suggest whether a homopolymer model is insufficient for describing a specific IDP and meets the challenge of quantitatively identifying specific, transient interactions from a background of nonspecific, weak interactions.
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Affiliation(s)
- Samuel Wohl
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
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4
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Luo S, Wohl S, Zheng W, Yang S. Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery. Biomolecules 2023; 13:biom13030530. [PMID: 36979465 PMCID: PMC10046839 DOI: 10.3390/biom13030530] [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: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.
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Affiliation(s)
- Shuqi Luo
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Samuel Wohl
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA
- Correspondence: (W.Z.); (S.Y.)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: (W.Z.); (S.Y.)
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5
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Dang X, Guelen L, Lutje Hulsik D, Ermakov G, Hsieh EJ, Kreijtz J, Stammen-Vogelzangs J, Lodewijks I, Bertens A, Bramer A, Guadagnoli M, Nazabal A, van Elsas A, Fischmann T, Juan V, Beebe A, Beaumont M, van Eenennaam H. Epitope mapping of monoclonal antibodies: a comprehensive comparison of different technologies. MAbs 2023; 15:2285285. [PMID: 38010385 PMCID: PMC10730160 DOI: 10.1080/19420862.2023.2285285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
Monoclonal antibodies have become an important class of therapeutics in the last 30 years. Because the mechanism of action of therapeutic antibodies is intimately linked to their binding epitopes, identification of the epitope of an antibody to the antigen plays a central role during antibody drug development. The gold standard of epitope mapping, X-ray crystallography, requires a high degree of proficiency with no guarantee of success. Here, we evaluated six widely used alternative methods for epitope identification (peptide array, alanine scan, domain exchange, hydrogen-deuterium exchange, chemical cross-linking, and hydroxyl radical footprinting) in five antibody-antigen combinations (pembrolizumab+PD1, nivolumab+PD1, ipilimumab+CTLA4, tremelimumab+CTLA4, and MK-5890+CD27). The advantages and disadvantages of each technique are demonstrated by our data and practical advice on when and how to apply specific epitope mapping techniques during the drug development process is provided. Our results suggest chemical cross-linking most accurately identifies the epitope as defined by crystallography.
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Affiliation(s)
- Xibei Dang
- Pharmacokinetics, Merck & Co. Inc, Kenilworth, NJ, USA
| | - Lars Guelen
- Research, Aduro Biotech Europe, Oss, The Netherlands
| | | | | | | | - Joost Kreijtz
- Research, Aduro Biotech Europe, Oss, The Netherlands
| | | | | | | | - Arne Bramer
- Research, Aduro Biotech Europe, Oss, The Netherlands
| | | | | | | | | | - Veronica Juan
- Pharmacokinetics, Merck & Co. Inc, Kenilworth, NJ, USA
| | - Amy Beebe
- Pharmacokinetics, Merck & Co. Inc, Kenilworth, NJ, USA
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6
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Paulikat M, Aranda J, Ippoliti E, Orozco M, Carloni P. Proton Transfers to DNA in Native Electrospray Ionization Mass Spectrometry: A Quantum Mechanics/Molecular Mechanics Study. J Phys Chem Lett 2022; 13:12004-12010. [PMID: 36540944 PMCID: PMC9806827 DOI: 10.1021/acs.jpclett.2c03100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Native electrospray ionization-ion mobility mass spectrometry (N-ESI/IM-MS) is a powerful approach for low-resolution structural studies of DNAs in the free state and in complex with ligands. Solvent vaporization is coupled with proton transfers from ammonium ions to the DNA, resulting in a reduction of the DNA charge. Here we provide insight into these processes by classical molecular dynamics and quantum mechanics/molecular mechanics free energy calculations on the d(GpCpGpApApGpC) heptamer, for which a wealth of experiments is available. Our multiscale simulations, consistent with experimental data, reveal a highly complex scenario. The proton either sits on one of the molecules or is fully delocalized on both, depending on the level of hydration of the analytes and the size of the droplets formed during the electrospray experiments. This work complements our previous study of the intramolecular proton transfer on the same heptamer occurring after the processes studied here, and together, they provide a first molecular view of proton transfer in N-ESI/IM-MS.
