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Ren G, Yang P, Cui J, Gao Y, Yin C, Bai Y, Zhao D, Chang J. Multiomics Analyses of Two Sorghum Cultivars Reveal the Molecular Mechanism of Salt Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:886805. [PMID: 35677242 PMCID: PMC9168679 DOI: 10.3389/fpls.2022.886805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/29/2022] [Indexed: 05/14/2023]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] is one of the most important cereal crops and contains many health-promoting substances. Sorghum has high tolerance to abiotic stress and contains a variety of flavonoids compounds. Flavonoids are produced by the phenylpropanoid pathway and performed a wide range of functions in plants resistance to biotic and abiotic stress. A multiomics analysis of two sorghum cultivars (HN and GZ) under different salt treatments time (0, 24, 48, and 72) was performed. A total of 45 genes, 58 secondary metabolites, and 246 proteins were recognized with significant differential abundances in different comparison models. The common differentially expressed genes (DEGs) were allocated to the "flavonoid biosynthesis" and "phenylpropanoid biosynthesis" pathways. The most enriched pathways of the common differentially accumulating metabolites (DAMs) were "flavonoid biosynthesis," followed by "phenylpropanoid biosynthesis" and "arginine and proline metabolism." The common differentially expressed proteins (DEPs) were mainly distributed in "phenylpropanoid biosynthesis," "biosynthesis of cofactors," and "RNA transport." Furthermore, considerable differences were observed in the accumulation of low molecular weight nonenzymatic antioxidants and the activity of antioxidant enzymes. Collectively, the results of our study support the idea that flavonoid biological pathways may play an important physiological role in the ability of sorghum to withstand salt stress.
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Affiliation(s)
- Genzeng Ren
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Puyuan Yang
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Jianghui Cui
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Yukun Gao
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Congpei Yin
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Yuzhe Bai
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Dongting Zhao
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
| | - Jinhua Chang
- College of Agronomy, Hebei Agricultural University, Baoding, China
- North China Key Laboratory for Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, China
- *Correspondence: Jinhua Chang,
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2
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Dutta S, Moitra A, Mukherjee D, Jarori GK. Functions of tryptophan residues in EWGWS insert of Plasmodium falciparum enolase. FEBS Open Bio 2017; 7:892-904. [PMID: 28680804 PMCID: PMC5494301 DOI: 10.1002/2211-5463.12242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 05/04/2017] [Indexed: 12/16/2022] Open
Abstract
Plasmodium falciparum enolase (Pfeno) is a dimeric enzyme with multiple moonlighting functions. This enzyme is thus a potential target for anti-malarial treatments. A unique feature of Pfeno is the presence of a pentapeptide insert 104 EWGWS 108. The functional role of tryptophan residues in this insert was investigated using site-directed mutagenesis. Replacement of these two Trp residues with alanines (or lysines) resulted in a near complete loss of enolase activity and dissociation of the normal dimeric form into monomers. Molecular modeling indicated that 340R forms π-cation bonds with the aromatic rings of 105W and 46Y. Mutation induced changes in the interactions among these three residues were presumably relayed to the inter-subunit interface via a coil formed by 46Y : 59Y, resulting in the disruption of a salt bridge between 11R : 425E and a π-cation interaction between 11R : 59Y. This led to a drop of ~ 4 kcal·mole-1 in the inter-subunit docking energy in the mutant, causing a ~ 103 fold decrease in affinity. Partial restoration of the inter-subunit interactions led to reformation of dimers and also restored a significant fraction of the lost enzyme activity. These results suggested that the perturbations in the conformation of the surface loop containing the insert sequence were relayed to the interface region, causing dimer dissociation that, in turn, disrupted the enzyme's active site. Since Plasmodium enolase is a moonlighting protein with multiple parasite-specific functions, it is likely that these functions may map on to the highly conserved unique insert region of this protein. ENZYMES Enolase(EC4.2.1.11).
