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Takemori A, Kaulich PT, Konno R, Kawashima Y, Hamazaki Y, Hoshino A, Tholey A, Takemori N. GeLC-FAIMS-MS workflow for in-depth middle-down proteomics. Proteomics 2024; 24:e2200431. [PMID: 37548120 DOI: 10.1002/pmic.202200431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/20/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Middle-down proteomics (MDP) is an analytical approach in which protein samples are digested with proteases such as Glu-C to generate large peptides (>3 kDa) that are analyzed by mass spectrometry (MS). This method is useful for characterizing high-molecular-weight proteins that are difficult to detect by top-down proteomics (TDP), in which intact proteins are analyzed by MS. In this study, we applied GeLC-FAIMS-MS, a multidimensional separation workflow that combines gel-based prefractionation with LC-FAIMS MS, for deep MDP. Middle-down peptides generated by optimized limited Glu-C digestion conditions were first size-fractionated by polyacrylamide gel electrophoresis, followed by C4 reversed-phase liquid chromatography separation and additional ion mobility fractionation, resulting in a significant increase in peptide length detectable by MS. In addition to global analysis, the GeLC-FAIMS-MS concept can also be applied to targeted MDP, where only proteins in the desired molecular weight range are gel-fractionated and their Glu-C digestion products are analyzed, as demonstrated by targeted analysis of integrins in exosomes. In-depth MDP achieved by global and targeted GeLC-FAIMS-MS supports the exploration of proteoform information not covered by conventional TDP by increasing the number of detectable protein groups or post-translational modifications (PTMs) and improving the sequence coverage.
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Affiliation(s)
- Ayako Takemori
- Advanced Research Support Center, Institute for Promotion of Science and Technology, Ehime University, Ehime, Japan
| | - Philipp T Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Yuto Hamazaki
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Ayuko Hoshino
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Nobuaki Takemori
- Advanced Research Support Center, Institute for Promotion of Science and Technology, Ehime University, Ehime, Japan
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Francis D, Bhairaddy A, Joy A, Hari GV, Francis A. Secretory proteins in the orchestration of microbial virulence: The curious case of Staphylococcus aureus. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 133:271-350. [PMID: 36707204 DOI: 10.1016/bs.apcsb.2022.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Microbial virulence showcases an excellent model for adaptive changes that enable an organism to survive and proliferate in a hostile environment and exploit host resources to its own benefit. In Staphylococcus aureus, an opportunistic pathogen of the human host, known for the diversity of the disease conditions it inflicts and the rapid evolution of antibiotic resistance, virulence is a consequence of having a highly plastic genome that is amenable to quick reprogramming and the ability to express a diverse arsenal of virulence factors. Virulence factors that are secreted to the host milieu effectively manipulate the host conditions to favor bacterial survival and growth. They assist in colonization, nutrient acquisition, immune evasion, and systemic spread. The structural and functional characteristics of the secreted virulence proteins have been shaped to assist S. aureus in thriving and disseminating effectively within the host environment and exploiting the host resources to its best benefit. With the aim of highlighting the importance of secreted virulence proteins in bacterial virulence, the present chapter provides a comprehensive account of the role of the major secreted proteins of S. aureus in orchestrating its virulence in the human host.
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Affiliation(s)
- Dileep Francis
- Department of Life Sciences, Kristu Jayanti College, Autonomous, Bengaluru, Karnataka, India.
| | - Anusha Bhairaddy
- Department of Life Sciences, Kristu Jayanti College, Autonomous, Bengaluru, Karnataka, India
| | - Atheene Joy
- Department of Life Sciences, Kristu Jayanti College, Autonomous, Bengaluru, Karnataka, India
| | | | - Ashik Francis
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
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Nishida H, Ishihama Y. One-Step Isolation of Protein C-Terminal Peptides from V8 Protease-Digested Proteins by Metal Oxide-Based Ligand-Exchange Chromatography. Anal Chem 2021; 94:944-951. [PMID: 34962382 DOI: 10.1021/acs.analchem.1c03722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed a one-step method to isolate protein C-terminal peptides from V8 protease-digested proteins by metal oxide-based ligand-exchange (MOLEX) chromatography. V8 protease cleaves the C-terminal side of Asp and Glu, affording a digested peptide with two carboxy groups at the C-terminus, whereas the protein C-terminal peptide has only one α-carboxy group. In MOLEX chromatography, a stable chelate is formed between dicarboxylates and metal atoms, so that the nonterminal (i.e., internal) peptide is retained, whereas the protein C-terminal peptide flows through the MOLEX column. After the optimization of the MOLEX chromatographic conditions, 1619 protein C-termini were identified from 30 μg of peptides (10 μg each, in triplicate) derived from human HeLa cells by means of nanoLC/MS/MS. When the MOLEX-isolated sample from 200 μg of HeLa peptides was further divided into six fractions by high-pH reversed-phase liquid chromatography (LC) prior to nanoLC/MS/MS, 2203 protein C-termini were identified with less than 3% contamination with internal peptides. We believe that this is the largest coverage with the highest purity reported to date in human protein C-terminomics. This fast, simple, sensitive, and selective method to isolate protein C-terminal peptides should be useful for profiling protein C-termini on a proteome-wide scale.
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Affiliation(s)
- Hiroshi Nishida
- Department of Molecular & Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,National Institute of Biomedical Innovation, Health and Nutrition, Laboratory of Clinical and Analytical Chemistry, Ibaraki, Osaka 567-0085, Japan
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Frey AM, Chaput D, Shaw LN. Insight into the human pathodegradome of the V8 protease from Staphylococcus aureus. Cell Rep 2021; 35:108930. [PMID: 33826899 PMCID: PMC8054439 DOI: 10.1016/j.celrep.2021.108930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/03/2020] [Accepted: 03/11/2021] [Indexed: 12/03/2022] Open
Abstract
Staphylococcus aureus possesses ten extracellular proteases with mostly unknown targets in the human proteome. To assist with bacterial protease target discovery, we have applied and compared two N-terminomics methods to investigate cleavage of human serum proteins by S. aureus V8 protease, discovering 85 host-protein targets. Among these are virulence-relevant complement, iron sequestration, clotting cascade, and host protease inhibitor proteins. Protein cleavage sites have been identified, providing insight into the disruption of host protein function by V8. Complement proteins are cleaved within peptidase and sushi domains, and host protease inhibitors are cleaved outside their protease-trapping motifs. Our data highlight the potential for further application of N-terminomics in discovery of bacterial protease substrates in other host niches and provide omics-scale insight into the role of the V8 protease in S. aureus pathogenesis. S. aureus-secreted proteases are central to disease causation, but the discovery of their host substrates has been limited. Frey et al. use N-terminomic approaches to uncover human serum targets of the V8 protease that are from virulence-relevant processes such as the host inflammatory network and nutrient sequestration.
