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Das D, Samanta D, Bhattacharya A, Basu A, Das A, Ghosh J, Chakrabarti A, Das Gupta C. A Possible Role of the Full-Length Nascent Protein in Post-Translational Ribosome Recycling. PLoS One 2017; 12:e0170333. [PMID: 28099529 PMCID: PMC5242463 DOI: 10.1371/journal.pone.0170333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/03/2017] [Indexed: 11/30/2022] Open
Abstract
Each cycle of translation initiation in bacterial cell requires free 50S and 30S ribosomal subunits originating from the post-translational dissociation of 70S ribosome from the previous cycle. Literature shows stable dissociation of 70S from model post-termination complexes by the concerted action of Ribosome Recycling Factor (RRF) and Elongation Factor G (EF-G) that interact with the rRNA bridge B2a/B2b joining 50S to 30S. In such experimental models, the role of full-length nascent protein was never considered seriously. We observed relatively slow release of full-length nascent protein from 50Sof post translation ribosome, and in that process, its toe prints on the rRNA in vivo and in in vitro translation with E.coli S30 extract. We reported earlier that a number of chemically unfolded proteins like bovine carbonic anhydrase (BCA), lactate dehydrogenase (LDH), malate dehydrogenase (MDH), lysozyme, ovalbumin etc., when added to free 70Sin lieu of the full length nascent proteins, also interact with identical RNA regions of the 23S rRNA. Interestingly the rRNA nucleotides that slow down release of the C-terminus of full-length unfolded protein were found in close proximity to the B2a/B2b bridge. It indicated a potentially important chemical reaction conserved throughout the evolution. Here we set out to probe that conserved role of unfolded protein conformation in splitting the free or post-termination 70S. How both the RRF-EFG dependent and the plausible nascent protein–EFG dependent ribosome recycling pathways might be relevant in bacteria is discussed here.
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Affiliation(s)
- Debasis Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
| | - Dibyendu Samanta
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
| | - Arpita Bhattacharya
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
| | - Arunima Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
- Department of Microbiology, Raidighi College, Raidighi, 24 Parganas (S), West Bengal, India
| | - Anindita Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
| | - Jaydip Ghosh
- Department of Microbiology, St. Xavier’s College, Kolkata, India
| | - Abhijit Chakrabarti
- Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, Kolkata, India
| | - Chanchal Das Gupta
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India
- Department of Life Sciences and Biotechnology, Jadavpur University, Kolkata, India
- * E-mail:
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2
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Electrospray Ionization. Mass Spectrom (Tokyo) 2017. [DOI: 10.1007/978-3-319-54398-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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3
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Bhadra PK, Hassanzadeh A, Arsic B, Allison DG, Morris GA, Barber J. Enhancement of the properties of a drug by mono-deuteriation: reduction of acid-catalysed formation of a gut-motilide enol ether from 8-deuterio-erythromycin B. Org Biomol Chem 2016; 14:6289-96. [DOI: 10.1039/c6ob00785f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient synthesis of 8-d-erythromycin B was achieved. A deuterium isotope effect suppresses formation of the corresponding enol ether, which may result in reduced gut-motilide effects.
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Affiliation(s)
| | | | - Biljana Arsic
- Manchester Pharmacy School
- University of Manchester
- Manchester
- UK
| | | | | | - Jill Barber
- Manchester Pharmacy School
- University of Manchester
- Manchester
- UK
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4
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Blake RC, Blake DA. Electrospray ionization-ion mobility spectrometry identified monoclonal antibodies that bind exclusively to either the monomeric or a dimeric form of prostate specific antigen. Anal Chem 2012; 84:6899-906. [PMID: 22827589 PMCID: PMC3413244 DOI: 10.1021/ac301527v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
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Macroion mobility spectrometry was used to distinguish
between
a monoclonal antibody (clone M612165) that bound exclusively to monomeric
prostate specific antigen and a different monoclonal antibody (clone
M612166) that bound exclusively to a dimeric form of the antigen that
only comprised 6.8% of the total protein. In the presence of excess
antigen, the mobility spectrum of M612165 was replaced by a composite
spectrum that represented a mixture of antibodies that included either
one or two equivalents of the protein antigen. In similar circumstances,
the mobility spectrum of M612166 was replaced by a composite spectrum
that represented a mixture of antibodies that included either two
or four equivalents of the protein antigen. When exposed to either
of the two antibodies, the mobility spectrum of the prostate specific
antigen showed a concomitant decrease in the monomeric antigen in
one case and in the dimeric antigen in the other case. While sensitive
kinetic exclusion assays demonstrated large differences in the antigen
binding behavior of the two antibodies, these functional studies alone
were insufficient to reveal the likely structural origins of the observed
differences. Macroion mobility measurements were shown to be a useful
and informative complement to functional studies in understanding
complex macromolecular interactions.
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Affiliation(s)
- Robert C Blake
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana 70125, USA.
