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Zheng T, Gao H, Liu Y, Sun S, Guan W, Wu L, Yang Y, Li G. Development of ovalbumin implants with different spatial configurations for treatment of peripheral nerve injury. Bioact Mater 2024; 35:401-415. [PMID: 38384987 PMCID: PMC10879707 DOI: 10.1016/j.bioactmat.2024.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/23/2024] Open
Abstract
Peripheral nerve injury (PNI) seriously affects the health and life of patients, and is an urgent clinical problem that needs to be resolved. Nerve implants prepared from various biomaterials have played a positive role in PNI, but the effect should be further improved and thus new biomaterials is urgently needed. Ovalbumin (OVA) contains a variety of bioactive components, low immunogenicity, tolerance, antimicrobial activity, non-toxicity and biodegradability, and has the ability to promote wound healing, cell growth and antimicrobial properties. However, there are few studies on the application of OVA in neural tissue engineering. In this study, OVA implants with different spatial structures (membrane, fiber, and lyophilized scaffolds) were constructed by casting, electrospinning, and freeze-drying methods, respectively. The results showed that the OVA implants had excellent physicochemical properties and were biocompatible without significant toxicity, and can promote vascularization, show good histocompatibility, without excessive inflammatory response and immunogenicity. The in vitro results showed that OVA implants could promote the proliferation and migration of Schwann cells, while the in vivo results confirmed that OVA implants (the E5/70% and 20 kV 20 μL/min groups) could effectively regulate the growth of blood vessels, reduce the inflammatory response and promote the repair of subcutaneous nerve injury. Further on, the high-throughput sequencing results showed that the OVA implants up-regulated differential expression of genes related to biological processes such as tumor necrosis factor-α (TNF-α), phosphatidylinositide 3-kinases/protein kinase B (PI3K-Akt) signaling pathway, axon guidance, cellular adhesion junctions, and nerve regeneration in Schwann cells. The present study is expected to provide new design concepts and theoretical accumulation for the development of a new generation of nerve regeneration implantable biomaterials.
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Affiliation(s)
- Tiantian Zheng
- Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610065, China
| | - Hongxia Gao
- Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Yaqiong Liu
- Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Shaolan Sun
- Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Wenchao Guan
- Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Linliang Wu
- The People's Hospital of Rugao, Affiliated Hospital of Nantong University, 226599, Nantong, China
| | - Yumin Yang
- Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Guicai Li
- Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
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2
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Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens RC, Sali A, Sun L, Shui W. Conformational Dynamics of the Activated GLP-1 Receptor-G s Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling. ACS CENTRAL SCIENCE 2023; 9:992-1007. [PMID: 37252352 PMCID: PMC10214531 DOI: 10.1021/acscentsci.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Indexed: 05/31/2023]
Abstract
Despite advances in characterizing the structures and functions of G protein-coupled receptors (GPCRs), our understanding of GPCR activation and signaling is still limited by the lack of information on conformational dynamics. It is particularly challenging to study the dynamics of GPCR complexes with their signaling partners because of their transient nature and low stability. Here, by combining cross-linking mass spectrometry (CLMS) with integrative structure modeling, we map the conformational ensemble of an activated GPCR-G protein complex at near-atomic resolution. The integrative structures describe heterogeneous conformations for a high number of potential alternative active states of the GLP-1 receptor-Gs complex. These structures show marked differences from the previously determined cryo-EM structure, especially at the receptor-Gs interface and in the interior of the Gs heterotrimer. Alanine-scanning mutagenesis coupled with pharmacological assays validates the functional significance of 24 interface residue contacts only observed in the integrative structures, yet absent in the cryo-EM structure. Through the integration of spatial connectivity data from CLMS with structure modeling, our study provides a new approach that is generalizable to characterizing the conformational dynamics of GPCR signaling complexes.
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Affiliation(s)
- Shijia Yuan
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Lisha Xia
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxi Wang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Wu
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Bingjie Zhang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Chen Pan
- National
Facility for Protein Science in Shanghai, Shanghai Advanced Research
Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Zhiran Fan
- Biocreater
(WuHan) Biotechnology Co., Ltd, Wuhan 430075, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory of
Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Department of
Chemical Biology, College of Chemistry and Molecular Engineering,
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Raymond C. Stevens
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Andrej Sali
- Quantitative
Biosciences Institute, University of California,
San Francisco, San Francisco, California 94143, United States
- Department
of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, United States
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, San
Francisco, California 94143, United States
| | - Liping Sun
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Wenqing Shui
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
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3
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del Caño-Ochoa F, Rubio-del-Campo A, Ramón-Maiques S. A Tailored Strategy to Crosslink the Aspartate Transcarbamoylase Domain of the Multienzymatic Protein CAD. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020660. [PMID: 36677714 PMCID: PMC9863657 DOI: 10.3390/molecules28020660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
CAD is a 1.5 MDa hexameric protein with four enzymatic domains responsible for initiating de novo biosynthesis of pyrimidines nucleotides: glutaminase, carbamoyl phosphate synthetase, aspartate transcarbamoylase (ATC), and dihydroorotase. Despite its central metabolic role and implication in cancer and other diseases, our understanding of CAD is poor, and structural characterization has been frustrated by its large size and sensitivity to proteolytic cleavage. Recently, we succeeded in isolating intact CAD-like particles from the fungus Chaetomium thermophilum with high yield and purity, but their study by cryo-electron microscopy is hampered by the dissociation of the complex during sample grid preparation. Here we devised a specific crosslinking strategy to enhance the stability of this mega-enzyme. Based on the structure of the isolated C. thermophilum ATC domain, we inserted by site-directed mutagenesis two cysteines at specific locations that favored the formation of disulfide bridges and covalent oligomers. We further proved that this covalent linkage increases the stability of the ATC domain without damaging the structure or enzymatic activity. Thus, we propose that this cysteine crosslinking is a suitable strategy to strengthen the contacts between subunits in the CAD particle and facilitate its structural characterization.
