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Haidar Y, Konermann L. Effects of Hydrogen/Deuterium Exchange on Protein Stability in Solution and in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023. [PMID: 37314114 DOI: 10.1021/jasms.3c00130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry (MS)-based techniques are widely used for probing protein structure and dynamics in solution. H/D exchange (HDX)-MS is one of the most common approaches in this context. HDX is often considered to be a "benign" labeling method, in that it does not perturb protein behavior in solution. However, several studies have reported that D2O pushes unfolding equilibria toward the native state. The origin, and even the existence of this protein stabilization remain controversial. Here we conducted thermal unfolding assays in solution to confirm that deuterated proteins in D2O are more stable, with 2-4 K higher melting temperatures than unlabeled proteins in H2O. Previous studies tentatively attributed this phenomenon to strengthened H-bonds after deuteration, an effect that may arise from the lower zero-point vibrational energy of the deuterated species. Specifically, it was proposed that strengthened water-water bonds (W···W) in D2O lower the solubility of nonpolar side chains. The current work takes a broader view by noting that protein stability in solution also depends on water-protein (W···P) and protein-protein (P···P) H-bonds. To help unravel these contributions, we performed collision-induced unfolding (CIU) experiments on gaseous proteins generated by native electrospray ionization. CIU profiles of deuterated and unlabeled proteins were indistinguishable, implying that P···P contacts are insensitive to deuteration. Thus, protein stabilization in D2O is attributable to solvent effects, rather than alterations of intraprotein H-bonds. Strengthening of W···W contacts represents one possible explanation, but the stabilizing effect of D2O can also originate from weakened W···P bonds. Future work will be required to elucidate which of these two scenarios is correct, or if both contribute to protein stabilization in D2O. In any case, the often-repeated adage that "D-bonds are more stable than H-bonds" does not apply to intramolecular contacts in native proteins.
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Affiliation(s)
- Yousef Haidar
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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2
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DeCaprio J, Kohl TO. Cross-Linking Antibodies to Beads with Disuccinimidyl Suberate (DSS). Cold Spring Harb Protoc 2019; 2019:2019/2/pdb.prot098632. [PMID: 30710026 DOI: 10.1101/pdb.prot098632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This protocol describes the cross-linking of antibodies to either Protein A or G agarose beads using disuccinimidyl suberate (DSS), a bifunctional cross-linker capable of directly reacting with two different amines to form stable amide bonds. Proteins, including antibodies, generally display several primary amines in the side chains of lysine (K) residues and the amino terminus of each polypeptide that represent available potential targets for N-hydroxysuccinimide (NHS)-ester cross-linking reagents. The antibody-bead cross-linking process generates a reusable resource of antibody and beads, commonly referred to as an antibody-specific resin, and can be repeatedly used for the immunoprecipitation of specific proteins if treated and stored correctly.
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3
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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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4
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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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5
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Kölbel K, Warnke S, Seo J, von Helden G, Moretti R, Meiler J, Pagel K, Sinz A. Conformational Shift of a β-Hairpin Peptide upon Complex Formation with an Oligo-proline Peptide Studied by Mass Spectrometry. ChemistrySelect 2016; 1:3651-3656. [PMID: 30547079 DOI: 10.1002/slct.201600934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
So-called super-secondary structures such as the β-hairpin, studied here, form an intermediate hierarchy between secondary and tertiary structures of proteins. Their sequence-derived 'pure' peptide backbone conformation is combined with 'remote' interstrand or interresidue contacts reminiscent of the 3D-structure of full-length proteins. This renders them ideally suited for studying potential nucleation sites of protein folding reactions as well as intermolecular interactions. But β-hairpins do not merely serve as model systems; their unique structure characteristics warrant a central role in structural studies on their own. In this study we applied photo cross-linking in combination with high-resolution mass spectrometry and computational modeling as well as with ion mobility-mass spectrometry to elucidate these structural properties. Using variants of a known β-hairpin representative, the so-called trpzip peptide and its ligands, we found evidence for a conformational transition of the β-hairpin and its impact on ligand binding.