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Affiliation(s)
- Andrew Michael Frey
- Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Dale Chaput
- Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Lindsey Neil Shaw
- Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, FL 33620, USA.
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Structural Determinants of Substrate Specificity of SplF Protease from Staphylococcus aureus. Int J Mol Sci 2021; 22:ijms22042220. [PMID: 33672341 PMCID: PMC7926377 DOI: 10.3390/ijms22042220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 11/17/2022] Open
Abstract
Accumulating evidence suggests that six proteases encoded in the spl operon of a dangerous human pathogen, Staphylococcus aureus, may play a role in virulence. Interestingly, SplA, B, D, and E have complementary substrate specificities while SplF remains to be characterized in this regard. Here, we describe the prerequisites of a heterologous expression system for active SplF protease and characterize the enzyme in terms of substrate specificity and its structural determinants. Substrate specificity of SplF is comprehensively profiled using combinatorial libraries of peptide substrates demonstrating strict preference for long aliphatic sidechains at the P1 subsite and significant selectivity for aromatic residues at P3. The crystal structure of SplF was provided at 1.7 Å resolution to define the structural basis of substrate specificity of SplF. The obtained results were compared and contrasted with the characteristics of other Spl proteases determined to date to conclude that the spl operon encodes a unique extracellular proteolytic system.
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Murphy J, Ramezanpour M, Stach N, Dubin G, Psaltis AJ, Wormald PJ, Vreugde S. Staphylococcus Aureus V8 protease disrupts the integrity of the airway epithelial barrier and impairs IL-6 production in vitro. Laryngoscope 2017; 128:E8-E15. [PMID: 28994126 DOI: 10.1002/lary.26949] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/03/2017] [Accepted: 09/07/2017] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Staphylococcus aureus (S. aureus) infection is known to contribute to the severity and recalcitrance of chronic rhinosinusitis (CRS), and its secreted products have been shown to alter the airway barrier. Extracellular proteases secreted by S. aureus are thought to be important in epithelial infection and immune evasion; however, their effect on airway mucosal barrier function is not known. METHODS To investigate the impact of extracellular proteases on airway epithelial integrity, the purified S. aureus proteases V8 protease, Staphopain A, Staphopain B, Exfoliative toxin A, and serine protease-like A-F were applied to human nasal epithelial cell air-liquid interface (HNEC-ALI) cultures. Transepithelial electrical resistance (TEER), permeability (Papp) measurements, and immuno-localization of the tight junction proteins claudin-1 and ZO-1 were used to assess barrier integrity. Effects of the proteases on inflammation and cell viability were measured using interleukin-6 (IL-6) ELISA and a lactate dehydrogenase assay. RESULTS Application of V8 protease to HNEC-ALI cultures caused a significant concentration and time-dependent decrease in TEER (22.67%, P < 0.0001), a reciprocal Papp increase (20.14-fold, P < 0.05), and a discontinuous ZO-1 immuno-localization compared to control. IL-6 production was significantly reduced in V8 protease-treated cells (153.5 pg/mL, P = 0.0069) compared to control (548.3 pg/mL), whereas no difference in cell viability was observed. CONCLUSION S. aureus V8 protease causes dysfunction of mucosal barrier structure and function indicative of a leaky barrier. A reduction in IL-6 levels suggests that the mucosal immunity is impaired by this protease and thus has the potential to contribute to CRS recalcitrance. LEVEL OF EVIDENCE NA. Laryngoscope, 128:E8-E15, 2018.
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Affiliation(s)
- Jae Murphy
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Woodville South, SA, Australia
| | - Mahnaz Ramezanpour
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Woodville South, SA, Australia
| | - Natalia Stach
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grzegorz Dubin
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alkis James Psaltis
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Woodville South, SA, Australia
| | - Peter-John Wormald
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Woodville South, SA, Australia
| | - Sarah Vreugde
- Department of Surgery-Otolaryngology, Head and Neck Surgery, The University of Adelaide, Woodville South, SA, Australia
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Östreicher C, Bartenbacher S, Pischetsrieder M. Targeted proteome analysis with isotope-coded protein labels for monitoring the influence of dietary phytochemicals on the expression of cytoprotective proteins in primary human colon cells. J Proteomics 2017; 166:27-38. [DOI: 10.1016/j.jprot.2017.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/19/2017] [Accepted: 06/29/2017] [Indexed: 02/07/2023]
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8
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Deng Z, Mao J, Wang Y, Zou H, Ye M. Enzyme Kinetics for Complex System Enables Accurate Determination of Specificity Constants of Numerous Substrates in a Mixture by Proteomics Platform. Mol Cell Proteomics 2017; 16:135-145. [PMID: 27852747 PMCID: PMC5217779 DOI: 10.1074/mcp.m116.062869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/20/2016] [Indexed: 01/05/2023] Open
Abstract
Many important experiments in proteomics including protein digestion, enzyme substrate screening, enzymatic labeling, etc., involve the enzymatic reactions in a complex system where numerous substrates coexists with an enzyme. However, the enzyme kinetics in such a system remains unexplored and poorly understood. Herein, we derived and validated the kinetics equations for the enzymatic reactions in complex system. We developed an iteration approach to depict the enzymatic reactions in complex system. It was validated by 630 time-course points from 24 enzymatic reaction experiments and was demonstrated to be a powerful tool to simulate the reactions in the complex system. By applying this approach, we found that the ratio of substrate depletion is independent of other coexisted substrates under specific condition. This observation was then validated by experiments. Based on this striking observation, a simplified model was developed to determine the catalytic efficiencies of numerous competing substrates presented in the complex enzyme reaction system. When coupled with high-throughput quantitative proteomics technique, this simplified model enabled the accurate determination of catalytic efficiencies for 2369 peptide substrates of a protease by using only one enzymatic reaction experiment. Thus, this study provided, in the first time, a validated model for the large scale determination of specificity constants which could enable the enzyme substrate screening approach turned from a qualitative method of identifying substrates to a quantitative method of identifying and prioritizing substrates. Data are available via ProteomeXchange with identifier PXD004665.