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Affiliation(s)
| | | | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia (IBV), CSIC, Jaime Roig 11, 46010 Valencia, Spain
- Group CB06/07/0077 at the Instituto de Biomedicina de Valencia (IBV-CSIC) of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Melchor Fernández Almagro 3, 28029 Madrid, Spain
- Correspondence:
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4
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Yassaghi G, Kukačka Z, Fiala J, Kavan D, Halada P, Volný M, Novák P. Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation. Anal Chem 2022; 94:9993-10002. [PMID: 35797180 DOI: 10.1021/acs.analchem.1c05476] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fast photochemical oxidation of proteins (FPOP) footprinting is a structural mass spectrometry method that maps proteins by fast and irreversible chemical reactions. The position of oxidative modification reflects solvent accessibility and site reactivity and thus provides information about protein conformation, structural dynamics, and interactions. Bottom-up mass spectrometry is an established standard method to analyze FPOP samples. In the bottom-up approach, all forms of the protein are digested together by a protease of choice, which results in a mixture of peptides from various subpopulations of proteins with varying degrees of photochemical oxidation. Here, we investigate the possibility to analyze a specifically selected population of only singly oxidized proteins. This requires utilization of more specific top-down mass spectrometry approaches. The key element of any top-down experiment is the selection of a suitable method of ion isolation, excitation, and fragmentation. Here, we employ and compare collision-induced dissociation, electron-transfer dissociation, and electron-capture dissociation combined with multi-continuous accumulation of selected ions. A singly oxidized subpopulation of FPOP-labeled ubiquitin was used to optimize the method. The top-down approach in FPOP is limited to smaller proteins, but its usefulness was demonstrated by using it to visualize structural changes induced by co-factor removal from the holo/apo myoglobin system. The top-down data were compared with the literature and with the bottom-up data set obtained on the same samples. The top-down results were found to be in good agreement, which indicates that monitoring a singly oxidized FPOP ion population by the top-down approach is a functional workflow for oxidative protein footprinting.
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Affiliation(s)
- Ghazaleh Yassaghi
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Jan Fiala
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 2 128 00, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 2 128 00, Czech Republic
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Michael Volný
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
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5
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Vermeire PJ, Stalmans G, Lilina AV, Fiala J, Novak P, Herrmann H, Strelkov SV. Molecular Interactions Driving Intermediate Filament Assembly. Cells 2021; 10:cells10092457. [PMID: 34572105 PMCID: PMC8466517 DOI: 10.3390/cells10092457] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 02/06/2023] Open
Abstract
Given the role of intermediate filaments (IFs) in normal cell physiology and scores of IF-linked diseases, the importance of understanding their molecular structure is beyond doubt. Research into the IF structure was initiated more than 30 years ago, and some important advances have been made. Using crystallography and other methods, the central coiled-coil domain of the elementary dimer and also the structural basis of the soluble tetramer formation have been studied to atomic precision. However, the molecular interactions driving later stages of the filament assembly are still not fully understood. For cytoplasmic IFs, much of the currently available insight is due to chemical cross-linking experiments that date back to the 1990s. This technique has since been radically improved, and several groups have utilized it recently to obtain data on lamin filament assembly. Here, we will summarize these findings and reflect on the remaining open questions and challenges of IF structure. We argue that, in addition to X-ray crystallography, chemical cross-linking and cryoelectron microscopy are the techniques that should enable major new advances in the field in the near future.
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Affiliation(s)
- Pieter-Jan Vermeire
- Laboratory for Biocrystallography, KU Leuven, 3000 Leuven, Belgium; (P.-J.V.); (G.S.); (A.V.L.)
| | - Giel Stalmans
- Laboratory for Biocrystallography, KU Leuven, 3000 Leuven, Belgium; (P.-J.V.); (G.S.); (A.V.L.)
| | - Anastasia V. Lilina
- Laboratory for Biocrystallography, KU Leuven, 3000 Leuven, Belgium; (P.-J.V.); (G.S.); (A.V.L.)
| | - Jan Fiala
- Department of Biochemistry, Charles University, 12800 Prague, Czech Republic; (J.F.); (P.N.)
- Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novak
- Department of Biochemistry, Charles University, 12800 Prague, Czech Republic; (J.F.); (P.N.)
- Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Harald Herrmann
- Institute of Neuropathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany;
| | - Sergei V. Strelkov
- Laboratory for Biocrystallography, KU Leuven, 3000 Leuven, Belgium; (P.-J.V.); (G.S.); (A.V.L.)
- Correspondence: ; Tel.: +32-1633-0845
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6
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Lee JG, Jeong JO, Jeong SI, Park JS. Radiation-Based Crosslinking Technique for Enhanced Thermal and Mechanical Properties of HDPE/EVA/PU Blends. Polymers (Basel) 2021; 13:2832. [PMID: 34451369 PMCID: PMC8401421 DOI: 10.3390/polym13162832] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/19/2021] [Accepted: 08/21/2021] [Indexed: 11/30/2022] Open
Abstract
Crosslinking of polyolefin-based polymers can improve their thermal and mechanical properties, which can then be used in various applications. Radiation-induced crosslinking can be done easily and usefully by irradiation without a crosslinking agent. In addition, polymer blending can improve thermal and mechanical properties, and chemical resistance, compared to conventional single polymers. In this study, high-density polyethylene (HDPE)/ethylene vinyl acetate (EVA)/polyurethane (PU) blends were prepared by radiation crosslinking to improve the thermal and mechanical properties of HDPE. This is because HDPE, a polyolefin-based polymer, has the weaknesses of low thermal resistance and flexibility, even though it has good mechanical strength and machinability. In contrast, EVA has good flexibility and PU has excellent thermal properties and wear resistance. The morphology and mechanical properties (e.g., tensile and flexure strength) were characterized using scanning electron microscopy (SEM) and a universal testing machine (UTM). The gel fraction, thermal shrinkage, and abrasion resistance of samples were confirmed. In particular, after storing at 180 °C for 1 h, the crosslinked HDPE-PU-EVA blends exhibited ~4-times better thermal stability compared to non-crosslinked HDPE. When subjected to a radiation dose of 100 kGy, the strength of HDPE increased, but the elongation sharply decreased (80%). On the other hand, the strength of the HDPE-PU-EVA blends was very similar to that of HDPE, and the elongation was more than 3-times better (320%). Finally, the abrasion resistance of crosslinked HDPE-PU-EVA was ~9-times better than the crosslinked HDPE. Therefore, this technology can be applied to various polymer products requiring high heat resistance and flexibility, such as electric cables and industrial pipes.
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Affiliation(s)
| | | | | | - Jong-Seok Park
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si 56212, Korea; (J.-G.L.); (J.-O.J.); (S.-I.J.)
