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Kaltashov IA. Mass spectrometry-based methods to study macromolecular higher order structure and interactions. Methods 2018; 144:1-2. [DOI: 10.1016/j.ymeth.2018.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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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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Vaughan RC, Kao CC. Mapping protein-RNA interactions by RCAP, RNA-cross-linking and peptide fingerprinting. Methods Mol Biol 2015; 1297:225-236. [PMID: 25896007 DOI: 10.1007/978-1-4939-2562-9_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
RNA nanotechnology often feature protein RNA complexes. The interaction between proteins and large RNAs are difficult to study using traditional structure-based methods like NMR or X-ray crystallography. RCAP, an approach that uses reversible-cross-linking affinity purification method coupled with mass spectrometry, has been developed to map regions within proteins that contact RNA. This chapter details how RCAP is applied to map protein-RNA contacts within virions.
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Affiliation(s)
- Robert C Vaughan
- Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne St., 201A Simon Hall, Bloomington, IN, 47405, USA,
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Abstract
Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.
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Wyttenbach T, Pierson NA, Clemmer DE, Bowers MT. Ion Mobility Analysis of Molecular Dynamics. Annu Rev Phys Chem 2014; 65:175-96. [DOI: 10.1146/annurev-physchem-040513-103644] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Wyttenbach
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106;
| | | | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405;
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106;
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Twenty years of gas phase structural biology. Structure 2014; 21:1541-50. [PMID: 24010713 DOI: 10.1016/j.str.2013.08.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/06/2013] [Accepted: 08/06/2013] [Indexed: 01/01/2023]
Abstract
Over the past two decades, mass spectrometry (MS) of protein complexes from their native state has made inroads into structural biology. To coincide with the 20(th) anniversary of Structure, and given that it is now approximately 20 years since the first mass spectra of noncovalent protein complexes were reported, it is timely to consider progress of MS as a structural biology tool. Early reports focused on soluble complexes, contributing to ligand binding studies, subunit interaction maps, and topological models. Recent discoveries have enabled delivery of membrane complexes, encapsulated in detergent micelles, prompting new opportunities. By maintaining interactions between membrane and cytoplasmic subunits in the gas phase, it is now possible to investigate the effects of lipids, nucleotides, and drugs on intact membrane assemblies. These investigations reveal allosteric and synergistic effects of small molecule binding and expose the consequences of posttranslational modifications. In this review, we consider recent progress in the study of protein complexes, focusing particularly on complexes extracted from membranes, and outline future prospects for gas phase structural biology.
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Deinhardt K, Darie CC. Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. Cell Mol Life Sci 2014; 71:205-28. [PMID: 23579629 PMCID: PMC11113707 DOI: 10.1007/s00018-013-1333-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 11/28/2022]
Abstract
Following the sequencing of the human genome and many other organisms, research on protein-coding genes and their functions (functional genomics) has intensified. Subsequently, with the observation that proteins are indeed the molecular effectors of most cellular processes, the discipline of proteomics was born. Clearly, proteins do not function as single entities but rather as a dynamic network of team players that have to communicate. Though genetic (yeast two-hybrid Y2H) and biochemical methods (co-immunoprecipitation Co-IP, affinity purification AP) were the methods of choice at the beginning of the study of protein-protein interactions (PPI), in more recent years there has been a shift towards proteomics-based methods and bioinformatics-based approaches. In this review, we first describe in depth PPIs and we make a strong case as to why unraveling the interactome is the next challenge in the field of proteomics. Furthermore, classical methods of investigation of PPIs and structure-based bioinformatics approaches are presented. The greatest emphasis is placed on proteomic methods, especially native techniques that were recently developed and that have been shown to be reliable. Finally, we point out the limitations of these methods and the need to set up a standard for the validation of PPI experiments.
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Affiliation(s)
- Armand G. Ngounou Wetie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Izabela Sokolowska
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Alisa G. Woods
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Urmi Roy
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
| | - Katrin Deinhardt
- Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
- Institute for Life Sciences, University of Southampton, Life Sciences Building 85, Southampton, SO17 1BJ UK
| | - Costel C. Darie
- Department of Chemistry and Biomolecular Science, Biochemistry and Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699-5810 USA
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Minsky BB, Nguyen TV, Peyton SR, Kaltashov IA, Dubin PL. Heparin decamer bridges a growth factor and an oligolysine by different charge-driven interactions. Biomacromolecules 2013; 14:4091-8. [PMID: 24107074 DOI: 10.1021/bm401227p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Full-length heparin is widely used in tissue engineering applications due its multiple protein-binding sites that allow it to retain growth factor affinity while associating with oligopeptide components of the tissue scaffold. However, the extent to which oligopeptide coupling interferes with cognate protein binding is difficult to predict. To investigate such simultaneous interactions, we examined a well-defined ternary system comprised of acidic fibroblast growth factor (FGF), tetralysine (K4), with a heparin decamer (dp10) acting as a noncovalent coupler. Electrospray ionization mass spectrometry was used to assess binding affinities and complex stoichiometries as a function of ionic strength for dp10·K4 and FGF·dp10. The ionic strength dependence of K4·dp10 formation is qualitatively consistent with binding driven by the release of condensed counterions previously suggested for native heparin with divalent oligopeptides (Mascotti, D. P.; Lohman, T. M. Biochemistry 1995, 34, 2908-2915). On the other hand, FGF binding displays more complex ionic strength dependence, with higher salt resistance. Remarkably, dp10 that can bind two FGF molecules can only bind one tetralysine. The limited binding of K4 to dp10 suggests that the tetralysine might not block growth factor binding, and the 1:1:1 ternary complex is indeed observed. The analysis of mass distribution of the bound dp10 chains in FGF·dp10, FGF2·dp10, and FGF·dp10·K4 complexes indicated that higher degrees of dp10 sulfation promote the formation of FGF2·dp10 and FGF·dp10·K4. Thus, the selectivity of appropriately chosen short heparin chains could be used to modulate growth factor sequestration and release in a way not feasible with heterogeneous native heparin. In support of this, human hepatocellular carcinoma cells (HEP3Bs) treated with FGF·dp10·K4 were found to exhibit biological activity similar to cells treated with FGF.