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Affiliation(s)
- Zhenzhen Deng
- From the ‡Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- §Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawei Mao
- From the ‡Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- §Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- From the ‡Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- §Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanfa Zou
- From the ‡Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Mingliang Ye
- From the ‡Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China;
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Noga MJ, Cerri M, Imholz N, Tulinski P, Şahin E, Bokinsky G. Mass-Spectrometry-Based Quantification of Protein-Bound Fatty Acid Synthesis Intermediates from Escherichia coli. J Proteome Res 2016; 15:3617-3623. [PMID: 27595277 DOI: 10.1021/acs.jproteome.6b00405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The production of fatty acids from simple nutrients occurs via a complex biosynthetic pathway with dozens of intermediate compounds and multiple branch points. Despite its importance for microbial physiology and biotechnology, critical aspects of fatty acid biosynthesis, especially dynamics of in vivo regulation, remain poorly characterized. We have developed a liquid chromatography/mass spectroscopy (LC-MS) method for relative quantification of fatty acid synthesis intermediates in Escherichia coli, a model organism for studies of fatty acid metabolism. The acyl carrier protein, a vehicle for the substrates and intermediates of fatty acid synthesis, is extracted from E. coli, proteolytically digested, resolved using reverse-phase LC, and detected using electrospray ionization coupled with a tandem MS. Our method reliably resolves 21 intermediates of fatty acid synthesis, with an average relative standard deviation in ratios of individual acyl-ACP species to total ACP concentrations of 20%. We demonstrate that fast sampling and quenching of cells is essential to accurately characterize intracellular concentrations of ACP species. We apply our method to examine the rapid response of fatty acid metabolism to the antibiotic cerulenin. We anticipate that our method will enable the characterization of in vivo regulation and kinetics of microbial fatty acid synthesis at unprecedented detail and will improve integration of fatty acid synthesis into models of microbial metabolism.
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Affiliation(s)
- Marek J Noga
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
| | - Mattia Cerri
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
| | - Nicole Imholz
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
| | - Pawel Tulinski
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
| | - Enes Şahin
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
| | - Gregory Bokinsky
- Department of Bionanoscience, Delft University of Technology, Kavli Institute of Nanoscience Delft , Lorentzweg 1, 2628CJ Delft, The Netherlands
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Autocatalytic activation of a thermostable glutamyl endopeptidase capable of hydrolyzing proteins at high temperatures. Appl Microbiol Biotechnol 2016; 100:10429-10441. [PMID: 27377749 DOI: 10.1007/s00253-016-7697-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/16/2016] [Accepted: 06/19/2016] [Indexed: 01/27/2023]
Abstract
Glutamyl endopeptidases (GSEs) specifically hydrolyze peptide bonds formed by α-carboxyl groups of Glu and Asp residues. We cloned the gene for a thermophilic GSE (designated TS-GSE) from Thermoactinomyces sp. CDF. A proform of TS-GSE that contained a 61-amino acid N-terminal propeptide and a 218-amino acid mature domain was produced in Escherichia coli. We found that the proform possessed two processing sites and was capable of autocatalytic activation via multiple pathways. The N-terminal propeptide could be autoprocessed at the Glu-1-Ser1 bond to directly generate the mature enzyme. It could also be autoprocessed at the Glu-12-Lys-11 bond to yield an intermediate, which was then converted into the mature form after removal of the remaining part of the propeptide. The segment surrounding the two processing sites was flexible, which allowed the proform and the intermediate form to be trans-processed into the mature form by either active TS-GSE or heterogeneous proteases. Deletion analysis revealed that the N-terminal propeptide is important for the correct folding and maturation of TS-GSE. The propeptide, even its last 11-amino acid peptide segment, could inhibit the activity of its cognate mature domain. The mature TS-GSE displayed a temperature optimum of 85 °C and retained approximately 90 % of its original activity after incubation at 70 °C for 6 h, representing the most thermostable GSE reported to date. Mutational analysis suggested that the disulfide bonds Cys32-Cys48 and Cys180-Cys183 cumulatively contributed to the thermostability of TS-GSE.
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Cui H, Li W, Lin L. Bacterial protease-triggered clove oil release from proteoliposomes against S. aureus biofilms on dried soybean curd. RSC Adv 2016. [DOI: 10.1039/c6ra03363f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The purpose of this study is to develop a new approach to deliver antimicrobials against bacterial infections by taking advantage of the hydrolysis of protease by casein.
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Affiliation(s)
- Haiying Cui
- School of Food and Biological Engineering
- Jiangsu University
- Zhenjiang 212013
- China
| | - Wei Li
- School of Food and Biological Engineering
- Jiangsu University
- Zhenjiang 212013
- China
| | - Lin Lin
- School of Food and Biological Engineering
- Jiangsu University
- Zhenjiang 212013
- China
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12
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Reactions of Cg10062, a cis-3-Chloroacrylic Acid Dehalogenase Homologue, with Acetylene and Allene Substrates: Evidence for a Hydration-Dependent Decarboxylation. Biochemistry 2015; 54:3009-23. [PMID: 25894805 DOI: 10.1021/acs.biochem.5b00240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cg10062 is a cis-3-chloroacrylic acid dehalogenase (cis-CaaD) homologue from Corynebacterium glutamicum with an unknown function and an uninformative genomic context. It shares 53% pairwise sequence similarity with cis-CaaD including the six active site amino acids (Pro-1, His-28, Arg-70, Arg-73, Tyr-103, and Glu-114) that are critical for cis-CaaD activity. However, Cg10062 is a poor cis-CaaD: it lacks catalytic efficiency and isomer specificity. Two acetylene compounds (propiolate and 2-butynoate) and an allene compound, 2,3-butadienoate, were investigated as potential substrates. Cg10062 functions as a hydratase/decarboxylase using propiolate as well as the cis-3-chloro- and 3-bromoacrylates, generating mixtures of malonate semialdehyde and acetaldehyde. The two activities occur sequentially at the active site using the initial substrate. With 2,3-butadienoate and 2-butynoate, Cg10062 functions as a hydratase and converts both to acetoacetate. Mutations of the proposed water-activating residues (E114Q, E114D, and Y103F) have a range of consequences from a reduction in wild type activity to a switch of activities (i.e., hydratase into a hydratase/decarboxylase or vice versa). The intermediates for the hydration and decarboxylation products can be trapped as covalent adducts to Pro-1 when NaCNBH3 is incubated with the E114D mutant and 2,3-butadienoate or 2-butynoate, and the Y103F mutant and 2-butynoate. Three mechanisms are presented to explain these findings. One mechanism involves the direct attack of water on the substrate, whereas the other two mechanisms use covalent catalysis in which a covalent bond forms between Pro-1 and the hydration product or the substrate. The strengths and weaknesses of the mechanisms and the implications for Cg10062 function are discussed.
