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Kaushik A, Than T, Petela NJ, Voulgaris M, Percival C, Daniels P, Rafferty JB, Nasmyth KA, Hu B. Conformational dynamics of cohesin/Scc2 loading complex are regulated by Smc3 acetylation and ATP binding. Nat Commun 2023; 14:5929. [PMID: 37739959 PMCID: PMC10516938 DOI: 10.1038/s41467-023-41596-w] [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: 12/02/2022] [Accepted: 09/11/2023] [Indexed: 09/24/2023] Open
Abstract
The ring-shaped cohesin complex is a key player in sister chromatid cohesion, DNA repair, and gene transcription. The loading of cohesin to chromosomes requires the loader Scc2 and is regulated by ATP. This process is hindered by Smc3 acetylation. However, the molecular mechanism underlying this inhibition remains mysterious. Here, using Saccharomyces cerevisiae as a model system, we identify a novel configuration of Scc2 with pre-engaged cohesin and reveal dynamic conformations of the cohesin/Scc2 complex in the loading reaction. We demonstrate that Smc3 acetylation blocks the association of Scc2 with pre-engaged cohesin by impairing the interaction of Scc2 with Smc3's head. Lastly, we show that ATP binding induces the cohesin/Scc2 complex to clamp DNA by promoting the interaction between Scc2 and Smc3 coiled coil. Our results illuminate a dynamic reconfiguration of the cohesin/Scc2 complex during loading and indicate how Smc3 acetylation and ATP regulate this process.
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Affiliation(s)
- Aditi Kaushik
- The Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Thane Than
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Naomi J Petela
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Charlotte Percival
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Peter Daniels
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - John B Rafferty
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Bin Hu
- The Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
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2
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Han CT, Nguyen KDQ, Berkow MW, Hussain S, Kiani A, Kinnebrew M, Idso MN, Baxter N, Chang E, Aye E, Winslow E, Rahman M, Seppälä S, O'Malley MA, Chmelka BF, Mertz B, Han S. Lipid membrane mimetics and oligomerization tune functional properties of proteorhodopsin. Biophys J 2023; 122:168-179. [PMID: 36352784 PMCID: PMC9822798 DOI: 10.1016/j.bpj.2022.11.012] [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: 12/21/2021] [Revised: 08/01/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2022] Open
Abstract
The functional properties of proteorhodopsin (PR) have been found to be strongly modulated by oligomeric distributions and lipid membrane mimetics. This study aims to distinguish and explain their effects by investigating how oligomer formation impacts PR's function of proton transport in lipid-based membrane mimetic environments. We find that PR forms stable hexamers and pentamers in both E. coli membranes and synthetic liposomes. Compared with the monomers, the photocycle kinetics of PR oligomers is ∼2 and ∼4.5 times slower for transitions between the K and M and the M and N photointermediates, respectively, indicating that oligomerization significantly slows PR's rate of proton transport in liposomes. In contrast, the apparent pKa of the key proton acceptor residue D97 (pKaD97) of liposome-embedded PR persists at 6.2-6.6, regardless of cross-protomer modulation of D97, suggesting that the liposome environment helps maintain PR's functional activity at neutral pH. By comparison, when extracted directly from E. coli membranes into styrene-maleic acid lipid particles, the pKaD97 of monomer-enriched E50Q PR drastically increases to 8.9, implying that there is a very low active PR population at neutral pH to engage in PR's photocycle. These findings demonstrate that oligomerization impacts PR's photocycle kinetics, while lipid-based membrane mimetics strongly affect PR's active population via different mechanisms.
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Affiliation(s)
- Chung-Ta Han
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Khanh Dinh Quoc Nguyen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California
| | - Maxwell W Berkow
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Sunyia Hussain
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Ahmad Kiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Maia Kinnebrew
- College of Creative Studies, Biology Department, University of California, Santa Barbara, Santa Barbara, California
| | - Matthew N Idso
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Naomi Baxter
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California
| | - Evelyn Chang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California
| | - Emily Aye
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California
| | - Elsa Winslow
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California
| | - Mohammad Rahman
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Bradley F Chmelka
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California; Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California.
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3
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Kim D, Tracey J, Becerra Flores M, Chaudhry K, Nasim R, Correa-Medina A, Knipling L, Chen Q, Stibitz S, Jenkins LM, Moon K, Cardozo T, Hinton D. Conformational change of the Bordetella response regulator BvgA accompanies its activation of the B. pertussis virulence gene fhaB. Comput Struct Biotechnol J 2022; 20:6431-6442. [DOI: 10.1016/j.csbj.2022.10.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 11/08/2022] Open
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4
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Trabjerg E, Keller A, Leitner A. pH Dependence of Succinimide-Ester-Based Protein Cross-Linking for Structural Mass Spectrometry Applications. ACS MEASUREMENT SCIENCE AU 2022; 2:132-138. [PMID: 36785722 PMCID: PMC9838815 DOI: 10.1021/acsmeasuresciau.1c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Within the research field of cross-linking mass spectrometry (XL-MS), the most commonly used cross-linking reagents are succinimide-ester-based (e.g., disuccinimidyl suberate (DSS)). These reagents primarily cross-link lysine side chains. So far, they have predominantly been used to investigate protein structures at neutral to slightly basic pH (7.0-8.5) to ensure the reactivity of the primary amine of the lysine side chain. However, disease-related molecular processes are not limited to such pH ranges; e.g., some important biological pathways are active in acidic intracellular compartments. The applicability of lysine-reactive cross-linking reagents to low-pH conditions remains unclear. Here, we cross-linked a mixture of eight model proteins at eight different pH conditions (pH 4.0-7.5) to investigate the pH dependency of DSS. DSS was able to cross-link proteins even at pH 4.0, but a clear decrease in the cross-linking efficiency was observed when the pH was lowered. Nevertheless, at pH 5.0, approximately half of the number of cross-links observed at pH 7.5 could still be identified. These findings highlight the ability of succinimide-based cross-linking reagents to be useful in probing the structure of proteins in a slightly acidic environment.
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5
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Petrotchenko EV, Borchers CH. Protein Chemistry Combined with Mass Spectrometry for Protein Structure Determination. Chem Rev 2021; 122:7488-7499. [PMID: 34968047 DOI: 10.1021/acs.chemrev.1c00302] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The advent of soft-ionization mass spectrometry for biomolecules has opened up new possibilities for the structural analysis of proteins. Combining protein chemistry methods with modern mass spectrometry has led to the emergence of the distinct field of structural proteomics. Multiple protein chemistry approaches, such as surface modification, limited proteolysis, hydrogen-deuterium exchange, and cross-linking, provide diverse and often orthogonal structural information on the protein systems studied. Combining experimental data from these various structural proteomics techniques provides a more comprehensive examination of the protein structure and increases confidence in the ultimate findings. Here, we review various types of experimental data from structural proteomics approaches with an emphasis on the use of multiple complementary mass spectrometric approaches to provide experimental constraints for the solving of protein structures.
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Affiliation(s)
- Evgeniy V Petrotchenko
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
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6
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Graziadei A, Rappsilber J. Leveraging crosslinking mass spectrometry in structural and cell biology. Structure 2021; 30:37-54. [PMID: 34895473 DOI: 10.1016/j.str.2021.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/11/2021] [Accepted: 11/17/2021] [Indexed: 12/18/2022]
Abstract
Crosslinking mass spectrometry (crosslinking-MS) is a versatile tool providing structural insights into protein conformation and protein-protein interactions. Its medium-resolution residue-residue distance restraints have been used to validate protein structures proposed by other methods and have helped derive models of protein complexes by integrative structural biology approaches. The use of crosslinking-MS in integrative approaches is underpinned by progress in estimating error rates in crosslinking-MS data and in combining these data with other information. The flexible and high-throughput nature of crosslinking-MS has allowed it to complement the ongoing resolution revolution in electron microscopy by providing system-wide residue-residue distance restraints, especially for flexible regions or systems. Here, we review how crosslinking-MS information has been leveraged in structural model validation and integrative modeling. Crosslinking-MS has also been a key technology for cell biology studies and structural systems biology where, in conjunction with cryoelectron tomography, it can provide structural and mechanistic insights directly in situ.
