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Abou-Diab M, Thibodeau J, Fliss I, Dhulster P, Nedjar N, Bazinet L. Impact of conductivity on the performances of electro-acidification and enzymatic hydrolysis phases of bovine hemoglobin by electrodialysis with bipolar membranes for the production of bioactive peptides. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.118650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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2
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Dulay MT, Eberlin LS, Zare RN. Protein Analysis by Ambient Ionization Mass Spectrometry Using Trypsin-Immobilized Organosiloxane Polymer Surfaces. Anal Chem 2015; 87:12324-30. [PMID: 26567450 DOI: 10.1021/acs.analchem.5b03669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the growing field of proteomic research, rapid and simple protein analysis is a crucial component of protein identification. We report the use of immobilized trypsin on hybrid organic-inorganic organosiloxane (T-OSX) polymers for the on-surface, in situ digestion of four model proteins: melittin, cytochrome c, myoglobin, and bovine serum albumin. Tryptic digestion products were sampled, detected, and identified using desorption electrospray ionization mass spectrometry (DESI-MS) and nanoDESI-MS. These novel, reusable T-OSX arrays on glass slides allow for protein digestion in methanol:water solvents (1:1, v/v) and analysis directly from the same polymer surface without the need for sample preparation, high temperature, and pH conditions typically required for in-solution trypsin digestions. Digestion reactions were conducted with 2 μL protein sample droplets (0.35 mM) at incubation temperatures of 4, 25, 37, and 65 °C and digestion reaction times between 2 and 24 h. Sequence coverages were dependent on the hydrophobicity of the OSX polymer support and varied by temperature and digestion time. Under the best conditions, the sequence coverages, determined by DESI-MS, were 100% for melittin, 100% for cytochrome c, 90% for myoglobin, and 65% for bovine serum albumin.
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Affiliation(s)
- Maria T Dulay
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Livia S Eberlin
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Richard N Zare
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L. Comparison of SDS- and methanol-assisted protein solubilization and digestion methods forEscherichia colimembrane proteome analysis by 2-D LC-MS/MS. Proteomics 2007; 7:484-493. [PMID: 17309111 DOI: 10.1002/pmic.200600518] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Both organic solvent and surfactant have been used for dissolving membrane proteins for shotgun proteomics. In this work, two methods of protein solubilization, namely using 60% methanol or 1% SDS, to dissolve and analyze the inner membrane fraction of an Escherichia coli K12 cell lysate were compared. A total of 358 proteins (1417 unique peptides) from the methanol-solubilized protein mixture and 299 proteins (892 peptides) from the SDS-solubilized sample-were identified by using trypsin digestion and 2-D LC-ESI MS/MS. It was found that the methanol method detected more hydrophobic peptides, resulting in a greater number of proteins identified, than the SDS method. We found that 159 out of 358 proteins (44%) and 120 out of 299 proteins (40%) detected from the methanol- and SDS-solubilized samples, respectively, are integral membrane proteins. Among the 190 integral membrane proteins 70 were identified exclusively in the methanol-solubilized sample, 89 were identified by both methods, and only 31 proteins were exclusively identified by the SDS method. It is shown that the integral membrane proteins reflected the theoretical proteome for number of transmembrane helices, length, functional class, and topology, indicating there was no bias in the proteins identified.
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Affiliation(s)
- Nan Zhang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Rui Chen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nelson Young
- Department of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - David Wishart
- Department of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - Philip Winter
- Institute for Biomolecular Design, University of Alberta, Edmonton, Alberta, Canada
| | - Joel H Weiner
- Institute for Biomolecular Design, University of Alberta, Edmonton, Alberta, Canada
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Jørgensen CS, Jagd M, Sørensen BK, McGuire J, Barkholt V, Højrup P, Houen G. Efficacy and compatibility with mass spectrometry of methods for elution of proteins from sodium dodecyl sulfate–polyacrylamide gels and polyvinyldifluoride membranes. Anal Biochem 2004; 330:87-97. [PMID: 15183766 DOI: 10.1016/j.ab.2004.03.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Indexed: 11/16/2022]
Abstract
The resolving power of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) combined with isoelectric focusing in two-dimensional gel electrophoresis has made it one of the most important techniques for resolving complex mixtures, and it is of great importance for proteome mapping projects. As a result of this, methods for postelectrophoretic protein characterization are of great interest as exemplified by in situ protease digestion combined with mass spectrometry (MS), which is the method of choice for identification of proteins. In this study we have developed and compared methods for recovering intact proteins from polyacrylamide gels and electroblotting membranes to define efficient methods compatible with MS. These methods complement in situ digestion protocols and allow determination of the molecular mass of whole proteins separated by SDS-PAGE. Passive elution of proteins from SDS-PAGE gels was efficient only in the presence of SDS, whereas electroelution was achieved using buffers without SDS. Surface-enhanced laser desorption/ionization MS (SELDI-MS) analysis of proteins eluted in the presence of SDS was possible using ion exchange ProteinChip arrays for concentration of sample and removal of SDS. Comparison of different electroblotting methods verified that the different membranes and buffers were equally efficient for transfer of proteins in the range 20-100 kDa. Elution from polyvinyldifluoride membranes was most efficient using either concentrated solutions of trifluoroacetic acid (TFA) or combinations of 8M urea and 1% Triton X-100, 1% Tween 20, or 40% isopropanol. The same result was obtained using nitrocellulose membranes, except that these were incompatible with organic solvent and TFA. Elution by TFA was compatible with matrix-assisted laser desorption/ionization MS (MALDI-MS) but was complicated by a high degree of trifluoroacetylation of the proteins. Alternatively, elution by 8M urea+1% Triton X-100, 1% Tween 20, or 40% isopropanol was compatible with both SELDI-MS and MALDI-MS. Eluted proteins were identified in MS experiments by intact mass determination, by peptide mapping, and by MS/MS analysis.
