1
|
Degliesposti G. Peptide-Based Mass Spectrometry for the Investigation of Protein Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:31-40. [PMID: 38507198 DOI: 10.1007/978-3-031-52193-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
In the last two decades, biological mass spectrometry has become the gold standard for the identification of proteins in biological samples. The technological advancement of mass spectrometers and the development of methods for ionization, gas phase transfer, peptide fragmentation as well as for acquisition of high-resolution mass spectrometric data marked the success of the technique. This chapter introduces peptide-based mass spectrometry as a tool for the investigation of protein complexes. It provides an overview of the main steps for sample preparation starting from protein fractionation, reduction, alkylation and focus on the final step of protein digestion. The basic concepts of biological mass spectrometry as well as details about instrumental analysis and data acquisition are described. Finally, the most common methods for data analysis and sequence determination are summarized with an emphasis on its application to protein-protein complexes.
Collapse
|
2
|
Xu H, Bygdell J, Wingsle G, Byström AS. Yeast Elongator protein Elp1p does not undergo proteolytic processing in exponentially growing cells. Microbiologyopen 2015; 4:867-78. [PMID: 26407534 PMCID: PMC4694139 DOI: 10.1002/mbo3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023] Open
Abstract
In eukaryotic organisms, Elongator is a six-subunit protein complex required for the formation of 5-carbamoylmethyl (ncm(5) ) and 5-methylcarboxymethyl (mcm(5) ) side chains on uridines present at the wobble position (U34 ) of tRNA. The open reading frame encoding the largest Elongator subunit Elp1p has two in-frame 5' AUG methionine codons separated by 48 nucleotides. Here, we show that the second AUG acts as the start codon of translation. Furthermore, Elp1p was previously shown to exist in two major forms of which one was generated by proteolysis of full-length Elp1p and this proteolytic cleavage was suggested to regulate Elongator complex activity. In this study, we found that the vacuolar protease Prb1p was responsible for the cleavage of Elp1p. The cleavage occurs between residues 203 (Lys) and 204 (Ala) as shown by amine reactive Tandem Mass Tag followed by LC-MS/MS (liquid chromatography mass spectrometry) analysis. However, using a modified protein extraction procedure, including trichloroacetic acid, only full-length Elp1p was observed, showing that truncation of Elp1p is an artifact occurring during protein extraction. Consequently, our results indicate that N-terminal truncation of Elp1p is not likely to regulate Elongator complex activity.
Collapse
Affiliation(s)
- Hao Xu
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Joakim Bygdell
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 87, Umeå, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| |
Collapse
|
3
|
Ye W, Wang H, Ma Y, Luo X, Zhang W, Wang J, Wang X. Characterization of the glutamate-specific endopeptidase from Bacillus licheniformis expressed in Escherichia coli. J Biotechnol 2013; 168:40-5. [PMID: 23965272 DOI: 10.1016/j.jbiotec.2013.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 08/08/2013] [Indexed: 11/30/2022]
Abstract
Glutamate-specific endopeptidase from Bacillus licheniformis (GSE-BL) is widely used in peptide recovery and synthesis because of its unique substrate specificity. However, the mechanism underlying its specificity is still not thoroughly understood. In this study, the roles of the prosegment and key amino acids involved in the proteolytic activity of GSE-BL were investigated. Loss of the GSE-BL prosegment severely restricted enzymatic activity toward Z-Phe-Leu-Glu-pNA. A homologous model of GSE-BL revealed that it contains the catalytic triad "His47, Asp96 and Ser 167", which was further confirmed by site-directed mutagenesis. In vitro mutagenesis further indicated that Val2, Arg89 and His190 are essential for enzymatic activity toward Z-Phe-Leu-Glu-pNA. Moreover, the catalytic efficiency of Phe57Ala GSE-BL toward Z-Phe-Leu-Glu-pNA was 50% higher than that of the native mature GSE-BL. This is the first study to fully elucidate the key amino acids for proteolytic activity of GSE-BL. Mature GSE-BL could be obtained through self-cleavage alone when Lys at -1 position was replaced by Glu, providing a new strategy for the preparation of mature GSE-BL. This study yielded some valuable insights into the substrate specificity of glutamate-specific endopeptidase, establishing a foundation for broadening the applications of GSE-BL.