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Affiliation(s)
- Sneha Dutta
- Department of Biological Sciences Tata Institute of Fundamental Research Mumbai India.,Present address: T. H. Chan School of Public Health Graduate School of Arts and Sciences Harvard University Boston MA USA
| | - Anasuya Moitra
- Department of Biological Sciences Tata Institute of Fundamental Research Mumbai India
| | - Debanjan Mukherjee
- Instituto de Medicina Molecular Faculdade de Medicina Universidade de Lisboa Portugal
| | - Gotam K Jarori
- Department of Biological Sciences Tata Institute of Fundamental Research Mumbai India
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3
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Ponniah G, Nowak C, Kita A, Cheng G, Kori Y, Liu H. Conformational changes of recombinant monoclonal antibodies by limited proteolytic digestion, stable isotope labeling, and liquid chromatography-mass spectrometry. Anal Biochem 2015; 497:1-7. [PMID: 26747642 DOI: 10.1016/j.ab.2015.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/28/2015] [Accepted: 12/14/2015] [Indexed: 01/10/2023]
Abstract
Limited proteolytic digestion is a method with a long history that has been used to study protein domain structures and conformational changes. A method of combining limited proteolytic digestion, stable isotope labeling, and mass spectrometry was established in the current study to investigate protein conformational changes. Recombinant monoclonal antibodies with or without the conserved oligosaccharides, and with or without oxidation of the conserved methionine residues, were used to test the newly proposed method. All of the samples were digested in ammonium bicarbonate buffer prepared in normal water. The oxidized deglycosylated sample was also digested in ammonium bicarbonate buffer prepared in (18)O-labeled water. The sample from the digestion in (18)O-water was spiked into each sample digested in normal water. Each mixed sample was subsequently analyzed by liquid chromatography-mass spectrometry (LC-MS). The molecular weight differences between the peptides digested in normal water versus (18)O-water were used to differentiate peaks from the samples. The relative peak intensities of peptides with or without the C-terminal incorporation of (18)O atoms were used to determine susceptibility of different samples to trypsin and chymotrypsin. The results demonstrated that the method was capable of detecting local conformational changes of the recombinant monoclonal antibodies caused by deglycosylation and oxidation.
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Affiliation(s)
| | - Christine Nowak
- Product Characterization, Alexion Pharmaceuticals, Cheshire, CT 06410, USA
| | - Adriana Kita
- Product Characterization, Alexion Pharmaceuticals, Cheshire, CT 06410, USA
| | - Guilong Cheng
- Product Characterization, Alexion Pharmaceuticals, Cheshire, CT 06410, USA
| | - Yekaterina Kori
- Product Characterization, Alexion Pharmaceuticals, Cheshire, CT 06410, USA
| | - Hongcheng Liu
- Product Characterization, Alexion Pharmaceuticals, Cheshire, CT 06410, USA.
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4
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Andreotti G, Monti MC, Citro V, Cubellis MV. Heterodimerization of Two Pathological Mutants Enhances the Activity of Human Phosphomannomutase2. PLoS One 2015; 10:e0139882. [PMID: 26488408 PMCID: PMC4619449 DOI: 10.1371/journal.pone.0139882] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/18/2015] [Indexed: 12/04/2022] Open
Abstract
The most frequent disorder of glycosylation is due to mutations in the gene encoding phosphomannomutase2 (PMM2-CDG). For this disease, which is autosomal and recessive, there is no cure at present. Most patients are composite heterozygous and carry one allele encoding an inactive mutant, R141H, and one encoding a hypomorphic mutant. Phosphomannomutase2 is a dimer. We reproduced composite heterozygosity in vitro by mixing R141H either with the wild type protein or the most common hypomorphic mutant F119L and compared the quaternary structure, the activity and the stability of the heterodimeric enzymes. We demonstrated that the activity of R141H/F119L heterodimers in vitro, which reproduces the protein found in patients, has the same activity of wild type/R141H, which reproduces the protein found in healthy carriers. On the other hand the stability of R141H/F119L appears to be reduced both in vitro and in vivo. These findings suggest that a therapy designed to enhance protein stability such as those based on pharmacological chaperones or modulation of proteostasis could be beneficial for PMM2-CDG patients carrying R141H/F119L genotype as well as for other genotypes where protein stability rather than specific activity is affected by mutations.