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7
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Hacene YC, Loiseau A, Maio VDP, Grenier P, Boisselier E, Bertrand N. Isolating Nanoparticles from Complex Biological Media by Immunoprecipitation. NANO LETTERS 2021; 21:4530-4538. [PMID: 34042452 DOI: 10.1021/acs.nanolett.0c05056] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polyethylene glycol (PEG) is considered the gold standard to prepare long circulating nanoparticles. The hydrophilic layer that sterically protects PEGylated nanomedicines also impedes their separation from biological media. In this study, we describe an immunoprecipitation method using AntiPEG antibodies cross-linked to magnetic beads to extract three types of radiolabeled PEGylated systems: polymeric nanoparticles, liposomes, and therapeutic proteins. The potential of the method is emphasized by isolating these systems after in vivo administration and ex vivo incubation in human biological fluids. Immunoprecipitation also allows a unique perspective on the size distribution of nanoparticles in the bloodstream after intravenous and intraperitoneal administrations. Further, we highlight the potential of the approach to inform on nanomaterial-associated drug in plasma as well as help characterize the protein corona. Altogether, we believe this method answers an unmet need in nanomedicine research and will contribute a fresh perspective on the interactions of nanomedicines with biological systems.
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Affiliation(s)
- Youcef Chakib Hacene
- Faculty of Pharmacy, CHU de Quebec Research Center, Université Laval, CHUL, 2705 Laurier Blvd, Québec G1 V 4G2, Canada
| | - Alexis Loiseau
- Faculty of Medicine, Department of Ophthalmology, CHU de Québec Research Center, Université Laval, Hôpital du Saint-Sacrement, CUO-Recherche, 1050, chemin Sainte-Foy, Québec, G1S 4L8, Canada
| | - Vanessa Dos Passos Maio
- Faculty of Pharmacy, CHU de Quebec Research Center, Université Laval, CHUL, 2705 Laurier Blvd, Québec G1 V 4G2, Canada
| | - Philippe Grenier
- Faculty of Pharmacy, CHU de Quebec Research Center, Université Laval, CHUL, 2705 Laurier Blvd, Québec G1 V 4G2, Canada
| | - Elodie Boisselier
- Faculty of Medicine, Department of Ophthalmology, CHU de Québec Research Center, Université Laval, Hôpital du Saint-Sacrement, CUO-Recherche, 1050, chemin Sainte-Foy, Québec, G1S 4L8, Canada
| | - Nicolas Bertrand
- Faculty of Pharmacy, CHU de Quebec Research Center, Université Laval, CHUL, 2705 Laurier Blvd, Québec G1 V 4G2, Canada
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8
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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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9
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The role of mechanical control of biofilm in the salivary pH after sucrose exposure in children with early childhood caries. Sci Rep 2021; 11:7496. [PMID: 33820926 PMCID: PMC8021547 DOI: 10.1038/s41598-021-86861-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 03/15/2021] [Indexed: 01/20/2023] Open
Abstract
This quasi-experimental study sought to investigate if the mechanical control of biofilm (3-times-a-day) modifies the saliva’s ability to buffer the oral environment after 20% sucrose rinse (SR20%) in children with early childhood caries (ECC). Here, SR20% reduced the saliva’s pH in both groups and the mechanical control of biofilm had a greater effect on this parameter after SR20% in CF children. The mechanical control of biofilm evidenced a higher buffering capacity in CF children before SR20%, which was not observed after SR20%. Otherwise, the absence of mechanical control of biofilm showed that buffering capacity was comparable in the two groups before SR20%, whereas after SR20% the saliva’s buffering capacity of CF children was higher than ECC children. When biofilm was mechanically controlled, carbonic anhydrase VI activity did not change after SR20% whereas the absence of mechanical control of biofilm reduced this enzyme activity after SR20%. In conclusion, the mechanical control of biofilm did not change saliva’s ability to buffer the oral environment after SR20% in children with ECC. On the other hand, CF children appeared to regulate more effectively the saliva’s pH than ECC children while the absence of mechanical control of biofilm mediated their pH-modifying ability after SR20%.
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10
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Nita LE, Chiriac AP, Ghilan A, Rusu AG, Tudorachi N, Timpu D. Alginate enriched with phytic acid for hydrogels preparation. Int J Biol Macromol 2021; 181:561-571. [PMID: 33798571 DOI: 10.1016/j.ijbiomac.2021.03.164] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/08/2021] [Accepted: 03/25/2021] [Indexed: 11/29/2022]
Abstract
Alginate hydrogels are extremely versatile and flexible biomaterials, with an enormous potential for bio-applications use. Their similarity with extracellular matrix is a key factor in their performance for cell and tissue regeneration. In this study superabsorbent high porous hydrogels based on sodium alginate physical crosslinked with a natural crosslinker compound namely phytic acid were prepared and evaluated from the viewpoint of their specific properties. The resulting hydrogels obtained with different ratios between alginate and phytic acid were characterized by Fourier transform infrared spectroscopy technique, scanning electron microscopy, XRD measurements, swelling tests in physiological environment, and thermal analysis by using a simultaneous TG/FT-IR/MS system. There are put into evidence the differences in physico-chemical properties of the hydrogels in relation with their composition, which endows them tunable properties and versatility.
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Affiliation(s)
- Loredana Elena Nita
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41-A, RO-700487, Iasi, Romania.
| | - Aurica P Chiriac
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41-A, RO-700487, Iasi, Romania
| | - Alina Ghilan
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41-A, RO-700487, Iasi, Romania
| | - Alina Gabriela Rusu
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41-A, RO-700487, Iasi, Romania
| | - Nita Tudorachi
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41-A, RO-700487, Iasi, Romania
| | - Daniel Timpu
- "Petru Poni" Institute of Macromolecular Chemistry, Grigore Ghica Voda Alley 41-A, RO-700487, Iasi, Romania
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11
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Joyce K, Fabra GT, Bozkurt Y, Pandit A. Bioactive potential of natural biomaterials: identification, retention and assessment of biological properties. Signal Transduct Target Ther 2021; 6:122. [PMID: 33737507 PMCID: PMC7973744 DOI: 10.1038/s41392-021-00512-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Biomaterials have had an increasingly important role in recent decades, in biomedical device design and the development of tissue engineering solutions for cell delivery, drug delivery, device integration, tissue replacement, and more. There is an increasing trend in tissue engineering to use natural substrates, such as macromolecules native to plants and animals to improve the biocompatibility and biodegradability of delivered materials. At the same time, these materials have favourable mechanical properties and often considered to be biologically inert. More importantly, these macromolecules possess innate functions and properties due to their unique chemical composition and structure, which increase their bioactivity and therapeutic potential in a wide range of applications. While much focus has been on integrating these materials into these devices via a spectrum of cross-linking mechanisms, little attention is drawn to residual bioactivity that is often hampered during isolation, purification, and production processes. Herein, we discuss methods of initial material characterisation to determine innate bioactivity, means of material processing including cross-linking, decellularisation, and purification techniques and finally, a biological assessment of retained bioactivity of a final product. This review aims to address considerations for biomaterials design from natural polymers, through the optimisation and preservation of bioactive components that maximise the inherent bioactive potency of the substrate to promote tissue regeneration.