Collapse
Affiliation(s)
- Wei Ye
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, PR China; State Key Laboratory of Applied Microbiology, South China (The Ministry-Province Joint Development), Guangdong Institute of Microbiology, GuangZhou 510070, PR China
| | | | | | | | | | | | | |
Collapse
|
4
|
Jahouh F, Hou SJ, Kováč P, Banoub JH. Determination of glycation sites by tandem mass spectrometry in a synthetic lactose-bovine serum albumin conjugate, a vaccine model prepared by dialkyl squarate chemistry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:749-58. [PMID: 22368054 PMCID: PMC3417241 DOI: 10.1002/rcm.6166] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE Neoglycoconjugate vaccines synthesized by the squaric acid spacer method allow single point attachment of the carbohydrate antigen to the protein carrier. However, the localization of the carbohydrate antigen sites of conjugation on the protein carrier has been an elusive task difficult to achieve. METHOD Covalent attachment of the lactose antigen to the bovine serum albumin (BSA) was prepared by the squaric acid method using a hapten:BSA ratio of 20:1. Different reaction times were used during the conjugation reaction and two different lactose-BSA glycoconjugate vaccines were obtained. The carbohydrate antigen hapten:BSA ratios of these lactose-BSA glycoconjugate vaccines were determined by MALDI-TOF/RTOF-MS and the glycation sites in the neoglycoconjugates were determined using nano-LC/ESI-QqTOF-MS/MS analysis of the trypsin and GluC V8 digests of the conjugates. RESULTS We have identified a total of 15 glycation sites located on the BSA lysine residues for the neoglycoconjugate vaccine formed with a hapten:BSA ratio of 5.1:1, However, the tryptic and GluC V8 digests of the hapten-BSA glycoconjugate with a hapten:BSA ratio of 19.0:1 allowed identification of 30 glycation sites located on the BSA. These last results seem to indicate that this conjugation results in formation of various glycoforms. CONCLUSIONS It was observed that the number of identified glycation sites increased when the hapten:BSA ratio of glycoconjugate formation increased, and that the location of the glycation sites appears to be mainly on the outer surface of the BSA carrier molecule which is in line with the assumption that the sterically more accessible lysine residues, namely those located on the outer surface of the BSA, would be conjugated preferentially.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Cattle
- Chromatography, Liquid
- Glycosylation
- Haptens/chemistry
- Haptens/metabolism
- Lactose/chemistry
- Lactose/immunology
- Lactose/metabolism
- Lysine/chemistry
- Lysine/metabolism
- Models, Molecular
- Molecular Sequence Data
- Peptide Fragments/chemistry
- Peptide Fragments/metabolism
- Serum Albumin, Bovine/chemistry
- Serum Albumin, Bovine/immunology
- Serum Albumin, Bovine/metabolism
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tandem Mass Spectrometry/methods
- Vaccines, Conjugate/chemistry
- Vaccines, Conjugate/immunology
- Vaccines, Conjugate/metabolism
- Vaccines, Subunit/chemistry
- Vaccines, Subunit/immunology
- Vaccines, Subunit/metabolism
Collapse
Affiliation(s)
- Farid Jahouh
- Department of Chemistry, Memorial University of Newfoundland, Saint John's, NL, Canada
| | - Shu-jie Hou
- NIDDK, LBC, National Institutes of Health, Bethesda, MD 20892-0815, USA
| | - Pavol Kováč
- NIDDK, LBC, National Institutes of Health, Bethesda, MD 20892-0815, USA
| | - Joseph H. Banoub
- Department of Chemistry, Memorial University of Newfoundland, Saint John's, NL, Canada
- Department of Fisheries and Oceans Canada, Science Branch, Special Projects, Saint John's, NL, A1C 5X1, Canada
| |
Collapse
|
5
|