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Affiliation(s)
- Knut Kölbel
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute for Pharmacy, Martin-Luther-Universit t Halle-Wittenberg W.-Langenbeck-Straße 4, 06120 Halle (Germany).,Chemistry Department Universiteit Antwerpen Campus Groenenborger, Groenenborgerlaan 171 G.V. 416, 2020 Antwer-pen (Belgi)
| | - Stephan Warnke
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-614195 Berlin (Germany)
| | - Jongcheol Seo
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-614195 Berlin (Germany)
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-614195 Berlin (Germany)
| | - Rocco Moretti
- Department of Chemistry and the Center for Structural Biology Vanderbilt University 465 21Ave South BIOSCi/MRBIII Nashville TN (USA)
| | - Jens Meiler
- Department of Chemistry and the Center for Structural Biology Vanderbilt University 465 21Ave South BIOSCi/MRBIII Nashville TN (USA)
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-614195 Berlin (Germany).,Freie Universit t Berlin Institute of Chemistry and Biochemistry Takustraße 3 14195 Berlin (Germany)
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute for Pharmacy, Martin-Luther-Universit t Halle-Wittenberg W.-Langenbeck-Straße 4, 06120 Halle (Germany)
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6
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Ouimet CM, Shao H, Rauch JN, Dawod M, Nordhues B, Dickey CA, Gestwicki JE, Kennedy RT. Protein Cross-Linking Capillary Electrophoresis for Protein-Protein Interaction Analysis. Anal Chem 2016; 88:8272-8. [PMID: 27434096 DOI: 10.1021/acs.analchem.6b02126] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Capillary electrophoresis (CE) has been identified as a useful platform for detecting, quantifying, and screening for modulators of protein-protein interactions (PPIs). In this method, one protein binding partner is labeled with a fluorophore, the protein binding partners are mixed, and then, the complex is separated from free protein to allow direct determination of bound to free ratios. Although it possesses many advantages for PPI studies, the method is limited by the need to have separation conditions that both prevent protein adsorption to capillary and maintain protein interactions during the separation. In this work, we use protein cross-linking capillary electrophoresis (PXCE) to overcome this limitation. In PXCE, the proteins are cross-linked under binding conditions and then separated. This approach eliminates the need to maintain noncovalent interactions during electrophoresis and facilitates method development. We report PXCE methods for an antibody-antigen interaction and heterodimer and homodimer heat shock protein complexes. Complexes are cross-linked by short treatments with formaldehyde after reaching binding equilibrium. Cross-linked complexes are separated by electrophoretic mobility using free solution CE or by size using sieving electrophoresis of SDS complexes. The method gives good quantitative results; e.g., a lysozyme-antibody interaction was found to have Kd = 24 ± 3 nM by PXCE and Kd = 17 ± 2 nM using isothermal calorimetry (ITC). Heat shock protein 70 (Hsp70) in complex with bcl2 associated athanogene 3 (Bag3) was found to have Kd = 25 ± 5 nM by PXCE which agrees with Kd values reported without cross-linking. Hsp70-Bag3 binding site mutants and small molecule inhibitors of Hsp70-Bag3 were characterized by PXCE with good agreement to inhibitory constants and IC50 values obtained by a bead-based flow cytometry protein interaction assay (FCPIA). PXCE allows rapid method development for quantitative analysis of PPIs.
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Affiliation(s)
- Claire M Ouimet
- Department of Chemistry, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Hao Shao
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California at San Francisco , 675 Nelson Rising Ln., San Francisco, California 94158, United States
| | - Jennifer N Rauch
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California at San Francisco , 675 Nelson Rising Ln., San Francisco, California 94158, United States
| | - Mohamed Dawod
- Department of Chemistry, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Bryce Nordhues
- Department of Molecular Medicine, University of South Florida , 4001 E. Fletcher Ave., MDC 36, Tampa, Florida 33613, United States
| | - Chad A Dickey
- Department of Molecular Medicine, University of South Florida , 4001 E. Fletcher Ave., MDC 36, Tampa, Florida 33613, United States
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California at San Francisco , 675 Nelson Rising Ln., San Francisco, California 94158, United States
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States.,Department of Pharmacology, University of Michigan , 1150 W. Medical Center Dr., Ann Arbor, Michigan 48109, United States
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7
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Clark AR, Carter AB, Hager LE, Price EM. In Vivo Neural Tissue Engineering: Cylindrical Biocompatible Hydrogels That Create New Neural Tracts in the Adult Mammalian Brain. Stem Cells Dev 2016; 25:1109-18. [PMID: 27295980 DOI: 10.1089/scd.2016.0069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Individuals with neurodegenerative disorders or brain injury have few treatment options and it has been proposed that endogenous adult neural stem cells can be harnessed to repopulate dysfunctional nonneurogenic regions of the brain. We have accomplished this through the development of rationally designed hydrogel implants that recruit endogenous cells from the adult subventricular zone to create new relatively long tracts of neuroblasts. These implants are biocompatible and biodegradable cylindrical hydrogels consisting of fibrin and immobilized neurotrophic factors. When implanted into rat brain such that the cylinder intersected the migratory path of endogenous neural progenitors (the rostral migratory stream) and led into the nonneurogenic striatum, we observed a robust neurogenic response in the form of migrating neuroblasts with long (>100 μm) complex neurites. The location of these new neural cells in the striatum was directly coincident with the original track of the fibrin implant, which itself had completely degraded, and covered a significant area and distance (>2.5 mm). We also observed a significant number of neuroblasts in the striatal region between the implant track and the lateral ventricle. When these fibrin cylinders were implanted into hemiparkinson rats, correction of parkinsonian behavior was observed. There were no obvious behavioral, inflammatory or tumorigenic sequelae as a consequence of the implants. In conclusion, we have successfully engineered neural tissue in vivo, using neurogenic biomaterials cast into a unique cylindrical architecture. These results represent a novel approach to efficiently induce neurogenesis in a controlled and targeted manner, which may lead toward a new therapeutic modality for neurological disorders.