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Affiliation(s)
- Andrea Graziadei
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
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7
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Orillard E, Anaya S, Johnson MS, Watts KJ. Oxygen-Induced Conformational Changes in the PAS-Heme Domain of the Pseudomonas aeruginosa Aer2 Receptor. Biochemistry 2021; 60:2610-2622. [PMID: 34383467 DOI: 10.1021/acs.biochem.1c00452] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Aer2 receptor from Pseudomonas aeruginosa has an O2-binding PAS-heme domain that stabilizes O2 via a Trp residue in the distal heme pocket. Trp rotates ∼90° to bond with the ligand and initiate signaling. Although the isolated PAS domain is monomeric, both in solution and in a cyanide-bound crystal structure, an unliganded structure forms a dimer. An overlay of the two structures suggests possible signaling motions but also predicts implausible clashes at the dimer interface when the ligand is bound. Moreover, in a full-length Aer2 dimer, PAS is sandwiched between multiple N- and C-terminal HAMP domains, which would feasibly restrict PAS motions. To explore the PAS dimer interface and signal-induced motions in full-length Aer2, we introduced Cys substitutions and used thiol-reactive probes to examine in vivo accessibility and residue proximities under both aerobic and anaerobic conditions. In vivo, PAS dimers were retained in full-length Aer2 in the presence and absence of O2, and the dimer interface was consistent with the isolated PAS dimer structure. O2-mediated changes were also consistent with structural predictions in which the PAS N-terminal caps move apart and the C-terminal DxT region moves closer together. The DxT motif links PAS to the C-terminal HAMP domains and was critical for PAS-HAMP signaling. Removing the N-terminal HAMP domains altered the distal PAS dimer interface and prevented signaling, even after signal-on lesions were introduced into PAS. The N-terminal HAMP domains thus facilitate the O2-dependent shift of PAS to the signal-on conformation, clarifying their role upstream of the PAS-sensing domain.
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Affiliation(s)
- Emilie Orillard
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, California 92350, United States
| | - Selina Anaya
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, California 92350, United States
| | - Mark S Johnson
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, California 92350, United States
| | - Kylie J Watts
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, California 92350, United States
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8
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Molecular Insight into the Regulation of Vimentin by Cysteine Modifications and Zinc Binding. Antioxidants (Basel) 2021; 10:antiox10071039. [PMID: 34203497 PMCID: PMC8300659 DOI: 10.3390/antiox10071039] [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] [Received: 05/22/2021] [Revised: 06/20/2021] [Accepted: 06/24/2021] [Indexed: 01/11/2023] Open
Abstract
The intermediate filament protein vimentin is involved in essential cellular processes, including cell division and stress responses, as well as in the pathophysiology of cancer, pathogen infection, and autoimmunity. The vimentin network undergoes marked reorganizations in response to oxidative stress, in which modifications of vimentin single cysteine residue, Cys328, play an important role, and is modulated by zinc availability. However, the molecular basis for this regulation is not fully understood. Here, we show that Cys328 displays a low pKa, supporting its reactivity, and is readily alkylated and oxidized in vitro. Moreover, combined oxidation and crosslinking assays and molecular dynamics simulations support that zinc ions interact with Cys328 in its thiolate form, whereas Glu329 and Asp331 stabilize zinc coordination. Vimentin oxidation can induce disulfide crosslinking, implying the close proximity of Cys328 from neighboring dimers in certain vimentin conformations, supported by our computational models. Notably, micromolar zinc concentrations prevent Cys328 alkylation, lipoxidation, and disulfide formation. Moreover, zinc selectively protects vimentin from crosslinking using short-spacer cysteine-reactive but not amine-reactive agents. These effects are not mimicked by magnesium, consistent with a lower number of magnesium ions hosted at the cysteine region, according to molecular dynamics simulations. Importantly, the region surrounding Cys328 is involved in interaction with several drugs targeting vimentin and is conserved in type III intermediate filaments, which include glial fibrillary acidic protein and desmin. Altogether, our results identify this region as a hot spot for zinc binding, which modulates Cys328 reactivity. Moreover, they provide a molecular standpoint for vimentin regulation through the interplay between cysteine modifications and zinc availability.
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9
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Dashnaw CM, Koone JC, Abdolvahabi A, Shaw BF. Measuring how two proteins affect each other's net charge in a crowded environment. Protein Sci 2021; 30:1594-1605. [PMID: 33928693 DOI: 10.1002/pro.4092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022]
Abstract
Theory predicts that the net charge (Z) of a protein can be altered by the net charge of a neighboring protein as the two approach one another below the Debye length. This type of charge regulation suggests that a protein's charge and perhaps function might be affected by neighboring proteins without direct binding. Charge regulation during protein crowding has never been directly measured due to analytical challenges. Here, we show that lysine specific protein crosslinkers (NHS ester-Staudinger pairs) can be used to mimic crowding by linking two non-interacting proteins at a maximal distance of ~7.9 Å. The net charge of the regioisomeric dimers and preceding monomers can then be determined with lysine-acyl "protein charge ladders" and capillary electrophoresis. As a proof of concept, we covalently linked myoglobin (Zmonomer = -0.43 ± 0.01) and α-lactalbumin (Zmonomer = -4.63 ± 0.05). Amide hydrogen/deuterium exchange and circular dichroism spectroscopy demonstrated that crosslinking did not significantly alter the structure of either protein or result in direct binding (thus mimicking crowding). Ultimately, capillary electrophoretic analysis of the dimeric charge ladder detected a change in charge of ΔZ = -0.04 ± 0.09 upon crowding by this pair (Zdimer = -5.10 ± 0.07). These small values of ΔZ are not necessarily general to protein crowding (qualitatively or quantitatively) but will vary per protein size, charge, and solvent conditions.
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Affiliation(s)
- Chad M Dashnaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Jordan C Koone
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Alireza Abdolvahabi
- Mass Spectrometry Core Facility, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
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10
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Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. Proc Natl Acad Sci U S A 2021; 118:e2020857118. [PMID: 33443187 PMCID: PMC7817115 DOI: 10.1073/pnas.2020857118] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/12/2020] [Indexed: 12/22/2022] Open
Abstract
N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.
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Affiliation(s)
- Lindy Abas
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria;
| | - Martina Kolb
- Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Johannes Stadlmann
- Department of Chemistry, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria
| | - Dorina P Janacek
- Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Kristina Lukic
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Claus Schwechheimer
- Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), 1190 Vienna, Austria
| | - Jiří Friml
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Ulrich Z Hammes
- Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany;
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11
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Kim JY, Sung GY, Park M. Efficient Portable Urea Biosensor Based on Urease Immobilized Membrane for Monitoring of Physiological Fluids. Biomedicines 2020; 8:biomedicines8120596. [PMID: 33322630 PMCID: PMC7764381 DOI: 10.3390/biomedicines8120596] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/01/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Numerous studies have addressed the utilization of glutaraldehyde (GA) as a homobifunctional cross-linker. However, its applicability has been impeded due to several issues, including the tendency of GA molecules to undergo polymerization. Herein, a portable urea biosensor was developed for the real-time monitoring of the flow of physiological fluids; this was achieved by using disuccinimidyl cross-linker-based urease immobilization. Urease was immobilized on a porous polytetrafluoroethylene (PTFE) solid support using different disuccinimidyl cross-linkers, namely disuccinimidyl glutarate (DSG), disuccinimidyl suberate (DSS) and bis-N-succinimidyl-(pentaethylene glycol) ester (BS(PEG)5). A urease activity test revealed that DSS exhibited the highest urease immobilizing efficiency, whereas FT-IR analysis confirmed that urease was immobilized on the PTFE membrane via DSS cross-linking. The membrane was inserted in a polydimethylsiloxane (PDMS) fluidic chamber that generated an electrochemical signal in the presence of a flowing fluid containing urea. Urea samples were allowed to flow into the urea biosensor (1.0 mL/min) and the signal was measured using chronoamperometry. The sensitivity of the DSS urea biosensor was the highest of all the trialed biosensors and was found to be superior to the more commonly used GA cross-linker. To simulate real-time monitoring in a human patient, flowing urea-spiked human serum was measured and the effective urease immobilization of the DSS urea biosensor was confirmed. The repeatability and interference of the urea biosensor were suitable for monitoring urea concentrations typically found in human patients.
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Affiliation(s)
- Jee Young Kim
- Cooperative Course of Nano-Medical Device Engineering, Hallym University, Chuncheon, Gangwon-do 24252, Korea; (J.Y.K.); (G.Y.S.)
- Integrative Materials Research Institute, Hallym University, Chuncheon, Gangwon-do 24252, Korea
| | - Gun Yong Sung
- Cooperative Course of Nano-Medical Device Engineering, Hallym University, Chuncheon, Gangwon-do 24252, Korea; (J.Y.K.); (G.Y.S.)
- Integrative Materials Research Institute, Hallym University, Chuncheon, Gangwon-do 24252, Korea
- Major in Materials Science and Engineering, Hallym University, Chuncheon, Gangwon-do 24252, Korea
| | - Min Park
- Cooperative Course of Nano-Medical Device Engineering, Hallym University, Chuncheon, Gangwon-do 24252, Korea; (J.Y.K.); (G.Y.S.)