Cloning, expression, purification, and characterization of a glutamate-specific endopeptidase from Bacillus licheniformis. Protein Expr Purif 2012; 82:138-43. [PMID: 22202650 DOI: 10.1016/j.pep.2011.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/05/2011] [Accepted: 12/06/2011] [Indexed: 11/17/2022]
|
6
|
Jahouh F, Hou SJ, Kováč P, Banoub JH. Determination of the glycation sites of Bacillus anthracis neoglycoconjugate vaccine by MALDI-TOF/TOF-CID-MS/MS and LC-ESI-QqTOF-tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:993-1003. [PMID: 22012665 PMCID: PMC3427925 DOI: 10.1002/jms.1980] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We present herein an efficient mass spectrometric method for the localization of the glycation sites of a model neoglycoconjugate vaccine formed by a construct of the tetrasaccharide side chain of the Bacillus anthracis exosporium and the protein carrier bovine serum albumin. The glycoconjugate was digested with both trypsin and GluC V8 endoproteinases, and the digests were then analyzed by MALDI-TOF/TOF-CID-MS/MS and nano-LC-ESI-QqTOF-CID-MS/MS. The sequences of the unknown peptides analyzed by MALDI-TOF/TOF-CID-MS/MS, following digestion with the GluC V8 endoproteinase, allowed us to recognize three glycopeptides whose glycation occupancies were, respectively, on Lys 235, Lys 420, and Lys 498. Similarly, the same analysis was performed on the tryptic digests, which permitted us to recognize two glycation sites on Lys 100 and Lys 374. In addition, we have also used LC-ESI-QqTOF-CID-MS/MS analysis for the identification of the tryptic digests. However, this analysis identified a higher number of glycopeptides than would be expected from a glycoconjugate composed of a carbohydrate-protein ratio of 5.4:1, which would have resulted in glycation occupancies of 18 specific sites. This discrepancy was due to the large number of glycoforms formed during the synthetic carbohydrate-spacer-carrier protein conjugation. Likewise, the LC-ESI-QqTOF-MS/MS analysis of the GluC V8 digest also identified 17 different glycation sites on the synthetic glycoconjugate.
Collapse
Affiliation(s)
- Farid Jahouh
- Department of Chemistry, Memorial University of Newfoundland, Saint John’s, NL, Canada
| | - Shu-jie Hou
- NIDDK, LBC, National Institutes of Health, Bethesda, MD 20892-0815, USA
| | - Pavol Kováč
- NIDDK, LBC, National Institutes of Health, Bethesda, MD 20892-0815, USA
| | - Joseph H. Banoub
- Department of Chemistry, Memorial University of Newfoundland, Saint John’s, NL, Canada
- Science Branch, Special Projects, Department of Fisheries and Oceans Canada, Saint John’s, NL A1C 5X1, Canada
| |
Collapse
|
7
|
Estève PO, Chang Y, Samaranayake M, Upadhyay AK, Horton JR, Feehery GR, Cheng X, Pradhan S. A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability. Nat Struct Mol Biol 2010; 18:42-8. [PMID: 21151116 DOI: 10.1038/nsmb.1939] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 09/29/2010] [Indexed: 12/17/2022]
Abstract
The protein lysine methyltransferase SET7 regulates DNA methyltransferase-1 (DNMT1) activity in mammalian cells by promoting degradation of DNMT1 and thus allows epigenetic changes via DNA demethylation. Here we reveal an interplay between monomethylation of DNMT1 Lys142 by SET7 and phosphorylation of DNMT1 Ser143 by AKT1 kinase. These two modifications are mutually exclusive, and structural analysis suggests that Ser143 phosphorylation interferes with Lys142 monomethylation. AKT1 kinase colocalizes and directly interacts with DNMT1 and phosphorylates Ser143. Phosphorylated DNMT1 peaks during DNA synthesis, before DNMT1 methylation. Depletion of AKT1 or overexpression of dominant-negative AKT1 increases methylated DNMT1, resulting in a decrease in DNMT1 abundance. In mammalian cells, phosphorylated DNMT1 is more stable than methylated DNMT1. These results reveal cross-talk on DNMT1, through modifications mediated by AKT1 and SET7, that affects cellular DNMT1 levels.