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Affiliation(s)
- Mirko Paulikat
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Juan Aranda
- Institute
for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Emiliano Ippoliti
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Modesto Orozco
- Institute
for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department
of Biochemistry and Biomedicine, University
of Barcelona, Avinguda
Diagonal 645, 08028 Barcelona, Spain
| | - Paolo Carloni
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
- Department
of Physics, RWTH Aachen University, Otto-Blumenthal-Straße, 52062 Aachen, Germany
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7
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Borotto NB, Richards TK. Rapid Online Oxidation of Proteins and Peptides via Electrospray-Accelerated Ozonation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2078-2086. [PMID: 36194498 DOI: 10.1021/jasms.2c00182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mass spectrometry-based analyses of protein conformation continue to grow in utilization due their speed, low sample requirements, and applicability to most protein systems. These techniques typically rely on chemical derivatization of proteins and as with all label-based analyses must ensure the integrity of the protein conformation throughout the duration of the labeling reaction. Hydroxyl radical footprinting of proteins and the recently developed fast fluoroalkylation of proteins attempt to bypass this consideration via rapid reactions that occur on time scales faster than protein folding, but they often require microfluidic setups or electromagnetic radiation sources. In this work, we demonstrate that ozonation of proteins and peptides, which normally occurs in the second to minute time scales, can be accelerated to the submillisecond to millisecond time scale with an electrospray ionization source. This rapid ozonation results in selective labeling of tryptophan and methionine residues. When applied to cytochrome C and carbonic anhydrase, this labeling technique is sensitive to solution conditions and correlates with solution-phase analyses of conformation. While significant work is still needed to characterize this fast chemical labeling strategy, it requires no complicated sample handling, electromagnetic radiation sources, or microfluidic systems outside of the electrospray source and may represent a facile alternative to other rapid labeling technologies that are utilized today.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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8
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Dafun AS, Marcoux J. Structural mass spectrometry of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140813. [PMID: 35750312 DOI: 10.1016/j.bbapap.2022.140813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The analysis of proteins and protein complexes by mass spectrometry (MS) has come a long way since the invention of electrospray ionization (ESI) in the mid 80s. Originally used to characterize small soluble polypeptide chains, MS has progressively evolved over the past 3 decades towards the analysis of samples of ever increasing heterogeneity and complexity, while the instruments have become more and more sensitive and resolutive. The proofs of concepts and first examples of most structural MS methods appeared in the early 90s. However, their application to membrane proteins, key targets in the biopharma industry, is more recent. Nowadays, a wealth of information can be gathered from such MS-based methods, on all aspects of membrane protein structure: sequencing (and more precisely proteoform characterization), but also stoichiometry, non-covalent ligand binding (metals, drug, lipids, carbohydrates), conformations, dynamics and distance restraints for modelling. In this review, we present the concept and some historical and more recent applications on membrane proteins, for the major structural MS methods.