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13
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Bacterial protease triggered release of biocides from microspheres with an oily core. Colloids Surf B Biointerfaces 2015; 127:200-5. [DOI: 10.1016/j.colsurfb.2015.01.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/13/2015] [Accepted: 01/21/2015] [Indexed: 12/17/2022]
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Craig M, Schuster E, Holmberg K. Biodegradable Nanofilms on Microcapsules for Controlled Release of Drugs to Infected Chronic Wounds. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.matpr.2015.04.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Liu M, Zhang Z, Cheetham J, Ren D, Zhou ZS. Discovery and characterization of a photo-oxidative histidine-histidine cross-link in IgG1 antibody utilizing ¹⁸O-labeling and mass spectrometry. Anal Chem 2014; 86:4940-8. [PMID: 24738698 PMCID: PMC4030806 DOI: 10.1021/ac500334k] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel photo-oxidative cross-linking
between two histidines (His-His)
has been discovered and characterized in an IgG1 antibody via the
workflow of XChem-Finder, 18O labeling and mass spectrometry
(2013, 85, 5900−590823634697). Its structure was elucidated by peptide
mapping with multiple proteases with various specificities (e.g.,
trypsin, Asp-N, and GluC combined with trypsin or Asp-N) and mass
spectrometry with complementary fragmentation modes (e.g., collision-induced
dissociation (CID) and electron-transfer dissociation (ETD)). Our
data indicated that cross-linking occurred across two identical conserved
histidine residues on two separate heavy chains in the hinge region,
which is highly flexible and solvent accessible. On the basis of model
studies with short peptides, it has been proposed that singlet oxygen
reacts with the histidyl imidazole ring to form an endoperoxide and
then converted to the 2-oxo-histidine (2-oxo-His) and His+32 intermediates, the latter is
subject to a
nucleophilic attack by the unmodified histidine; and finally, elimination
of a water molecule leads to the final adduct with a net mass increase
of 14 Da. Our findings are consistent with this mechanism. Successful
discovery of cross-linked His-His again demonstrates the broad applicability
and utility of our XChem-Finder approach in the discovery and elucidation
of protein cross-linking, particularly without a priori knowledge of the chemical nature and site of cross-linking.
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Affiliation(s)
- Min Liu
- Analytical Research and Development, Amgen , One Amgen Center Drive, Thousand Oaks, California 91320, United States
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16
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Polypeptide multilayer self-assembly studied by ellipsometry. JOURNAL OF DRUG DELIVERY 2014; 2014:424697. [PMID: 24660065 PMCID: PMC3934801 DOI: 10.1155/2014/424697] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 12/21/2013] [Accepted: 12/31/2013] [Indexed: 12/04/2022]
Abstract
A polypeptide nanofilm made by layer-by-layer (LbL) self-assembly was built on a surface that mimics nonwoven, a material commonly used in wound dressings. Poly-L-lysine (PLL) and poly-L-glutamic acid (PLGA) are the building blocks of the nanofilm, which is intended as an enzymatically degradable lid for release of bactericides to chronic wounds. Chronic wounds often carry infection originating from bacteria such as Staphylococcus aureus and a release system triggered by the degree of infection is of interest. The dry nanofilm was studied with ellipsometry. The thickness of the nanofilm was 60% less in its dry state than in its wet state. The measurements showed that a primer was not necessary to build a stable nanofilm, which is practically important in our case because a nondegradable primer is highly unwanted in a wound care dressing. Added V8 (glutamyl endopeptidase) enzymes only showed adsorption on the nanofilm at room temperature, indicating that the PLL/PLGA “lid” may remain intact until the dressing has been filled with wound exudate at the elevated temperature typical of that of the wound.
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Tucher J, Linke D, Koudelka T, Cassidy L, Tredup C, Wichert R, Pietrzik C, Becker-Pauly C, Tholey A. LC-MS based cleavage site profiling of the proteases ADAM10 and ADAM17 using proteome-derived peptide libraries. J Proteome Res 2014; 13:2205-14. [PMID: 24635658 DOI: 10.1021/pr401135u] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A Disintegrin and Metalloproteinase 10 (ADAM10) and ADAM17 catalyze ectodomain shedding of a number of cell surface proteins important for embryonic development and tissue homeostasis. Changes in the expression levels or dysregulated proteolytic activity of ADAM10 and ADAM17 have been shown to play important roles in multiple diseases such as inflammation, cancer, and neurodegenerative disorders. Despite the well documented substrate repertoire of ADAM10 and ADAM17, little is known about their cleavage site specificity. We optimized Q-PICS (Quantitative Proteomics for the Identification of Cleavage Sites) to elucidate the cleavage site specificity of recombinant murine ADAM10 and ADAM17. Two different yeast proteome-derived peptide libraries were used and samples were analyzed by LC-MALDI and LC-ESI MS in parallel. We show that the largest difference in the cleavage site specificities of ADAM10 and ADAM17 is at the P1' site: while both enzymes cleave N-terminal of leucine, only ADAM10 shows additional preference toward aromatic amino acids, whereas ADAM17 exhibits the highest preference for valine. Together with further amino acid preferences more adjacent to the scissile bond, our data is in good agreement with ADAM10/17 cleavage sites previously identified in native substrates. Overall, the precise identification of ADAM10 and ADAM17 cleavage site specificity provides the basis for better substrate identification in vivo and the generation of specific inhibitors or activity based probes.
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Affiliation(s)
- Joanna Tucher
- AG Systematische Proteomforschung, Institut für Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel , Niemannsweg 11, 24105 Kiel, Germany
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18
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Prikryl P, Ticha M, Kucerova Z. Immobilized endoproteinase Glu-C to magnetic bead cellulose as a tool in proteomic analysis. J Sep Sci 2013; 36:2043-8. [DOI: 10.1002/jssc.201300118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/01/2013] [Accepted: 04/01/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Petr Prikryl
- Institute of Pathological Physiology; First Faculty of Medicine; Charles University; Prague Czech Republic
| | - Marie Ticha
- Institute of Pathological Physiology; First Faculty of Medicine; Charles University; Prague Czech Republic
- Department of Biochemistry; Faculty of Science; Charles University; Prague Czech Republic
| | - Zdenka Kucerova
- Institute of Pathological Physiology; First Faculty of Medicine; Charles University; Prague Czech Republic
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19
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Kartner N, Yao Y, Bhargava A, Manolson MF. Topology, glycosylation and conformational changes in the membrane domain of the vacuolar H+-ATPaseasubunit. J Cell Biochem 2013; 114:1474-87. [DOI: 10.1002/jcb.24489] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 12/21/2012] [Indexed: 11/08/2022]
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20
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Jakoby T, van den Berg BHJ, Tholey A. Quantitative Protease Cleavage Site Profiling using Tandem-Mass-Tag Labeling and LC–MALDI-TOF/TOF MS/MS Analysis. J Proteome Res 2012; 11:1812-20. [DOI: 10.1021/pr201051e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Thomas Jakoby
- AG Systematische Proteomforschung, Institut für
Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Germany
| | - Bart HJ van den Berg
- AG Systematische Proteomforschung, Institut für
Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Germany
| | - Andreas Tholey
- AG Systematische Proteomforschung, Institut für
Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Germany
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21
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Gupta N, Hixson KK, Culley DE, Smith RD, Pevzner PA. Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry. Proteomics 2010; 10:2833-44. [PMID: 20597098 DOI: 10.1002/pmic.200900821] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Although trypsin remains the most commonly used protease in MS, other proteases may be employed for increasing peptide coverage or generating overlapping peptides. Knowledge of the accurate specificity rules of these proteases is helpful for database search tools to detect peptides, and becomes crucial when label-free MS is used to discover in vivo proteolytic cleavages. Since in vivo cleavages are inferred by subtracting digestion-induced cleavages from all observed cleavages, it is important to ensure that the specificity rule used to identify digestion-induced cleavages are broad enough to capture even minor cleavages produced in digestion, to avoid erroneously identifying them as in vivo cleavages. In this study, we describe MS-Proteolysis, a software tool for identifying putative sites of in vivo proteolytic cleavage using label-free MS. The tool is used in conjunction with digestion by trypsin and three other proteases, whose specificity rules are revised and extended before inferring proteolytic cleavages. Finally, we show that comparative analysis of multiple proteases can be used to detect putative in vivo proteolytic sites on a proteome-wide scale.