- Integrative Materials Research Institute, Hallym University, Chuncheon, Gangwon-do 24252, Korea
- Major in Materials Science and Engineering, Hallym University, Chuncheon, Gangwon-do 24252, Korea
- Correspondence:
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12
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Gnanapradeepan K, Leu JIJ, Basu S, Barnoud T, Good M, Lee JV, Quinn WJ, Kung CP, Ahima R, Baur JA, Wellen KE, Liu Q, Schug ZT, George DL, Murphy ME. Increased mTOR activity and metabolic efficiency in mouse and human cells containing the African-centric tumor-predisposing p53 variant Pro47Ser. eLife 2020; 9:e55994. [PMID: 33170774 PMCID: PMC7661039 DOI: 10.7554/elife.55994] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/28/2020] [Indexed: 01/24/2023] Open
Abstract
The Pro47Ser variant of p53 (S47) exists in African-descent populations and is associated with increased cancer risk in humans and mice. Due to impaired repression of the cystine importer Slc7a11, S47 cells show increased glutathione (GSH) accumulation compared to cells with wild -type p53. We show that mice containing the S47 variant display increased mTOR activity and oxidative metabolism, as well as larger size, improved metabolic efficiency, and signs of superior fitness. Mechanistically, we show that mTOR and its positive regulator Rheb display increased association in S47 cells; this is due to an altered redox state of GAPDH in S47 cells that inhibits its ability to bind and sequester Rheb. Compounds that decrease glutathione normalize GAPDH-Rheb complexes and mTOR activity in S47 cells. This study reveals a novel layer of regulation of mTOR by p53, and raises the possibility that this variant may have been selected for in early Africa.
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Affiliation(s)
- Keerthana Gnanapradeepan
- Program in Molecular and Cellular Oncogenesis, The Wistar InstitutePhiladelphiaUnited States
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Julia I-Ju Leu
- Department of Genetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Subhasree Basu
- Program in Molecular and Cellular Oncogenesis, The Wistar InstitutePhiladelphiaUnited States
| | - Thibaut Barnoud
- Program in Molecular and Cellular Oncogenesis, The Wistar InstitutePhiladelphiaUnited States
| | - Madeline Good
- Program in Molecular and Cellular Oncogenesis, The Wistar InstitutePhiladelphiaUnited States
| | - Joyce V Lee
- Department of Cancer Biology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - William J Quinn
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Che-Pei Kung
- Washington University in St. LouisSt LouisUnited States
| | - Rexford Ahima
- Division of Endocrinology, Diabetes & Metabolism, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Joseph A Baur
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Kathryn E Wellen
- Department of Cancer Biology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Qin Liu
- Program in Molecular and Cellular Oncogenesis, The Wistar InstitutePhiladelphiaUnited States
| | - Zachary T Schug
- Program in Molecular and Cellular Oncogenesis, The Wistar InstitutePhiladelphiaUnited States
| | - Donna L George
- Department of Genetics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Maureen E Murphy
- Program in Molecular and Cellular Oncogenesis, The Wistar InstitutePhiladelphiaUnited States
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13
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Liess AKL, Kucerova A, Schweimer K, Schlesinger D, Dybkov O, Urlaub H, Mansfeld J, Lorenz S. Dimerization regulates the human APC/C-associated ubiquitin-conjugating enzyme UBE2S. Sci Signal 2020; 13:eaba8208. [PMID: 33082289 PMCID: PMC7613103 DOI: 10.1126/scisignal.aba8208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
At the heart of protein ubiquitination cascades, ubiquitin-conjugating enzymes (E2s) form reactive ubiquitin-thioester intermediates to enable efficient transfer of ubiquitin to cellular substrates. The precise regulation of E2s is thus crucial for cellular homeostasis, and their deregulation is frequently associated with tumorigenesis. In addition to driving substrate ubiquitination together with ubiquitin ligases (E3s), many E2s can also autoubiquitinate, thereby promoting their own proteasomal turnover. To investigate the mechanisms that balance these disparate activities, we dissected the regulatory dynamics of UBE2S, a human APC/C-associated E2 that ensures the faithful ubiquitination of cell cycle regulators during mitosis. We uncovered a dimeric state of UBE2S that confers autoinhibition by blocking a catalytically critical ubiquitin binding site. Dimerization is stimulated by the lysine-rich carboxyl-terminal extension of UBE2S that is also required for the recruitment of this E2 to the APC/C and is autoubiquitinated as substrate abundance becomes limiting. Consistent with this mechanism, we found that dimerization-deficient UBE2S turned over more rapidly in cells and did not promote mitotic slippage during prolonged drug-induced mitotic arrest. We propose that dimerization attenuates the autoubiquitination-induced turnover of UBE2S when the APC/C is not fully active. More broadly, our data illustrate how the use of mutually exclusive macromolecular interfaces enables modulation of both the activities and the abundance of E2s in cells to facilitate precise ubiquitin signaling.
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Affiliation(s)
- Anna K L Liess
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Alena Kucerova
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | | | - Dörte Schlesinger
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Olexandr Dybkov
- Department for Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, 37077 Göttingen, Germany
- Bioanalytics Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jörg Mansfeld
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany.
- Institute of Cancer Research, London SW7 3RP, UK
| | - Sonja Lorenz
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany.
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14
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Mitra G. Emerging Role of Mass Spectrometry-Based Structural Proteomics in Elucidating Intrinsic Disorder in Proteins. Proteomics 2020; 21:e2000011. [PMID: 32959512 DOI: 10.1002/pmic.202000011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/30/2020] [Indexed: 12/14/2022]
Abstract
Inherent disorder is an integral part of all proteomes, represented as fully or partially unfolded proteins. The lack of order in intrinsically disordered proteins (IDPs) results in an incredibly flexible, floppy, and heterogeneous ensemble, contrary to the well-structured and unique organization of folded proteins. Despite such unusual demeanor, IDPs are crucial for numerous cellular processes and are increasingly being associated with disease-causing pathologies. These warrant more intensive investigation of this atypical class of protein. Traditional biophysical tools, however, fall short of analyzing IDPs, thus making their structure-function characterization challenging. Mass spectrometry (MS) in recent years has evolved as a valuable tool for elucidating the unusual conformational facets of IDPs. In this review, the features of advanced MS techniques such as Hydrogen-deuterium exchange (HDX)-MS, native MS, limited proteolysis (LiP)-MS, chemical cross-linking (XL)-MS, and Fast photochemical oxidation of proteins (FPOP)-MS are briefly discussed. Recent MS studies on IDPs and the unique advantages/shortfalls associated with the above methods while evaluating structural proteomics of IDPs, are illustrated. Eventually the future scope of the MS methods in further decoding the unexplored landscapes of IDPs is presented.
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Affiliation(s)
- Gopa Mitra
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St John's Medical College, St. John's National Academy of Health Sciences, 100 Feet Road, Koramangala, Bangalore, Karnataka, 560034, India
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15
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Carey Hulyer AR, Briggs DA, O'Mara ML, Kerr ID, Harmer JR, Callaghan R. Cross-linking, DEER-spectroscopy and molecular dynamics confirm the inward facing state of P-glycoprotein in a lipid membrane. J Struct Biol 2020; 211:107513. [PMID: 32339763 DOI: 10.1016/j.jsb.2020.107513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/09/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
The drug efflux pump P-glycoprotein (P-gp) displays a complex transport mechanism involving multiple drug binding sites and two centres for nucleotide hydrolysis. Elucidating the molecular mechanism of transport remains elusive and the availability of P-gp structures in distinct natural and ligand trapped conformations will accelerate our understanding. The present investigation sought to provide biochemical data to validate specific features of these structures; with particular focus on the transmembrane domain that provides the transport conduit. Hence our focus was on transmembrane helices six and twelve (TM6/TM12), which are believed to participate in drug binding, as they line the central transport conduit and provide a direct link to the catalytic centres. A series of P-gp mutants were generated with a single cysteine in both TM6 and TM12 to facilitate measurement of inter-helical distances using cross-linking and DEER strategies. Experimental results were compared to published structures per se and those refined by MD simulations. This analysis revealed that the refined inward-facing murine structure (4M1M) of P-gp provides a good representation of the proximity, topography and relative motions of TM6 and TM12 in reconstituted human P-gp.
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Affiliation(s)
- Alex R Carey Hulyer
- Research School of Biology, and the Medical School, Australian National University, Canberra, ACT 2601, Australia
| | - Deborah A Briggs
- Centre for Biochemistry and Cell Biology, School of Biomedical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Megan L O'Mara
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Ian D Kerr
- Centre for Biochemistry and Cell Biology, School of Biomedical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Jeffrey R Harmer
- The Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Richard Callaghan
- Research School of Biology, and the Medical School, Australian National University, Canberra, ACT 2601, Australia.