Collapse
|
8
|
Buttle DJ, Bramwell H, Hollander AP. Proteolytic mechanisms of cartilage breakdown: a target for arthritis therapy? Mol Pathol 2010; 48:M167-77. [PMID: 16696000 PMCID: PMC407956 DOI: 10.1136/mp.48.4.m167] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- D J Buttle
- Institute for Bone & Joint Medicine, Department of Human Metabolism & Clinical Biochemistry, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX
| | | | | |
Collapse
|
9
|
Yang H, Gurgel PV, Williams DK, Bobay BG, Cavanagh J, Muddiman DC, Carbonell RG. Binding site on human immunoglobulin G for the affinity ligand HWRGWV. J Mol Recognit 2010; 23:271-82. [PMID: 20049844 PMCID: PMC3906645 DOI: 10.1002/jmr.967] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Affinity ligand HWRGWV has demonstrated the ability to isolate human immunoglobulin G (hIgG) from mammalian cell culture media. The ligand specifically binds hIgG through its Fc portion. This work shows that deglycosylation of hIgG has no influence on its binding to the HWRGWV ligand and the ligand does not compete with Protein A or Protein G in binding hIgG. It is suggested by the mass spectrometry (MS) data and docking simulation that HWRGWV binds to the pFc portion of hIgG and interacts with the amino acids in the loop Ser383-Asn389 (SNGQPEN) located in the C(H)3 domain. Subsequent modeling has suggested a possible three-dimensional minimized solution structure for the interaction of hIgG and the HWRGWV ligand. The results support the fact that a peptide as small as a hexamer can have specific interactions with large proteins such as hIgG.
Collapse
Affiliation(s)
- Haiou Yang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Patrick V. Gurgel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - D. Keith Williams
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Benjamin G. Bobay
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- North Carolina Research Campus, Kannapolis, Kannapolis, NC 28081, USA
| | - John Cavanagh
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - David C. Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Ruben G. Carbonell
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| |
Collapse
|
10
|
Two-dimensional gel electrophoresis-based proteomics of mycobacteria. Methods Mol Biol 2009. [PMID: 20560054 DOI: 10.1007/978-1-59745-207-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Two-dimensional gel electrophoresis (2-DE) in combination with mass spectrometry (MS) is the classic proteomics approach used to monitor the dynamics of protein abundance and posttranslational modifications in biological systems. In this chapter, we provide detailed protocols for 2-DE-based proteomics of mycobacteria. Adequate standard operating procedures for mycobacterial culture, subcellular fractionation, and selective enrichment of proteins are indispensable prerequisites for targeted proteome analyses. Therefore, we also provide approved protocols for selective and efficient extraction of cytosolic, secreted, and hydrophobic plasma membrane proteins of mycobacteria, as well as for isolation of mycobacteria from infected macrophages.
Collapse
|
11
|
De Leo F, Volpicella M, Sciancalepore M, Gallerani R, Ceci LR. One of the three proteinase inhibitor genes newly identified in theBrassica napusgenome codes for an inhibitor of glutamyl endopeptidase. FEBS Lett 2006; 580:948-54. [PMID: 16438970 DOI: 10.1016/j.febslet.2006.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 01/09/2006] [Indexed: 10/25/2022]
Abstract
Three proteinase inhibitor genes have been identified in the rapeseed (Brassica napus) genome. They are highly homologous to other genes of the mustard inhibitor (MSI) family of proteinase inhibitors characteristic of Cruciferae. In germinating seeds, only the transcript of one gene, coding for a trypsin inhibitor, is detectable by Northern analysis. The other two genes are transcribed at basal levels detectable only by reverse transcription PCR. One of the other two genes (rti-2) encodes a polypeptide with a glutamic residue in the P1 position, characteristic of glutamyl proteinase inhibitors. The recombinant RTI-2 protein strongly inhibits (Ki=44 nM) a glutamyl proteinase from Streptomyces griseus.