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Affiliation(s)
- Amanda R Clark
- Department of Biology, Marshall University , Huntington, West Virginia
| | - Arrin B Carter
- Department of Biology, Marshall University , Huntington, West Virginia
| | - Lydia E Hager
- Department of Biology, Marshall University , Huntington, West Virginia
| | - Elmer M Price
- Department of Biology, Marshall University , Huntington, West Virginia
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8
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Marcoux J, Cianférani S. Towards integrative structural mass spectrometry: Benefits from hybrid approaches. Methods 2015; 89:4-12. [DOI: 10.1016/j.ymeth.2015.05.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/06/2015] [Accepted: 05/25/2015] [Indexed: 01/10/2023] Open
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9
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Chen F, Gerber S, Korkhov VM, Mireku S, Bucher M, Locher KP, Zenobi R. On the efficiency of NHS ester cross-linkers for stabilizing integral membrane protein complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:493-498. [PMID: 25404159 DOI: 10.1007/s13361-014-1035-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 06/04/2023]
Abstract
We have previously presented a straightforward approach based on high-mass matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) to study membrane proteins. In addition, the stoichiometry of integral membrane protein complexes could be determined by MALDI-MS, following chemical cross-linking via glutaraldehyde. However, glutaraldehyde polymerizes in solution and reacts nonspecifically with various functional groups of proteins, limiting its usefulness for structural studies of protein complexes. Here, we investigated the capability of N-hydroxysuccinimide (NHS) esters, which react much more specifically, to cross-link membrane protein complexes such as PglK and BtuC(2)D(2). We present clear evidence that NHS esters are capable of stabilizing membrane protein complexes in situ, in the presence of detergents such as DDM, C12E8, and LDAO. The stabilization efficiency strongly depends on the membrane protein structure (i.e, the number of primary amine groups and the distances between primary amines). A minimum number of primary amine groups is required, and the distances between primary amines govern whether a cross-linker with a specific spacer arm length is able to bridge two amine groups.
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Affiliation(s)
- Fan Chen
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
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10
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Remmele RL, Bee JS, Phillips JJ, Mo WD, Higazi DR, Zhang J, Lindo V, Kippen AD. Characterization of Monoclonal Antibody Aggregates and Emerging Technologies. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1202.ch005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Richard L. Remmele
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jared S. Bee
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jonathan J. Phillips
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Wenjun David Mo
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Daniel R. Higazi
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jifeng Zhang
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Vivian Lindo
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Alistair D. Kippen
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
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11
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Weidmann S, Mikutis G, Barylyuk K, Zenobi R. Mass discrimination in high-mass MALDI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1396-1404. [PMID: 23836380 DOI: 10.1007/s13361-013-0686-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 05/27/2013] [Accepted: 05/28/2013] [Indexed: 06/02/2023]
Abstract
In high-mass matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), the accessible m/z range is limited by the detector used. Therefore, special high-mass detectors based on ion conversion dynodes (ICDs) have been developed. Recently, we have found that mass bias may exist when such ICD detectors are used [Weidmann et al., Anal. Chem. 85(6), 3425-3432 (2013)]. In this contribution, the mass-dependent response of an ICD detector was systematically studied, the response factors for proteins with molecular weights from 35.9 to 129.9 kDa were determined, and the reasons for mass bias were identified. Compared with commonly employed microchannel plate detectors, we found that the mass discrimination is less pronounced, although ions with higher masses are weakly favored when using an ICD detector. The relative response was found to depend on the laser power used for MALDI; low-mass ions are discriminated against with higher laser power. The effect of mutual ion suppression in dependence of the proteins used and their molar ratio is shown. Mixtures consisting of protein oligomers that only differ in mass show less mass discrimination than mixtures consisting of different proteins with similar masses. Furthermore, mass discrimination increases for molar ratios far from 1. Finally, we present clear guidelines that help to choose the experimental parameters such that the response measured matches the actual molar fraction as closely as possible.