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Affiliation(s)
| | - Maria Chiara Monti
- Dipartimento di Farmacia, Università degli Studi di Salerno, Fisciano, Italy
| | - Valentina Citro
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
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5
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Dutta S, Mukherjee D, Jarori GK. Replacement of Ser108 in Plasmodium falciparum enolase results in weak Mg(II) binding: role of a parasite-specific pentapeptide insert in stabilizing the active conformation of the enzyme. FEBS J 2015; 282:2296-308. [PMID: 25787157 DOI: 10.1111/febs.13272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 03/06/2015] [Accepted: 03/16/2015] [Indexed: 01/20/2023]
Abstract
A distinct structural feature of Plasmodium falciparum enolase (Pfeno) is the presence of a five amino acid insert -104EWGWS108- that is not found in host enolases. Its conservation among apicomplexan enolases has raised the possibility of its involvement in some important physiological function(s). Deletion of this sequence is known to lower k(cat)/K(m), increase K(a) for Mg(II) and convert dimer into monomers (Vora HK, Shaik FR, Pal-Bhowmick I, Mout R & Jarori GK (2009) Arch Biochem Biophys 485, 128-138). These authors also raised the possibility of the formation of an H-bond between Ser108 and Leu49 that could stabilize the apo-Pfeno in an active closed conformation that has high affinity for Mg(II). Here, we examined the effect of replacement of Ser108 with Gly/Ala/Thr on enzyme activity, Mg(II) binding affinity, conformational states and oligomeric structure and compared it with native recombinant Pfeno. The results obtained support the view that Ser108 is likely to be involved in the formation of certain crucial H-bonds with Leu49. The presence of these interactions can stabilize apo-Pfeno in an active closed conformation similar to that of Mg(II) bound yeast enolase. As predicted, S108G/A-Pfeno variants (where Ser108-Leu49 H-bonds are likely to be disrupted) were found to exist in an open conformation and had low affinity for Mg(II). They also required Mg(II) induced conformational changes to acquire the active closed conformational state essential for catalysis. The possible physiological relevance of apo-Pfeno being in such an active state is discussed.
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Affiliation(s)
- Sneha Dutta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Debanjan Mukherjee
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Gotam K Jarori
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
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6
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Aghajanian S, Hovsepyan M, Geoghegan KF, Chrunyk BA, Engel PC. A thermally sensitive loop in clostridial glutamate dehydrogenase detected by limited proteolysis. J Biol Chem 2003; 278:1067-74. [PMID: 12414808 DOI: 10.1074/jbc.m206099200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structural flexibility and thermostability of glutamate dehydrogenase (GDH) from Clostridium symbiosum were examined by limited proteolysis using three proteinases with different specificities, trypsin, chymotrypsin, and endoproteinase Glu-C. Clostridial GDH resisted proteolysis by any of these enzymes at 25 degrees C. Above 30 degrees C, however, GDH became cleavable by chymotrypsin, apparently at a single site. SDS-PAGE indicated the formation of one large fragment with a molecular mass of approximately 44 kDa and one small one of <10 kDa. Proteolysis was accompanied by the loss of enzyme activity, which outran peptide cleavage, suggesting a cooperative conformational change. Proteolysis was prevented by either of the substrates 2-oxoglutarate or l-glutamate but not by the coenzymes NAD(+) or NADH. Circular dichroism spectroscopy indicated that the protective effects of these ligands resulted from fixation of flexible regions of the native structure of the enzyme. Size-exclusion chromatography and SDS-PAGE studies of chymotrypsin-treated GDH showed that the enzyme retained its hexameric structure and all of its proteolytic fragments. However, circular dichroism spectroscopy and analytical ultracentrifugation showed global conformational changes affecting the overall compactness of the protein structure. Chymotrypsin-catalyzed cleavage also diminished the thermostability of GDH and the cooperativity of the transition between its native and denatured states. N-terminal amino acid sequencing and mass spectrometry showed that heat-induced sensitivity to chymotrypsin emerged in the loop formed by residues 390-393 that lies between helices alpha(15) and alpha(16) in the folded structure of the enzyme.