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5
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Deroo S, Hyung SJ, Marcoux J, Gordiyenko Y, Koripella RK, Sanyal S, Robinson CV. Mechanism and rates of exchange of L7/L12 between ribosomes and the effects of binding EF-G. ACS Chem Biol 2012; 7:1120-7. [PMID: 22489843 PMCID: PMC4058753 DOI: 10.1021/cb300081s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ribosomal stalk complex binds and recruits translation factors to the ribosome during protein biosynthesis. In Escherichia coli the stalk is composed of protein L10 and four copies of L7/L12. Despite the crucial role of the stalk, mechanistic details of L7/L12 subunit exchange are not established. By incubating isotopically labeled intact ribosomes with their unlabeled counterparts we monitored the exchange of the labile stalk proteins by recording mass spectra as a function of time. On the basis of kinetic analysis, we proposed a mechanism whereby exchange proceeds via L7/L12 monomers and dimers. We also compared exchange of L7/L12 from free ribosomes with exchange from ribosomes in complex with elongation factor G (EF-G), trapped in the posttranslocational state by fusidic acid. Results showed that binding of EF-G reduces the L7/L12 exchange reaction of monomers by ~27% and of dimers by ~47% compared with exchange from free ribosomes. This is consistent with a model in which binding of EF-G does not modify interactions between the L7/L12 monomers but rather one of the four monomers, and as a result one of the two dimers, become anchored to the ribosome-EF-G complex preventing their free exchange. Overall therefore our results not only provide mechanistic insight into the exchange of L7/L12 monomers and dimers and the effects of EF-G binding but also have implications for modulating stability in response to environmental and functional stimuli within the cell.
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Affiliation(s)
- Stéphanie Deroo
- University of Oxford, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Suk-Joon Hyung
- University of Michigan, Department of Chemistry, 930 N. University, Ann Arbor, MI 48109-1055, USA
| | - Julien Marcoux
- University of Oxford, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Yuliya Gordiyenko
- University of Oxford, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - Ravi Kiran Koripella
- Uppsala University, Department of Cell and Molecular Biology, BMC, Box-596, S-75 124 Uppsala, Sweden
| | - Suparna Sanyal
- Uppsala University, Department of Cell and Molecular Biology, BMC, Box-596, S-75 124 Uppsala, Sweden
| | - Carol V. Robinson
- University of Oxford, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
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6
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Robinson CV. Finding the right balance - a personal journey from individual proteins to membrane-embedded motors. FEBS J 2012; 279:663-77. [DOI: 10.1111/j.1742-4658.2011.08460.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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7
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Abstract
The comprehensive analysis of intact proteins down to the level of their individual amino acid sequence and the entirety of post-translational modifications is an area that can hardly be covered by the typical workflow in MS based protein analysis, which comprises enzymatic digestion, mass spectrometric analysis and subsequent database search. This approach typically provides 20-80% sequence coverage, which is not sufficient for the characterization of biopharmaceuticals, for example. This generates the requirement for a comprehensive analysis of the protein, without the risk of losing sequence information due to undetected peptides. Top-down sequencing of proteins starts from the intact protein, typically by determining the intact protein mass in the first step, a fragmentation of the intact protein is then performed within the mass spectrometer, resulting in fragment ions that allow us to pinpoint the protein sequence, as well as potential modifications or mutations in their localization and structure. A number of technologies have been developed for this task in the last few years, based on various different mass spectrometric instrument configurations, but typically based on the same technology platforms as used for bottom-up strategies. Thus, the use of one specific instrument often allows the application of top-down and bottom-up technologies in a complementary way, providing much more detailed information about the proteins of interest than either of the approaches alone.
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9
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Gordiyenko Y, Videler H, Zhou M, McKay AR, Fucini P, Biegel E, Müller V, Robinson CV. Mass spectrometry defines the stoichiometry of ribosomal stalk complexes across the phylogenetic tree. Mol Cell Proteomics 2010; 9:1774-83. [PMID: 20467040 DOI: 10.1074/mcp.m000072-mcp201] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribosomal stalk complex plays a crucial role in delivering translation factors to the catalytic site of the ribosome. It has a very similar architecture in all cells, although the protein components in bacteria are unrelated to those in archaea and eukaryotes. Here we used mass spectrometry to investigate ribosomal stalk complexes from bacteria, eukaryotes, and archaea in situ on the ribosome. Specifically we targeted ribosomes with different optimal growth temperatures. Our results showed that for the mesophilic bacterial ribosomes we investigated the stalk complexes are exclusively pentameric or entirely heptameric in the case of thermophilic bacteria, whereas we observed only pentameric stalk complexes in eukaryotic species. We also found the surprising result that for mesophilic archaea, Methanococcus vannielii, Methanococcus maripaludis, and Methanosarcina barkeri, both pentameric and heptameric stoichiometries are present simultaneously within a population of ribosomes. Moreover the ratio of pentameric to heptameric stalk complexes changed during the course of cell growth. We consider these differences in stoichiometry within ribosomal stalk complexes in the context of convergent evolution.