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Russell WK, Park ZY, Russell DH. Proteolysis in mixed organic-aqueous solvent systems: applications for peptide mass mapping using mass spectrometry. Anal Chem 2001; 73:2682-5. [PMID: 11403317 DOI: 10.1021/ac001332p] [Citation(s) in RCA: 225] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rate of protein digestion imposes significant limitations on high-throughput protein identification using mass spectrometry. In this report, we demonstrate that proteins are readily digested by trypsin in the presence of organic solvents such as methanol, acetone, 2-propanol, and acetonitrile. The rates of protein digestion in organic solvents, as indicated by the abundances of digest fragment ions in the mass spectrum, are increased relative to aqueous solution. In addition, amino acid coverage for the analyzed proteins increases in the presence of the organic solvents, and proteins that are resistant to proteolysis are readily digested. For example, a 68% amino acid sequence coverage was attained from a tryptic digest of myoglobin in < 5 min from an 80% acetonitrile solution, whereas no digest fragments were detected from a 5 min digestion in an aqueous solution. Moreover, the tryptic digestion of a complex protein mixture in an organic-aqueous solvent system showed significantly enhanced digestion for nearly all of the protein components. Enzymatic digestion in an organic-aqueous solvent system is a rapid, simple, and effective peptide mass-mapping technique.
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Affiliation(s)
- W K Russell
- Department of Chemistry, Texas A&M University, College Station 77843, USA
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Zhu G, Huang Q, Wang Z, Qian M, Jia Y, Tang Y. X-ray studies on two forms of bovine beta-trypsin crystals in neat cyclohexane. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1429:142-50. [PMID: 9920392 DOI: 10.1016/s0167-4838(98)00226-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Two orthorhombic forms (Vm values are 2.3 and 3.0 A3/Da) of bovine beta-trypsin crystals in neat cyclohexane were determined to 1.93 A resolution, by X-ray diffraction. Both structures in organic solvent are similar to those in aqueous solution. In the high packing density form, one cyclohexane molecule is found in a hydrophobic site near the active center. One sulfate locates at the active site with hydrogen or salt bond to the Ser-His catalytic diad, and five more sulfates bind on the molecular surface. The conformation of the side chains near the sulfates changed greatly. In the low packing density form, one cyclohexane and three sulfates are found. In both structures, one benzamidine molecule locates at the hydrophobic pocket of the active center. Most water molecules on the enzyme surface are retained except some with high temperature factors.
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Affiliation(s)
- G Zhu
- Department of Chemistry, Peking University, Beijing, PR China
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Laureto PP, Filippis V, Scaramella E, Zambonin M, Fontana A. Limited Proteolysis of Lysozyme in Trifluoroethanol. Isolation and Characterization of a Partially Active Enzyme Derivative. ACTA ACUST UNITED AC 1995. [DOI: 10.1111/j.1432-1033.1995.0779h.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Chen L, Fincher G, Høj P. Evolution of polysaccharide hydrolase substrate specificity. Catalytic amino acids are conserved in barley 1,3-1,4- and 1,3-beta-glucanases. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)38654-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Pepinsky B, Hession C, Chen L, Moy P, Burkly L, Jakubowski A, Chow E, Benjamin C, Chi-Rosso G, Luhowskyj S. Structure/function studies on vascular cell adhesion molecule-1. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)37117-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Protein sequencing strategies designed for DNA cloning. Protein J 1992. [DOI: 10.1007/bf01673759] [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]
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