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Affiliation(s)
- Suren Aghajanian
- Department of Biochemistry and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
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7
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Nowicki C, Hunter GR, Montemartini-Kalisz M, Blankenfeldt W, Hecht H, Kalisz HM. Recombinant tyrosine aminotransferase from Trypanosoma cruzi: structural characterization and site directed mutagenesis of a broad substrate specificity enzyme. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1546:268-81. [PMID: 11295433 DOI: 10.1016/s0167-4838(01)00136-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The gene encoding tyrosine aminotransferase (TAT, EC 2.6.1.5) from the parasitic protozoan Trypanosoma cruzi was amplified from genomic DNA, cloned into the pET24a expression vector and functionally expressed as a C-terminally His-tagged protein in Escherichia coli BL21(DE3)pLysS. Purified recombinant TAT exhibited identical electrophoretic and enzymatic properties as the authentic enzyme from T. cruzi. Both recombinant and authentic T. cruzi TATs were highly resistant to limited tryptic cleavage and contained no disulfide bonds. Comprehensive analysis of its substrate specificity demonstrated TAT to be a broad substrate aminotransferase, with leucine, methionine as well as tyrosine, phenylalanine, tryptophan and alanine being utilized efficiently as amino donors. Valine, isoleucine and dicarboxylic amino acids served as poor substrates while polar aliphatic amino acids could not be transaminated. TAT also accepted several 2-oxoacids, including 2-oxoisocaproate and 2-oxomethiobutyrate, in addition to pyruvate, oxaloacetate and 2-oxoglutarate. The functionality of the expression system was confirmed by constructing two variants; one (Arg389) being a completely inactive enzyme; the other (Arg283) retaining its full activity, as predicted from the recently solved three-dimensional structure of T. cruzi TAT. Thus, only one of the two strictly conserved arginines which are essential for the enzymatic activity of subfamily Ialpha aspartate and aromatic aminotransferases is critical for T. cruzi's TAT activity.
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Affiliation(s)
- C Nowicki
- Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, Junin 956, 1113 Buenos Aires, Argentina.
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8
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Li ZY, Zhou JM. Conformational change of dihydrofolate reductase near the active site after thiol modification: detected by limited proteolysis. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1481:37-44. [PMID: 10962090 DOI: 10.1016/s0167-4838(00)00121-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Kinetic studies of chicken liver dihydrofolate reductase (CL-DHFR) and Chinese hamster ovary DHFR (CH-DHFR) activated following p-hydroxymercuribenzoate (p-HMB) modification indicate a conformational change at the active site, suggesting a loosening of the enzyme structure upon SH modification. In the present study, limited proteolysis was applied to detect the subtle conformational changes in SH-modified DHFRs. The digested peptide fragments were separated by Tricine SDS-PAGE and sequenced by Edman auto-degradation. The thiol modifier N-iodoacetyl-N'-(5-sulfo-1-nophthyl) ethylenediamine (IAEANS), which activates these DHFRs only weakly, was used as a control. The results of sequencing showed that compared to native enzyme, there is one additional cleavage site near the active site in p-HMB-modified CL-DHFR, two additional sites in p-HMB-modified CH-DHFR, but no additional site for IAEANS-modified DHFRs. These results indicate that activation of DHFRs following thiol modification is accompanied by a conformational change at or near the active site. This subtle change in the active site conformation results in a pronounced change in enzyme activity. This provides further evidence that flexibility at the active site is essential for full expression of enzyme catalytic activity. Comparing results obtained from previous experiments on guanidine- and urea-activated CL-DHFR, this shows that a conformational change near helix(28-39) is sufficient for full activation of DHFR.
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Affiliation(s)
- Z Y Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Chaoyang District, Beijing 100101, PR China
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9
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Caporale C, Caruso C, Facchiano A, Nobile M, Leonardi L, Bertini L, Colonna G, Buonocore V. Probing the modelled structure of Wheatwin1 by controlled proteolysis and sequence analysis of unfractionated digestion mixtures. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19990801)36:2<192::aid-prot5>3.0.co;2-l] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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10
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Dieckmann R, Pavela-Vrancic M, von Döhren H, Kleinkauf H. Probing the domain structure and ligand-induced conformational changes by limited proteolysis of tyrocidine synthetase 1. J Mol Biol 1999; 288:129-40. [PMID: 10329131 DOI: 10.1006/jmbi.1999.2671] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The boundaries of the structural domains in peptide synthetases and the conformational changes related to catalysis were investigated by limited proteolysis of tyrocidine synthetase 1 (TY1). Four regions sensitive to proteolysis were detected (cleavage site at Arg13, Arg424, Arg509 and Arg602) that, in addition to an N-terminal extension, accurately delineate the domain boundaries of the adenylate-forming domain, the aminoacyl carrier domain, and the epimerisation domain. Limited proteolysis of an active N-terminal truncated deletion mutant, His6DeltaTY1, generated two stable and structurally independent subunits, corresponding to the subdomains of the adenylation domain. The structural integrity of the carrier domain was substantiated by its resistance to proteolytic degradation. Evidence is provided that the C-terminal "spacer" region with epimerising and/or condensing activity folds into an autonomous domain stable against degradation by limited proteoly sis. In the presence of substrates, reduced susceptibility to proteolysis was observed in the linker region connecting the subdomains of the adenylation domain, and corresponding to a peptide stretch of low electron density in the X-ray structure of the homologous firefly luciferase. Sequence analysis has shown that the respective linker contains conserved residues, whereas the linker regions connecting the structural domains are of low homology with a significant content of Pro, Ala, Glu and polar residues. A combination of kinetic and proteolytic studies using ATP analogues with substitutions in the phosphate chain, AMP-PcP, AMP-PNP and AMP-cPP, strongly suggests that the generation of a productive complex is associated with the ability of the beta, gamma-pyrophosphate moiety of ATP to adopt the proper active-site conformation. These data substantiate the observation that peptide synthetases undergo a series of conformational changes in the process of adenylate formation and product release.