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Affiliation(s)
- Angelique Sanchez Dafun
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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9
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Jain R, Dhillon NS, Farquhar ER, Wang B, Li X, Kiselar J, Chance MR. Multiplex Chemical Labeling of Amino Acids for Protein Footprinting Structure Assessment. Anal Chem 2022; 94:9819-9825. [PMID: 35763792 PMCID: PMC9983563 DOI: 10.1021/acs.analchem.2c01640] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein footprinting with mass spectrometry is an established structural biology technique for mapping solvent accessibility and assessing molecular-level interactions of proteins. In hydroxyl radical protein footprinting (HRPF), hydroxyl (OH) radicals generated by water radiolysis or other methods covalently label protein side chains. Because of the wide dynamic range of OH reactivity, not all side chains are easily detected in a single experiment. Novel reagent development and the use of radical chain reactions for labeling, including trifluoromethyl radicals, is a potential approach to normalize the labeling across a diverse set of residues. HRPF in the presence of a trifluoromethylation reagent under the right conditions could provide a "one-pot" reaction for multiplex labeling of protein side chains. Toward this goal, we have systematically evaluated amino acid labeling with the recently investigated Langlois' reagent (LR) activated by X-ray-mediated water radiolysis, followed by three different mass spectrometry methods. We compared the reactivity of CF3 and OH radical labeling for all 20 protein side chains in a competition-free environment. We found that all 20 amino acids exhibited CF3 or OH labeling in LR. Our investigations provide the evidence and knowledge set to perfect hydroxyl radical-activated trifluoromethyl chemistry as "one-pot" reaction for multiplex labeling of protein side chains to achieve higher resolution in HRPF.
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Affiliation(s)
- Rohit Jain
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Nanak S. Dhillon
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Erik R. Farquhar
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Benlian Wang
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Xiaolin Li
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Janna Kiselar
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Mark R. Chance
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Corresponding Author: Mark R. Chance - Center for Synchrotron Biosciences; Center for Proteomics and Bioinformatics; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
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10
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Blackburn MR, Minkoff BB, Sussman MR. Mass spectrometry-based technologies for probing the 3D world of plant proteins. PLANT PHYSIOLOGY 2022; 189:12-22. [PMID: 35139210 PMCID: PMC9070838 DOI: 10.1093/plphys/kiac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/30/2021] [Indexed: 05/03/2023]
Abstract
Over the past two decades, mass spectrometric (MS)-based proteomics technologies have facilitated the study of signaling pathways throughout biology. Nowhere is this needed more than in plants, where an evolutionary history of genome duplications has resulted in large gene families involved in posttranslational modifications and regulatory pathways. For example, at least 5% of the Arabidopsis thaliana genome (ca. 1,200 genes) encodes protein kinases and protein phosphatases that regulate nearly all aspects of plant growth and development. MS-based technologies that quantify covalent changes in the side-chain of amino acids are critically important, but they only address one piece of the puzzle. A more crucially important mechanistic question is how noncovalent interactions-which are more difficult to study-dynamically regulate the proteome's 3D structure. The advent of improvements in protein 3D technologies such as cryo-electron microscopy, nuclear magnetic resonance, and X-ray crystallography has allowed considerable progress to be made at this level, but these methods are typically limited to analyzing proteins, which can be expressed and purified in milligram quantities. Newly emerging MS-based technologies have recently been developed for studying the 3D structure of proteins. Importantly, these methods do not require protein samples to be purified and require smaller amounts of sample, opening the wider proteome for structural analysis in complex mixtures, crude lysates, and even in intact cells. These MS-based methods include covalent labeling, crosslinking, thermal proteome profiling, and limited proteolysis, all of which can be leveraged by established MS workflows, as well as newly emerging methods capable of analyzing intact macromolecules and the complexes they form. In this review, we discuss these recent innovations in MS-based "structural" proteomics to provide readers with an understanding of the opportunities they offer and the remaining challenges for understanding the molecular underpinnings of plant structure and function.
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Affiliation(s)
- Matthew R Blackburn
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Benjamin B Minkoff
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
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11
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Sun J, Li W, Gross ML. Advances in mass spectrometry-based footprinting of membrane proteins. Proteomics 2022; 22:e2100222. [PMID: 35290716 PMCID: PMC10493193 DOI: 10.1002/pmic.202100222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
Structural biology is entering an exciting time where many new high-resolution structures of large complexes and membrane proteins (MPs) are determined regularly. These advances have been driven by over 15 years of technological improvements, first in macromolecular crystallography, and recently in cryo-electron microscopy. Obtaining information about MP higher order structure and interactions is also a frontier, important but challenging owing to their unique properties and the need to choose suitable detergents/lipids for their study. The development of mass spectrometry (MS), both instruments and methodology in the past 10 years, has also advanced it as a complementary method to study MP structure and interactions. In this review, we discuss advances in MS-based footprinting for MPs and highlight recent methodologies that offer new promise for MP study by chemical footprinting and mass spectrometry.