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Affiliation(s)
- Simon Weidmann
- Department of Chemistry and Applied Biosciences, ETH (Swiss Federal Institute of Technology) Zürich, Zürich, Switzerland
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12
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Merkley ED, Cort JR, Adkins JN. Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze. ACTA ACUST UNITED AC 2013; 14:77-90. [PMID: 23917845 DOI: 10.1007/s10969-013-9160-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 07/26/2013] [Indexed: 12/12/2022]
Abstract
Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature. These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes.
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Affiliation(s)
- Eric D Merkley
- MS K8-98, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Loo JA, Darie CC. Investigation of stable and transient protein-protein interactions: Past, present, and future. Proteomics 2013. [PMID: 23193082 DOI: 10.1002/pmic.201200328] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (PPIs) with a focus on their function within cells, organs, and organisms. The significance of PTMs within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPIs, with particular emphasis on electrophoresis-based and MS-based investigation of PPIs, including specific examples. The validation of PPIs is emphasized and the limitations of the current methods for studying stable and transient PPIs are discussed. Perspectives regarding PPIs, with focus on bioinformatics and transient PPIs are also provided.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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14
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Zinn N, Hopf C, Drewes G, Bantscheff M. Mass spectrometry approaches to monitor protein-drug interactions. Methods 2012; 57:430-40. [PMID: 22687620 DOI: 10.1016/j.ymeth.2012.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/16/2012] [Accepted: 05/28/2012] [Indexed: 12/16/2022] Open
Abstract
Recent advances in mass spectrometry-based approaches have enabled the investigation of drug-protein interactions in various ways including the direct detection of drug-target complexes, the examination of drug-induced changes in the target protein structure, and the monitoring of enzymatic target activity. Mass spectrometry-based proteomics methods also permit the unbiased analysis of changes in protein abundance and post-translational modifications induced by drug action. Finally, chemoproteomic affinity enrichment studies enable the deconvolution of drug targets under close to physiological conditions. This review provides an overview of current methods for the characterization of drug-target interactions by mass spectrometry and describes a protocol for chemoproteomic target binding studies using immobilized bioactive molecules.
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Affiliation(s)
- Nico Zinn
- Cellzome AG, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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15
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Mädler S, Barylyuk K, Boeri Erba E, Nieckarz RJ, Zenobi R. Compelling advantages of negative ion mode detection in high-mass MALDI-MS for homomeric protein complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:213-224. [PMID: 22131225 DOI: 10.1007/s13361-011-0274-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/04/2011] [Accepted: 10/08/2011] [Indexed: 05/31/2023]
Abstract
Chemical cross-linking in combination with high-mass MALDI mass spectrometry allows for the rapid identification of interactions and determination of the complex stoichiometry of noncovalent protein-protein interactions. As the molecular weight of these complexes increases, the fraction of multiply charged species typically increases. In the case of homomeric complexes, signals from multiply charged multimers overlap with singly charged subunits. Remarkably, spectra recorded in negative ion mode show lower abundances of multiply charged species, lower background, higher reproducibility, and, thus, overall cleaner spectra compared with positive ion mode spectra. In this work, a dedicated high-mass detector was applied for measuring high-mass proteins (up to 200 kDa) by negative ion mode MALDI-MS. The influences of sample preparation and instrumental parameters were carefully investigated. Relative signal integrals of multiply charged anions were relatively independent of any of the examined parameters and could thus be approximated easily for the spectra of cross-linked complexes. For example, the fraction of doubly charged anions signals overlapping with the signals of singly charged subunits could be more precisely estimated than in positive ion mode. Sinapinic acid was found to be an excellent matrix for the analysis of proteins and cross-linked protein complexes in both ion modes. Our results suggest that negative ion mode data of chemically cross-linked protein complexes are complementary to positive ion mode data and can in some cases represent the solution phase situation better than positive ion mode.