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16
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Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
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17
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Esch P, Fischer M, Heiles S, Schäfer M. Olefinic reagents tested for peptide derivatization with switchable properties: Stable upon collision induced dissociation and cleavable by in-source Paternò-Büchi reactions. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:976-986. [PMID: 31729095 DOI: 10.1002/jms.4474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
This contribution is part of our ongoing efforts to develop innovative cross-linking (XL) reagents and protocols for facilitated peptide mixture analysis and efficient assignment of cross-linked peptide products. In this report, we combine in-source Paternò-Büchi (PB) photo-chemistry with a tandem mass spectrometry approach to selectively address the fragmentation of a tailor-made cross-linking reagent. The PB photochemistry, so far exclusively used for the identification of unsaturation sites in lipids and in lipidomics, is now introduced to the field of chemical cross-linking. Based on trans-3-hexenedioic acid, an olefinic homo bifunctional amine reactive XL reagent was designed and synthesized for this proof-of-principle study. Condensation products of the olefinic reagent with a set of exemplary peptides are used to test the feasibility of the concept. Benzophenone is photochemically reacted in the nano-electrospray ion source and forms oxetane PB reaction products. Subsequent CID-MS triggered retro-PB reaction of the respective isobaric oxetane molecular ions and delivers reliably and predictably two sets of characteristic fragment ions of the cross-linker. Based on these signature ion sets, a straightforward identification of covalently interconnected peptides in complex digests is proposed. Furthermore, CID-MSn experiments of the retro-PB reaction products deliver peptide backbone characteristic fragment ions. Additionally, the olefinic XL reagents exhibit a pronounced robustness upon CID-activation, without previous UV-excitation. These experiments document that a complete backbone fragmentation is possible, while the linker-moiety remains intact. This feature renders the new olefinic linkers switchable between a stable, noncleavable cross-linking mode and an in-source PB cleavable mode.
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Affiliation(s)
- Patrick Esch
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich Buff Ring 17, D-35392 Giessen, Germany
| | - Moritz Fischer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstraße 4, D-50939, Cologne, Germany
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich Buff Ring 17, D-35392 Giessen, Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstraße 4, D-50939, Cologne, Germany
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18
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Gotte G, Menegazzi M. Biological Activities of Secretory RNases: Focus on Their Oligomerization to Design Antitumor Drugs. Front Immunol 2019; 10:2626. [PMID: 31849926 PMCID: PMC6901985 DOI: 10.3389/fimmu.2019.02626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ribonucleases (RNases) are a large number of enzymes gathered into different bacterial or eukaryotic superfamilies. Bovine pancreatic RNase A, bovine seminal BS-RNase, human pancreatic RNase 1, angiogenin (RNase 5), and amphibian onconase belong to the pancreatic type superfamily, while binase and barnase are in the bacterial RNase N1/T1 family. In physiological conditions, most RNases secreted in the extracellular space counteract the undesired effects of extracellular RNAs and become protective against infections. Instead, if they enter the cell, RNases can digest intracellular RNAs, becoming cytotoxic and having advantageous effects against malignant cells. Their biological activities have been investigated either in vitro, toward a number of different cancer cell lines, or in some cases in vivo to test their potential therapeutic use. However, immunogenicity or other undesired effects have sometimes been associated with their action. Nevertheless, the use of RNases in therapy remains an appealing strategy against some still incurable tumors, such as mesothelioma, melanoma, or pancreatic cancer. The RNase inhibitor (RI) present inside almost all cells is the most efficacious sentry to counteract the ribonucleolytic action against intracellular RNAs because it forms a tight, irreversible and enzymatically inactive complex with many monomeric RNases. Therefore, dimerization or multimerization could represent a useful strategy for RNases to exert a remarkable cytotoxic activity by evading the interaction with RI by steric hindrance. Indeed, the majority of the mentioned RNases can hetero-dimerize with antibody derivatives, or even homo-dimerize or multimerize, spontaneously or artificially. This can occur through weak interactions or upon introducing covalent bonds. Immuno-RNases, in particular, are fusion proteins representing promising drugs by combining high target specificity with easy delivery in tumors. The results concerning the biological features of many RNases reported in the literature are described and discussed in this review. Furthermore, the activities displayed by some RNases forming oligomeric complexes, the mechanisms driving toward these supramolecular structures, and the biological rebounds connected are analyzed. These aspects are offered with the perspective to suggest possible efficacious therapeutic applications for RNases oligomeric derivatives that could contemporarily lack, or strongly reduce, immunogenicity and other undesired side-effects.
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Affiliation(s)
- Giovanni Gotte
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Marta Menegazzi
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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19
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Steigenberger B, Pieters RJ, Heck AJR, Scheltema RA. PhoX: An IMAC-Enrichable Cross-Linking Reagent. ACS CENTRAL SCIENCE 2019; 5:1514-1522. [PMID: 31572778 PMCID: PMC6764163 DOI: 10.1021/acscentsci.9b00416] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Indexed: 05/02/2023]
Abstract
Chemical cross-linking mass spectrometry is rapidly emerging as a prominent technique to study protein structures. Structural information is obtained by covalently connecting peptides in close proximity by small reagents and identifying the resulting peptide pairs by mass spectrometry. However, substoichiometric reaction efficiencies render routine detection of cross-linked peptides problematic. Here, we present a new trifunctional cross-linking reagent, termed PhoX, which is decorated with a stable phosphonic acid handle. This makes the cross-linked peptides amenable to the well-established immobilized metal affinity chromatography (IMAC) enrichment. The handle allows for 300× enrichment efficiency and 97% specificity. We exemplify the approach on various model proteins and protein complexes, e.g., resulting in a structural model of the LRP1/RAP complex. Almost completely removing linear peptides allows PhoX, although noncleavable, to be applied to complex lysates. Focusing the database search to the 1400 most abundant proteins, we were able to identify 1156 cross-links in a single 3 h measurement.
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Affiliation(s)
- Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Department of Chemical Biology & Drug Discovery,
Utrecht Institute for Pharmaceutical Sciences, Utrecht
University, P.O. Box 80082, 3508 TB Utrecht, The
Netherlands
| | - Roland J. Pieters
- Department of Chemical Biology & Drug Discovery,
Utrecht Institute for Pharmaceutical Sciences, Utrecht
University, P.O. Box 80082, 3508 TB Utrecht, The
Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Phone: +31 30 253 6797. Fax: +31 30
253 69 18. E-mail:
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Phone: +31 30 253 45 64. Fax: +31 30
253 69 18. E-mail:
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20
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Jones AX, Cao Y, Tang YL, Wang JH, Ding YH, Tan H, Chen ZL, Fang RQ, Yin J, Chen RC, Zhu X, She Y, Huang N, Shao F, Ye K, Sun RX, He SM, Lei X, Dong MQ. Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers. Nat Commun 2019; 10:3911. [PMID: 31477730 PMCID: PMC6718413 DOI: 10.1038/s41467-019-11917-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) is widely used to study protein-protein interactions (PPI), protein structures, and even protein dynamics. However, structural information provided by CXMS is still limited, partly because most CXMS experiments use lysine-lysine (K-K) cross-linkers. Although superb in selectivity and reactivity, they are ineffective for lysine deficient regions. Herein, we develop aromatic glyoxal cross-linkers (ArGOs) for arginine-arginine (R-R) cross-linking and the lysine-arginine (K-R) cross-linker KArGO. The R-R or K-R cross-links generated by ArGO or KArGO fit well with protein crystal structures and provide information not attainable by K-K cross-links. KArGO, in particular, is highly valuable for CXMS, with robust performance on a variety of samples including a kinase and two multi-protein complexes. In the case of the CNGP complex, KArGO cross-links covered as much of the PPI interface as R-R and K-K cross-links combined and improved the accuracy of Rosetta docking substantially. Cross-linking mass spectrometry can provide insights into protein structures and interactions but its scope depends on the reactivity of the cross-linker. Here, the authors develop Arg-Arg and Lys-Arg cross-linkers, which provide structural information elusive to the widely used Lys-Lys cross-linkers.
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Affiliation(s)
- Alexander X Jones
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Yong Cao
- School of Life Sciences, Peking University, 100871, Beijing, China.,National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Yu-Liang Tang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Jian-Hua Wang
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Yue-He Ding
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Hui Tan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Zhen-Lin Chen
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Run-Qian Fang
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jili Yin
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Rong-Chang Chen
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xing Zhu
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yang She
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Niu Huang
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Feng Shao
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Keqiong Ye
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Rui-Xiang Sun
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China
| | - Si-Min He
- Key Lab of Intelligent Information Processing, Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, 100049, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
| | - Meng-Qiu Dong
- National Institute of Biological Sciences (NIBS), 102206, Beijing, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206, Beijing, China.
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21
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Keller A, Chavez JD, Felt KC, Bruce JE. Prediction of an Upper Limit for the Fraction of Interprotein Cross-Links in Large-Scale In Vivo Cross-Linking Studies. J Proteome Res 2019; 18:3077-3085. [PMID: 31267744 DOI: 10.1021/acs.jproteome.9b00189] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical cross-linking and mass spectrometry is of growing use for establishment of distance constraints on protein conformations and interactions. Whereas intraprotein cross-links can arise from proteins in isolation, interprotein cross-links reflect proximity of two interacting proteins in the sample. Prediction of expected ratios of the number of interprotein to intraprotein cross-links is hindered by lacking comprehensive knowledge on the interactome network and global occupancy levels for all interacting complex subunits. Here we determine the theoretical number of possible inter- and intraprotein cross-links in available PDB structures of proteins bound in complexes to predict a maximum expected fraction of interprotein cross-links in large scale in vivo cross-linking studies. We show how the maximum fraction can guide interpretation of reported interprotein fractions with respect to the extent of sample protein binding, comparing whole cell and lysate cross-linked samples as an example. We also demonstrate how an observation of interprotein cross-link fractions greater than the maximum value can result from the presence of false positive cross-links which are predominantly interprotein, their number estimable from the observed surplus fraction of interprotein cross-links.