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Affiliation(s)
- Jie Sun
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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12
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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13
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Borotto NB, Osho KE, Richards TK, Graham KA. Collision-Induced Unfolding of Native-like Protein Ions Within a Trapped Ion Mobility Spectrometry Device. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:83-89. [PMID: 34870999 DOI: 10.1021/jasms.1c00273] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Native mass spectrometry and collision-induced unfolding (CIU) workflows continue to grow in utilization due to their ability to rapidly characterize protein conformation and stability. To perform these experiments, the instrument must be capable of collisionally activating ions prior to ion mobility spectrometry (IMS) analyses. Trapped ion mobility spectrometry (TIMS) is an ion mobility implementation that has been increasingly adopted due to its inherently high resolution and reduced instrumental footprint. In currently deployed commercial instruments, however, typical modes of collisional activation do not precede IMS analysis, and thus, the instruments are incapable of performing CIU. In this work, we expand on a recently developed method of activating protein ions within the TIMS device and explore its analytical utility toward the unfolding of native-like protein ions. We demonstrate the unfolding of native-like ions of ubiquitin, cytochrome C, β-lactoglobulin, and carbonic anhydrase. These ions undergo extensive unfolding upon collisional activation. Additionally, the improved resolution provided by the TIMS separation uncovers previously obscured unfolding complexity.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | - Kemi E Osho
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
| | | | - Katherine A Graham
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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14
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Basciu A, Callea L, Motta S, Bonvin AM, Bonati L, Vargiu AV. No dance, no partner! A tale of receptor flexibility in docking and virtual screening. VIRTUAL SCREENING AND DRUG DOCKING 2022. [DOI: 10.1016/bs.armc.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Pan X, Vachet RW. MEMBRANE PROTEIN STRUCTURES AND INTERACTIONS FROM COVALENT LABELING COUPLED WITH MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2022; 41:51-69. [PMID: 33145813 PMCID: PMC8093322 DOI: 10.1002/mas.21667] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 05/31/2023]
Abstract
Membrane proteins are incredibly important biomolecules because they mediate interactions between a cell's external and internal environment. Obtaining information about membrane protein structure and interactions is thus important for understanding these essential biomolecules. Compared with the analyses of water-soluble proteins, the structural analysis of membrane proteins is more challenging owing to their unique chemical properties and the presence of lipid components that are necessary to solubilize them. The combination of covalent labeling (CL) and mass spectrometry (MS) has recently been applied with great success to study membrane protein structure and interactions. These studies have demonstrated the many advantages that CL-MS methods have over other traditional biophysical techniques. In this review, we discuss both amino acid-specific and non-specific labeling approaches and the special considerations needed to address the unique challenges associated with interrogating membrane proteins. This review highlights the aspects of this approach that require special care to be applied correctly and provides a comprehensive review of the membrane protein systems that have been studied by CL-MS. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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16
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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17
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Garman EF, Weik M. Radiation damage to biological samples: still a pertinent issue. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1278-1283. [PMID: 34475277 PMCID: PMC8415327 DOI: 10.1107/s1600577521008845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
An understanding of radiation damage effects suffered by biological samples during structural analysis using both X-rays and electrons is pivotal to obtain reliable molecular models of imaged molecules. This special issue on radiation damage contains six papers reporting analyses of damage from a range of biophysical imaging techniques. For X-ray diffraction, an in-depth study of multi-crystal small-wedge data collection single-wavelength anomalous dispersion phasing protocols is presented, concluding that an absorbed dose of 5 MGy per crystal was optimal to allow reliable phasing. For small-angle X-ray scattering, experiments are reported that evaluate the efficacy of three radical scavengers using a protein designed to give a clear signature of damage in the form of a large conformational change upon the breakage of a disulfide bond. The use of X-rays to induce OH radicals from the radiolysis of water for X-ray footprinting are covered in two papers. In the first, new developments and the data collection pipeline at the NSLS-II high-throughput dedicated synchrotron beamline are described, and, in the second, the X-ray induced changes in three different proteins under aerobic and low-oxygen conditions are investigated and correlated with the absorbed dose. Studies in XFEL science are represented by a report on simulations of ultrafast dynamics in protic ionic liquids, and, lastly, a broad coverage of possible methods for dose efficiency improvement in modalities using electrons is presented. These papers, as well as a brief synopsis of some other relevant literature published since the last Journal of Synchrotron Radiation Special Issue on Radiation Damage in 2019, are summarized below.