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Affiliation(s)
- Kieran Joyce
- School of Medicine, National University of Ireland, Galway, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
| | - Georgina Targa Fabra
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
| | - Yagmur Bozkurt
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland
| | - Abhay Pandit
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland, Galway, Ireland.
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12
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Filandrová R, Vališ K, Černý J, Chmelík J, Slavata L, Fiala J, Rosůlek M, Kavan D, Man P, Chum T, Cebecauer M, Fabris D, Novák P. Motif orientation matters: Structural characterization of TEAD1 recognition of genomic DNA. Structure 2020; 29:345-356.e8. [PMID: 33333006 DOI: 10.1016/j.str.2020.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 11/29/2022]
Abstract
TEAD transcription factors regulate gene expression through interactions with DNA and other proteins. They are crucial for the development of eukaryotic organisms and to control the expression of genes involved mostly in cell proliferation and differentiation; however, their deregulation can lead to tumorigenesis. To study the interactions of TEAD1 with M-CAT motifs and their inverted versions, the KD of each complex was determined, and H/D exchange, quantitative chemical cross-linking, molecular docking, and smFRET were utilized for structural characterization. ChIP-qPCR was employed to correlate the results with a cell line model. The results obtained showed that although the inverted motif has 10× higher KD, the same residues were affected by the presence of M-CAT in both orientations. Molecular docking and smFRET revealed that TEAD1 binds the inverted motif rotated 180°. In addition, the inverted motif was proven to be occupied by TEAD1 in Jurkat cells, suggesting that the low-affinity binding sites present in the human genome may possess biological relevance.
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Affiliation(s)
- Růžena Filandrová
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Karel Vališ
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec 252 50, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Lukáš Slavata
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Jan Fiala
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Michal Rosůlek
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - Tomáš Chum
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague 182 00, Czech Republic
| | - Marek Cebecauer
- J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague 182 00, Czech Republic
| | - Daniele Fabris
- University of Connecticut, Department of Chemistry, 55 N. Eagleville Road, Storrs, CT 06269, USA
| | - Petr Novák
- Institute of Microbiology, Czech Academy of Sciences, Prague 142 20, Czech Republic; Faculty of Science, Charles University, Prague 128 43, Czech Republic.
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13
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Structure of the human clamp loader reveals an autoinhibited conformation of a substrate-bound AAA+ switch. Proc Natl Acad Sci U S A 2020; 117:23571-23580. [PMID: 32907938 DOI: 10.1073/pnas.2007437117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
DNA replication requires the sliding clamp, a ring-shaped protein complex that encircles DNA, where it acts as an essential cofactor for DNA polymerases and other proteins. The sliding clamp needs to be opened and installed onto DNA by a clamp loader ATPase of the AAA+ family. The human clamp loader replication factor C (RFC) and sliding clamp proliferating cell nuclear antigen (PCNA) are both essential and play critical roles in several diseases. Despite decades of study, no structure of human RFC has been resolved. Here, we report the structure of human RFC bound to PCNA by cryogenic electron microscopy to an overall resolution of ∼3.4 Å. The active sites of RFC are fully bound to adenosine 5'-triphosphate (ATP) analogs, which is expected to induce opening of the sliding clamp. However, we observe the complex in a conformation before PCNA opening, with the clamp loader ATPase modules forming an overtwisted spiral that is incapable of binding DNA or hydrolyzing ATP. The autoinhibited conformation observed here has many similarities to a previous yeast RFC:PCNA crystal structure, suggesting that eukaryotic clamp loaders adopt a similar autoinhibited state early on in clamp loading. Our results point to a "limited change/induced fit" mechanism in which the clamp first opens, followed by DNA binding, inducing opening of the loader to release autoinhibition. The proposed change from an overtwisted to an active conformation reveals an additional regulatory mechanism for AAA+ ATPases. Finally, our structural analysis of disease mutations leads to a mechanistic explanation for the role of RFC in human health.
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14
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Sinnott M, Malhotra S, Madhusudhan MS, Thalassinos K, Topf M. Combining Information from Crosslinks and Monolinks in the Modeling of Protein Structures. Structure 2020; 28:1061-1070.e3. [DOI: 10.1016/j.str.2020.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/08/2020] [Accepted: 05/22/2020] [Indexed: 11/30/2022]
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15
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Belsom A, Rappsilber J. Anatomy of a crosslinker. Curr Opin Chem Biol 2020; 60:39-46. [PMID: 32829152 DOI: 10.1016/j.cbpa.2020.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/17/2022]
Abstract
Crosslinking mass spectrometry has become a core technology in structural biology and is expanding its reach towards systems biology. Its appeal lies in a rapid workflow, high sensitivity and the ability to provide data on proteins in complex systems, even in whole cells. The technology depends heavily on crosslinking reagents. The anatomy of crosslinkers can be modular, sometimes comprising combinations of functional groups. These groups are defined by concepts including: reaction selectivity to increase information density, enrichability to improve detection, cleavability to enhance the identification process and isotope-labelling for quantification. Here, we argue that both concepts and functional groups need more thorough experimental evaluation, so that we can show exactly how and where they are useful when applied to crosslinkers. Crosslinker design should be driven by data, not only concepts. We focus on two crosslinker concepts with large consequences for the technology, namely reactive group reaction kinetics and enrichment groups.
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Affiliation(s)
- Adam Belsom
- 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, Edinburgh, EH9 3BF, UK.