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Affiliation(s)
- Yuliya Gordiyenko
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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10
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Fabris D. A role for the MS analysis of nucleic acids in the post-genomics age. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1-13. [PMID: 19897384 DOI: 10.1016/j.jasms.2009.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Revised: 09/04/2009] [Accepted: 09/04/2009] [Indexed: 05/28/2023]
Abstract
The advances of mass spectrometry in the analysis of nucleic acids have tracked very closely the exciting developments of instrumentation and ancillary technologies, which have taken place over the years. However, their diffusion in the broader life sciences community has been and will be linked to the ever evolving focus of biomedical research and its changing demands. Before the completion of the Human Genome Project, great emphasis was placed on sequencing technologies that could help accomplish this project of exceptional scale. After the publication of the human genome, the emphasis switched toward techniques dedicated to the exploration of sequences not coding for actual protein products, which amount to the vast majority of transcribed elements. The broad range of capabilities offered by mass spectrometry is rapidly advancing this platform to the forefront of the technologies employed for the structure-function investigation of these noncoding elements. Increasing focus on the characterization of functional assemblies and their specific interactions has prompted a re-evaluation of what has been traditionally construed as nucleic acid analysis by mass spectrometry. Inspired by the accelerating expansion of the broader field of nucleic acid research, new applications to fundamental biological studies and drug discovery will help redefine the evolving role of MS-analysis of nucleic acids in the post-genomics age.
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Affiliation(s)
- Daniele Fabris
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21228, USA.
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11
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Hernández H, Makarova OV, Makarov EM, Morgner N, Muto Y, Krummel DP, Robinson CV. Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP. PLoS One 2009; 4:e7202. [PMID: 19784376 PMCID: PMC2747018 DOI: 10.1371/journal.pone.0007202] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 08/13/2009] [Indexed: 12/24/2022] Open
Abstract
Most human protein-encoding genes contain multiple exons that are spliced together, frequently in alternative arrangements, by the spliceosome. It is established that U1 snRNP is an essential component of the spliceosome, in human consisting of RNA and ten proteins, several of which are post-translationally modified and exist as multiple isoforms. Unresolved and challenging to investigate are the effects of these post translational modifications on the dynamics, interactions and stability of the particle. Using mass spectrometry we investigate the composition and dynamics of the native human U1 snRNP and compare native and recombinant complexes to isolate the effects of various subunits and isoforms on the overall stability. Our data reveal differential incorporation of four protein isoforms and dynamic interactions of subunits U1-A, U1-C and Sm-B/B'. Results also show that unstructured post-translationally modified C-terminal tails are responsible for the dynamics of Sm-B/B' and U1-C and that their interactions with the Sm core are controlled by binding to different U1-70k isoforms and their phosphorylation status in vivo. These results therefore provide the important functional link between proteomics and structure as well as insight into the dynamic quaternary structure of the native U1 snRNP important for its function.
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Affiliation(s)
- Helena Hernández
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Olga V. Makarova
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Evgeny M. Makarov
- Division of Bioscience, School of Health and Social Care, Brunel University, Uxbridge, United Kingdom
| | - Nina Morgner
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Yutaka Muto
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Carol V. Robinson
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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12
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Morgner N, Barth HD, Schmidt TL, Heckel A, Scheffer U, Göbel M, Fucini P, Brutschy B. Detecting Specific Ligand Binding to Nucleic Acids: A Test for Ultrasoft Laser Mass Spectrometry. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zpch.2007.221.5.689] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Results from a new laser based mass spectrometry method termed LILBID (laser induced liquid bead ion desorption) are presented, which demonstrate the potential for the soft mass analysis of nucleic acids and their specific complexes in solution. On-demand micro droplets, injected into vacuum, are irradiated by intense mid IR-laser pulses. A subsequent explosive phase transition leads to the emission of solvated biomolecular ions into vacuum, which are then mass analyzed by time of flight mass spectrometry. The method is very soft and allows the detection of specific noncovalent complexes. Furthermore it is very tolerant against various buffers and detergents and the charge states of the observed ions reflect qualitatively the charge state in solution. With a required volume of analyte solution in the micro litre range at micromolar concentration, the total consumption of analyte is in the picomolar region. Regarding a single droplet only it is even three orders of magnitude lower, underlining the very high sensitivity of this method. Here we present first examples of the LILBID mass analysis of single stranded DNA (up to a 77mer) and of specific DNA duplices, which show nearly no dissociation under ultrasoft desorption conditions. In case of model hairpin DNA, forming duplices, a sequence specific binding of Dervan-type polyamides into the minor groove of the DNA was observed, and in case of a Tat-TAR model complex strong indications for a specific binding of the Tat protein into the bulge of the wt-RNA was found. Mass spectra of the ribosome of thermos thermophilus give evidence of the applicability of LILBID-MS to analyze large RNA/protein complexes even in the MDa region.