Collapse
Affiliation(s)
- Francesca De Leo
- Institute of Biomembranes and Bioenergetic, Italian National Research Council, CNR, Via Amendola, 165/A, 70126 Bari, Italy
| | | | | | | | | |
Collapse
|
12
|
|
13
|
Supuran CT, Scozzafava A, Mastrolorenzo A. Bacterial proteases: current therapeutic use and future prospects for the development of new antibiotics. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.11.2.221] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
14
|
Shaw L, Golonka E, Potempa J, Foster SJ. The role and regulation of the extracellular proteases of Staphylococcus aureus. MICROBIOLOGY-SGM 2004; 150:217-228. [PMID: 14702415 DOI: 10.1099/mic.0.26634-0] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Staphylococcus aureus has several extracellular proteases with proposed roles in virulence. SspA (serine protease), SspB (cysteine protease) and Aur (metalloprotease) have been characterized previously and SspA and SspB were found to be cotranscribed. The coding region for the cysteine protease ScpA has been identified and characterized. It is in a probable bi-cistronic operon with scpA located immediately upstream of a coding region for a 108 aa protein that is a specific inhibitor of ScpA. Using primer extension analysis promoters have been mapped and it was found that sigmaA is the only sigma factor involved in the transcription of scpA, sspABC and aur. The transcription of all the genes occurs maximally at post-exponential phase, being positively regulated by agr (accessory gene regulator) and negatively regulated by sarA (staphylococcal accessory regulator). Furthermore sigmaB represses transcription from the aur and scp operons similarly to the previously shown effect on ssp [Horsburgh, M., Aish, J., White, I., Shaw, L., Lithgow, J. & Foster, S. (2002). J Bacteriol 184, 5457-5467]. Using mutations in each protease gene the proteolytic cascade of activation has been analysed. Aur, SspA, SspB and ScpA are all produced as zymogens, activated by proteolytic cleavage. Although the metalloprotease, Aur, does catalyse activation of the SspA zymogen, it is not the sole agent capable of conducting this process. Site-directed mutagenesis revealed that Aur is not capable of undergoing auto-proteolysis to achieve activation. The cysteine protease, ScpA, appears to reside outside this cascade of activation, as mature ScpA was observed in the aur, sspA and sspB mutant strains. Using a mouse abscess model, it has been shown that insertional inactivation of sspA or sspB results in significant attenuation of virulence, whilst mutations in aur or scpA do not. It is likely the attenuation observed in the sspA strain is due to polarity on the sspB gene.
Collapse
Affiliation(s)
- Lindsey Shaw
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Ewa Golonka
- Department of Microbiology, Faculty of Biotechnology, Jagiellonian University, 7 Gronostajowa St, 30-387 Kraków, Poland
| | - Jan Potempa
- Department of Microbiology, Faculty of Biotechnology, Jagiellonian University, 7 Gronostajowa St, 30-387 Kraków, Poland
| | - Simon J Foster
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| |
Collapse
|
15
|
Abstract
Serine-, cysteine-, and metalloproteases are widely spread in many pathogenic bacteria, where they play critical functions related to colonization and evasion of host immune defenses, acquisition of nutrients for growth and proliferation, facilitation of dissemination, or tissue damage during infection. Since all the antibiotics used clinically at the moment share a common mechanism of action, acting as inhibitors of the bacterial cell wall biosynthesis or affecting protein synthesis on ribosomes, resistance to these pharmacological agents represents a serious medical problem, which might be resolved by using new generation of antibiotics, possessing a different mechanism of action. Bacterial protease inhibitors constitute an interesting such possibility, due to the fact that many specific as well as ubiquitous proteases have recently been characterized in some detail in both gram-positive as well as gram-negative pathogens. Few potent, specific inhibitors for such bacterial proteases have been reported at this moment except for some signal peptidase, clostripain, Clostridium histolyticum collagenase, botulinum neurotoxin, and tetanus neurotoxin inhibitors. No inhibitors of the critically important and ubiquitous AAA proteases, degP or sortase have been reported, although such compounds would presumably constitute a new class of highly effective antibiotics. This review presents the state of the art in the design of such enzyme inhibitors with potential therapeutic applications, as well as recent advances in the use of some of these proteases in therapy.
Collapse
Affiliation(s)
- Claudiu T Supuran
- University of Florence, Dipartimento di Chimica, Laboratorio di Chimica Inorganica e Bioinorganica, Firenze, Italy.
| | | | | |
Collapse
|
16
|
Ferjani A, Abe S, Ishikawa Y, Henmi T, Nishi Y, Tamura N, Yamamoto Y. Characterization of the stromal protease(s) degrading the cross-linked products of the D1 protein generated by photoinhibition of photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1503:385-95. [PMID: 11115650 DOI: 10.1016/s0005-2728(00)00233-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
When photosystem (PS) II-enriched membranes are exposed to strong light, cross-linking of the intrinsic D1 protein with the surrounding polypeptides and degradation of the D1 protein take place. The cross-linking of the D1 protein with the alpha-subunit of cytochrome b(559) is suggested to be an early event of photoinduced damage to the D1 protein (Barbato et al., FEBS Lett. 309 (1992) 165-169). The relationship between the cross-linking and the degradation of the D1 protein, however, is not yet clear. In the present study, we show that the addition of stromal extract from chloroplasts degrades the 41 kDa cross-linked product of D1/cytochrome b(559) alpha-subunit and enhances the degradation of the D1 protein. Incubation of the preilluminated PS II-enriched membranes with the stromal extract at 25 degrees C causes the degradation of the cross-linked product by more than 70%. The activity of the stromal extract showed a pH optimum at 8.0, and was enhanced by the addition of ATP or GTP. Consistent with the nucleotide effect, this stromal activity was eliminated by the preincubation of the stromal extract with apyrase, which hydrolyzes nucleotides. Also, the stromal activity was nearly fully inhibited by a serine-type protease inhibitor, 3,4-dichloroisocoumarin, which suggests participation of a serine-type protease(s).