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Affiliation(s)
- Nitin Gupta
- Bioinformatics Program, University of California San Diego, La Jolla, CA 92093, USA.
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22
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Kosters H, Wierenga P, Gruppen H. SELDI-TOF-MS as a rapid tool to study food related protein–peptide interactions. Food Hydrocoll 2010. [DOI: 10.1016/j.foodhyd.2010.03.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Anderson DC, Green GR, Smith K, Selker EU. Extensive and varied modifications in histone H2B of wild-type and histone deacetylase 1 mutant Neurospora crassa. Biochemistry 2010; 49:5244-57. [PMID: 20462202 DOI: 10.1021/bi100391w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA methylation is deficient in a histone deacetylase 1 (HDA1) mutant (hda-1) strain of Neurospora crassa with inactivated histone deacetylase 1. Difference two-dimensional (2D) gels identified the primary histone deacetylase 1 target as histone H2B. Acetylation was identified by LC-MS/MS at five different lysines in wild-type H2B and at 11 lysines in hda-1 H2B, suggesting Neurospora H2B is a complex combination of different acetylated species. Individual 2D gel spots were shifted by single lysine acetylations. FTICR MS-observed methylation ladders identify an ensemble of 20-25 or more modified forms for each 2D gel spot. Twelve different lysines or arginines were methylated in H2B from the wild type or hda-1; only two were in the N-terminal tail. Arginines were modified by monomethylation, dimethylation, or deimination. H2B from wild-type and hda-1 ensembles may thus differ by acetylation at multiple sites, and by additional modifications. Combined with asymmetry-generated diversity in H2B structural states in nucleosome core particles, the extensive modifications identified here can create substantial histone-generated structural diversity in nucleosome core particles.
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Affiliation(s)
- D C Anderson
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA.
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24
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BONGERS JACOB, LIU WEN, LAMBROS THEODORE, BREDDAM KLAUS, CAMPBELL ROBERTM, FELIX ARTHURM, HEIMER EDGARP. Peptide synthesis catalyzed by the Glu/Asp-specific endopeptidase. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1994.tb00566.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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26
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Poelarends GJ, Serrano H, Person MD, Johnson WH, Whitman CP. Characterization of Cg10062 from Corynebacterium glutamicum: implications for the evolution of cis-3-chloroacrylic acid dehalogenase activity in the tautomerase superfamily. Biochemistry 2008; 47:8139-47. [PMID: 18598055 PMCID: PMC2659011 DOI: 10.1021/bi8007388] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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A 149-amino acid protein designated Cg10062 is encoded by a gene from Corynebacterium glutamicum. The physiological function of Cg10062 is unknown, and the gene encoding this protein has no obvious genomic context. Sequence analysis links Cg10062 to the cis-3-chloroacrylic acid dehalogenase (cis-CaaD) family, one of the five known families of the tautomerase superfamily. The characterized tautomerase superfamily members have two distinctive characteristics: a β−α−β structure motif and a catalytic amino-terminal proline. Pro-1 is present in the Cg10062 amino acid sequence along with His-28, Arg-70, Arg-73, Tyr-103, and Glu-114, all of which have been implicated as critical residues for cis-CaaD activity. The gene for Cg10062 has been cloned and the protein overproduced, purified, and subjected to kinetic and mechanistic characterization. Like cis-CaaD, Cg10062 functions as a hydratase: it converts 2-oxo-3-pentynoate to acetopyruvate and processes 3-bromopropiolate to a species that inactivates the enzyme by acylation of Pro-1. Kinetic and 1H NMR spectroscopic studies also show that Cg10062 processes both isomers of 3-chloroacrylic acid at low levels with a clear preference for the cis isomer. Pro-1 is critical for the dehalogenase and hydratase activities because the P1A mutant no longer catalyzes either reaction. The presence of the six key catalytic residues and the hydratase activity coupled with the absence of an efficient cis-CaaD activity and the lack of isomer specificity implicate factors beyond this core set of residues in cis-CaaD catalysis and specificity. This work sets the stage for in-depth mechanistic and structural studies of Cg10062, which could identify the additional features necessary for a fully active and highly specific cis-CaaD. Such results will also shed light on how cis-CaaD emerged in the tautomerase superfamily because Cg10062 could be characteristic of an intermediate along the evolutionary pathway for this dehalogenase.