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Affiliation(s)
- Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
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18
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Jain R, Abel D, Rakitin M, Sullivan M, Lodowski DT, Chance MR, Farquhar ER. New high-throughput endstation to accelerate the experimental optimization pipeline for synchrotron X-ray footprinting. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1321-1332. [PMID: 34475281 PMCID: PMC8415340 DOI: 10.1107/s1600577521005026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 05/30/2023]
Abstract
Synchrotron X-ray footprinting (XF) is a growing structural biology technique that leverages radiation-induced chemical modifications via X-ray radiolysis of water to produce hydroxyl radicals that probe changes in macromolecular structure and dynamics in solution states of interest. The X-ray Footprinting of Biological Materials (XFP) beamline at the National Synchrotron Light Source II provides the structural biology community with access to instrumentation and expert support in the XF method, and is also a platform for development of new technological capabilities in this field. The design and implementation of a new high-throughput endstation device based around use of a 96-well PCR plate form factor and supporting diagnostic instrumentation for synchrotron XF is described. This development enables a pipeline for rapid comprehensive screening of the influence of sample chemistry on hydroxyl radical dose using a convenient fluorescent assay, illustrated here with a study of 26 organic compounds. The new high-throughput endstation device and sample evaluation pipeline now available at the XFP beamline provide the worldwide structural biology community with a robust resource for carrying out well optimized synchrotron XF studies of challenging biological systems with complex sample compositions.
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Affiliation(s)
- Rohit Jain
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Donald Abel
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Maksim Rakitin
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Michael Sullivan
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - David T. Lodowski
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Mark R. Chance
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Erik R. Farquhar
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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19
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Kursula P. Small-angle X-ray scattering for the proteomics community: current overview and future potential. Expert Rev Proteomics 2021; 18:415-422. [PMID: 34210208 DOI: 10.1080/14789450.2021.1951242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Proteins are biological nanoparticles. For structural proteomics and hybrid structural biology, complementary methods are required that allow both high throughput and accurate automated data analysis. Small-angle X-ray scattering (SAXS) is a method for observing the size and shape of particles, such as proteins and complexes, in solution. SAXS data can be used to model both the structure, oligomeric state, conformational changes, and flexibility of biomolecular samples.Areas covered: The key principles of SAXS, its sample requirements, and its current and future applications for structural proteomics are briefly reviewed. Recent technical developments in SAXS experiments are discussed, and future potential of the method in structural proteomics is evaluated.Expert opinion: SAXS is a method suitable for several aspects of integrative structural proteomics, with current technical developments allowing for higher throughput and time-resolved studies, as well as the analysis of complex samples, such as membrane proteins. Increasing automation and streamlined data analysis are expected to equip SAXS for structure-based screening workflows. Originally, structural genomics had a heavy focus on folded, crystallizable proteins and complexes - SAXS is a method allowing an expansion of this focus to flexible and disordered systems.