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Affiliation(s)
- R Dieckmann
- Max-Volmer-Institut für Biophysikalische Chemie und Biochemie, Technische Universität Berlin, Berlin, Germany
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11
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Azzariti A, Vacca RA, Giannattasio S, Merafina RS, Marra E, Doonan S. Kinetic properties and thermal stabilities of mutant forms of mitochondrial aspartate aminotransferase. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1386:29-38. [PMID: 9675237 DOI: 10.1016/s0167-4838(98)00057-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Kinetic properties and thermal stabilities of the precursor form of mitochondrial aspartate aminotransferase, the mature form lacking 9 amino acids from the N-terminus, and forms of the mature protein in which cysteine-166 had been mutated to serine or alanine were compared with those of the mature enzyme. The precursor and the cysteine mutants showed moderately impaired catalytic properties consistent with decreased ability to undergo transition from the open to the closed conformation which is an integral part of the mechanism of action of the enzyme. The deletion mutant had a kcat only 2% of that of the mature enzyme but also much reduced Km values for both substrates. In addition it showed enhanced reactivity of cysteine-166 with 5,5'-dithiobis(2-nitrobenzoate), which is characteristic of the closed form of the enzyme, with no enhancement of reactivity in the presence of substrates. This is taken to show that the deletion mutant adopts a conformation that is significantly different from that of the mature enzyme particularly in respect of the small domain. The deletion mutant was found to be more resistant to thermal inactivation over a range of temperatures than were the other forms of the enzyme consistent with its having a more tightly packed small domain.
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Affiliation(s)
- A Azzariti
- Centro di Studio sui Mitocondri e Metabolismo Energetico, CNR, Bari and Trani, Italy
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12
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Yang HH, Li XC, Amft M, Grotemeyer J. Protein conformational changes determined by matrix-assisted laser desorption mass spectrometry. Anal Biochem 1998; 258:118-26. [PMID: 9527857 DOI: 10.1006/abio.1997.2549] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is shown that simultaneously to the unfolding of hen egg white lysozyme and horse heart cytochrome c the sequential conformational changes and molten globule states can be detected by the combination of proteolysis and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). This is demonstrated by the differences among the products and the time courses of native lysozyme as well as those unfolded in 1 and 3 M guanidine hydrochloride (GuHCl) when they were proteolyzed by proteinase K and analyzed by MALDI-MS. Due to the absence of disulfide bonds in the cytochrome c molecule, it is more sensitive to the disturbance of the denaturant. The partially unfolded state as detected at low concentrations of guanidine hydrochloride in our experiment resemble the molten globule state. One of the unique properties of the method described herein is to measure directly the peptide fragment liberated from proteolysis of the protein. It allows the identification of the sensitive sites susceptible to denaturation, which are subsequently cleaved by proteinase K proteolysis.
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Affiliation(s)
- H H Yang
- Institut für Physikalische Chemie, Universität Würzburg, Marcusstrasse 9/11, Würzburg, D-97070, Germany
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13
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Yang H, Amft M, Grundwürmer JM, Li X, Grotemeyer J. Primary structures of proteins characterized by proteinase K digestion and matrix-assisted laser desorption/ionization mass spectrometry. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1997; 50:402-6. [PMID: 9401926 DOI: 10.1111/j.1399-3011.1997.tb01201.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To improve the sequence ions of a protein in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), proteinase K was used to digest the protein followed by MALDI-MS characterization of the peptide fragments. The primary structures of three proteins, insulin B chain, cytochrome c and lysozyme, were determined by this method. A series of peptide fragments including those differentiated by one residue can be produced from the protein by using proteinase K digestion, thus providing support to the protein sequence. The peptide fragments liberated from proteinase K proteolysis of the insulin B chain allow the protein to be partially sequenced. Furthermore, some of the residues are double or triple checked by generating a variety of fragments. The same method was used to investigate cytochrome c and lysozyme denaturated in 3 M guanidine hydrochloride. The success of the method relies on the intrinsic properties of proteinase K and accurate determination of the peptide fragments by MALDI-MS.