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Affiliation(s)
- Gerrit J Poelarends
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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27
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Broomell CC, Chase SF, Laue T, Waite JH. Cutting Edge Structural Protein from the Jaws of Nereis virens. Biomacromolecules 2008; 9:1669-77. [DOI: 10.1021/bm800200a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chris C. Broomell
- University of California at Santa Barbara, Santa Barbara, California 93106, and Center to Advance Molecular Interaction Science, University of New Hampshire, Durham, New Hampshire 03824
| | - Sue F. Chase
- University of California at Santa Barbara, Santa Barbara, California 93106, and Center to Advance Molecular Interaction Science, University of New Hampshire, Durham, New Hampshire 03824
| | - Tom Laue
- University of California at Santa Barbara, Santa Barbara, California 93106, and Center to Advance Molecular Interaction Science, University of New Hampshire, Durham, New Hampshire 03824
| | - J. Herbert Waite
- University of California at Santa Barbara, Santa Barbara, California 93106, and Center to Advance Molecular Interaction Science, University of New Hampshire, Durham, New Hampshire 03824
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28
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Branca RMM, Bodó G, Bagyinka C, Prokai L. De novo sequencing of a 21-kDa cytochrome c4 from Thiocapsa roseopersicina by nanoelectrospray ionization ion-trap and Fourier-transform ion-cyclotron resonance mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:1569-1582. [PMID: 18085548 DOI: 10.1002/jms.1337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have determined the primary structure of cytochrome c(4) from Thiocapsa roseopersicina by de novo protein sequencing using the 'bottom up' approach. Three different enzymes (trypsin, endoproteinase Lys-C, and endoproteinase Glu-C) were employed to prepare four different sets of proteolytic digests. The digestion strategy was designed to permit a gradual buildup of smaller peptides into larger ones that were overlapped to yield the complete protein sequence. In this way we countered the main problem: peptides larger than about 1500 Da were difficult to sequence fully by tandem mass spectrometry. Direct infusion and online liquid chromatography were used on a linear ion trap Fourier-transform ion-cyclotron resonance hybrid instrument. The high resolving power, high mass accuracy and the availability of electron capture dissociation and collision-induced dissociation were essential to achieve full sequence coverage. The software DeNovoX complemented by manual interpretation was used to generate sequence information from tandem mass spectra. The predominantly automated nature of data acquisition and handling allowed for a relatively straightforward and fast procedure, which could compete with the mainstream alternative of nucleotide sequence determination.
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Affiliation(s)
- Rui Miguel Mamede Branca
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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29
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Metz B, Kersten GFA, Baart GJE, de Jong A, Meiring H, ten Hove J, van Steenbergen MJ, Hennink WE, Crommelin DJA, Jiskoot W. Identification of Formaldehyde-Induced Modifications in Proteins: Reactions with Insulin. Bioconjug Chem 2006; 17:815-22. [PMID: 16704222 DOI: 10.1021/bc050340f] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formaldehyde is frequently used to inactivate, stabilize, or immobilize proteins. The treatment results in a large variety of chemical modifications in proteins, such as the formation of methylol groups, Schiff bases, and methylene bridges. The purpose of the present study was to identify the stable formaldehyde-induced modifications in a small protein. Therefore, insulin was treated with excess formaldehyde (CH2O) or deuterated formaldehyde (CD2O). In a separate experiment, insulin was modified by formaldehyde (CH2O vs CD2O) and glycine. The mixture of CH2O-treated and CD2O-treated insulin was digested by the proteinase Glu-C. The peptide fragments obtained were analyzed by liquid chromatography-mass spectrometry (LC-MS). Seven intramolecular cross-links were identified in formaldehyde-treated insulin. Furthermore, eight out of the sixteen potentially reactive sites of the insulin molecule were modified by incubation with formaldehyde and glycine. Both the location and the chemical nature of the modifications could be assigned based on the mass increase of potential adducts as elucidated in our previous study (B. Metz et al. (2004) J. Biol. Chem. 279, 6235-6243). To confirm the assigned structures, LC-MS measurements with collision-induced dissociation (LC-MS/MS) were performed on insulin fragments. The results of the LC-MS/MS analyses agreed excellently with the assignments. The study showed that arginine, tyrosine, and lysine residues were very reactive. However, eight theoretically reactive residues did not show detectable modifications, probably because of their low intrinsic reactivity, inaccessibility, or both. The asparagine, glutamine, and histidine residues were not converted in insulin. The N-termini of insulin were partly converted to the expected imidazolidinone adducts, indicating that the protein conformation affects the accessibility and reactivity of these residues. In conclusion, this study shows that, based on our current insights in the chemistry of the reactions between proteins and formaldehyde, we are able to elucidate the location and nature of formaldehyde-induced modifications in a small protein. The approach followed in this study may be generally applicable to larger formaldehyde-treated proteins, such as toxoids used in vaccines.
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Affiliation(s)
- Bernard Metz
- Unit Research and Development, The Netherlands Vaccine Institute (NVI), Bilthoven, The Netherlands.
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30
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Reed DC, Barnard GC, Anderson EB, Klein LT, Gerngross TU. Production and purification of self-assembling peptides in Ralstonia eutropha. Protein Expr Purif 2005; 46:179-88. [PMID: 16249097 DOI: 10.1016/j.pep.2005.08.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2005] [Revised: 08/25/2005] [Accepted: 08/26/2005] [Indexed: 10/25/2022]
Abstract
Self-assembling peptides have emerged as an attractive scaffold material for tissue engineering, yet the expense associated with solid phase chemical synthesis has limited their broad use. In addition, the fidelity of chemical synthesis constrains the length of polypeptides that can be produced homogeneously by this method. Template-derived biosynthesis by recombinant DNA technology may overcome both of these problems. However, recovery of polypeptides from recombinant protein expression systems typically involves multi-step purification schemes. In this study, we report an integrated approach to recombinantly produce and purify self-assembling peptides from the recently developed expression host Ralstonia eutropha. The purification is based on the specific affinity of carbohydrate binding modules (CBMs) to cellulose. In a first step, we identified CBMs that express well in R. eutropha by assembling a fusion library of green fluorescent protein (GFP) and CBMs and determining the fluorescence of cell-free extracts. Three GFP::CBM fusions were found to express at levels similar to GFP alone, of which two CBMs were able to mediate cellulose binding of the GFP::CBM fusion. These two CBMs were then fused to multiple repeats of the self-assembling peptide RAD16-I::E (N-RADARADARADARADAE-C). The fusion protein CBM::E::(RAD16-I::E)4 was expressed in R. eutropha and purified using the CBM's affinity for cellulose. Subsequent proteolytic cleavage with endoproteinase GluC liberated RAD16-I::E peptide monomers with similar properties to the chemically synthesized counterpart RAD16-I.
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Affiliation(s)
- David C Reed
- Thayer School of Engineering, Dartmouth College, 8000 Cummings Hall, Hanover, NH 03755, USA
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31
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Grange PA, Marcelin AG, Calvez V, Chauvel C, Escande JP, Dupin N. Salivary lactoferrin is recognized by the human herpesvirus-8. J Invest Dermatol 2005; 124:1249-58. [PMID: 15955101 DOI: 10.1111/j.0022-202x.2005.23756.x] [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: 11/30/2022]
Abstract
Human herpesvirus-8 (HHV-8) is commonly detected in all epidemiologic forms of Kaposi's sarcoma. Despite the broad cellular tropism of HHV-8, studies on mucosal shedding of HHV-8 have shown that infectious particles are restricted to saliva isolated from the oropharynx. We used biotinylated purified HHV-8 particles in a direct binding assay to whole clarified human salivary samples isolated from HHV-8-infected and uninfected individuals. We found that the major binding activity was carried out by a protein of 78-kDa size, which was further characterized as human lactoferrin (hLf) using 2-D electrophoresis and MALDI-ToF analysis. Preliminary comparison of HHV-8 binding activity of 76 salivary samples from HHV-8-infected and uninfected individuals showed that 7.8% of the uninfected population exhibited a form of Lf not recognized by HHV-8. Deglycosylation of hLf by PNGase F did not reduce HHV-8 binding activity, whereas endoproteinase cleavage of native hLf generated a non-glycosylated 8-kDa peptide recognized by HHV-8 particles and was located at the position Ala606-Tyr679 in the native hLf amino acid sequence, corresponding to the C-terminal region of the glycoprotein. This work identify the lactoferrin in saliva as a ligand for HHV-8 and suggests that this glycoprotein could be used as a carrier for the viral particles.