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Affiliation(s)
- Andrew Keller
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 United States
| | - Juan D Chavez
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 United States
| | - Kevin C Felt
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 United States
| | - James E Bruce
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 United States
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22
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Cline EN, Das A, Bicca MA, Mohammad SN, Schachner LF, Kamel JM, DiNunno N, Weng A, Paschall JD, Bu RL, Khan FM, Rollins MG, Ives AN, Shekhawat G, Nunes-Tavares N, de Mello FG, Compton PD, Kelleher NL, Klein WL. A novel crosslinking protocol stabilizes amyloid β oligomers capable of inducing Alzheimer's-associated pathologies. J Neurochem 2019; 148:822-836. [PMID: 30565253 DOI: 10.1111/jnc.14647] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 12/09/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022]
Abstract
Amyloid β oligomers (AβOs) accumulate early in Alzheimer's disease (AD) and experimentally cause memory dysfunction and the major pathologies associated with AD, for example, tau abnormalities, synapse loss, oxidative damage, and cognitive dysfunction. In order to develop the most effective AβO-targeting diagnostics and therapeutics, the AβO structures contributing to AD-associated toxicity must be elucidated. Here, we investigate the structural properties and pathogenic relevance of AβOs stabilized by the bifunctional crosslinker 1,5-difluoro-2,4-dinitrobenzene (DFDNB). We find that DFDNB stabilizes synthetic Aβ in a soluble oligomeric conformation. With DFDNB, solutions of Aβ that would otherwise convert to large aggregates instead yield solutions of stable AβOs, predominantly in the 50-300 kDa range, that are maintained for at least 12 days at 37°C. Structures were determined by biochemical and native top-down mass spectrometry analyses. Assayed in neuronal cultures and i.c.v.-injected mice, the DFDNB-stabilized AβOs were found to induce tau hyperphosphorylation, inhibit choline acetyltransferase, and provoke neuroinflammation. Most interestingly, DFDNB crosslinking was found to stabilize an AβO conformation particularly potent in inducing memory dysfunction in mice. Taken together, these data support the utility of DFDNB crosslinking as a tool for stabilizing pathogenic AβOs in structure-function studies.
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Affiliation(s)
- Erika N Cline
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Arighno Das
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | | | - Saad N Mohammad
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Luis F Schachner
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Josette M Kamel
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Nadia DiNunno
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Anthea Weng
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Jacob D Paschall
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Riana Lo Bu
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Faraz M Khan
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Madeline G Rollins
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
| | - Ashley N Ives
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Gajendra Shekhawat
- Department of Material Science and Engineering, Northwestern University, Evanston, Illinois, USA
| | - Nilson Nunes-Tavares
- Instituo de Biofisica Carlo Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando G de Mello
- Instituo de Biofisica Carlo Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - William L Klein
- Department of Neurobiology, Northwestern University, Evanston, Illinois, USA
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Nguyen TK, Negishi H, Abe S, Ueno T. Construction of supramolecular nanotubes from protein crystals. Chem Sci 2019; 10:1046-1051. [PMID: 30774900 PMCID: PMC6346403 DOI: 10.1039/c8sc04167a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/26/2018] [Indexed: 01/26/2023] Open
Abstract
Investigations involving the design of protein assemblies for the development of biomaterials are receiving significant attention. In nature, proteins can be driven into assemblies frequently by various non-covalent interactions. Assembly of proteins into supramolecules can be conducted under limited conditions in solution. These factors force the assembly process into an equilibrium state with low stability. Here, we report a new method for preparing assemblies using protein crystals as non-equilibrium molecular scaffolds. Protein crystals provide an ideal environment with a highly ordered packing of subunits in which the supramolecular assembled structures are formed in the crystalline matrix. Based on this feature, we demonstrate the self-assembly of supramolecular nanotubes constructed from protein crystals triggered by co-oxidation with cross-linkers. The assembly of tubes is driven by the formation of disulfide bonds to retain the intermolecular interactions within each assembly in the crystalline matrix after dissolution of the crystals.
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Affiliation(s)
- Tien Khanh Nguyen
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Hashiru Negishi
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Satoshi Abe
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
| | - Takafumi Ueno
- School of Life Science and Technology , Tokyo Institute of Technology , Nagatsuta-cho , Midori-ku , Yokohama 226-8501 , Japan .
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24
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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25
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Micheel M, Ahner J, Frey M, Neumann C, Hager MD, Dietzek B. Photophysics of a Bis-Furan-Functionalized 4,7-bis
(Phenylethynyl)-2,1,3-benzothiadiazole: A Building Block for Dynamic Polymers. CHEMPHOTOCHEM 2018. [DOI: 10.1002/cptc.201800149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mathias Micheel
- Institute of Physical Chemistry; Friedrich Schiller University Jena; Helmholtzweg 4 07743 Jena Germany
- Leibniz Institute of Photonic Technology (IPHT) e.V.; Albert-Einstein-Straße 9 07745 Jena Germany
| | - Johannes Ahner
- Jena Center for Soft Matter (JCSM); Friedrich Schiller University Jena; Philosophenweg 7 07743 Jena Germany
- Laboratory of Organic and Macromolecular Chemistry (IOMC); Friedrich Schiller University Jena; Humboldtstraße 10 07743 Jena Germany
| | - Martha Frey
- Institute of Physical Chemistry; Friedrich Schiller University Jena; Helmholtzweg 4 07743 Jena Germany
| | - Clara Neumann
- Institute of Physical Chemistry; Friedrich Schiller University Jena; Helmholtzweg 4 07743 Jena Germany
| | - Martin D. Hager
- Jena Center for Soft Matter (JCSM); Friedrich Schiller University Jena; Philosophenweg 7 07743 Jena Germany
- Laboratory of Organic and Macromolecular Chemistry (IOMC); Friedrich Schiller University Jena; Humboldtstraße 10 07743 Jena Germany
| | - Benjamin Dietzek
- Institute of Physical Chemistry; Friedrich Schiller University Jena; Helmholtzweg 4 07743 Jena Germany
- Leibniz Institute of Photonic Technology (IPHT) e.V.; Albert-Einstein-Straße 9 07745 Jena Germany
- Jena Center for Soft Matter (JCSM); Friedrich Schiller University Jena; Philosophenweg 7 07743 Jena Germany
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26
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Ramezanpour M, Lee J, Taneva SG, Tieleman DP, Cornell RB. An auto-inhibitory helix in CTP:phosphocholine cytidylyltransferase hijacks the catalytic residue and constrains a pliable, domain-bridging helix pair. J Biol Chem 2018. [PMID: 29519816 DOI: 10.1074/jbc.ra118.002053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The activity of CTP:phosphocholine cytidylyltransferase (CCT), a key enzyme in phosphatidylcholine synthesis, is regulated by reversible interactions of a lipid-inducible amphipathic helix (domain M) with membrane phospholipids. When dissociated from membranes, a portion of the M domain functions as an auto-inhibitory (AI) element to suppress catalysis. The AI helix from each subunit binds to a pair of α helices (αE) that extend from the base of the catalytic dimer to create a four-helix bundle. The bound AI helices make intimate contact with loop L2, housing a key catalytic residue, Lys122 The impacts of the AI helix on active-site dynamics and positioning of Lys122 are unknown. Extensive MD simulations with and without the AI helix revealed that backbone carbonyl oxygens at the point of contact between the AI helix and loop L2 can entrap the Lys122 side chain, effectively competing with the substrate, CTP. In silico, removal of the AI helices dramatically increased αE dynamics at a predicted break in the middle of these helices, enabling them to splay apart and forge new contacts with loop L2. In vitro cross-linking confirmed the reorganization of the αE element upon membrane binding of the AI helix. Moreover, when αE bending was prevented by disulfide engineering, CCT activation by membrane binding was thwarted. These findings suggest a novel two-part auto-inhibitory mechanism for CCT involving capture of Lys122 and restraint of the pliable αE helices. We propose that membrane binding enables bending of the αE helices, bringing the active site closer to the membrane surface.
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Affiliation(s)
- Mohsen Ramezanpour
- From the Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 and
| | - Jaeyong Lee
- the Departments of Molecular Biology and Biochemistry and
| | | | - D Peter Tieleman
- From the Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 and
| | - Rosemary B Cornell
- the Departments of Molecular Biology and Biochemistry and .,Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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27
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Goyal N, Rossi MJ, Mazina OM, Chi Y, Moritz RL, Clurman BE, Mazin AV. RAD54 N-terminal domain is a DNA sensor that couples ATP hydrolysis with branch migration of Holliday junctions. Nat Commun 2018; 9:34. [PMID: 29295984 PMCID: PMC5750232 DOI: 10.1038/s41467-017-02497-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/28/2017] [Indexed: 11/08/2022] Open
Abstract
In eukaryotes, RAD54 catalyzes branch migration (BM) of Holliday junctions, a basic process during DNA repair, replication, and recombination. RAD54 also stimulates RAD51 recombinase and has other activities. Here, we investigate the structural determinants for different RAD54 activities. We find that the RAD54 N-terminal domain (NTD) is responsible for initiation of BM through two coupled, but distinct steps; specific binding to Holliday junctions and RAD54 oligomerization. Furthermore, we find that the RAD54 oligomeric state can be controlled by NTD phosphorylation at S49, a CDK2 consensus site, which inhibits RAD54 oligomerization and, consequently, BM. Importantly, the effect of phosphorylation on RAD54 oligomerization is specific for BM, as it does not affect stimulation of RAD51 recombinase by RAD54. Thus, the transition of the oligomeric states provides an important control of the biological functions of RAD54 and, likely, other multifunctional proteins.