Collapse
Affiliation(s)
- A Ferjani
- Department of Biology, Faculty of Science, Okayama University, Japan
| | | | | | | | | | | | | |
Collapse
|
17
|
Folate assay of foods by traditional and tri-enzyme treatments using cryoprotected Lactobacillus casei. Food Chem 2000. [DOI: 10.1016/s0308-8146(00)00210-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
18
|
Pałyga J, Górnicka-Michalska E, Kowalski A, Ksiazkiewicz J. Natural allelic variation of duck erythrocyte histone H1b. Int J Biochem Cell Biol 2000; 32:665-75. [PMID: 10785363 DOI: 10.1016/s1357-2725(99)00153-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In our previous work (J. Palyga, Genetic polymorphisms of histone H1. b in duck erythrocytes. Hereditas 114, 85-89, 1991) we reported a genetic polymorphism of duck erythrocyte histone H1.b. Here, we screened H1 preparations in a two-dimensional polyacrylamide gel to refine the distribution of allelic forms of H1.b in fifteen duck populations. We have revealed that the frequency of H1.b allelic variants was significantly different among many conservative and breeding duck groups. While b(1) and b(3) were common in all populations screened, the allele b(2), with a slightly lower apparent molecular weight, was confined mainly to brown-feathered ducks (Khaki Campbell and Orpington) and descendent lines. The C- and N-terminal peptides released upon cleavage with N-bromosuccinimide and Staphylococcus aureus protease V8 from duck allelic histones H1. b2 and H1.b3, respectively, migrated differently in the gel, probably as a result of potential amino acid variation in a C-terminal domain.
Collapse
Affiliation(s)
- J Pałyga
- Department of Genetics, Wyzsza Szkola Pedagogiczna, ul. Konopnickiej 15, 25-406, Kielce, Poland.
| | | | | | | |
Collapse
|
19
|
Kumaran S, Datta D, Roy RP. An enigmatic peptide ligation reaction: protease-catalyzed oligomerization of a native protein segment in neat aqueous solution. Protein Sci 2000; 9:734-41. [PMID: 10794415 PMCID: PMC2144614 DOI: 10.1110/ps.9.4.734] [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: 10/19/2022]
Abstract
We report an enigmatic peptide ligation reaction catalyzed by Glu-specific Staphylococcus aureus V8 protease that occurs in neat aqueous solution around neutral pH utilizing a totally unprotected peptide substrate containing free alpha-carboxyl and alpha-amino groups. V8 protease catalyzed a chain of ligation steps between pH 6 and 8 at 4 degrees C, producing a gamut of covalent oligomers (dimer through octamer or higher) of a native protein segment TAAAKFE (S39) derived from ribonuclease A (RNAse A). Size-exclusion chromatography suggested the absence of strong interaction between the reacting peptides. The circular dichroism spectra of monomer through pentamer showed length-dependent enhancement of secondary structure in the oligomers, suggesting that protease-catalyzed ligation of a monomer to an oligomer resulted in a product that was more structured than its precursor. The relative conformational stability of the oligomers was reflected in their ability to resist proteolysis, indicating that the oligomerization reaction was facilitated as a consequence of the "conformational trapping" of the product. The ligation reaction proceeded in two phases-slow formation and accumulation of the dimer followed by a fast phase of oligomerization, implying that the conformational trap encountered in the oligomerization reaction was a two-step process. The Gly substitution at any position of the TAAAKFE sequence was deleterious, suggesting that the first step of the conformational trap, namely the dimerization reaction, that proceeded very slowly even with the parent peptide, was quite sensitive to amino acid sequence. In contrast, the oligomerization reaction of an Ala analog, AAAAKFE, occurred in much the same way as S39, albeit with faster rate, suggesting that Ala substitution stabilized the overall conformational trapping process. The results suggest the viability of the product-directed "conformational trap" as a mechanism to achieve peptide ligation of totally unprotected peptide fragments in neat aqueous solution. Further, the study projects the presence of considerable innate synthetic potential in V8 protease, baring rich possibilities of protein engineering of this enzyme to generate a "V8 peptide ligase."