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Affiliation(s)
- H Yang
- Institute of Physical Chemistry, Wuerzburg University, Germany.
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14
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Andreotti G, Cubellis MV, Palo MD, Fessas D, Sannia G, Marino G. Stability of a thermophilic TIM-barrel enzyme: indole-3-glycerol phosphate synthase from the thermophilic archaeon Sulfolobus solfataricus. Biochem J 1997; 323 ( Pt 1):259-64. [PMID: 9173891 PMCID: PMC1218304 DOI: 10.1042/bj3230259] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The stability and activity of indole-3-glycerol phosphate synthase from Sulfolobus solfataricus were studied as a function of pH and temperature. In this paper we focus on three points: (1) the long-term stability of the protein to irreversible denaturation at high temperature; (2) the short-term stability of the protein to reversible temperature-driven unfolding; and (3) the dependence of its activity on temperature. Results can be summarized as follows: (a) the same first-order kinetic constant (0.020+/-0.003 min-1) was determined at different pH values (6.5, 8.0 and 9.5) from long-term stability experiments at 80 degrees C; (b) short-term stability experiments revealed different behaviour in two different pH ranges (6.5-8.0, 8.5-9.5), suggesting that the melting temperature is higher at alkaline than at neutral pH; (c) the dependence of activity on temperature was investigated at pH 7.0 and 9.0, and a discontinuity was observed in the Arrhenius plot of kcat values at pH 9.0. We also investigated the stability in the presence of guanidinium chloride at 20 degrees C either at pH 7.0 or at pH 9.0, and we present data that indicate that the unfolding mechanism closely approaches a two-state model at pH 7.0 and a more complex mechanism at pH 9.0. Satisfactory fitting of the equilibrium unfolding transition obtained by fluorescence measurements at pH 9.0 required a model that involves a stable intermediate in addition to the native and unfolded forms. At 20 degrees C the folded conformation is more stable than the unfolded conformation by (14. 7+/-1.2) kJ/mol at pH 7.0 and by (25.5+/-1.8) kJ/mol at pH 9.0.
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Affiliation(s)
- G Andreotti
- Dipartimento di Chimica Organica e Biologica, Via Mezzocannone 16, Universit à di Napoli 'Federico II', 80134 Napoli, Italy
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15
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Tutino ML, Tosco A, Marino G, Sannia G. Expression of Sulfolobus solfataricus trpE and trpG genes in E. coli. Biochem Biophys Res Commun 1997; 230:306-10. [PMID: 9016772 DOI: 10.1006/bbrc.1996.5951] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The genes trpE and trpG of the hyperthermophilic archaeon Sulfolobus solfataricus, encoding the components I and II of anthranilate synthase, were cloned and co-expressed in Escherichia coli. The properties of the recombinant protein were determined and compared to those of the wild type complex. Gel filtration chromatography revealed an alpha2beta2 composition. The heteromeric enzyme is fully active above 85 degrees C and can be considered to be an "extremozyme" according to Adams et al.[1]. Sulfolobus solfataricus anthranilate synthase is subject to feedback inhibition by L-tryptophan even if it lacks the co-operativity that has been observed for all the other tetrameric anthranilate synthases.
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Affiliation(s)
- M L Tutino
- Dipartimento di Chimica Organica e Biologica, Università di Napoli Federico II, Italy
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16
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Zappacosta F, Pessi A, Bianchi E, Venturini S, Sollazzo M, Tramontano A, Marino G, Pucci P. Probing the tertiary structure of proteins by limited proteolysis and mass spectrometry: the case of Minibody. Protein Sci 1996; 5:802-13. [PMID: 8732752 PMCID: PMC2143402 DOI: 10.1002/pro.5560050502] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A strategy that combines limited proteolysis experiments and mass spectrometric analysis of the fragments generated has been developed to probe protease-accessible sites on the protein surface. This integrated approach has been employed to investigate the tertiary structure of the Minibody, a de novo designed 64-residue protein consisting of a beta-sheet scaffold based on the heavy-chain variable-domain structure of a mouse immunoglobulin and containing two segments corresponding to the hypervariable H1 and H2 regions. The low solubility of the protein prevented a detailed characterization by NMR and/or X-ray. Different proteases were used under strictly controlled conditions and the cleavage sites were mapped onto the anticipated Minibody model, leading to the identification of the most exposed regions. A single-residue mutant was constructed and characterized, following the same procedure, showing a slightly higher correspondence with the predicted model. This strategy can be used to effectively supplement NMR and X-ray investigations of protein tertiary structure, where these procedures cannot provide definitive data, or to verify and refine protein models.