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13
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Liu X, Reilly JP. Correlating the Chemical Modification of Escherichia coli Ribosomal Proteins with Crystal Structure Data. J Proteome Res 2009; 8:4466-78. [DOI: 10.1021/pr9002382] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaohui Liu
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
| | - James P. Reilly
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405
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14
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Li Z, Song F, Zhuang Z, Dunaway-Mariano D, Anderson KS. Monitoring enzyme catalysis in the multimeric state: direct observation of Arthrobacter 4-hydroxybenzoyl-coenzyme A thioesterase catalytic complexes using time-resolved electrospray ionization mass spectrometry. Anal Biochem 2009; 394:209-16. [PMID: 19635449 DOI: 10.1016/j.ab.2009.07.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 07/06/2009] [Accepted: 07/20/2009] [Indexed: 11/19/2022]
Abstract
The ability to examine real-time reaction kinetics for multimeric enzymes in their native state may offer unique insights into understanding the catalytic mechanism and its interplay with three-dimensional structure. In this study, we have used a time-resolved electrospray mass spectrometry approach to probe the kinetic mechanism of 4-hydroxybenzoyl-coenzyme A (4-HBA-CoA) thioesterase from Arthrobacter sp. strain SU in the millisecond time domain. Intact tetrameric complexes of 4-HBA-CoA thioesterase with up to four natural substrate (4-HBA-CoA) molecules bound were detected at times as early as 6 ms using an online rapid-mixing device directly coupled to an electrospray ionization time-of-flight mass spectrometer. Species corresponding to the formation of a folded tetramer of the thioesterase at charge states 16+, 17+, 18+, and 19+ around m/z 3800 were observed and assigned as individual tetramers of thioesterase and noncovalent complexes of the tetramers with up to four substrate and/or product molecules. Real-time evaluation of the reaction kinetics was accomplished by monitoring change in peak intensity corresponding to the substrate and product complexes of the tetrameric protein. The mass spectral data suggest that product 4-HBA is released from the active site of the enzyme prior to the release of product CoA following catalytic turnover. This study demonstrates the utility of this technique to provide additional molecular details for an understanding of the individual enzyme states during the thioesterase catalysis and ability to observe real-time interactions between enzyme and substrates and/or products in the millisecond time range.
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Affiliation(s)
- Zhili Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
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15
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Rutkowska A, Beerbaum M, Rajagopalan N, Fiaux J, Schmieder P, Kramer G, Oschkinat H, Bukau B. Large-scale purification of ribosome-nascent chain complexes for biochemical and structural studies. FEBS Lett 2009; 583:2407-13. [DOI: 10.1016/j.febslet.2009.06.041] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 06/17/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
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16
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Hirokawa G, Iwakura N, Kaji A, Kaji H. The role of GTP in transient splitting of 70S ribosomes by RRF (ribosome recycling factor) and EF-G (elongation factor G). Nucleic Acids Res 2008; 36:6676-87. [PMID: 18948280 PMCID: PMC2588517 DOI: 10.1093/nar/gkn647] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ribosome recycling factor (RRF), elongation factor G (EF-G) and GTP split 70S ribosomes into subunits. Here, we demonstrated that the splitting was transient and the exhaustion of GTP resulted in re-association of the split subunits into 70S ribosomes unless IF3 (initiation factor 3) was present. However, the splitting was observed with sucrose density gradient centrifugation (SDGC) without IF3 if RRF, EF-G and GTP were present in the SDGC buffer. The splitting of 70S ribosomes causes the decrease of light scattering by ribosomes. Kinetic constants obtained from the light scattering studies are sufficient to account for the splitting of 70S ribosomes by RRF and EF-G/GTP during the lag phase for activation of ribosomes for the log phase. As the amount of 70S ribosomes increased, more RRF, EF-G and GTP were necessary to split 70S ribosomes. In the presence of a physiological amount of polyamines, GTP and factors, even 0.6 microM 70S ribosomes (12 times higher than the 70S ribosomes for routine assay) were split. Spermidine (2 mM) completely inhibited anti-association activity of IF3, and the RRF/EF-G/GTP-dependent splitting of 70S ribosomes.
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Affiliation(s)
- Go Hirokawa
- Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Jefferson Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
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17
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Guan H, Kiss-Toth E. Advanced technologies for studies on protein interactomes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 110:1-24. [PMID: 18219467 DOI: 10.1007/10_2007_092] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
One of the key challenges of biology in the post-genomic era is to assign function to the many genes revealed by large-scale sequencing programmes, since only a small fraction of gene function can be directly inferred from the coding sequence. Identifying interactions between proteins is a substantial part in understanding their function. The main technologies for investigating protein-protein interactions and assigning functions to proteins include direct detection intermolecular interactions through protein microarray, yeast two-hybrid system, mass spectrometry fluorescent techniques to visualize protein complexes or pull-down assays, as well as technologies detecting functional interactions between genes, such as RNAi knock down or functional screening of cDNA libraries. Over recent years, considerable advances have been made in the above techniques. In this review, we discuss some recent developments and their impact on the gene function annotation.