Collapse
Affiliation(s)
- S Kumaran
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | | | | |
Collapse
|
20
|
Dormady SJ, Lei J, Regnier FE. Eliminating disulfide exchange during glutamyl endopeptidase digestion of native protein. J Chromatogr A 1999; 864:237-45. [PMID: 10669291 DOI: 10.1016/s0021-9673(99)01028-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Numerous advantages of using immobilized enzymes over free-solution protein digests have been cited in the literature. This investigation examines both the rate of hydrolysis and the extent of disulfide bond exchange in disulfide bridged dipeptide fragments formed during proteolysis of native protein. Glutamyl endopeptidase as both an immobilized enzyme and in free solution was used in these studies. It was found that extensive hydrolysis of insulin was achieved in 2 min with immobilized enzyme cartridges operated in the stopped-flow mode orders. This is orders of magnitude faster than was seen in free solution. Other advantages ranging from ease of use and reduction in sample size to the potential for automation were also noted with the immobilized enzyme cartridge. Normal free-solution proteolysis generally requires 12-24 h, based on the lower enzyme-to-substrate ratio in solution. A disturbing feature noted in these lengthy free-solution reactions was the tendency to form disulfide bridged peptide artifacts. This could lead to the erroneous conclusion that disulfide bonding in a sample was not that of the native protein. It is concluded that the advantage of immobilized enzymes over free-solution reactions will be most important in the pharmaceutical industry where proteolytic fragment "fingerprinting" of recombinant proteins is being used to confirm structure.
Collapse
Affiliation(s)
- S J Dormady
- Department of Chemistry, Purdue University, Lafayette, IN 47907, USA
| | | | | |
Collapse
|
21
|
Zambrano R, Briones E, Avila J, Ballesta JP. Phosphorylation of P'(1) serine inhibits peptide bond sensitivity to Staphylococcus aureus V8 protease. Arch Biochem Biophys 1999; 368:207-9. [PMID: 10415129 DOI: 10.1006/abbi.1999.1301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- R Zambrano
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid and Consejo Superior de Investigaciones Científicas, Canto Blanco, Madrid, 28049, Spain
| | | | | | | |
Collapse
|
22
|
Lecchi P, Loh YP, Snell CR, Pannell LK. The structure of synenkephalin (pro-enkephalin 1-73) is dictated by three disulfide bridges. Biochem Biophys Res Commun 1997; 232:800-5. [PMID: 9126357 DOI: 10.1006/bbrc.1997.6373] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mass spectrometry of fragments produced by limited proteolytic digestion of pro-enkephalin was used to locate the disulfide bridges in synenkephalin (pro-enkephalin 1-73), a domain which contains sorting information for targeting the pro-neuropeptide to the granules of the regulated secretory pathway in neuroendocrine cells. Mass spectrometric analysis was optimized by using chemicals that gave low interference with the ionization and desorption processes, and computer software which simplified the identification of all possible disulfide-linked peptide fragments. Three disulfide bridges between Cys2-Cys24, Cys6-Cys28, and Cys9-Cys41 were identified. Protein conformational prediction of synenkephalin1-42 shows beta-turns which facilitate the formation of these disulfide bonds.