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16
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Gong Z, Ye SX, Tang C. Tightening the Crosslinking Distance Restraints for Better Resolution of Protein Structure and Dynamics. Structure 2020; 28:1160-1167.e3. [PMID: 32763142 DOI: 10.1016/j.str.2020.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/04/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022]
Abstract
Chemical crosslinking coupled with mass spectrometry (CXMS) has been increasingly used in structural biology. CXMS distance restraints are usually applied to Cα or Cβ atoms of the crosslinked residues, with upper bounds typically over 20 Å. The incorporation of loose CXMS restraints only marginally improves the resolution of the calculated structures. Here, we present a revised format of CXMS distance restraints, which works by first modifying the crosslinked residue with a rigid extension derived from the crosslinker. With the flexible side chain explicitly represented, the reformatted restraint can be applied to the modification group instead, with an upper bound of 6 Å or less. The short distance restraint can be represented and back-calculated simply with a straight line. The use of tighter restraints not only afford better-resolved structures but also uncover protein dynamics. Together, our approach enables more information extracted from the CXMS data.
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Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Shang-Xiang Ye
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei Province 430074, China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei Province 430074, China; Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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17
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Addressing the Molecular Mechanism of Longitudinal Lamin Assembly Using Chimeric Fusions. Cells 2020; 9:cells9071633. [PMID: 32645958 PMCID: PMC7407374 DOI: 10.3390/cells9071633] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/28/2022] Open
Abstract
The molecular architecture and assembly mechanism of intermediate filaments have been enigmatic for decades. Among those, lamin filaments are of particular interest due to their universal role in cell nucleus and numerous disease-related mutations. Filament assembly is driven by specific interactions of the elementary dimers, which consist of the central coiled-coil rod domain flanked by non-helical head and tail domains. We aimed to investigate the longitudinal 'head-to-tail' interaction of lamin dimers (the so-called ACN interaction), which is crucial for filament assembly. To this end, we prepared a series of recombinant fragments of human lamin A centred around the N- and C-termini of the rod. The fragments were stabilized by fusions to heterologous capping motifs which provide for a correct formation of parallel, in-register coiled-coil dimers. As a result, we established crystal structures of two N-terminal fragments one of which highlights the propensity of the coiled-coil to open up, and one C-terminal rod fragment. Additional studies highlighted the capacity of such N- and C-terminal fragments to form specific complexes in solution, which were further characterized using chemical cross-linking. These data yielded a molecular model of the ACN complex which features a 6.5 nm overlap of the rod ends.
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18
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Influence of cross-linker polarity on selectivity towards lysine side chains. J Proteomics 2020; 218:103716. [DOI: 10.1016/j.jprot.2020.103716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/02/2020] [Accepted: 02/19/2020] [Indexed: 11/19/2022]
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19
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Evaluation of chemical cross-linkers for in-depth structural analysis of G protein-coupled receptors through cross-linking mass spectrometry. Anal Chim Acta 2020; 1102:53-62. [DOI: 10.1016/j.aca.2019.12.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/12/2019] [Accepted: 12/15/2019] [Indexed: 01/05/2023]
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20
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Zeman J, Itoh Y, Kukačka Z, Rosůlek M, Kavan D, Kouba T, Jansen ME, Mohammad MP, Novák P, Valášek LS. Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes. Nucleic Acids Res 2019; 47:8282-8300. [PMID: 31291455 PMCID: PMC6735954 DOI: 10.1093/nar/gkz570] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/12/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
eIF3 is a large multiprotein complex serving as an essential scaffold promoting binding of other eIFs to the 40S subunit, where it coordinates their actions during translation initiation. Perhaps due to a high degree of flexibility of multiple eIF3 subunits, a high-resolution structure of free eIF3 from any organism has never been solved. Employing genetics and biochemistry, we previously built a 2D interaction map of all five yeast eIF3 subunits. Here we further improved the previously reported in vitro reconstitution protocol of yeast eIF3, which we cross-linked and trypsin-digested to determine its overall shape in 3D by advanced mass-spectrometry. The obtained cross-links support our 2D subunit interaction map and reveal that eIF3 is tightly packed with its WD40 and RRM domains exposed. This contrasts with reported cryo-EM structures depicting eIF3 as a molecular embracer of the 40S subunit. Since the binding of eIF1 and eIF5 further fortified the compact architecture of eIF3, we suggest that its initial contact with the 40S solvent-exposed side makes eIF3 to open up and wrap around the 40S head with its extended arms. In addition, we mapped the position of eIF5 to the region below the P- and E-sites of the 40S subunit.
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Affiliation(s)
- Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Yuzuru Itoh
- Institute of Genetics and Molecular and Cellular Biology, CNRS UMR7104, INSERM UMR964, Illkirch, France
| | - Zdeněk Kukačka
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Michal Rosůlek
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Daniel Kavan
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Tomáš Kouba
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Myrte E Jansen
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Mahabub P Mohammad
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
| | - Leoš S Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Videnska 1083, 142 20, The Czech Republic
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21
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Hanozin E, Grifnée E, Gattuso H, Matagne A, Morsa D, Pauw ED. Covalent Cross-Linking as an Enabler for Structural Mass Spectrometry. Anal Chem 2019; 91:12808-12818. [PMID: 31490660 DOI: 10.1021/acs.analchem.9b02491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The number of studies referring to the structural elucidation of intact biomolecular systems using mass spectrometry techniques has gradually increased in the post-2000s literature topics. As part of native mass spectrometry, this domain capitalizes on the kinetic trapping of physiological folds in view of probing solution-like conformational properties of isolated molecules or complexes after their electrospray transfer to the gas phase. Despite its efficiency for a wide array of analytes, this approach is expected to be pushed to its limits when considering highly dynamic systems or when dealing with nonideal operating conditions. To circumvent these limitations, we challenge the adequacy of an original strategy based on cross-linkers to improve the gas-phase stability of isolated proteins and ensure the preservation of folded conformations when measuring with strong transmission voltages, by spraying from denaturing solvents, or trapping for extended periods of time. Tested on cytochrome c, myoglobin, and β-lactoglobulin cross-linked using BS3, we validated the process as structurally nonintrusive in solution using far-ultraviolet circular dichroism and unraveled the preservation of folded conformations showing better resilience to denaturation on cross-linked species using ion mobility. The resulting collision cross sections were found in agreement with the native fold, and a preservation of the proteins' secondary and tertiary structures was evidenced using molecular dynamics simulations. Our results provide new insights concerning the fate of electro-sprayed cross-linked conformers in the gas phase, while constituting promising evidence for the validation of this technique as part of future structural mass spectrometry workflows.