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Affiliation(s)
- Hongtao Guan
- Cardiovascular Research Unit, University of Sheffield, Royal Hallamshire Hospital, Glossop road, S10 2JF, Sheffield, UK
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18
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Gordiyenko Y, Deroo S, Zhou M, Videler H, Robinson CV. Acetylation of L12 increases interactions in the Escherichia coli ribosomal stalk complex. J Mol Biol 2008; 380:404-14. [PMID: 18514735 DOI: 10.1016/j.jmb.2008.04.067] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 04/23/2008] [Accepted: 04/26/2008] [Indexed: 11/18/2022]
Abstract
The ribosomal stalk complex in Escherichia coli consists of L10 and four copies of L7/L12, and is largely responsible for binding and recruiting translation factors. Structural characterisation of this stalk complex is difficult, primarily due to its dynamics. Here, we apply mass spectrometry to follow post-translational modifications and their effect on structural changes of the stalk proteins on intact ribosomes. Our results show that increased acetylation of L12 occurs during the stationary phase on ribosomes harvested from cells grown under optimal conditions. For cells grown in minimal medium, L12 acetylation and processing is altered, resulting in deficient removal of N-terminal methionine in approximately 50% of the L12 population, while processed L12 is almost 100% acetylated. Our results show also that N-acetylation of L12 correlates with an increased stability of the stalk complex in the gas phase. To investigate further the basis of this increased stability, we applied a solution phase hydrogen deuterium exchange protocol to compare the rate of deuterium incorporation in the proteins L9, L10, L11 and L12 as well as the acetylated form of L12 (L7), in situ on the ribosome. Results show that deuterium incorporation is consistently slower for L7 relative to L12 and for L10 when L7 is predominant. Our results imply a tightening of the interaction between L7 and L10 relative to that between L12 and L10. Since acetylation is predominant when cells are grown in minimal medium, we propose that these modifications form part of the cell's strategy to increase stability of the stalk complex under conditions of stress. More generally, our results demonstrate that it is possible to discern the influence of a 42 Da post-translational modification by mass spectrometry and to record subtle changes in hydrogen/deuterium exchange within the context of an intact 2.5 MDa particle.
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Affiliation(s)
- Yuliya Gordiyenko
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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19
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Wysocki VH, Joyce KE, Jones CM, Beardsley RL. Surface-induced dissociation of small molecules, peptides, and non-covalent protein complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:190-208. [PMID: 18191578 PMCID: PMC2709493 DOI: 10.1016/j.jasms.2007.11.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 10/23/2007] [Accepted: 11/03/2007] [Indexed: 05/12/2023]
Abstract
This article provides a perspective on collisions of ions with surfaces, including surface-induced dissociation (SID) and reactive ion scattering spectrometry (RISS). The content is organized into sections on surface-induced dissociation of small ions, surface characterization of organic thin films by collision of well-characterized ions into surfaces, the use of SID to probe peptide fragmentation, and the dissociation of large non-covalent complexes by SID. Examples are given from the literature with a focus on experiments from the authors' laboratory. The article is not a comprehensive review but is designed to provide the reader with an overview of the types of results possible by collisions of ions into surfaces.
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Affiliation(s)
- Vicki H Wysocki
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA.
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20
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Abstract
The fact that ions of macromolecular complexes produced by electrospray ionization can be maintained intact in a mass spectrometer has stimulated exciting new lines of research. In this review we chart the progress of this research from the observation of simple homo-oligomers to complex heterogeneous macromolecular assemblies of mega-Dalton proportions. The applications described herein not only confirm the status of mass spectrometry (MS) as a structural biology approach to complement X-ray analysis or electron microscopy, but also highlight unique attributes of the methodology. This is exemplified in studies of the biogenesis of macromolecular complexes and in the exchange of subunits between macromolecular complexes. Moreover, recent successes in revealing the overall subunit architecture of complexes are set to promote MS from a complementary approach to a structural biology tool in its own right.
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Affiliation(s)
- Michal Sharon
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
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Sharon M, Taverner T, Ambroggio XI, Deshaies RJ, Robinson CV. Structural organization of the 19S proteasome lid: insights from MS of intact complexes. PLoS Biol 2006; 4:e267. [PMID: 16869714 PMCID: PMC1523230 DOI: 10.1371/journal.pbio.0040267] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Accepted: 06/09/2006] [Indexed: 11/26/2022] Open
Abstract
The 26S proteasome contains a 19S regulatory particle that selects and unfolds ubiquitinated substrates for degradation in the 20S catalytic particle. To date there are no high-resolution structures of the 19S assembly, nor of the lid or base subcomplexes that constitute the 19S. Mass spectra of the intact lid complex from
Saccharomyces cerevisiae show that eight of the nine subunits are present stoichiometrically and that a stable tetrameric subcomplex forms in solution. Application of tandem mass spectrometry to the intact lid complex reveals the subunit architecture, while the coupling of a cross-linking approach identifies further interaction partners. Taking together our results with previous analyses we are able to construct a comprehensive interaction map. In summary, our findings allow us to identify a scaffold for the assembly of the particle and to propose a regulatory mechanism that prevents exposure of the active site until assembly is complete. More generally, the results highlight the potential of mass spectrometry to add crucial insight into the structural organization of an endogenous, wild-type complex.
Tandem mass spectrometry coupled with structural cross-linking enabled a depiction of how components of the 19S proteasome lid interact and the active site remains hidden until assembly is complete.