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Affiliation(s)
- F Zappacosta
- Servizio di Spettrometria di Massa del CNR, Napoli, Italy
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17
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Fan YX, Ju M, Zhou JM, Tsou CL. Activation of chicken liver dihydrofolate reductase by urea and guanidine hydrochloride is accompanied by conformational change at the active site. Biochem J 1996; 315 ( Pt 1):97-102. [PMID: 8670138 PMCID: PMC1217202 DOI: 10.1042/bj3150097] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
It has been reported that the activation of dihydrofolate reductase (DHFR) from L1210 mouse leukaemia cells by KCl or thiol modifiers is accompanied by increased digestibility by proteinases [Duffy, Beckman, Peterson, Vitols and Huennekens (1987) J. Biol. Chem. 262, 7028-7033], suggesting a loosening up of the general compact structure of the enzyme. In the present study, the peptide fragments liberated from the chicken liver enzyme by digestion with trypsin in dilute solutions of urea or guanidine hydrochloride (GuHCl) have been separated by FPLC and sequenced. The sequences obtained are unique when compared with the known sequence of DHFR and thus allow the points of proteolytic cleavage identified for the urea- and GuHCl-activated enzyme to be at or near the active site. It was also indicated by the enhanced fluorescence of 2-p-toluidinylnaphthalene 6-sulfonate that conformational changes at the active site in dilute GuHCl parallel GuHCl activation. The above results indicate that the activation of DHFR in dilute denaturants is accompanied by a loosening up of its compact structure especially at or near the active site, suggesting that the flexibility at its active site is essential for the full expression of its catalytic activity.
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Affiliation(s)
- Y X Fan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing, China
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18
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Tsou CL. Inactivation precedes overall molecular conformation changes during enzyme denaturation. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1253:151-62. [PMID: 8519796 DOI: 10.1016/0167-4838(95)00172-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- C L Tsou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing, People's Republic of China
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19
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Yang HJ, Tsou CL. Inactivation during denaturation of ribonuclease A by guanidinium chloride is accompanied by unfolding at the active site. Biochem J 1995; 305 ( Pt 2):379-84. [PMID: 7832749 PMCID: PMC1136372 DOI: 10.1042/bj3050379] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Inactivation of pancreatic RNAase A occurs in guanidinium chloride (GdmCl) at low concentrations before the unfolding of the molecule as a whole can be detected [Liu and Tsou (1987) Biochim. Biophys. Acta 916, 455-464]. We have now shown that the rate of digestion of the RNAase molecule by either trypsin or proteinase K increases significantly at low concentrations of GdmCl where the enzyme is largely inactivated, but fluorescence and absorption measurements reveal no conformational changes. N-Terminal sequence analysis of the peptide fragments generated shows that proteolysis occurs primarily at or near the active site. The decrease in activity of RNAase at low concentrations of GdmCl is therefore due to partial unfolding of the molecule, particularly at the active site and not to an inhibition by the denaturant.
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Affiliation(s)
- H J Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing, China
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20
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Zappacosta F, Sannia G, Savoy LA, Marino G, Pucci P. Post-translational modifications in aspartate aminotransferase from Sulfolobus solfataricus. Detection of N-epsilon-methyllysines by mass spectrometry. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 222:761-7. [PMID: 8026489 DOI: 10.1111/j.1432-1033.1994.tb18922.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Advanced mass spectrometric procedures have been extensively used to provide an accurate structural characterization of aspartate aminotransferase from Sulfolobus solfataricus. The amino acid sequence of this enzyme had previously been deduced from the DNA sequence. The accurate molecular mass of the protein, determined using electrospray mass spectrometry, demonstrated that the amino acid sequence deduced was correct and ruled out the possible presence of large covalent modifications which had been postulated to fit the much higher molecular mass obtained from previous SDS/PAGE experiments. The definition of the entire primary structure of aspartate aminotransferase from S. solfataricus was achieved by exploiting a new mass spectrometric mapping strategy. Initially, the molecular mass of relatively large protein fragments produced by CNBr hydrolysis was accurately determined using electrospray mass spectrometry. The protein regions where structural modifications had occurred were easily identified from their anomalous mass values. The corresponding CNBr fragments were then subdigested with suitable proteases and the resulting peptide mixtures were analysed by fast-atom-bombardment mass spectrometry. This mapping approach led to the detection of two partially modified lysine residues at positions 202 and 384, which had been converted to their N-epsilon-methyl derivatives to a substoichiometric extent.