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Affiliation(s)
- Philippe A Grange
- Laboratoire de Microbiologie Cutanée, Pavillon Tarnier, Groupe Hospitalier Cochin-Port Royal, Université Paris V, Paris, France.
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Weinrick B, Dunman PM, McAleese F, Murphy E, Projan SJ, Fang Y, Novick RP. Effect of mild acid on gene expression in Staphylococcus aureus. J Bacteriol 2005; 186:8407-23. [PMID: 15576791 PMCID: PMC532443 DOI: 10.1128/jb.186.24.8407-8423.2004] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During staphylococcal growth in glucose-supplemented medium, the pH of a culture starting near neutrality typically decreases by about 2 units due to the fermentation of glucose. Many species can comfortably tolerate the resulting mildly acidic conditions (pH, approximately 5.5) by mounting a cellular response, which serves to defend the intracellular pH and, in principle, to modify gene expression for optimal performance in a mildly acidic infection site. In this report, we show that changes in staphylococcal gene expression formerly thought to represent a glucose effect are largely the result of declining pH. We examine the cellular response to mild acid by microarray analysis and define the affected gene set as the mild acid stimulon. Many of the genes encoding extracellular virulence factors are affected, as are genes involved in regulation of virulence factor gene expression, transport of sugars and peptides, intermediary metabolism, and pH homeostasis. Key results are verified by gene fusion and Northern blot hybridization analyses. The results point to, but do not define, possible regulatory pathways by which the organism senses and responds to a pH stimulus.
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Affiliation(s)
- Brian Weinrick
- Program in Molecular Pathogenesis, Skirball Institute, and Department of Microbiology, New York University School of Medicine, 540 First Ave., New York, NY 10016, USA
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Livney YD, Schwan AL, Dalgleish DG. A Study of β-Casein Tertiary Structure by Intramolecular Crosslinking and Mass Spectrometry. J Dairy Sci 2004; 87:3638-47. [PMID: 15483147 DOI: 10.3168/jds.s0022-0302(04)73502-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The objective of this study was to obtain experimental evidence to extend the discussion on the 3-D structure of beta-casein (beta-CN). The approach involved the preparation of homobifunctional crosslinkers, bis(sulfosuccinimidyl) derivatives of dicarboxylic acids of several lengths, which specifically react with primary amines of lysinyl residues or the N-terminal in the protein. The intramolecular crosslinks formed were determined by enzymatic digestion and by matrix-assisted laser desorption and ionization time-of-flight mass spectrometry combined with comparison against the theoretical digestion patterns. This procedure allowed the measurement of distances between the crosslinked residues. Ten different masses arising from 8 different specific intramolecular crosslinks were identified. Of these, 5 crosslinks were in good agreement with a published model (Kumosinski et al., 1993). Two other crosslinks each connected 2 residues that are much closer together, according to the model, than the maximum length of the crosslink. However, one of the crosslinks apparently connected 2 residues that are predicted by the model to be 16.7 A farther apart than the crosslink's stretched length. This disparity might be explained by structural flexibility. The structure expressed by the model is probably one of several energetically favorable conformations of the beta-CN molecule, whose structure is best described as rheomorphic rather than either a fixed structure or a random coil.
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Affiliation(s)
- Y D Livney
- Department of Food Science, University of Guelph, ON, Canada N1G 2W1
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34
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Tan YV, Couvineau A, Laburthe M. Diffuse pharmacophoric domains of vasoactive intestinal peptide (VIP) and further insights into the interaction of VIP with the N-terminal ectodomain of human VPAC1 receptor by photoaffinity labeling with [Bpa6]-VIP. J Biol Chem 2004; 279:38889-94. [PMID: 15247290 DOI: 10.1074/jbc.m404460200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The widespread 28-amino acid neuropeptide vasoactive intestinal peptide (VIP) exerts its many biological effects through interaction with serpentine class II G protein-coupled receptors named VPAC receptors. We previously provided evidence for a physical contact between the side chain at position 22 of VIP and the N-terminal ectodomain of the hVPAC1 receptor (Tan, Y. V., Couvineau, A., Van Rampelbergh, J., and Laburthe, M. (2003) J. Biol. Chem. 278, 36531-36536). We explored here the contact site between hVPAC1 receptor and the side chain at position 6 of VIP by photoaffinity labeling. The photoreactive para-benzoyl-l-Phe (Bpa) was substituted for Phe(6) in VIP resulting in [Bpa(6)]-VIP, which was shown to be a hVPAC1 receptor agonist in Chinese hamster ovary cells stably expressing the recombinant receptor. After obtaining the covalent (125)I-[Bpa(6)-VIP].hVPAC1 receptor complex, it was sequentially cleaved by cyanogen bromide, peptide N-glycosidase F, endopeptidase Glu-C, and trypsin, and the cleavage products were analyzed by electrophoresis. The data demonstrated that (125)I-[Bpa(6)-VIP] were covalently attached to the short 104-108 fragment within the N-terminal ectodomain of the receptor. The data were confirmed by creation of a receptor mutant with new CNBr cleavage site. In a three-dimensional model of the receptor N-terminal ectodomain, this fragment was located on one edge of the putative VIP-binding groove and was adjacent to the fragment covalently attached to the side chain at position 22 of VIP. Altogether these data showed that the central part of VIP, at least between Phe(6) and Tyr(22), interacts with the N-terminal ectodomain of the hVPAC1 receptor.