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Affiliation(s)
- Michal Sharon
- 1Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Thomas Taverner
- 1Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Xavier I Ambroggio
- 2Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Raymond J Deshaies
- 2Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Carol V Robinson
- 1Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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22
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Kitova EN, Daneshfar R, Marcato P, Mulvey GL, Armstrong G, Klassen JS. Stability of the homopentameric B subunits of shiga toxins 1 and 2 in solution and the gas phase as revealed by nanoelectrospray fourier transform ion cyclotron resonance mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1957-68. [PMID: 16242954 DOI: 10.1016/j.jasms.2005.07.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 07/07/2005] [Accepted: 07/12/2005] [Indexed: 05/05/2023]
Abstract
The assembly of the B subunits of Shiga toxins (Stx) 1 and 2 and the influence of solution conditions (protein concentration, temperature, pH, and ionic strength) on it are investigated using temperature-controlled nanoflow electrospray (nano-ES) ionization and Fourier-transform ion cyclotron resonance mass spectrometry. Despite the similar higher order structure predicted by X-ray crystallography analysis, the B(5) homopentamers of Stx1 and Stx2 exhibit differences in stability under the solution conditions investigated. At solution temperatures ranging from 0 to 60 degrees C and subunit concentrations ranging from 5 to 85 microM, the Stx1 B subunit exists almost entirely as the homopentamer in aqueous solutions, independent of the ionic strength. In contrast, the degree of assembly of Stx2 B subunit is strongly dependent on temperature, subunit concentration, and ionic strength. At subunit concentrations of more than 50 microM, the Stx2 B subunit exists predominantly as a pentamer, although smaller multimers (dimer, trimer, and tetramer) are also evident. At lower concentrations, the Stx2 B subunit exists predominantly as monomer and dimer. The relative abundance of multimeric species of the Stx2 B subunit was insensitive to the ion source conditions, suggesting that gas-phase dissociation of the pentamer ions in the source does not influence the mass spectrum. Blackbody infrared radiative dissociation of the protonated B(5) ions of Stx2 at the +12 and +13 charge states proceeds, at reaction temperatures of 120 to 180 degrees C, predominantly by the ejection of a single subunit from the complex. Dissociation into dimer and trimer ions constitutes a minor pathway. It follows that the dimer and trimer ions and, likely, the monomer ions observed in the nano-ES mass spectra of Stx2 B subunit originated in solution and not from gas-phase reactions. It is concluded that, under the solution conditions investigated, the homopentamer of Stx2 B subunit is thermodynamically less stable than that of Stx1 B subunit. Arrhenius activation parameters determined for the protonated Stx2 B(5) ions at the +12 and +13 charge states were compared with values reported for the corresponding B(5) ions of Stx1 B subunit. In contrast to the differential stability of the Stx1 and Stx2 B pentamers in solution, the dissociation activation energies (E(a)) determined for the gaseous complexes are indistinguishable at a given charge state. The similarity in the E(a) values suggests that the protonated pentamer ions of both toxins are stabilized by similar intersubunit interactions in the gas phase, a result that is in agreement with the X-ray crystal structures of the holotoxins.
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Affiliation(s)
- Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Canada
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23
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Borch J, Jørgensen TJD, Roepstorff P. Mass spectrometric analysis of protein interactions. Curr Opin Chem Biol 2005; 9:509-16. [PMID: 16125435 DOI: 10.1016/j.cbpa.2005.08.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2005] [Accepted: 08/11/2005] [Indexed: 11/20/2022]
Abstract
Mass spectrometry is a powerful tool for identification of interaction partners and structural characterization of protein interactions because of its high sensitivity, mass accuracy and tolerance towards sample heterogeneity. Several tools that allow studies of protein interaction are now available and recent developments that increase the confidence of studies of protein interaction by mass spectrometry include quantification of affinity-purified proteins by stable isotope labeling and reagents for surface topology studies that can be identified by mass-contributing reporters (e.g. isotope labels, cleavable cross-linkers or fragment ions. The use of mass spectrometers to study protein interactions using deuterium exchange and for analysis of intact protein complexes recently has progressed considerably.
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Affiliation(s)
- Jonas Borch
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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24
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Ilag LL, Videler H, McKay AR, Sobott F, Fucini P, Nierhaus KH, Robinson CV. Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria. Proc Natl Acad Sci U S A 2005; 102:8192-7. [PMID: 15923259 PMCID: PMC1149426 DOI: 10.1073/pnas.0502193102] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosomes are universal translators of the genetic code into protein and represent macromolecular structures that are asymmetric, often heterogeneous, and contain dynamic regions. These properties pose considerable challenges for modern-day structural biology. Despite these obstacles, high-resolution x-ray structures of the 30S and 50S subunits have revealed the RNA architecture and its interactions with proteins for ribosomes from Thermus thermophilus, Deinococcus radiodurans, and Haloarcula marismortui. Some regions, however, remain inaccessible to these high-resolution approaches because of their high conformational dynamics and potential heterogeneity, specifically the so-called L7/L12 stalk complex. This region plays a vital role in protein synthesis by interacting with GTPase factors in translation. Here, we apply tandem MS, an approach widely applied to peptide sequencing for proteomic applications but not previously applied to MDa complexes. Isolation and activation of ions assigned to intact 30S and 50S subunits releases proteins S6 and L12, respectively. Importantly, this process reveals, exclusively while attached to ribosomes, a phosphorylation of L12, the protein located in multiple copies at the tip of the stalk complex. Moreover, through tandem MS we discovered a stoichiometry for the stalk protuberance on Thermus thermophilus and other thermophiles and contrast this assembly with the analogous one on ribosomes from mesophiles. Together with evidence for a potential interaction with the degradosome, these results show that important findings on ribosome structure, interactions, and modifications can be discovered by tandem MS, even on well studied ribosomes from Thermus thermophilus.
