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Karataş E, Tülek A, Çakar MM, Tamtürk F, Aktaş F, Binay B. From secretion in Pichia pastoris to application in apple juice processing: Exo-polygalacturonase from Sporothrix schenckii 1099-18. Protein Pept Lett 2021; 28:817-830. [PMID: 33413052 DOI: 10.2174/1871530321666210106110400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Polygalacturonases are a group of enzymes under pectinolytic enzymes related to enzymes that hydrolyse pectic substances. Polygalacturonases have been used in various industrial applications such as fruit juice clarification, retting of plant fibers, wastewater treatment drinks fermentation, and oil extraction. OBJECTIVES The study was evaluated at the heterologous expression, purification, biochemical characterization, computational modeling, and performance in apple juice clarification of a new exo-polygalacturonase from Sporothrix schenckii 1099-18 (SsExo-PG) in Pichia pastoris. METHODS Recombinant DNA technology was used in this study. Two different pPIC9K plasmids were constructed with native signal sequence-ssexo-pg and alpha signal sequence-ssexo-pg separately. Protein expression and purification performed after plasmids transformed into the Pichia pastoris. Biochemical and structural analyses were performed by using pure SsExo-PG. RESULTS The purification of SsExo-PG was achieved using a Ni-NTA chromatography system. The enzyme was found to have a molecular mass of approximately 52 kDa. SsExo-PG presented as stable at a wide range of temperature and pH values, and to be more storage stable than other commercial pectinolytic enzyme mixtures. Structural analysis revealed that the catalytic residues of SsExo-PG are somewhat similar to other Exo-PGs. The KM and kcat values for the degradation of polygalacturonic acid (PGA) by the purified enzyme were found to be 0.5868 µM and 179 s-1, respectively. Cu2+ was found to enhance SsExo-PG activity while Ag2+ and Fe2+ almost completely inhibited enzyme activity. The enzyme reduced turbidity up to 80% thus enhanced the clarification of apple juice. SsExo-PG showed promising performance when compared with other commercial pectinolytic enzyme mixtures. CONCLUSION The clarification potential of SsExo-PG was revealed by comparing it with commercial pectinolytic enzymes. The following parameters of the process of apple juice clarification processes showed that SsExo-PG is highly stable and has a novel performance.
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Affiliation(s)
- Ersin Karataş
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze 41400, Kocaeli. Turkey
| | - Ahmet Tülek
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze 41400, Kocaeli. Turkey
| | - Mehmet Mervan Çakar
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze 41400, Kocaeli. Turkey
| | - Faruk Tamtürk
- Döhler Food & Beverage Ingredients, 70100 Merkez, Karaman. Turkey
| | - Fatih Aktaş
- Department of Environment Engineering, Duzce University, Konuralp 81100, Düzce. Turkey
| | - Barış Binay
- Department of Bioengineering, Gebze Technical University, Gebze 41400, Kocaeli. Turkey
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Biochemical and kinetic characterization of the recombinant GH28 Stereum purpureum endopolygalacturonase and its biotechnological application. Int J Biol Macromol 2019; 137:469-474. [DOI: 10.1016/j.ijbiomac.2019.06.165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 11/19/2022]
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3
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Hamada S, Toda K, Ogawa S, Kubota K, Miyairi K. Characterization of the effects of C-terminal pro-sequence on self-inactivation ofStereum purpureumendopolygalacturonase I. FEMS Microbiol Lett 2015; 362:fnv134. [DOI: 10.1093/femsle/fnv134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2015] [Indexed: 11/13/2022] Open
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4
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The Pro-Form ofStereum purpureumEndopolygalacturonase I Is Inactivated by a Pro-Sequence in the C-Terminal Region. Biosci Biotechnol Biochem 2014; 74:558-62. [DOI: 10.1271/bbb.90754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Argôlo Santos Carvalho H, de Andrade Silva EM, Carvalho Santos S, Micheli F. Polygalacturonases from Moniliophthora perniciosa are regulated by fermentable carbon sources and possible post-translational modifications. Fungal Genet Biol 2013; 60:110-21. [DOI: 10.1016/j.fgb.2013.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 09/30/2013] [Accepted: 10/06/2013] [Indexed: 11/30/2022]
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6
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Active suppression of EndoPG IV by ligation of the pro-sequence from Stereum purpureum Pro-EndoPG I. Biosci Biotechnol Biochem 2012; 76:196-8. [PMID: 22232258 DOI: 10.1271/bbb.110611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We attempted to inactivate endopolygaolacturonase from Stereum purpureum (EndoPG) IV of identical origin by linking the pro-sequence of S. purpureum Pro-EndoPG I to the C-terminus. The recombinant Pro-EndoPG IV, expressed in Escherichia coli, had no polygalacturonase (PG) activity, but activity was acquired after partial degradation of the pro-sequence with V8 protease, as was the case for Pro-EndoPG I. These results indicate that the pro-sequence of Pro-EndoPG I can suppress the PG activity of EndoPG IV.