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Affiliation(s)
- Stefanie Mädler
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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Pacholarz KJ, Garlish RA, Taylor RJ, Barran PE. Mass spectrometry based tools to investigate protein–ligand interactions for drug discovery. Chem Soc Rev 2012; 41:4335-55. [DOI: 10.1039/c2cs35035a] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Mädler S, Boeri Erba E, Zenobi R. MALDI-ToF mass spectrometry for studying noncovalent complexes of biomolecules. Top Curr Chem (Cham) 2012; 331:1-36. [PMID: 22371170 DOI: 10.1007/128_2011_311] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been demonstrated to be a valuable tool to investigate noncovalent interactions of biomolecules. The direct detection of noncovalent assemblies is often more troublesome than with electrospray ionization. Using dedicated sample preparation techniques and carefully optimized instrumental parameters, a number of biomolecule assemblies were successfully analyzed. For complexes dissociating under MALDI conditions, covalent stabilization with chemical cross-linking is a suitable alternative. Indirect methods allow the detection of noncovalent assemblies by monitoring the fading of binding partners or altered H/D exchange patterns.
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Affiliation(s)
- Stefanie Mädler
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
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Chavez JD, Liu NL, Bruce JE. Quantification of protein-protein interactions with chemical cross-linking and mass spectrometry. J Proteome Res 2011; 10:1528-37. [PMID: 21222489 DOI: 10.1021/pr100898e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Chemical cross-linking in combination with mass spectrometry has largely been used to study protein structures and protein-protein interactions. Typically, it is used in a qualitative manner to identify cross-linked sites and provide a low-resolution topological map of the interacting regions of proteins. Here, we investigate the capability of chemical cross-linking to quantify protein-protein interactions using a model system of calmodulin and substrates melittin and mastoparan. Calmodulin is a well-characterized protein which has many substrates. Melittin and mastoparan are two such substrates which bind to calmodulin in 1:1 ratios in the presence of calcium. Both the calmodulin-melittin and calmodulin-mastoparan complexes have had chemical cross-linking strategies successfully applied in the past to investigate topological properties. We utilized an excess of immobilized calmodulin on agarose beads and formed complexes with varying quantities of mastoparan and melittin. Then, we applied disuccinimidyl suberate (DSS) chemical cross-linker, digested and detected cross-links through an LC-MS analytical method. We identified five interpeptide cross-links for calmodulin-melittin and three interpeptide cross-links for calmodulin-mastoparan. Using cross-linking sites of calmodulin-mastoparan, we demonstrated that mastoparan also binds in two orientations to calmodulin. We quantitatively demonstrated that both melittin and mastoparan preferentially bind to calmodulin in a parallel fashion, which is opposite to the preferred binding mode of the majority of known calmodulin binding peptides. We also demonstrated that the relative abundances of cross-linked peptide products quantitatively reflected the abundances of the calmodulin peptide complexes formed.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, PO Box 358050, Seattle, Washington 98195, United States
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Rappsilber J. The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J Struct Biol 2010; 173:530-40. [PMID: 21029779 PMCID: PMC3043253 DOI: 10.1016/j.jsb.2010.10.014] [Citation(s) in RCA: 319] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/21/2010] [Accepted: 10/21/2010] [Indexed: 11/17/2022]
Abstract
After more than a decade of method development, cross-linking in combination with mass spectrometry and bioinformatics is finally coming of age. This technology now provides improved opportunities for modelling by mapping structural details of functional complexes in solution. The structure of proteins or protein complexes is ascertained by identifying amino acid pairs that are positioned in close proximity to each other. The validity of this technique has recently been benchmarked for large multi-protein complexes, by comparing cross-link data with that from a crystal structure of RNA polymerase II. Here, the specific nature of this cross-linking data will be discussed to assess the technical challenges and opportunities for model building. We believe that once remaining technological challenges of cross-linking/mass spectrometry have been addressed and cross-linking/mass spectrometry data has been incorporated into modelling algorithms it will quickly become an indispensable companion of protein and protein complex modelling and a corner-stone of integrated structural biology.
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Affiliation(s)
- Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, King's Buildings, Mayfield Road, Edinburgh, EH9 3JR Scotland, UK.
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