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Affiliation(s)
- Leopold L Ilag
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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25
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Catalina MI, van den Heuvel RHH, van Duijn E, Heck AJR. Decharging of Globular Proteins and Protein Complexes in Electrospray. Chemistry 2005; 11:960-8. [PMID: 15593239 DOI: 10.1002/chem.200400395] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) is a valuable tool in structural biology for investigating globular proteins and their biomolecular interactions. During the electrospray ionization process, proteins become desolvated and multiply charged, which may influence their structure. Reducing the net charge obtained during the electrospray process may be relevant for studying globular proteins. In this report we demonstrate the effect of a series of inorganic and organic gas-phase bases on the number of charges that proteins and protein complexes attain. Solution additives with very strong gas-phase basicities (GB) were identified among the so-called "proton sponges". The gas-phase proton affinities (PA) of the compounds that were added to the aqueous protein solutions ranged from 700 to 1050 kJ mol(-1). Circular dichroism studies showed that in these solutions the proteins retain their globular structures. The size of the proteins investigated ranged from the 14.3 kDa lysozyme up to the 800 kDa tetradecameric chaperone complex GroEL. Decharging of the proteins in the electrospray process by up to 60 % could be achieved by adding the most basic compounds rather than the more commonly used ammonium acetate additive. This decharging process probably results from proton competition events between the multiply protonated protein ions and the basic additives just prior to the final desolvation. We hypothesize that such globular protein species, which attain relatively few charges during the ionization event, obtain a gas-phase structure that more closely resembles their solution-phase structure. Thus, these basic additives can be useful in the study of the biologically relevant properties of globular proteins by using mass spectrometry.
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Affiliation(s)
- M Isabel Catalina
- Department of Biomolecular Mass Spectrometry, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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26
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Videler H, Ilag LL, McKay ARC, Hanson CL, Robinson CV. Mass spectrometry of intact ribosomes. FEBS Lett 2004; 579:943-7. [PMID: 15680979 DOI: 10.1016/j.febslet.2004.12.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 12/06/2004] [Accepted: 12/06/2004] [Indexed: 11/17/2022]
Abstract
The ability to maintain intact ribosomes in the mass spectrometer has enabled research into their changes in conformation and interactions. In the mass spectrometer, it is possible to induce dissociation of proteins from the intact ribosome and, in conjunction with atomic structures, to understand the factors governing their release. We have applied this knowledge to interpret the structural basis for release of proteins from ribosomes for which no high resolution structures are available, such as complexes with elongation factor G and ribosomes from yeast. We also describe how improvements in technology and understanding have widened the scope of our research and lead to dramatic improvements in quality and information available from spectra of intact ribosomes.
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Affiliation(s)
- Hortense Videler
- The University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK
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27
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Abstract
The minutiae of subtle changes that occur in response to ligand binding in multiprotein complexes are often difficult to assess without resource to high resolution X-ray analysis. Recent developments in mass spectrometry, however, are providing insight into dynamic changes within components. In this article we review recent applications of MS for selection of ligands and definition of their binding characteristics for individual protein targets through to macromolecular complexes such as ribosomes.
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Affiliation(s)
- Margaret G McCammon
- Cambridge University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK
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28
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Lengqvist J, Svensson R, Evergren E, Morgenstern R, Griffiths WJ. Observation of an Intact Noncovalent Homotrimer of Detergent-solubilized Rat Microsomal Glutathione Transferase-1 by Electrospray Mass Spectrometry. J Biol Chem 2004; 279:13311-6. [PMID: 14726533 DOI: 10.1074/jbc.m310958200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Microsomal glutathione transferase-1 (MGST1) is a membrane-bound enzyme involved in the detoxification of xenobiotics and the protection of cells against oxidative stress. The proposed active form of the enzyme is a noncovalently associated homotrimer that binds one substrate glutathione molecule/trimer. In this study, this complex has been directly observed by electrospray mass spectrometry analysis of active rat liver MGST1 reconstituted in a minimum amount of detergent. The measured mass of the homotrimer is 53 kDa, allowing for the mass of three MGST molecules in complex with one glutathione molecule. Collision-induced dissociation of the trimer complex resulted in the formation of monomer and homodimer ion species. Two distinct species of homodimer were observed, one unliganded and one identified as a homodimer.glutathione complex. Activation of the enzyme by N-ethylmaleimide through modification of Cys(49) (Svensson, R., Rinaldi, R., Swedmark, S., and Morgenstern, R. (2000) Biochemistry 39, 15144-15149) was monitored by the observation of an appropriate increase in mass in both the denatured monomeric and native trimeric forms of MGST1. Together, the data correspond well with the proposed functional organization of MGST1. These results also represent the first example of direct electrospray mass spectrometry analysis of a detergent-solubilized multimeric membrane protein complex in its native state.
