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Tomioka Y, Akuta T, Tokunaga M, Arakawa T. Different behavior of Ferguson plot between agarose and polyacrylamide gels. Biophys Chem 2024; 307:107200. [PMID: 38367540 DOI: 10.1016/j.bpc.2024.107200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
In this study, we conducted Ferguson plot analyses using both agarose and polyacrylamide gels in native electrophoresis and SDS-PAGE. The results revealed intriguing differences in the behavior of bovine serum albumin (BSA) and other model proteins. Specifically, BSA exhibited Ferguson plot slopes that were dependent on the oligomer size in agarose native gel electrophoresis, while such size-dependent behavior was not observed in native-PAGE or SDS-PAGE. These findings suggest that Ferguson plot analysis is a suitable approach when using agarose gel under the electrophoretic conditions employed in this study. Furthermore, our investigation extended to model proteins with acidic isoelectric points and larger molecular weights, namely Ferritin and caseinolytic peptidase B (ClpB). Notably, these proteins displayed distinct Ferguson plot slopes when subjected to agarose gel electrophoresis. Intriguingly, when polyacrylamide gel was employed, ClpB exhibited multiple bands, each with its unique Ferguson plot slope, deviating from the expected behavior based on molecular size. This divergence in Ferguson plot characteristics between agarose and polyacrylamide gels points to an interesting and complex interplay between protein properties and gel electrophoresis conditions.
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Affiliation(s)
- Yui Tomioka
- Product Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan.
| | - Teruo Akuta
- Product Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26, Aza-Asayama, Kamitezuna Takahagi-shi, Ibaraki 318-0004, Japan.
| | - Masao Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima-shi 890-0065, Japan
| | - Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Rd, San Diego, CA 92130, USA.
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Arumugam M, Ajitkumar P. Histidine 117 in the His-Gly-Ser-Asp motif is Required for the Biochemical Activities of Nucleoside Diphosphate Kinase of Mycobacterium smegmatis. Open Biochem J 2012; 6:71-7. [PMID: 22888372 PMCID: PMC3414718 DOI: 10.2174/1874091x01206010071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 04/16/2012] [Accepted: 04/19/2012] [Indexed: 11/28/2022] Open
Abstract
Nucleoside diphosphate kinase (NDK), which is widely conserved in both prokaryotes and eukaryotes, maintains a balanced pool of nucleotide triphosphates and their deoxy derivatives. NDKs from bacterial and other systems contain the conserved HGSD motif, where the His residue is required for the biochemical activities, namely the NTPase (AT-Pase and GTPase), NTP synthesising, and autophosphorylation activities of the enzyme. Amino acid sequence homology comparison of the NDK of Mycobacterium smegmatis (MsmNDK) with the NDKs of other bacterial genera showed the presence of H117GSD motif. While the recombinant wild type MsmNDK showed the NTPase, NTP synthesising, and autophosphorylation activities, the H117Q mutation abolished the biochemical activities of the recombinant MsmNDK-H117Q mutant protein in vitro. These observations demonstrate that the H117 residue in the HGSD motif is required for the biochemical activities of MsmNDK.
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Affiliation(s)
- Muthu Arumugam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
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Bracken CD, Neighbor AM, Lamlenn KK, Thomas GC, Schubert HL, Whitby FG, Howard BR. Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G. BMC STRUCTURAL BIOLOGY 2011; 11:23. [PMID: 21569248 PMCID: PMC3112382 DOI: 10.1186/1472-6807-11-23] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 05/10/2011] [Indexed: 01/07/2023]
Abstract
BACKGROUND Malate synthase, one of the two enzymes unique to the glyoxylate cycle, is found in all three domains of life, and is crucial to the utilization of two-carbon compounds for net biosynthetic pathways such as gluconeogenesis. In addition to the main isoforms A and G, so named because of their differential expression in E. coli grown on either acetate or glycolate respectively, a third distinct isoform has been identified. These three isoforms differ considerably in size and sequence conservation. The A isoform (MSA) comprises ~530 residues, the G isoform (MSG) is ~730 residues, and this third isoform (MSH-halophilic) is ~430 residues in length. Both isoforms A and G have been structurally characterized in detail, but no structures have been reported for the H isoform which has been found thus far only in members of the halophilic Archaea. RESULTS We have solved the structure of a malate synthase H (MSH) isoform member from Haloferax volcanii in complex with glyoxylate at 2.51 Å resolution, and also as a ternary complex with acetyl-coenzyme A and pyruvate at 1.95 Å. Like the A and G isoforms, MSH is based on a β8/α8 (TIM) barrel. Unlike previously solved malate synthase structures which are all monomeric, this enzyme is found in the native state as a trimer/hexamer equilibrium. Compared to isoforms A and G, MSH displays deletion of an N-terminal domain and a smaller deletion at the C-terminus. The MSH active site is closely superimposable with those of MSA and MSG, with the ternary complex indicating a nucleophilic attack on pyruvate by the enolate intermediate of acetyl-coenzyme A. CONCLUSIONS The reported structures of MSH from Haloferax volcanii allow a detailed analysis and comparison with previously solved structures of isoforms A and G. These structural comparisons provide insight into evolutionary relationships among these isoforms, and also indicate that despite the size and sequence variation, and the truncated C-terminal domain of the H isoform, the catalytic mechanism is conserved. Sequence analysis in light of the structure indicates that additional members of isoform H likely exist in the databases but have been misannotated.