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Affiliation(s)
- F Zappacosta
- Servizio di Spettrometria di Massa del CNR, Napoli, Italy
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Andreotti G, Cubellis MV, Nitti G, Sannia G, Mai X, Marino G, Adams MW. Characterization of aromatic aminotransferases from the hyperthermophilic archaeon Thermococcus litoralis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 220:543-9. [PMID: 8125113 DOI: 10.1111/j.1432-1033.1994.tb18654.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The hyperthermophilic archaeon (formerly archaebacterium) Thermococcus litoralis grows at temperatures up to 98 degrees C using peptides and proteins as the sole sources of carbon and nitrogen. Cell-free extracts of the organism contained two distinct types of aromatic aminotransferases (EC 2.6.1.57) which were separated and purified to electrophoretic homogeneity. Both enzymes are homodimers with subunit masses of approximately 47 kDa and 45 kDa. Using 2-oxoglutarate as the amino acceptor, each catalyzed the pyridoxal-5'-phosphate-dependent transamination of the three aromatic amino acids but showed virtually no activity towards aspartic acid, alanine, valine or isoleucine. From the determination of Km and kcat values using 2-oxoglutarate, phenylalanine, tyrosine and tryptophan as substrates, both enzymes were shown to be highly efficient at transaminating phenylalanine (kcat/Km approximately 400 s-1 mM-1); the 47-kDa enzyme showed more activity towards tyrosine and tryptophan compared to the 45-kDa one. Kinetic analyses indicated a two-step mechanism with a pyridoxamine intermediate. Both enzymes were virtually inactive at 30 degrees C and exhibited maximal activity between 95-100 degrees C. They showed no N-terminal sequence similarity with each other (approximately 30 residues), nor with the complete amino acid sequences of aromatic aminotransferases from Escherichia coli and rat liver. The catalytic properties of the two enzymes are distinct from bacterial aminotransferases, which have broad substrate specificities, but are analogous to two aromatic aminotransferases which play a biosynthetic role in a methanogenic archaeon. In contrast, it is proposed that one or both play a catabolic role in proteolytic T. litoralis in which they generate glutamate and an arylpyruvate. These serve as substrates for glutamate dehydrogenase and indolepyruvate ferredoxin oxidoreductase in a novel pathway for the utilization of aromatic amino acids.
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Affiliation(s)
- G Andreotti
- Dipartimento di Chimica Organica e Biologica, Università di Napoli, Italy
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Arnone MI, Birolo L, Cubellis MV, Nitti G, Marino G, Sannia G. Expression of a hyperthermophilic aspartate aminotransferase in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1160:206-12. [PMID: 1445947 DOI: 10.1016/0167-4838(92)90009-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The gene for an archaebacterial hyperthermophilic enzyme, aspartate aminotransferase from Sulfolobus solfataricus (AspATSs), was expressed in Escherichia coli and the enzyme purified to homogeneity. A suitable expression vector and host strain were selected and culture conditions were optimized so that 6-7 mg of pure enzyme per litre of culture were obtained repeatedly. The recombinant enzyme and the authentic AspATSs are indistinguishable: in fact, they have the same molecular weight, estimated by means of SDS-PAGE and gel filtration, the same Km values for 2-oxo-glutarate and cysteine sulphinate and the same UV-visible spectra. Moreover, recombinant AspATSs is thermophilic and thermostable just as the enzyme extracted from Sulfolobus solfataricus. The protocol described may be used to produce thermostable arachaebacterial enzymes in mesophilic hosts.
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Affiliation(s)
- M I Arnone
- Dipartimento di Chimica Organica e Biologica, Università di Napoli, Italy
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