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Affiliation(s)
- Johan Lengqvist
- Department of Medical Biochemistry and Biophysics, Lüdwig Institute for Cancer Research, Stockholm, Sweden
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29
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Hanson CL, Robinson CV. Protein-nucleic acid interactions and the expanding role of mass spectrometry. J Biol Chem 2004; 279:24907-10. [PMID: 15056667 DOI: 10.1074/jbc.r300037200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mass spectrometry methods are being developed that enable detection of protein interactions with nucleic acids. By mass measuring complexes a direct determination of the stoichiometry of protein-nucleic acid interactions is revealed. For more complex assemblies, using a different approach it is possible to gain information about subcomplexes and even the spatial arrangement of proteins in macromolecular machines. To illustrate these different approaches we review progress and problems encountered in evaluating complexes from bimolecular interactions through to macromolecular machines such as ribosomes.
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Affiliation(s)
- Charlotte L Hanson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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30
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Li A, Fenselau C. Contact regions in the dimer of Alzheimer beta-amyloid domain [1-28] studied by mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2004; 10:309-316. [PMID: 15103108 DOI: 10.1255/ejms.642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Information is provided about the amino acid residues in the [1-28] domain of the Alzheimer b- amyloid protein, which participate in interstrand pairing and initiate fibillogenesis. The study was carried out using electrospray ionization on a four sector mass spectrometer, measuring kinetic energy release for a fragmentation process, and modeling the transition state with molecular dynamics calculations. The results eliminate the sequence [11-24] proposed earlier as the central core, and are consistent with, but do not distinguish between, residues [17-28] and [17-23] proposed by others based on biochemical studies.
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Affiliation(s)
- Aiqun Li
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Catonsville, MD 21250, USA
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31
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Suh MJ, Limbach PA. Investigation of methods suitable for the matrix-assisted laser desorption/ionization mass spectrometric analysis of proteins from ribonucleoprotein complexes. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2004; 10:89-99. [PMID: 15100481 DOI: 10.1255/ejms.626] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A variety of protein isolation and purification techniques for ribonucleoprotein (RNP) complexes were investigated for their compatibility with downstream analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Ribosomal proteins from Escherichia coli 70S ribosomes were obtained using methods such as phenol extraction and precipitation by organic solvents or acids. Under optimal conditions, more than 90% of the expected ribosomal proteins were detected in a single MALDI-MS experiment. The most effective approach combined ribosome denaturation by buffer exchange with acid precipitation of the ribosomal ribonucleic acids. An improved acid precipitation approach, involving the sequential additions of acetic and trifluoroacetic acid, yielded more complete protein coverage while minimizing loss of ion signal from lower molecular weight proteins. With phenol extraction, substantial gains in ion abundance of higher molecular weight proteins are noted, although some of the lower molecular weight proteins were not efficiently extracted. These results illustrate several effective approaches for protein isolation from protein complexes such as RNPs that are MALDI-MS compatible, and these approaches should extend the use of MALDI-MS for proteomics-based analyses of other protein-nucleic acid complexes.
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Affiliation(s)
- Moo-Jin Suh
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221, USA
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32
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Jurchen JC, Garcia DE, Williams ER. Gas-phase dissociation pathways of multiply charged peptide clusters. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2003; 14:1373-86. [PMID: 14652186 PMCID: PMC1343450 DOI: 10.1016/j.jasms.2003.07.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Numerous studies of cluster formation and dissociation have been conducted to determine properties of matter in the transition from the condensed phase to the gas phase using materials as diverse as atomic nuclei, noble gases, metal clusters, and amino acids. Here, electrospray ionization is used to extend the study of cluster dissociation to peptides including leucine enkephalin with 7-19 monomer units and 2-5 protons, and somatostatin with 5 monomer units and 4 protons under conditions where its intramolecular disulfide bond is either oxidized or reduced. Evaporation of neutral monomers and charge separation by cluster fission are the competing dissociation pathways of both peptides. The dominant fission product for all leucine enkephalin clusters studied is a proton-bound dimer, presumably due to the high gas-phase stability of this species. The branching ratio of the fission and evaporation processes for leucine enkephalin clusters appears to be determined by the value of z2/n for the cluster where z is the charge and n the number of monomer units in the cluster. Clusters with low and high values of z2/n dissociate primarily by evaporation and cluster fission respectively, with a sharp transition between dissociation primarily by evaporation and primarily by fission measured at a z2/n value of approximately 0.5. The dependence of the dissociation pathway of a cluster on z2/n is similar to the dissociation of atomic nuclei and multiply charged metal clusters indicating that leucine enkephalin peptide clusters exist in a state that is more disordered, and possibly fluid, rather than highly structured in the dissociative transition state. The branching ratio, but not the dissociation pathway of [somatostatin5 + 4H]4+ is altered by the reduction of its internal disulfide bond indicating that monomer conformational flexibility plays a role in peptide cluster dissociation.
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Affiliation(s)
- John C. Jurchen
- Department of Chemistry, University of California, Berkeley, California, USA
| | - David E. Garcia
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California, USA
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33
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2003; 38:588-595. [PMID: 12794882 DOI: 10.1002/jms.408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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Abstract
Recent successes illustrate the role of mass spectrometry-based proteomics as an indispensable tool for molecular and cellular biology and for the emerging field of systems biology. These include the study of protein-protein interactions via affinity-based isolations on a small and proteome-wide scale, the mapping of numerous organelles, the concurrent description of the malaria parasite genome and proteome, and the generation of quantitative protein profiles from diverse species. The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.
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Affiliation(s)
- Ruedi Aebersold
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103-8904, USA.
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