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Affiliation(s)
- Colten D Bracken
- Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA
| | - Amber M Neighbor
- Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA
| | - Kenneth K Lamlenn
- Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA,Department of Pharmacology, Georgetown University Medical Center, Washington, DC. 20057-1411, USA
| | - Geoffrey C Thomas
- Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA,Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA
| | - Frank G Whitby
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA
| | - Bruce R Howard
- Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA
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Ishibashi M, Oda K, Arakawa T, Tokunaga M. Cloning, expression, purification and activation by Na ion of halophilic alkaline phosphatase from moderate halophile Halomonas sp. 593. Protein Expr Purif 2011; 76:97-102. [DOI: 10.1016/j.pep.2010.09.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 09/22/2010] [Accepted: 09/22/2010] [Indexed: 10/19/2022]
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Tokunaga H, Arakawa T, Tokunaga M. Engineering of halophilic enzymes: two acidic amino acid residues at the carboxy-terminal region confer halophilic characteristics to Halomonas and Pseudomonas nucleoside diphosphate kinases. Protein Sci 2008; 17:1603-10. [PMID: 18573868 DOI: 10.1110/ps.035725.108] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Nucleoside diphosphate kinase from Halomonas sp. 593 (HaNDK) exhibits halophilic characteristics. Residues 134 and 135 in the carboxy-terminal region of HaNDK are Glu-Glu, while those of its homologous counterpart of non-halophilic Pseudomonas NDK (PaNDK) are Ala-Ala. The double mutation, E134A-E135A, in HaNDK results in the loss of the halophilic characteristics, and, conversely, the double mutation of A134E-A135E in PaNDK confers halophilic characters to this enzyme, indicating that the charged state of these two residues that are located in the C-terminal region plays a critical role in determining halophilic characteristics. The importance of these two residues versus the net negative charges will be discussed in relation to the halophilicity of NDK.
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Affiliation(s)
- Hiroko Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
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Yonezawa Y, Izutsu KI, Tokunaga H, Maeda H, Arakawa T, Tokunaga M. Dimeric structure of nucleoside diphosphate kinase from moderately halophilic bacterium: contrast to the tetramericPseudomonascounterpart. FEMS Microbiol Lett 2007; 268:52-8. [PMID: 17227453 DOI: 10.1111/j.1574-6968.2007.00626.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Light scattering and chemical cross-linking analyses of nucleoside diphosphate kinase (NDK) from moderate halophile, Halomonas sp. 593 (HaNDK), unambiguously demonstrated that this enzyme formed a dimeric structure, in contrast to the Pseudomonas NDK (PaNDK), a nonhalophilic counterpart, and other NDKs from Gram-negative bacteria, which all formed a tetrameric structure. Comparison of HaNDK and PaNDK showed that the HaNDK was less thermally stable than the PaNDK: the optimum temperature of PaNDK enzyme activity was 20 degrees C higher than that of HaNDK. However, the HaNDK readily refolded and reassembled back to the active dimeric structure, upon heat denaturation at 0.2 M NaCl, as soon as the temperature was lowered. On the contrary, the thermally more stable PaNDK was irreversibly denatured at its melting temperature.