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Affiliation(s)
- Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway.,Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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20
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Sharp JS, Chea EE, Misra SK, Orlando R, Popov M, Egan RW, Holman D, Weinberger SR. Flash Oxidation (FOX) System: A Novel Laser-Free Fast Photochemical Oxidation Protein Footprinting Platform. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1601-1609. [PMID: 33872496 PMCID: PMC8812269 DOI: 10.1021/jasms.0c00471] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Hydroxyl radical protein footprinting (HRPF) is a powerful and flexible technique for probing changes in protein topography. With the development of the fast photochemical oxidation of proteins (FPOP), it became possible for researchers to perform HRPF in their laboratory on a very short time scale. While FPOP has grown significantly in popularity since its inception, adoption remains limited due to technical and safety issues involved in the operation of a hazardous Class IV UV laser and irreproducibility often caused by improper laser operation and/or differential radical scavenging by various sample components. Here, we present a new integrated FOX (Flash OXidation) Protein Footprinting System. This platform delivers sample via flow injection to a facile and safe-to-use high-pressure flash lamp with a flash duration of 10 μs fwhm. Integrated optics collect the radiant light and focus it into the lumen of a capillary flow cell. An inline radical dosimeter measures the hydroxyl radical dose delivered and allows for real-time compensation for differential radical scavenging. A programmable fraction collector collects and quenches only the sample that received the desired effective hydroxyl radical dose, diverting the carrier liquid and improperly oxidized sample to waste. We demonstrate the utility of the FOX Protein Footprinting System by determining the epitope of TNFα recognized by adalimumab. We successfully identify the surface of the protein that serves as the epitope for adalimumab, identifying four of the five regions previously noted by X-ray crystallography while seeing no changes in peptides not involved in the epitope interface. The FOX Protein Footprinting System allows for FPOP-like experiments with real-time dosimetry in a safe, compact, and integrated benchtop platform.
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Affiliation(s)
- Joshua S. Sharp
- GenNext Technologies, Inc., Half Moon Bay, CA 94019
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi 38677
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677
- Correspondence to Joshua S. Sharp,
| | | | - Sandeep K. Misra
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi 38677
| | - Ron Orlando
- GenNext Technologies, Inc., Half Moon Bay, CA 94019
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602
- GlycoScientific, Athens, GA 30602
| | | | | | - David Holman
- GenNext Technologies, Inc., Half Moon Bay, CA 94019
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Ruan H, Kiselar J, Zhang W, Li S, Xiong R, Liu Y, Yang S, Lai L. Integrative structural modeling of a multidomain polo-like kinase. Phys Chem Chem Phys 2020; 22:27581-27589. [PMID: 33236741 DOI: 10.1039/d0cp05030j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polo-like kinase 1 (PLK1) is a key regulator and coordinator for mitotic signaling that contains two major functional units of a kinase domain (KD) and a polo-box domain (PBD). While individual domain structures of the KD and the PBD are known, how they interact and assemble into a functional complex remains an open question. The structural model from the KD-PBD-Map205PBM heterotrimeric crystal structure of zebrafish PLK1 represents a major step in understanding the KD and the PBD interactions. However, how these two domains interact when connected by a linker in the full length PLK1 needs further investigation. By integrating different sources of structural data from small-angle X-ray scattering, hydroxyl radical protein footprinting, and computational sampling, here we report an overall architecture for PLK1 multidomain assembly between the KD and the PBD. Our model revealed that the KD uses its C-lobe to interact with the PBD via the site near the phosphopeptide binding site in its auto-inhibitory state in solution. Disruption of this auto-inhibition via site-directed mutagenesis at the KD-PBD interface increases its kinase activity, supporting the functional role of KD-PBD interactions predicted for regulating the PLK1 kinase function. Our results indicate that the full length human PLK1 takes dynamic structures with a variety of domain-domain interfaces in solution.
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Affiliation(s)
- Hao Ruan
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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22
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Affiliation(s)
- Sichun Yang
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
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