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Ogawa S, Ito M, Ohki H, Kimura T, Shimizu T, Matsuda M, Miyairi K. Glycosylation Status and Conformational Stability of Recombinant Stereum purpureum Endopolygalacturonase IVs Produced in an Aspergillus oryzae Expression System. J Appl Glycosci (1999) 2012. [DOI: 10.5458/jag.jag.jag-2011_017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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8
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Cloning, expression and characterization of an acidic endo-polygalacturonase from Bispora sp. MEY-1 and its potential application in juice clarification. Process Biochem 2011. [DOI: 10.1016/j.procbio.2010.08.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Massa C, Guarnaccia C, Lamba D, Anselmi C. Insight into the structure of an endopolygalacturonase from the phytopathogen Burkholderia cepacia: a biochemical and computational study. Biochimie 2010; 92:1445-53. [PMID: 20637827 DOI: 10.1016/j.biochi.2010.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 07/07/2010] [Indexed: 11/30/2022]
Abstract
We have recently investigated and characterized the mode of action of BcPeh28A, an endopolygalacturonase (endoPG) from the phytopathogen Burkholderia cepacia. EndoPGs belong to glycoside hydrolase family 28 and are responsible for the hydrolysis of the non-esterified regions of pectins. Here we report a 3-D structural model of BcPeh28A by combining mass spectrometry (MS) analysis, aimed at disulphide bridges mapping, and computational modelling tools. MS analyses have revealed the complete pattern of disulphide bridges in BcPeh28A, pointing out the presence of three disulphide bonds, defined as Cys3-25, Cys216-244 and Cys309-421. A 3-D model of BcPeh28A was generated by computational methods based on profile-profile sequence alignments and fold recognition algorithms. The final model exhibits a right-handed β-helix fold with eleven β-helical coils and includes the disulphide bonds as additional spatial restraints. Molecular dynamics simulations have been performed to test the conformational stability of the model. Finally, the structural analysis of the BcPeh28A model allows defining the architecture and the amino acid topology of the subsites involved in the catalysis and in the substrate binding specificity.
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Affiliation(s)
- Claudia Massa
- Structural Biology Laboratory, Sincrotrone Trieste S.C.p.A., AREA Science Park - Basovizza Strada Statale 14, km 163,5, I-34149 Trieste, Italy.
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Miyairi K, Ogawa S, Kimura T, Shimizu T, Okuno T. Auto-inactivation of Stereum purpureum Proendopolygalacturonase I by C-terminal 44 Amino Acid Residues. J Appl Glycosci (1999) 2010. [DOI: 10.5458/jag.57.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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11
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Ogawa S, Shimizu T, Ohki H, Araya T, Okuno T, Miyairi K. Expression, purification, and analyses of glycosylation and disulfide bonds of Stereum purpureum endopolygalacturonase I in Pichia pastoris. Protein Expr Purif 2009; 65:15-22. [PMID: 19174189 DOI: 10.1016/j.pep.2008.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 12/09/2008] [Accepted: 12/09/2008] [Indexed: 10/21/2022]
Abstract
We have succeeded in the expression of Stereum purpureum endopolygalacturonase I (EndoPG I) using the Pichia expression system and in purification of the three kinds of recombinant EndoPG I, which have one to three sugar chains by using CM52 column chromatography. The sugar chains which were added to EndoPG I were the M8, M9, and/or M10 high-mannose type. The results of LC-MS analysis showed that recombinant EndoPG Is were randomly glycosylated at four N-glycosylation sites. From the thermal denaturation curves of the recombinant enzymes, it was suggested that EndoPG I differing in thermal stability was included in the sample after purification. Therefore, we investigated the disulfide bonds of recombinant EndoPG I by LC-MS analysis. As a result, peptides without a second or third disulfide bond were detected. This result is the first indicating that there are incomplete enzymes in terms of disulfide bonds in the Pichia expression system.