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Affiliation(s)
- Nadish Goyal
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Matthew J Rossi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Olga M Mazina
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Yong Chi
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Bruce E Clurman
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Alexander V Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
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28
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Hage C, Falvo F, Schäfer M, Sinz A. Novel Concepts of MS-Cleavable Cross-linkers for Improved Peptide Structure Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2022-2038. [PMID: 28653243 DOI: 10.1007/s13361-017-1712-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/03/2017] [Accepted: 05/07/2017] [Indexed: 06/07/2023]
Abstract
The chemical cross-linking/mass spectrometry (MS) approach is gaining increasing importance as an alternative method for studying protein conformation and for deciphering protein interaction networks. This study is part of our ongoing efforts to develop innovative cross-linking principles for a facile and efficient assignment of cross-linked products. We evaluate two homobifunctional, amine-reactive, and MS-cleavable cross-linkers regarding their potential for automated analysis of cross-linked products. We introduce the bromine phenylurea (BrPU) linker that possesses a unique structure yielding a distinctive fragmentation pattern on collisional activation. Moreover, BrPU delivers the characteristic bromine isotope pattern and mass defect for all cross-linker-decorated fragments. We compare the fragmentation behavior of the BrPU linker with that of our previously described MS-cleavable TEMPO-Bz linker (which consists of a 2,2,6,6-tetramethylpiperidine-1-oxy moiety connected to a benzyl group) that was developed to perform free-radical-initiated peptide sequencing. Comparative collisional activation experiments (collision-induced dissociation and higher-energy collision-induced dissociation) with both cross-linkers were conducted in negative electrospray ionization mode with an Orbitrap Fusion mass spectrometer using five model peptides. As hypothesized in a previous study, the presence of a cross-linked N-terminal aspartic acid residue seems to be the prerequisite for the loss of an intact peptide from the cross-linked products. As the BrPU linker combines a characteristic mass shift with an isotope signature, it presents a more favorable combination for automated assignment of cross-linked products compared with the TEMPO-Bz linker. ᅟ.
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Affiliation(s)
- Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Francesco Falvo
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
- Eurofins Umwelt West GmbH, Vorgebirgsstr. 20, 50389, Wesseling, Germany
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany.
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29
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Iacobucci C, Hage C, Schäfer M, Sinz A. A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2039-2053. [PMID: 28717933 DOI: 10.1007/s13361-017-1744-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS3 experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies. Graphical Abstract ᅟ.
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Affiliation(s)
- Claudio Iacobucci
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany.
| | - Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstr. 4, D-50939, Kӧln, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany.
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30
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31
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Iacobucci C, Sinz A. To Be or Not to Be? Five Guidelines to Avoid Misassignments in Cross-Linking/Mass Spectrometry. Anal Chem 2017; 89:7832-7835. [DOI: 10.1021/acs.analchem.7b02316] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Claudio Iacobucci
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), Germany
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32
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Friedhoff P, Manelyte L, Giron-Monzon L, Winkler I, Groothuizen FS, Sixma TK. Use of Single-Cysteine Variants for Trapping Transient States in DNA Mismatch Repair. Methods Enzymol 2017; 592:77-101. [PMID: 28668131 DOI: 10.1016/bs.mie.2017.03.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
DNA mismatch repair (MMR) is necessary to prevent incorporation of polymerase errors into the newly synthesized DNA strand, as they would be mutagenic. In humans, errors in MMR cause a predisposition to cancer, called Lynch syndrome. The MMR process is performed by a set of ATPases that transmit, validate, and couple information to identify which DNA strand requires repair. To understand the individual steps in the repair process, it is useful to be able to study these large molecular machines structurally and functionally. However, the steps and states are highly transient; therefore, the methods to capture and enrich them are essential. Here, we describe how single-cysteine variants can be used for specific cross-linking and labeling approaches that allow trapping of relevant transient states. Analysis of these defined states in functional and structural studies is instrumental to elucidate the molecular mechanism of this important DNA MMR process.
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Affiliation(s)
- Peter Friedhoff
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany.
| | - Laura Manelyte
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | - Luis Giron-Monzon
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | - Ines Winkler
- Institute for Biochemistry, Justus-Liebig-University, Giessen, Germany
| | | | - Titia K Sixma
- Netherlands Cancer Institute, Amsterdam, The Netherlands.
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33
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Steinhagen M, Gräbner A, Meyer J, Horst AE, Drews A, Holtmann D, Ansorge-Schumacher MB. Bridging the bridge—Stabilization of CalB against H2O2 and its application in epoxidation reactions. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2017.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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34
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Silván U, Hyotyla J, Mannherz HG, Ringler P, Müller SA, Aebi U, Maier T, Schoenenberger CA. Contributions of the lower dimer to supramolecular actin patterning revealed by TIRF microscopy. J Struct Biol 2016; 195:159-166. [PMID: 27189866 DOI: 10.1016/j.jsb.2016.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/13/2016] [Accepted: 05/14/2016] [Indexed: 11/25/2022]
Abstract
Two distinct dimers are formed during the initial steps of actin polymerization. The first one, referred to as the 'lower dimer' (LD) was discovered many years ago by means of chemical crosslinking. Owing to its transient nature, a biological relevance had long been precluded when, using LD-specific antibodies, we detected LD-like contacts in actin assemblies that are associated with the endolysosomal compartment in a number of different cell lines. Moreover, immunofluorescence showed the presence of LD-related structures at the cell periphery of migrating fibroblasts, in the nucleus, and in association with the centrosome of interphase cells. Here, we explore contributions of the LD to the assembly of supramolecular actin structures in real time by total internal reflection fluorescence (TIRF) microscopy. Our data shows that while LD on its own cannot polymerize under filament forming conditions, it is able to incorporate into growing F-actin filaments. This incorporation of LD triggers the formation of X-shaped filament assemblies with barbed ends that are pointing in the same direction in the majority of cases. Similarly, an increased frequency of junction sites was observed when filaments were assembled in the presence of oxidized actin. This data suggests that a disulfide bridge between Cys374 residues might stabilize LD-contacts. Based on our findings, we propose two possible models for the molecular mechanism underlying the supramolecular actin patterning in LD-related structures.
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Affiliation(s)
- Unai Silván
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Janne Hyotyla
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Hans-Georg Mannherz
- Department of Anatomy and Molecular Embryology, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Philippe Ringler
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Shirley A Müller
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Ueli Aebi
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Timm Maier
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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35
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Davydov DR. Molecular organization of the microsomal oxidative system: a new connotation for an old term. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2016. [DOI: 10.1134/s1990750816010042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Decker CG, Wang Y, Paluck SJ, Shen L, Loo JA, Levine AJ, Miller LS, Maynard HD. Fibroblast growth factor 2 dimer with superagonist in vitro activity improves granulation tissue formation during wound healing. Biomaterials 2016; 81:157-168. [PMID: 26731578 PMCID: PMC4715972 DOI: 10.1016/j.biomaterials.2015.12.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/04/2015] [Accepted: 12/11/2015] [Indexed: 01/13/2023]
Abstract
Site-specific chemical dimerization of fibroblast growth factor 2 (FGF2) with the optimal linker length resulted in a FGF2 homodimer with improved granulation tissue formation and blood vessel formation at exceptionally low concentrations. Homodimers of FGF2 were synthesized through site-specific linkages to both ends of different molecular weight poly(ethylene glycols) (PEGs). The optimal linker length was determined by screening dimer-induced metabolic activity of human dermal fibroblasts and found to be that closest to the inter-cysteine distance, 70 Å, corresponding to 2 kDa PEG. A straightforward analysis of the kinetics of second ligand binding as a function of tether length showed that, as the polymerization index (the number of monomer repeat units in the polymer, N) of the tether decreases, the mean time for second ligand capture decreases as ∼N(3/2), leading to an enhancement of the number of doubly bound ligands in steady-state for a given (tethered) ligand concentration. FGF2-PEG2k-FGF2 induced greater fibroblast metabolic activity than FGF2 alone, all other dimers, and all monoconjugates, at each concentration tested, with the greatest difference observed at low (0.1 ng/mL) concentration. FGF2-PEG2k-FGF2 further exhibited superior activity compared to FGF2 for both metabolic activity and migration in human umbilical vein endothelial cells, as well as improved angiogenesis in a coculture model in vitro. Efficacy in an in vivo wound healing model was assessed in diabetic mice. FGF2-PEG2k-FGF2 increased granulation tissue and blood vessel density in the wound bed compared to FGF2. The results suggest that this rationally designed construct may be useful for improving the fibroblast matrix formation and angiogenesis in chronic wound healing.