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22
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MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex. Biomolecules 2019; 9:biom9100535. [PMID: 31561554 PMCID: PMC6843354 DOI: 10.3390/biom9100535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/18/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023] Open
Abstract
The limited information available on the structure of complexes involving transcription factors and cognate DNA response elements represents a major obstacle in the quest to understand their mechanism of action at the molecular level. We implemented a concerted structural proteomics approach, which combined hydrogen-deuterium exchange (HDX), quantitative protein-protein and protein-nucleic acid cross-linking (XL), and homology analysis, to model the structure of the complex between the full-length DNA binding domain (DBD) of Forkhead box protein O4 (FOXO4) and its DNA binding element (DBE). The results confirmed that FOXO4-DBD assumes the characteristic forkhead topology shared by these types of transcription factors, but its binding mode differs significantly from those of other members of the family. The results showed that the binding interaction stabilized regions that were rather flexible and disordered in the unbound form. Surprisingly, the conformational effects were not limited only to the interface between bound components, but extended also to distal regions that may be essential to recruiting additional factors to the transcription machinery. In addition to providing valuable new insights into the binding mechanism, this project provided an excellent evaluation of the merits of structural proteomics approaches in the investigation of systems that are not directly amenable to traditional high-resolution techniques.
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23
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24
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Dülfer J, Kadek A, Kopicki JD, Krichel B, Uetrecht C. Structural mass spectrometry goes viral. Adv Virus Res 2019; 105:189-238. [PMID: 31522705 DOI: 10.1016/bs.aivir.2019.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the last 20 years, mass spectrometry (MS), with its ability to analyze small sample amounts with high speed and sensitivity, has more and more entered the field of structural virology, aiming to investigate the structure and dynamics of viral proteins as close to their native environment as possible. The use of non-perturbing labels in hydrogen-deuterium exchange MS allows for the analysis of interactions between viral proteins and host cell factors as well as their dynamic responses to the environment. Cross-linking MS, on the other hand, can analyze interactions in viral protein complexes and identify virus-host interactions in cells. Native MS allows transferring viral proteins, complexes and capsids into the gas phase and has broken boundaries to overcome size limitations, so that now even the analysis of intact virions is possible. Different MS approaches not only inform about size, stability, interactions and dynamics of virus assemblies, but also bridge the gap to other biophysical techniques, providing valuable constraints for integrative structural modeling of viral complex assemblies that are often inaccessible by single technique approaches. In this review, recent advances are highlighted, clearly showing that structural MS approaches in virology are moving towards systems biology and ever more experiments are performed on cellular level.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alan Kadek
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany.
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25
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Müller F, Graziadei A, Rappsilber J. Quantitative Photo-crosslinking Mass Spectrometry Revealing Protein Structure Response to Environmental Changes. Anal Chem 2019; 91:9041-9048. [PMID: 31274288 PMCID: PMC6639777 DOI: 10.1021/acs.analchem.9b01339] [Citation(s) in RCA: 16] [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: 03/15/2019] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
Abstract
Protein structures respond to changes in their chemical and physical environment. However, studying such conformational changes is notoriously difficult, as many structural biology techniques are also affected by these parameters. Here, the use of photo-crosslinking, coupled with quantitative crosslinking mass spectrometry (QCLMS), offers an opportunity, since the reactivity of photo-crosslinkers is unaffected by changes in environmental parameters. In this study, we introduce a workflow combining photo-crosslinking using sulfosuccinimidyl 4,4'-azipentanoate (sulfo-SDA) with our recently developed data-independent acquisition (DIA)-QCLMS. This novel photo-DIA-QCLMS approach is then used to quantify pH-dependent conformational changes in human serum albumin (HSA) and cytochrome C by monitoring crosslink abundances as a function of pH. Both proteins show pH-dependent conformational changes resulting in acidic and alkaline transitions. 93% and 95% of unique residue pairs (URP) were quantifiable across triplicates for HSA and cytochrome C, respectively. Abundance changes of URPs and hence conformational changes of both proteins were visualized using hierarchical clustering. For HSA we distinguished the N-F and the N-B form from the native conformation. In addition, we observed for cytochrome C acidic and basic conformations. In conclusion, our photo-DIA-QCLMS approach distinguished pH-dependent conformers of both proteins.
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Affiliation(s)
- Fränze Müller
- Bioanalytics,
Institute of Biotechnology, Technische Universität
Berlin, 13355 Berlin, Germany
| | - 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, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom
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26
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Chavez JD, Mohr JP, Mathay M, Zhong X, Keller A, Bruce JE. Systems structural biology measurements by in vivo cross-linking with mass spectrometry. Nat Protoc 2019; 14:2318-2343. [PMID: 31270507 DOI: 10.1038/s41596-019-0181-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 04/18/2019] [Indexed: 12/23/2022]
Abstract
This protocol describes a workflow for utilizing large-scale cross-linking with mass spectrometry (XL-MS) to make systems-level structural biology measurements in complex biological samples, including cells, isolated organelles, and tissue samples. XL-MS is a structural biology technique that provides information on the molecular structure of proteins and protein complexes using chemical probes that report the proximity of probe-reactive amino acids within proteins, typically lysine residues. Information gained through XL-MS studies is often complementary to more traditional methods, such as X-ray crystallography, nuclear magnetic resonance, and cryo-electron microscopy. The use of MS-cleavable cross-linkers, including protein interaction reporter (PIR) technologies, enables XL-MS studies on protein structures and interactions in extremely complex biological samples, including intact living cells. PIR cross-linkers are designed to contain chemical bonds at specific locations within the cross-linker molecule that can be selectively cleaved by collision-induced dissociation or UV light. When broken, these bonds release the intact peptides that were cross-linked, as well as a reporter ion. Conservation of mass dictates that the sum of the two released peptide masses and the reporter mass equals the measured precursor mass. This relationship is used to identify cross-linked peptide pairs. Release of the individual peptides permits accurate measurement of their masses and independent amino acid sequence determination by tandem MS, allowing the use of standard proteomics search engines such as Comet for peptide sequence assignment, greatly simplifying data analysis of cross-linked peptide pairs. Search results are processed with XLinkProphet for validation and can be uploaded into XlinkDB for interaction network and structural analysis.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jared P Mohr
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Martin Mathay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xuefei Zhong
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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27
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Dixit SM, Ruotolo BT. A Semi-Empirical Framework for Interpreting Traveling Wave Ion Mobility Arrival Time Distributions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:956-966. [PMID: 30815838 DOI: 10.1007/s13361-019-02133-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/12/2018] [Accepted: 01/04/2019] [Indexed: 06/09/2023]
Abstract
The inherent structural heterogeneity of biomolecules is an important biophysical property that is essential to their function, but is challenging to characterize experimentally. We present a workflow that rapidly and quantitatively assesses the conformational heterogeneity of peptides and proteins in the gas phase using traveling wave ion mobility (TWIM) arrival time distributions (ATDs). We have established a set of semi-empirical equations that model the TWIM ATD peak width and resolution across a wide range of wave amplitudes (V) and wave velocities (v). In addition, a conformational broadening parameter, δ, can be extracted from this analysis that reports on the contribution of conformational heterogeneity to the broadening of TWIM ATD peak width during ion mobility separation. We use this δ value to evaluate the conformational heterogeneity of a set of helical peptides, and our analysis correlates well with previous peak width observations reported for these ions. Furthermore, we use molecular dynamics simulations to independently investigate the general flexibility of these peptides in the gas phase, and generate similar trends found in experimental TWIM data. Finally, we extended our analysis to Avidin, a 64-kDa homotetramer, and quantify the structural heterogeneity of this intact complex using TWIM ATD data as a function of cross-linking. We observe an initial reduction in δ values as a function of cross-linker concentration, demonstrating the sensitivity of our δ value analysis to changes in flexibility of the assembly.