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Affiliation(s)
- Shun Ogawa
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Aomori Prefecture, Hirosaki 036-8561, Japan
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Ogawa S, Saka M, Yoshizaki T, Shimizu T, Okuno T, Miyairi K. Purification, Characterization and Amino Acid Sequence of Endopolygalacturonases IVa and IVb from Fungus Stereum purpureum. J Appl Glycosci (1999) 2009. [DOI: 10.5458/jag.56.261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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13
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Comparative biochemical and structural characterizations of fungal polygalacturonases. Biologia (Bratisl) 2008. [DOI: 10.2478/s11756-008-0018-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Yamamoto K, Watanabe N, Matsuda H, Oohara K, Araya T, Hashimoto M, Miyairi K, Okazaki I, Saito M, Shimizu T, Kato H, Okuno T. Design, synthesis, and enzymatic property of a sulfur-substituted analogue of trigalacturonic acid. Bioorg Med Chem Lett 2005; 15:4932-5. [PMID: 16169214 DOI: 10.1016/j.bmcl.2005.08.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 07/18/2005] [Accepted: 08/06/2005] [Indexed: 11/25/2022]
Abstract
A sulfur-substituted analogue of trigalacturonic acid (3) was synthesized. The synthesis features the application of 3-cyano-3-(tert-butyldimethylsilyl)oxypropylthioether (CSP) as a novel protective group for thiols. This analogue was designed with the expectation that it would be a stable analogous substrate for endo-polygalacturonase isolated from Stereum purpureum based on computer modeling experiments. Surface plasmon resonance experiments revealed that 3 forms a stable complex with the target enzyme.
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Affiliation(s)
- Kazunori Yamamoto
- Faculty of Agriculture and Lifescience, Hirosaki University, 3-Bunkyo-cho, Hirosaki 036-8561, Japan
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Shimizu T, Shibata H, Araya T, Nakatsu T, Miyairi K, Okuno T, Kato H. Expression, purification, and crystallization of endopolygalacturonase from a pathogenic fungus, Stereum purpureum, in Escherichia coli. Protein Expr Purif 2005; 44:130-5. [PMID: 16061394 DOI: 10.1016/j.pep.2005.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Revised: 05/30/2005] [Accepted: 06/02/2005] [Indexed: 11/20/2022]
Abstract
Endopolygalacturonases (EC 3.2.1.15) catalyze random hydrolysis of the alpha-1,4 glycosidic linkages in polygalacturonic acid, a component of pectin. Previously, we reported crystal structures of endogenously produced Stereum purprureum endopolygalacturonase I (endoPG I), both in its native form and complexed with its product, galacturonate. However, the substrate-binding mechanism of endoPG I is still unclear, because crystals have not yet been obtained with a substrate analog, or with mutant enzymes that can bind substrates. We describe here an expression system using Escherichia coli and a purification method to prepare functionally active endoPG I for such mutation and crystallographic studies. Expression in E. coli strain Origami (DE3) provided a soluble and active enzyme with proper disulfide bond formation, whereas the enzyme expressed in BL21 (DE3) was localized in inclusion bodies. A sufficient amount of recombinant endoPG I produced by Origami (DE3) was purified by a single-step procedure using cation exchange chromatography. The specific activity of recombinant endoPG I was equivalent to that of the enzyme produced by S. purpureum. Recombinant endoPG I was crystallized under the same conditions as those used for the native enzyme produced by S. purpureum. The crystals diffracted beyond 1.0 A resolution with synchrotron radiation.
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Affiliation(s)
- Tetsuya Shimizu
- Kinetic Crystallography Research Team, Membrane Dynamics Research Group, RIKEN, Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
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16
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Xie M, Krooshof GH, Benen JAE, Atwood JA, King D, Bergmann C, Orlando R. Post-translational modifications of recombinant B. cinerea EPG 6. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:3389-97. [PMID: 16259040 DOI: 10.1002/rcm.2194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The fungus Botrytis cinerea is a ubiquitous plant pathogen that infects more than 200 different plant species and causes substantial economic losses in a wide range of agricultural crops and harvested products. Endopolygalacturonases (EPGs) are among the first array of cell-wall-degrading enzymes secreted by fungi during infection. Up to 13 EPG glycoforms have been described for B. cinerea. The presence of multiple N-linked glycosylation modifications in BcPG1-6 is predicted by their deduced amino acid sequences. In this work, the glycosylation sites and the attached oligosaccharide structures on BcPG6 were analyzed. The molecular mass of the intact glycoprotein was determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOFMS) analysis. BcPG6 contains seven potential N-linked glycosylation sites. Occupancy of these glycosylation sites and the attached carbohydrate structures were analyzed by tryptic digestion followed by liquid chromatography/mass spectrometry (LC/MS) using a stepped orifice voltage approach. Five out of seven potential N-linked sites present in BcPG6 were determined to be occupied by high-mannose-type oligosaccharides. Four of them were readily determined to be at Asn58 (T3 peptide), Asn198 (T7 peptide), Asn237 (T9 peptide) and Asn256 (T11 peptide), respectively. Another was located on the T8 peptide, which contained two potential N-linked sites, Asn224 and Asn227 (SNNN224VTN227ITFK). LC/MS/MS of a sample treated with N-glycanase placed the glycan in this peptide at Asn224 rather than at Asn227. The potential glycosylation site on Asn146 (T6 peptide) was not glycosylated. In addition, two disulfide bonds were observed, linking the Cys residues within the T13 and T16 peptides.