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Affiliation(s)
- Burcu Baykal Minsky
- Departments of †Chemistry and ‡Chemical Engineering, University of Massachusetts , 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
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The potential for clinical applications using a new ionization method combined with ion mobility spectrometry-mass spectrometry. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12127-013-0131-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Meyer T, Gabelica V, Grubmüller H, Orozco M. Proteins in the gas phase. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1130] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Salbo R, Bush MF, Naver H, Campuzano I, Robinson CV, Pettersson I, Jørgensen TJD, Haselmann KF. Traveling-wave ion mobility mass spectrometry of protein complexes: accurate calibrated collision cross-sections of human insulin oligomers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1181-1193. [PMID: 22499193 DOI: 10.1002/rcm.6211] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE The collision cross-section (Ω) of a protein or protein complex ion can be measured using traveling-wave (T-wave) ion mobility (IM) mass spectrometry (MS) via calibration with compounds of known Ω. The T-wave Ω-values depend strongly on instrument parameters and calibrant selection. Optimization of instrument parameters and calibration standards are crucial for obtaining accurate T-wave Ω-values. METHODS Human insulin and the fast-acting insulin aspart under native-like conditions (ammonium acetate, physiological pH) were analyzed on Waters SYNAPT G1 and G2 HDMS instruments. The calibrated T-wave Ω-values of insulin monomer, dimer, and hexamer ions were measured using many different combinations of denatured and native-like calibrants (masses between 2.85 and 256 kDa) and T-wave conditions. Drift-tube Ω-values were obtained on a modified SYNAPT G1. RESULTS Insulin T-wave Ω-values were measured at 26 combinations of T-wave velocity and amplitude. Optimal sets of calibrants were identified that yield Ω-values with minimal dependence on T-wave conditions and calibration plots with high R(2)-values. The T-wave Ω-values determined under conditions satisfying these criteria had absolute errors <2%. Structural differences between human insulin and fast-acting insulin aspart were probed with IM-MS. Insulin aspart monomers have increased flexibility, while hexamers are more compact than human insulin. CONCLUSIONS Accurate T-wave Ω-values that are indistinguishable from drift-tube values are obtained when using (1) native-like calibrants with masses that closely bracket that of the analyte, (2) T-wave velocities that maximize the R(2) of the calibration plot for those calibrants, and (3) at least three replicates at T-wave velocities that yield calibration plots with high R(2).
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Affiliation(s)
- Rune Salbo
- Diabetes Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
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Brélivet Y, Rochel N, Moras D. Structural analysis of nuclear receptors: from isolated domains to integral proteins. Mol Cell Endocrinol 2012; 348:466-73. [PMID: 21888944 DOI: 10.1016/j.mce.2011.08.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/28/2011] [Accepted: 08/12/2011] [Indexed: 11/26/2022]
Abstract
Nuclear receptors (NRs) are ligand dependent transcription factors that regulate gene expression. A number of in depth structure-function relationship studies have been performed, in particular with drug design perspectives. Recent structural results concerning integral receptors in diverse functional states, obtained using a combination of different methods, now allow a better understanding of the mechanisms involved in molecular regulation. The structural data highlight the importance of DNA sequences for binding selectivity and the role of promoter response elements in the spatial organization of the protein domains into functional complexes. The solution structures of several heterodimer complexes reveal how the DNA directs the positioning of coactivators. In the case of PPARγ-RXRα the comparison with the crystal structure reveals two different conformational states that illustrate the flexibility of the receptors. The results shed light on the dynamics of the molecular recognition process.
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Affiliation(s)
- Yann Brélivet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Institut National de la Santé et de la Recherche Médicale U964/Centre National de Recherche Scientifique UMR7104/Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch, France
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Stengel F, Aebersold R, Robinson CV. Joining forces: integrating proteomics and cross-linking with the mass spectrometry of intact complexes. Mol Cell Proteomics 2011; 11:R111.014027. [PMID: 22180098 PMCID: PMC3316738 DOI: 10.1074/mcp.r111.014027] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein assemblies are critical for cellular function and understanding their physical organization is the key aim of structural biology. However, applying conventional structural biology approaches is challenging for transient, dynamic, or polydisperse assemblies. There is therefore a growing demand for hybrid technologies that are able to complement classical structural biology methods and thereby broaden our arsenal for the study of these important complexes. Exciting new developments in the field of mass spectrometry and proteomics have added a new dimension to the study of protein-protein interactions and protein complex architecture. In this review, we focus on how complementary mass spectrometry-based techniques can greatly facilitate structural understanding of protein assemblies.
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Affiliation(s)
- Florian Stengel
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, OX1 3TA United Kingdom
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