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Affiliation(s)
- Caitlin G Decker
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive South, Los Angeles, CA 90095-1569, United States
| | - Yu Wang
- Department of Dermatology, Johns Hopkins University School of Medicine, 1550 Orleans St., Baltimore, MD 21231, United States
| | - Samantha J Paluck
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive South, Los Angeles, CA 90095-1569, United States
| | - Lu Shen
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive South, Los Angeles, CA 90095-1569, United States
| | - Joseph A Loo
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive South, Los Angeles, CA 90095-1569, United States; Department of Biological Chemistry, David Geffen School of Medicine, and UCLA/DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, United States
| | - Alex J Levine
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive South, Los Angeles, CA 90095-1569, United States; Department of Physics and Astronomy, University of California, Los Angeles, CA 90095-1569, United States; Department of Biomathematics, University of California, Los Angeles, CA 90095-1569, United States
| | - Lloyd S Miller
- Department of Dermatology, Johns Hopkins University School of Medicine, 1550 Orleans St., Baltimore, MD 21231, United States
| | - Heather D Maynard
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive South, Los Angeles, CA 90095-1569, United States.
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Funke JJ, Dietz H. Placing molecules with Bohr radius resolution using DNA origami. NATURE NANOTECHNOLOGY 2016; 11:47-52. [PMID: 26479026 DOI: 10.1038/nnano.2015.240] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/09/2015] [Indexed: 05/17/2023]
Abstract
Molecular self-assembly with nucleic acids can be used to fabricate discrete objects with defined sizes and arbitrary shapes. It relies on building blocks that are commensurate to those of biological macromolecular machines and should therefore be capable of delivering the atomic-scale placement accuracy known today only from natural and designed proteins. However, research in the field has predominantly focused on producing increasingly large and complex, but more coarsely defined, objects and placing them in an orderly manner on solid substrates. So far, few objects afford a design accuracy better than 5 nm, and the subnanometre scale has been reached only within the unit cells of designed DNA crystals. Here, we report a molecular positioning device made from a hinged DNA origami object in which the angle between the two structural units can be controlled with adjuster helices. To test the positioning capabilities of the device, we used photophysical and crosslinking assays that report the coordinate of interest directly with atomic resolution. Using this combination of placement and analysis, we rationally adjusted the average distance between fluorescent molecules and reactive groups from 1.5 to 9 nm in 123 discrete displacement steps. The smallest displacement step possible was 0.04 nm, which is slightly less than the Bohr radius. The fluctuation amplitudes in the distance coordinate were also small (±0.5 nm), and within a factor of two to three of the amplitudes found in protein structures.
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Affiliation(s)
- Jonas J Funke
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748 Garching near Munich, Germany
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748 Garching near Munich, Germany
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38
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Protein Structural Analysis via Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:397-431. [PMID: 27975228 DOI: 10.1007/978-3-319-41448-5_19] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: (1) hydrogen/deuterium exchange (HDX), (2) limited proteolysis, and (3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography.
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Robaszkiewicz K, Ostrowska Z, Marchlewicz K, Moraczewska J. Tropomyosin isoforms differentially modulate the regulation of actin filament polymerization and depolymerization by cofilins. FEBS J 2015; 283:723-37. [DOI: 10.1111/febs.13626] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/30/2015] [Accepted: 12/10/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Katarzyna Robaszkiewicz
- Department of Biochemistry and Cell Biology; Faculty of Natural Sciences; Kazimierz Wielki University in Bydgoszcz; Poland
| | - Zofia Ostrowska
- Department of Biochemistry and Cell Biology; Faculty of Natural Sciences; Kazimierz Wielki University in Bydgoszcz; Poland
| | - Kamila Marchlewicz
- Department of Biochemistry and Cell Biology; Faculty of Natural Sciences; Kazimierz Wielki University in Bydgoszcz; Poland
| | - Joanna Moraczewska
- Department of Biochemistry and Cell Biology; Faculty of Natural Sciences; Kazimierz Wielki University in Bydgoszcz; Poland
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Davydov DR. [Molecular organization of the microsomal oxidative system: a new connotation for an old term]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:176-87. [PMID: 25978385 DOI: 10.18097/pbmc20156102176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The central role that cytochromes P450 play in the metabolism of drugs and other xenobiotics makes these enzymes a major subject for studies of drug disposition, adverse drug effects and drug-drug interactions. Although there has been tremendous success in delineating P450 mechanisms, the concept of the drug-metabolizing ensemble as a functionally integrated system remains undeveloped. However, eukaryotic cells typically possess a multitude of different P450 enzymes that are co-localized in the membrane of endoplasmic reticulum (ER) and interact with each other with the formation of dynamic heteromeric complexes (mixed oligomers). Appreciation of the importance of developing an integral, systems approach to the ensemble of cytochromes P450 as an integral system inspired growing interest of researchers to the molecular organization of microsomal monooxygenase, which remained in the focus of research of academician Archakov for over 40 years. Fundamental studies carried out under his guidance have an important impact on our current concepts in this area. Further exploration of the molecular organization of the system of microsomal monooxygenase as an integral multienzyme and multifunctional system will have an essential impact on our understanding of the key factors that determine the changes in human drug metabolism and other P450-related functions in development, aging, and disease, as well as under influence of drugs, food ingredients, and environmental contaminants.
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Affiliation(s)
- D R Davydov
- Institute of Biomedical Chemistry, Moscow, Russia; Department of Chemistry, Washington State University, Washington, USA
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41
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Shiota T, Imai K, Qiu J, Hewitt VL, Tan K, Shen HH, Sakiyama N, Fukasawa Y, Hayat S, Kamiya M, Elofsson A, Tomii K, Horton P, Wiedemann N, Pfanner N, Lithgow T, Endo T. Molecular architecture of the active mitochondrial protein gate. Science 2015; 349:1544-8. [DOI: 10.1126/science.aac6428] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP. Protein Neighbors and Proximity Proteomics. Mol Cell Proteomics 2015; 14:2848-56. [PMID: 26355100 PMCID: PMC4638030 DOI: 10.1074/mcp.r115.052902] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 12/31/2022] Open
Abstract
Within cells, proteins can co-assemble into functionally integrated and spatially restricted multicomponent complexes. Often, the affinities between individual proteins are relatively weak, and proteins within such clusters may interact only indirectly with many of their other protein neighbors. This makes proteomic characterization difficult using methods such as immunoprecipitation or cross-linking. Recently, several groups have described the use of enzyme-catalyzed proximity labeling reagents that covalently tag the neighbors of a targeted protein with a small molecule such as fluorescein or biotin. The modified proteins can then be isolated by standard pulldown methods and identified by mass spectrometry. Here we will describe the techniques as well as their similarities and differences. We discuss their applications both to study protein assemblies and to provide a new way for characterizing organelle proteomes. We stress the importance of proteomic quantitation and independent target validation in such experiments. Furthermore, we suggest that there are biophysical and cell-biological principles that dictate the appropriateness of enzyme-catalyzed proximity labeling methods to address particular biological questions of interest.
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Affiliation(s)
- Johanna S Rees
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW, the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Xue-Wen Li
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Sarah Perrett
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Kathryn S Lilley
- the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Antony P Jackson
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW,
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43
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Tran BQ, Goodlett DR, Goo YA. Advances in protein complex analysis by chemical cross-linking coupled with mass spectrometry (CXMS) and bioinformatics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:123-9. [PMID: 26025770 DOI: 10.1016/j.bbapap.2015.05.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/07/2015] [Accepted: 05/18/2015] [Indexed: 01/12/2023]
Abstract
For the analysis of protein-protein interactions and protein conformations, cross-linking coupled with mass spectrometry (CXMS) has become an essential tool in recent years. A variety of cross-linking reagents are used to covalently link interacting amino acids to identify protein-binding partners. The spatial proximity of cross-linked amino acid residues is used to elucidate structural models of protein complexes. The main challenges for mapping protein-protein interaction are low stoichiometry and low frequency of cross-linked peptides relative to unmodified linear peptides as well as accurate and efficient matches to corresponding peptide sequences with low false discovery rates for identifying the site of cross-link. We evaluate the current state of chemical cross-linking and mass spectrometry applications with the special emphasis on the recent development of informatics data processing and analysis tools that help complexity of interpreting CXMS data. This article is part of a Special Issue entitled:Physiological Enzymology and Protein Functions.