Collapse
Affiliation(s)
- P Lecchi
- Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | |
Collapse
|
23
|
James F, Brouquisse R, Suire C, Pradet A, Raymond P. Purification and biochemical characterization of a vacuolar serine endopeptidase induced by glucose starvation in maize roots. Biochem J 1996; 320 ( Pt 1):283-92. [PMID: 8947499 PMCID: PMC1217929 DOI: 10.1042/bj3200283] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
An endopeptidase (designated RSIP, for root-starvation-induced protease) was purified to homogeneity from glucose-starved maize roots. The molecular mass of the enzyme was 59 kDa by SDS/PAGE under reducing conditions and 62 kDa by gel filtration on a Sephacryl S-200 column. The isoelectric point of RSIP was 4.55. The purified enzyme was stable, with no auto-proteolytic activity. The enzyme activity was strongly inhibited by proteinaceous trypsin inhibitors, di-isopropylfluorophosphate, 3,4-dichloroisocoumarin and PMSF, suggesting that the enzyme is a serine protease. The maximum proteolytic activity against different protein substrates occurred at pH 6.5. With the exception of succinyl-Leu-Leu-Val-Tyr-4-methylcoumarin, no hydrolysis was detected with synthetic tryptic, chymotryptic or peptidylglutamate substrates. The determination of the cleavage sites in the oxidized B-Chain of insulin showed specificity for hydrophobic residues at the P2 and P3 positions, indicating that RSIP is distinct from other previously characterized maize endopeptidases. Both subcellular fractionation and immuno-detection in situ indicated that RSIP is localized in the vacuole of the root cells. RSIP is the first vacuolar serine endopeptidase to be identified. Glucose starvation induced RSIP: after 4 days of starvation, RSIP was estimated to constitute 80% of total endopeptidase activity in the root tip. These results suggest that RSIP is implicated in vacuolar autophagic processes triggered by carbon limitation.
Collapse
Affiliation(s)
- F James
- Institut National de la Recherche Agronomique, Station de Physiologie, Végétale Villenave d'Ornon, France
| | | | | | | | | |
Collapse
|
24
|
Sprecher CA, Morgenstern KA, Mathewes S, Dahlen JR, Schrader SK, Foster DC, Kisiel W. Molecular cloning, expression, and partial characterization of two novel members of the ovalbumin family of serine proteinase inhibitors. J Biol Chem 1995; 270:29854-61. [PMID: 8530382 DOI: 10.1074/jbc.270.50.29854] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A human placental lambda gt11 cDNA library was screened for sequences encoding proteins related to human proteinase inhibitor 6 (PI6), and two plaques were identified that displayed weak hybridization at high stringency. Isolation and characterization of the DNA inserts revealed two novel sequences encoding proteins composed of 376 and 374 amino acids with predicted molecular masses of approximately 42 kDa. The novel proteins displayed all of the structural features unique to the ovalbumin family of intracellular serpins including the apparent absence of a cleavable N-terminal signal sequence. The degree of amino acid sequence identity between the novel serpins and PI6 (63-68%) significantly exceeds that of any other combination of known intracellular serpins. The two novel serpins encoded by the two novel cDNA sequences have been designated as proteinase inhibitor 8 (PI8) and proteinase inhibitor 9 (PI9). The putative reactive center P1-P1' residues for PI8 and PI9 were identified as Arg339-Cys340 and Glu340-Cys341, respectively. PI9 appears to be unique in that it is the first human serpin identified with an acidic residue in the reactive center P1 position. In addition, the reactive center loop of PI9 exhibits 54% identity with residues found in the reactive center loop of the cowpox virus CrmA serpin. Two PI8 transcripts of 1.4 kilobases (kb) and 3.8 kb were detected by Northern analysis in equal and greatest abundance in liver and lung, while the 1.4-kb mRNA was in excess over the 3.8-kb mRNA in skeletal muscle and heart. Two PI9 transcripts of 3.4 and 4.4 kb were detected in equal and greatest abundance in lung and placenta and were weakly detected in all other tissues. PI8 and PI9 were expressed in baby hamster kidney and yeast cells, respectively. Immunoblot analyses using rabbit anti-PI6 IgG indicated the presence of PI8 in the cytosolic fraction of stably transfected cells that formed an SDS-stable 67-kDa complex with human thrombin. PI9 was purified to homogeneity from the yeast cell lysate by a combination of heparin-agarose chromatography and Mono Q fast protein liquid chromatography and migrated as a single band in SDS-polyacrylamide gel electrophoresis with an apparent molecular mass of 42 kDa. Purified recombinant PI9 failed to inhibit the amidolytic activities of trypsin, papain, thrombin, or Staphylococcus aureus endoproteinase Glu-C and did not form an SDS-stable complex when incubated with thrombin. The cognate intracellular proteinases that interact with PI8 and PI9 are unknown.
Collapse
Affiliation(s)
- C A Sprecher
- ZymoGenetics, Inc., Seattle, Washington 98102, USA
| | | | | | | | | | | | | |
Collapse
|