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Affiliation(s)
- Sugyan M Dixit
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, USA.
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28
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Hernychová L, Rosůlek M, Kádek A, Mareška V, Chmelík J, Adámková L, Grobárová V, Šebesta O, Kukačka Z, Skála K, Spiwok V, Černý J, Novák P. The C-type lectin-like receptor Nkrp1b: Structural proteomics reveals features affecting protein conformation and interactions. J Proteomics 2019; 196:162-172. [DOI: 10.1016/j.jprot.2018.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 11/24/2022]
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Ouimet CM, Dawod M, Grinias J, Assimon VA, Lodge J, Mapp AK, Gestwicki JE, Kennedy RT. Protein cross-linking capillary electrophoresis at increased throughput for a range of protein-protein interactions. Analyst 2019; 143:1805-1812. [PMID: 29565056 DOI: 10.1039/c7an02098h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tools for measuring affinities and stoichiometries of protein-protein complexes are valuable for elucidating the role of protein-protein interactions (PPIs) in governing cell functions and screening for PPI modulators. Such measurements can be challenging because PPIs can span a wide range of affinities and include stoichiometries from dimers to high order oligomers. Also, most techniques require large amounts of protein which can hamper research for difficult to obtain proteins. Protein cross-linking capillary electrophoresis (PXCE) has the potential to directly measure PPIs and even resolve multiple PPIs while consuming attomole quantities. Previously PXCE has only been used for high affinity, 1 : 1 complexes; here we expand the utility of PXCE to access a wide range of PPIs including weak and multimeric oligomers. Use of glutaraldehyde as the cross-linking agent was key to advancing the method because of its rapid reaction kinetics. A 10 s reaction time was found to be sufficient for cross-linking and quantification of seven different PPIs with Kd values ranging from low μM to low nM including heat shock protein 70 (Hsp70) interacting with heat shock organizing protein (3.8 ± 0.7 μM) and bcl2 associated anthanogene (26 ± 6 nM). Non-specific cross-linking of protein aggregates was found to be minimal at protein concentrations <20 μM as assessed by size exclusion chromatography. PXCE was sensitive enough to measure changes in PPI affinity induced by the protein nucleotide state or point mutations in the protein-binding site. Further, several interactions could be resolved in a single run, including Hsp70 monomer, homodimer and Hsp70 complexed the with c-terminus of Hsp70 interacting protein (CHIP). Finally, the throughput of PXCE was increased to 1 min per sample suggesting potential for utility in screening.
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Affiliation(s)
- Claire M Ouimet
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Mohamed Dawod
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - James Grinias
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA. and Department of Chemistry, Rowan University, Glassboro, NJ 08028, USA
| | - Victoria A Assimon
- Department of Pharmaceutical Chemistry, University of California at San Francisco, California 94158, USA
| | - Jean Lodge
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA. and Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California at San Francisco, California 94158, USA
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA. and Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
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30
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Downard KM, Maleknia SD. Mass spectrometry in structural proteomics: The case for radical probe protein footprinting. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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31
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Ziemianowicz DS, Ng D, Schryvers AB, Schriemer DC. Photo-Cross-Linking Mass Spectrometry and Integrative Modeling Enables Rapid Screening of Antigen Interactions Involving Bacterial Transferrin Receptors. J Proteome Res 2018; 18:934-946. [DOI: 10.1021/acs.jproteome.8b00629] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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32
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Calabrese AN, Radford SE. Mass spectrometry-enabled structural biology of membrane proteins. Methods 2018; 147:187-205. [DOI: 10.1016/j.ymeth.2018.02.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/30/2018] [Accepted: 02/21/2018] [Indexed: 01/01/2023] Open
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Yoshimoto M, Schweizer T, Rathlef M, Pleij T, Walde P. Immobilization of Carbonic Anhydrase in Glass Micropipettes and Glass Fiber Filters for Flow-Through Reactor Applications. ACS OMEGA 2018; 3:10391-10405. [PMID: 31459167 PMCID: PMC6645021 DOI: 10.1021/acsomega.8b01517] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/20/2018] [Indexed: 05/20/2023]
Abstract
There are various ways of immobilizing carbonic anhydrase (CA) on solid materials. One of the final aims is to apply immobilized CA for the catalytic hydration of carbon dioxide (CO2) as a first step in the conversion of gaseous CO2 into solid products. The immobilization method investigated allows a straightforward, stable, and quantifiable immobilization of bovine erythrocyte carbonic anhydrase (BCA) on silicate surfaces. The method is based on the use of a water-soluble, polycationic second-generation dendronized polymer with on average 1000 repeating units, abbreviated as de-PG21000. Several copies of BCA were first covalently linked to de-PG21000 through stable bisaryl hydrazone (BAH) bonds. Then, the de-PG21000-BAH-BCA conjugates obtained were adsorbed noncovalently either on microscopy glass coverslips, inside glass micropipettes, or in porous glass fiber filters. The apparent density of the immobilized BCA on the glass surfaces was about 8-10 pmol/cm2. In all three cases, the immobilized enzyme was highly active and stable when tested with p-nitrophenyl acetate as a model enzyme substrate at room temperature. The micropipettes and the glass fiber filters were applied as flow-through systems for continuous operation at room temperature. In the case of the glass fiber filters, the filters were placed inside a homemade flow-through filter holder which allows flow-through runs with more than one filter connected in series. This offers the opportunity of increasing the substrate conversion by increasing the number of BCA-containing filters.