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Affiliation(s)
- Min Xie
- Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, 315 Riverbend Road, Athens, GA 30602-4712, USA
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Shimizu T, Nakatsu T, Miyairi K, Okuno T, Kato H. Reaction Mechanism Based on X-ray Crystallography at Atomic Resolution of Endopolygalacutronase I from Fungus Stereum purpureum. J Appl Glycosci (1999) 2004. [DOI: 10.5458/jag.51.161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Tetsuya Shimizu
- Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Toru Nakatsu
- Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Kazuo Miyairi
- Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Sciences, Hirosaki University
| | - Toshikatsu Okuno
- Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Sciences, Hirosaki University
| | - Hiroaki Kato
- Graduate School of Pharmaceutical Sciences, Kyoto University
- RIKEN, Harima Institute at SPring-8
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Shimizu T, Nakatsu T, Miyairi K, Okuno T, Kato H. Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution. Biochemistry 2002; 41:6651-9. [PMID: 12022868 DOI: 10.1021/bi025541a] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Crystal structures of endopolygalacturonase from Stereum purpureum were solved in native and two galacturonic acid complex states at atomic resolution. Endopolygalacturonase catalyzes the hydrolysis of alpha-1,4-glycosidic linkage of polygalacturonate in pectin. The native structure was determined by the multiple wavelength anomalous dispersion method and was refined anisotropically with SHELXL-97, with an R factor of 11.4% and an R(free) factor of 14.0% at 0.96 A resolution. The enzyme folds into a right-handed parallel beta-helix with 10 complete turns. The crystal structures of its binary complex with one D-galacturonate and its ternary complex with two D-galacturonates were also determined to identify the substrate binding site at 1.0 and 1.15 A resolutions, respectively. In the binary complex, one beta-D-galactopyranuronate was found in the +1 subsite, thus proving the strong affinity of the +1 subsite expected from the bond cleavage frequency on oligogalacturonates. In the ternary complex, an additional beta-D-galactofuranuronate was found in the -1 subsite. In both subsites, the recognition of the galacturonate carboxy group is important in galacturonate binding. In the +1 subsite, the carboxy group interacts with three basic residues, His195, Arg226, and Lys228, which were conserved in all endopolygalacturonases. In the -1 subsite, the unique nonprolyl cis-peptide bond is believed to be involved in binding the carboxy group of the substrate. The active site architecture of the complexes provides insight into the mechanism of inverting glycosyl hydrolases and also sheds light on the basis of the differences between the family 28 and the other inverting glycosyl hydrolases.
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Affiliation(s)
- Tetsuya Shimizu
- Kinetic Crystallography Research Team, Membrane Dynamics Research Group, RIKEN, Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148 Japan
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Affiliation(s)
- Yehia Mechref
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2000; 35:1148-1155. [PMID: 11006610 DOI: 10.1002/1096-9888(200009)35:9<1148::aid-jms982>3.0.co;2-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In order to keep subscribers up-to-date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of mass spectrometry. Each bibliography is divided into 11 sections: 1 Books, Reviews & Symposia; 2 Instrumental Techniques & Methods; 3 Gas Phase Ion Chemistry; 4 Biology/Biochemistry: Amino Acids, Peptides & Proteins; Carbohydrates; Lipids; Nucleic Acids; 5 Pharmacology/Toxicology; 6 Natural Products; 7 Analysis of Organic Compounds; 8 Analysis of Inorganics/Organometallics; 9 Surface Analysis; 10 Environmental Analysis; 11 Elemental Analysis. Within each section, articles are listed in alphabetical order with respect to author (3 Weeks journals - Search completed at 28th. June 2000)
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