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Affiliation(s)
- Bao Quoc Tran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| | - David R Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
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44
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Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 390] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
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Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
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Hofmann T, Fischer AW, Meiler J, Kalkhof S. Protein structure prediction guided by crosslinking restraints--A systematic evaluation of the impact of the crosslinking spacer length. Methods 2015; 89:79-90. [PMID: 25986934 DOI: 10.1016/j.ymeth.2015.05.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/21/2015] [Accepted: 05/12/2015] [Indexed: 11/15/2022] Open
Abstract
Recent development of high-resolution mass spectrometry (MS) instruments enables chemical crosslinking (XL) to become a high-throughput method for obtaining structural information about proteins. Restraints derived from XL-MS experiments have been used successfully for structure refinement and protein-protein docking. However, one formidable question is under which circumstances XL-MS data might be sufficient to determine a protein's tertiary structure de novo? Answering this question will not only include understanding the impact of XL-MS data on sampling and scoring within a de novo protein structure prediction algorithm, it must also determine an optimal crosslinker type and length for protein structure determination. While a longer crosslinker will yield more restraints, the value of each restraint for protein structure prediction decreases as the restraint is consistent with a larger conformational space. In this study, the number of crosslinks and their discriminative power was systematically analyzed in silico on a set of 2055 non-redundant protein folds considering Lys-Lys, Lys-Asp, Lys-Glu, Cys-Cys, and Arg-Arg reactive crosslinkers between 1 and 60Å. Depending on the protein size a heuristic was developed that determines the optimal crosslinker length. Next, simulated restraints of variable length were used to de novo predict the tertiary structure of fifteen proteins using the BCL::Fold algorithm. The results demonstrate that a distinct crosslinker length exists for which information content for de novo protein structure prediction is maximized. The sampling accuracy improves on average by 1.0 Å and up to 2.2 Å in the most prominent example. XL-MS restraints enable consistently an improved selection of native-like models with an average enrichment of 2.1.
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Affiliation(s)
- Tommy Hofmann
- Department of Proteomics, Helmholtz-Centre for Environmental Research - UFZ, Leipzig D-04318, Germany
| | - Axel W Fischer
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
| | - Stefan Kalkhof
- Department of Proteomics, Helmholtz-Centre for Environmental Research - UFZ, Leipzig D-04318, Germany; Department of Bioanalytics, University of Applied Sciences and Arts of Coburg, D-96450 Coburg, Germany.
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Zheng X, Podariu M, Bi C, Hage DS. Development of enhanced capacity affinity microcolumns by using a hybrid of protein cross-linking/modification and immobilization. J Chromatogr A 2015; 1400:82-90. [PMID: 25981291 DOI: 10.1016/j.chroma.2015.04.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 11/29/2022]
Abstract
A hybrid method was examined for increasing the binding capacity and activity of protein-based affinity columns by using a combination of protein cross-linking/modification and covalent immobilization. Various applications of this approach in the study of drug-protein interactions and in use with affinity microcolumns were considered. Human serum albumin (HSA) was utilized as a model protein for this work. Bismaleimidohexane (BMH, a homobifunctional maleimide) was used to modify and/or cross-link HSA through the single free sulfhydryl group that is present on this protein. Up to a 75-113% increase in protein content was obtained when comparing affinity supports that were prepared with BMH versus reference supports that were made by using only covalent immobilization. Several drugs that are known to bind HSA (e.g., warfarin, verapamil and carbamazepine) were further found to have a significant increase in retention on HSA microcolumns that were treated with BMH (i.e., a 70-100% increase in protein-based retention). These BMH-treated HSA microcolumns were used in chiral separations and in ultrafast affinity extraction to measure free drug fractions in drug/protein mixtures, with the latter method giving association equilibrium constants that had good agreement with literature values. In addition, it was found that the reversible binding of HSA with ethacrynic acid, an agent that can combine irreversibly with the free sulfhydryl group on this protein, could be examined by using the BMH-treated HSA microcolumns. The same hybrid immobilization method could be extended to other proteins or alternative applications that may require protein-based affinity columns with enhanced binding capacities and activities.
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Affiliation(s)
- Xiwei Zheng
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Maria Podariu
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Cong Bi
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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Davydov DR, Davydova NY, Sineva EV, Halpert JR. Interactions among cytochromes P450 in microsomal membranes: oligomerization of cytochromes P450 3A4, 3A5, and 2E1 and its functional consequences. J Biol Chem 2015; 290:3850-64. [PMID: 25533469 PMCID: PMC4319048 DOI: 10.1074/jbc.m114.615443] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/02/2014] [Indexed: 12/31/2022] Open
Abstract
The body of evidence of physiologically relevant P450-P450 interactions in microsomal membranes continues to grow. Here we probe oligomerization of human CYP3A4, CYP3A5, and CYP2E1 in microsomal membranes. Using a technique based on luminescence resonance energy transfer, we demonstrate that all three proteins are subject to a concentration-dependent equilibrium between the monomeric and oligomeric states. We also observed the formation of mixed oligomers in CYP3A4/CYP3A5, CYP3A4/CYP2E1, and CYP3A5/CYP2E1 pairs and demonstrated that the association of either CYP3A4 or CYP3A5 with CYP2E1 causes activation of the latter enzyme. Earlier we hypothesized that the intersubunit interface in CYP3A4 oligomers is similar to that observed in the crystallographic dimers of some microsomal drug-metabolizing cytochromes P450 (Davydov, D. R., Davydova, N. Y., Sineva, E. V., Kufareva, I., and Halpert, J. R. (2013) Pivotal role of P450-P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone. Biochem. J. 453, 219-230). Here we report the results of intermolecular cross-linking of CYP3A4 oligomers with thiol-reactive bifunctional reagents as well as the luminescence resonance energy transfer measurements of interprobe distances in the oligomers of labeled CYP3A4 single-cysteine mutants. The results provide compelling support for the physiological relevance of the dimer-specific peripheral ligand-binding site observed in certain CYP3A4 structures. According to our interpretation, these results reveal an important general mechanism that regulates the activity and substrate specificity of the cytochrome P450 ensemble through interactions between multiple P450 species. As a result of P450-P450 cross-talk, the catalytic properties of the cytochrome P450 ensemble cannot be predicted by simple summation of the properties of the individual P450 species.
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Affiliation(s)
- Dmitri R Davydov
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093 and the V. N. Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaya Str., Moscow 119832, Russia
| | - Nadezhda Y Davydova
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093 and
| | - Elena V Sineva
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093 and
| | - James R Halpert
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093 and
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An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin. Proc Natl Acad Sci U S A 2015; 112:2204-9. [PMID: 25646411 DOI: 10.1073/pnas.1423754112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular electrostatic interaction with K336 of the adjacent monomer on completion of the prepore complex. The signal generated throughout the prepore complex by this interaction irrevocably commits it to the formation of the membrane-inserted giant β-barrel pore. This interaction supplies the free energy to overcome the energy barrier (determined here to be ∼ 19 kcal/mol) to the prepore-to-pore transition by the coordinated disruption of a critical interface within each monomer. These studies provide the first insight to our knowledge into the molecular mechanism that controls the prepore-to-pore transition for a βPFT.
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Functional consequences of the oligomeric assembly of proteorhodopsin. J Mol Biol 2015; 427:1278-1290. [PMID: 25597999 PMCID: PMC4374980 DOI: 10.1016/j.jmb.2015.01.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/21/2014] [Accepted: 01/08/2015] [Indexed: 11/24/2022]
Abstract
The plasma membrane is the crucial interface between the cell and its exterior, packed with embedded proteins experiencing simultaneous protein-protein and protein-membrane interactions. A prominent example of cell membrane complexity is the assembly of transmembrane proteins into oligomeric structures, with potential functional consequences that are not well understood. From the study of proteorhodopsin (PR), a prototypical seven-transmembrane light-driven bacterial proton pump, we find evidence that the inter-protein interaction modulated by self-association yields functional changes observable from the protein interior. We also demonstrate that the oligomer is likely a physiologically relevant form of PR, as crosslinking of recombinantly expressed PR reveals an oligomeric population within the Escherichia coli membrane (putatively hexameric). Upon chromatographic isolation of oligomeric and monomeric PR in surfactant micelles, the oligomer exhibits distinctly different optical absorption properties from monomeric PR, as reflected in a prominent decrease in the pKa of the primary proton acceptor residue (D97) and slowing of the light-driven conformational change. These functional effects are predominantly determined by specific PR-PR contacts over nonspecific surfactant interactions. Interestingly, varying the surfactant type alters the population of oligomeric states and the proximity of proteins within an oligomer, as determined by sparse electron paramagnetic resonance distance measurements. Nevertheless, the dynamic surfactant environment retains the key function-tuning property exerted by oligomeric contacts. A potentially general design principle for transmembrane protein function emerges from this work, one that hinges on specific oligomeric contacts that can be modulated by protein expression or membrane composition.
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Hendricks NG, Julian RR. Characterizing gaseous peptide structure with action-EET and simulated annealing. Phys Chem Chem Phys 2015; 17:25822-7. [DOI: 10.1039/c5cp01617g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Distance-sensitive energy transfer and molecular dynamics are used to generate experimentally corroborated structures for peptides in the gas phase.
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Affiliation(s)
| | - Ryan R. Julian
- Department of Chemistry
- University of California
- Riverside
- USA
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