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Affiliation(s)
- Yasushi Yonezawa
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
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Lee MS, Joo WA, Kim CW. Identification of a novel protein D3UPCA from Halobacterium salinarum and prediction of its function. Proteomics 2005; 4:3622-31. [PMID: 15449372 DOI: 10.1002/pmic.200400978] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Halobacterium salinarum is an extremely halophilic archaea, which is able to live in highly saline environments. In a recent study, several halophilic archaea were found to have the ability to biodegrade organic hydrocarbon pollutants, but protein information regarding hydrocarbon degradation and tolerance in halophilic archaea has been relatively rare. In this study, the protein expression profile of H. salinarum cultured under different diesel concentrations (0, 2 and 4%) was investigated by two-dimensional gel electrophoresis. Proteins which increased their expression levels in diesel media were identified using matrix-assisted laser desorption/ionization-time of flight and electrospray ionization-tandem mass spectrometry analysis. Among these, a protein spot (named D3UPCA) which was up-regulated about nine-fold and found to have COG3388, an uncharacterized protein conserved in archaea, was selected in order to further characterize its functions. The D3UPCA coding gene (named d3upca) was cloned and expressed in Escherichia coli, and purified by the glutathione-S-transferase-fusion method. The function of the protein was estimated using various bioinformatics tools and was predicted to be related to the regulation of transcription and/or translation of genes needed to tolerate stresses associated within the presence of diesel oil.
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Affiliation(s)
- Moon-Sup Lee
- Graduate School of Life Sciences and Biotechnology, Korea University, Seoul, Korea
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Madern D, Zaccai G. Molecular adaptation: the malate dehydrogenase from the extreme halophilic bacterium Salinibacter ruber behaves like a non-halophilic protein. Biochimie 2005; 86:295-303. [PMID: 15194233 DOI: 10.1016/j.biochi.2004.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2004] [Accepted: 04/01/2004] [Indexed: 11/30/2022]
Abstract
Malate dehydrogenase from the extreme halophilic bacterium, Salinibacter ruber (Sr MalDH) was purified and characterised as a tetramer by sedimentation velocity measurements, showing the enzyme belongs to the LDH-like group of MalDHs. In contrast to most other halophilic enzymes, which unfold when incubated at low salt concentration, Sr MalDH is completely stable in absence of salt. Its amino acid composition does not display the strong acidic character specific of halophilic proteins. The enzyme displays a strong KCl-concentration dependent variation in K(m) for oxaloacetate, but not for the NADH co-factor. Its activity is reduced by high salt concentration, but remains sufficient for the enzyme to sustain catalysis at approximately 30% of its maximal rates in 3 M KCl. The properties of the protein were compared with those from other LDH-like MalDHs of bacterial and archaeal origins, showing that Sr MalDH in fact behaves like a non-halophilic enzyme.
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Affiliation(s)
- Dominique Madern
- Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale CEA-CNRS-UJF, UMR 5075, 41, rue Jules-Horowitz, Grenoble 38042, France.
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Mizuki T, Kamekura M, Ishibashi M, Usami R, Yoshida Y, Tokunaga M, Horikoshi K. Nucleoside diphosphate kinase of halobacteria. ACTA ACUST UNITED AC 2004. [DOI: 10.3118/jjse.3.1_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Yonezawa Y, Tokunaga H, Ishibashi M, Taura S, Tokunaga M. Cloning, expression, and efficient purification in Escherichia coli of a halophilic nucleoside diphosphate kinase from the moderate halophile Halomonas sp. #593. Protein Expr Purif 2003; 27:128-33. [PMID: 12509994 DOI: 10.1016/s1046-5928(02)00594-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most typical halophilic enzymes from extremely halophilic archaea require high concentrations of salt for their activity and stability. These enzymes are inactive in Escherichia coli unless refolded in the presence of salts in vitro. In this report, we describe cloning of the ndk gene of nucleoside diphosphate kinase from a moderately halophilic eubacterium and overexpression of the protein in E. coli as an N-terminal hexa-His fusion to facilitate its purification on Ni-NTA affinity resin. We demonstrate evidence that the protein is properly folded and exhibits the same specific activity and stability as the native protein from Halomonas cells.
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Affiliation(s)
- Yasushi Yonezawa
- Laboratory of Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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