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Affiliation(s)
- Makoto Yoshimoto
- Department
of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
- Department
of Applied Chemistry, Yamaguchi University, Tokiwadai 2-16-1, Ube 755-8611, Japan
| | - Thomas Schweizer
- Department
of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
| | - Marco Rathlef
- Department
of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
| | - Tazio Pleij
- Department
of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
| | - Peter Walde
- Department
of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland
- E-mail:
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Chavez JD, Bruce JE. Chemical cross-linking with mass spectrometry: a tool for systems structural biology. Curr Opin Chem Biol 2018; 48:8-18. [PMID: 30172868 DOI: 10.1016/j.cbpa.2018.08.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 01/14/2023]
Abstract
Biological processes supporting life are orchestrated by a highly dynamic array of protein structures and interactions comprising the interactome. Defining the interactome, visualizing how structures and interactions change and function to support life is essential to improved understanding of fundamental molecular processes, but represents a challenge unmet by any single analytical technique. Chemical cross-linking with mass spectrometry provides identification of proximal amino acid residues within proteins and protein complexes, yielding low resolution structural information. This approach has predominantly been employed to provide structural insight on isolated protein complexes, and has been particularly useful for molecules that are recalcitrant to conventional structural biology studies. Here we discuss recent developments in cross-linking and mass spectrometry technologies that are providing large-scale or systems-level interactome data with successful applications to isolated organelles, cell lysates, virus particles, intact bacterial and mammalian cultured cells and tissue samples.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
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Kim HS, Hong SG, Woo KM, Teijeiro Seijas V, Kim S, Lee J, Kim J. Precipitation-Based Nanoscale Enzyme Reactor with Improved Loading, Stability, and Mass Transfer for Enzymatic CO2 Conversion and Utilization. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00606] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Han Sol Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Sung-Gil Hong
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Kie Moon Woo
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Vanesa Teijeiro Seijas
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Seongbeen Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Kyungbuk 37673, Republic of Korea
| | - Jinwoo Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Kyungbuk 37673, Republic of Korea
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
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Chu F, Thornton DT, Nguyen HT. Chemical cross-linking in the structural analysis of protein assemblies. Methods 2018; 144:53-63. [PMID: 29857191 DOI: 10.1016/j.ymeth.2018.05.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/22/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
For decades, chemical cross-linking of proteins has been an established method to study protein interaction partners. The chemical cross-linking approach has recently been revived by mass spectrometric analysis of the cross-linking reaction products. Chemical cross-linking and mass spectrometric analysis (CXMS) enables the identification of residues that are close in three-dimensional (3D) space but not necessarily close in primary sequence. Therefore, this approach provides medium resolution information to guide de novo structure prediction, protein interface mapping and protein complex model building. The robustness and compatibility of the CXMS approach with multiple biochemical methods have made it especially appealing for challenging systems with multiple biochemical compositions and conformation states. This review provides an overview of the CXMS approach, describing general procedures in sample processing, data acquisition and analysis. Selection of proper chemical cross-linking reagents, strategies for cross-linked peptide identification, and successful application of CXMS in structural characterization of proteins and protein complexes are discussed.
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Affiliation(s)
- Feixia Chu
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States; Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, United States.
| | - Daniel T Thornton
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
| | - Hieu T Nguyen
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, United States
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Fioramonte M, de Jesus HCR, Ferrari AJR, Lima DB, Drekener RL, Correia CRD, Oliveira LG, Neves-Ferreira AGDC, Carvalho PC, Gozzo FC. XPlex: An Effective, Multiplex Cross-Linking Chemistry for Acidic Residues. Anal Chem 2018; 90:6043-6050. [PMID: 29565564 DOI: 10.1021/acs.analchem.7b05135] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cross-linking/Mass spectrometry (XLMS) is a consolidated technique for structural characterization of proteins and protein complexes. Despite its success, the cross-linking chemistry currently used is mostly based on N-hydroxysuccinimide (NHS) esters, which react primarily with lysine residues. One way to expand the current applicability of XLMS into several new areas is to increase the number of cross-links obtainable for a target protein. We introduce a multiplex chemistry (denoted XPlex) that targets Asp, Glu, Lys, and Ser residues. XPlex can generate significantly more cross-links with reactions occurring at lower temperatures and enables targeting proteins that are not possible with NHS ester-based cross-linkers. We demonstrate the effectiveness of our approach in model proteins as well as a target Lys-poor protein, SalBIII. Identification of XPlex spectra requires a search engine capable of simultaneously considering multiple cross-linkers on the same run; to achieve this, we updated the SIM-XL search algorithm with a search mode tailored toward XPlex. In summary, we present a complete chemistry/computational solution for significantly increasing the number of possible distance constraints by mass spectrometry experiments, and thus, we are convinced that XPlex poses as a real complementary approach for structural proteomics studies.
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Affiliation(s)
- Mariana Fioramonte
- Institute of Chemistry , University of Campinas , CP 6154 , Campinas , Sao Paulo 13083-970 , Brazil
| | | | | | - Diogo Borges Lima
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteu , Paris , France
| | - Roberta Lopes Drekener
- Institute of Chemistry , University of Campinas , CP 6154 , Campinas , Sao Paulo 13083-970 , Brazil
| | | | - Luciana Gonzaga Oliveira
- Institute of Chemistry , University of Campinas , CP 6154 , Campinas , Sao Paulo 13083-970 , Brazil
| | | | - Paulo Costa Carvalho
- Laboratory for Proteomics and Protein Engineering , Carlos Chagas Institute , Fiocruz , Parana , Brazil
| | - Fabio Cesar Gozzo
- Institute of Chemistry , University of Campinas , CP 6154 , Campinas , Sao Paulo 13083-970 , Brazil
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