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Affiliation(s)
- Yossan-Var Tan
- INSERM U410, Neuroendocrinologie et Biologie Cellulaire Digestives, Institut National de la Santé et de la Recherche Médicale, Faculté de Médecine Xavier Bichat, Paris F-75018, France
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35
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Mehndiratta P, Walton WJ, Hare JT, Pulido S, Parthasarathy G, Emmett MR, Marshall AG, Logan TM. Expression, purification, and characterization of avian Thy-1 from Lec1 mammalian and Tn5 insect cells. Protein Expr Purif 2004; 33:274-87. [PMID: 14711516 DOI: 10.1016/j.pep.2003.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Structural studies of asparagine-linked glycoproteins are complicated by the oligosaccharide heterogeneity inherent to individual glycosylation sites. Herein, we report the cloning of a novel isoform of avian Thy-1 and the subsequent expression, purification, and characterization of a soluble form of Thy-1 from Lec1 mammalian and Tn5 insect cells. The novel isoform of Thy-1 differs from the previously reported chicken isoform by eight amino acid residues, but these changes do not alter the secondary structure content, the disulfide bond pattern, or the sites of glycosylation. The disulfide linkage pattern and glycoform distribution on each N-glycosylation site of recombinant chicken Thy-1 from both cell lines were determined by a combination of amino-terminal sequencing and mass spectrometry. The mass spectral data showed that the amino-terminal glutamine was modified to pyroglutamate. Recombinant Thy-1 from Lec1 cells contained (GlcNAc)(2)(Man)(5) on asparagine 60, whereas the oligosaccharides on asparagine 23 and 100 contained approximately 80% (GlcNAc)(2)(Man)(4) and approximately 20% (GlcNAc)(2)(Man)(5). The glycoforms on Thy-1 expressed in Tn5 cells were more heterogeneous, with the oligosaccharides ranging over (GlcNAc)(2)(Fuc)(0-2)(Man)(2-3) on each site. The ability to generate recombinant glycoproteins with restricted carbohydrate heterogeneity is the first step toward the systematic study of structure-function relationships in intact glycoproteins.
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Affiliation(s)
- Promod Mehndiratta
- Graduate Program in Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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36
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Tan YV, Couvineau A, Van Rampelbergh J, Laburthe M. Photoaffinity labeling demonstrates physical contact between vasoactive intestinal peptide and the N-terminal ectodomain of the human VPAC1 receptor. J Biol Chem 2003; 278:36531-6. [PMID: 12807902 DOI: 10.1074/jbc.m304770200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Vasoactive intestinal peptide (VIP) is a prominent neuropeptide whose actions are mediated by VPAC receptors belonging to class II G protein-coupled receptors. To identify contact sites between VIP and its VPAC1 receptor, an analog of VIP substituted with a photoreactive para-benzoyl-l-Phe (Bpa) at position 22 has been synthesized and evaluated in Chinese hamster ovary cells stably expressing the recombinant human receptor. Bpa22-VIP and native VIP are equipotent in stimulating adenylyl cyclase activity in cell membranes. Cyanogen bromide cleavage of the covalent 125I-[Bpa22-VIP]-hVPAC1R complex yielded a single labeled fragment of 30 kDa that shifted to 11 after deglycosylation, most consistent with the 67-137 fragment of the receptor N-terminal ectodomain. Further cleavage of this fragment with V8 endoproteinase and creation of receptor mutants with new CNBr cleavage sites (XàMet), demonstrated that 125I-[Bpa22-VIP] was covalently attached to the short receptor 109-120 fragment (GWTHLEPGPYPI). In a three-dimensional model of the receptor N-terminal ectodomain, this fragment is located on one edge of the putative VIP binding groove and encompasses several amino acids previously shown to be crucial for VIP binding (reviewed in Laburthe, M., Couvineau, A., and Marie, J. C. (2002) Receptors Channels 8, 137-153). Our data provide the first direct evidence for a physical contact between VIP and the N-terminal ectodomain of the hVPAC1 receptor.
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Affiliation(s)
- Yossan-Var Tan
- INSERM U410, Neuroendocrinologie et Biologie Cellulaire Digestives, Institut National de la Santé et de la Recherche Médicale, Faculté de Médecine Xavier Bichat, Paris F-75018, France
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37
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Affiliation(s)
- Brian G Rowan
- Department of Biochemistry and Molecular Biology, Medical College of Ohio, Toledo, Ohio 43614, USA
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38
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Brand GD, Leite JRSA, Silva LP, Albuquerque S, Prates MV, Azevedo RB, Carregaro V, Silva JS, Sá VCL, Brandão RA, Bloch C. Dermaseptins from Phyllomedusa oreades and Phyllomedusa distincta. Anti-Trypanosoma cruzi activity without cytotoxicity to mammalian cells. J Biol Chem 2002; 277:49332-40. [PMID: 12379643 DOI: 10.1074/jbc.m209289200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amphibian skin secretions are known as a rich source of biologically active molecules, most of which are alkaloids, biogenic amines, and peptides. Dermaseptins are a class of antimicrobial peptides present in tree frogs of the Phyllomedusa genus. They are cationic molecules of 28-34 residues that permeabilize the membrane of Gram-positive and Gram-negative bacteria, yeasts, and filamentous fungi, showing little or no hemolytic activity. This work reports the isolation, molecular mass analysis, primary structure determination, biological activities, and potential therapeutic applications of an antimicrobial peptide found in the skin secretion of Phyllomedusa oreades, which is a newly described amphibian species endemic of the Brazilian savanna. DS 01 is a 29-residue-long peptide with a molecular mass of 2793.39 Da showing antibacterial properties against Gram-positive and Gram-negative bacteria in the range of 3-25 microm. Anti-protozoan activity was investigated using T. cruzi in its trypomatigote and epimastigote forms cultivated in both cell culture and blood media. Within 2 h after incubation with DS 01 at a final concentration of approximately 6 microm, no protozoan cells were detected. Two synthetic dermaseptins, described previously by our group and named dermadistinctins K and L (DD K and DD L), also had their anti-Trypanosoma cruzi activity investigated and demonstrated similar properties. Toxicity of DS 01 to mouse erythrocytes and white blood cells was evaluated by means of atomic force microscopy and flow cytometry. No morphological alterations were observed at a lytic concentration of DS 01, suggesting its therapeutic value especially as an anti-T. cruzi agent to prevent infections during blood transfusion.
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Affiliation(s)
- Guilherme D Brand
- Laboratório de Espectrometria de Massa, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) - Recursos Genéticos e Biotecnologia, Estação Parque Biológico, Final W5, Asa Norte, Brasilia, DF, 70770-900 Brazil
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39
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Abstract
Bacterial proteases secreted into an infected host may exhibit a wide range of pathogenic potentials. Staphylococci, in particular Staphylococcus aureus, are known to produce several extracellular proteases, including serine-, cysteine- and metalloenzymes. Their insensitivity to most human plasma protease inhibitors and, even more, the ability to inactivate some of these make the proteases potentially harmful. Indeed, several recent studies have shown that staphylococcal proteases are able to interact with the host defense mechanisms and tissue components as well as to modify other pathogen-derived virulence factors. A tight, cell density-dependent control of proteolytic activity expression, similar to that of the well-defined virulence determinants, further suggests the role of staphylococcal proteases in the infection process. Consistently, alterations in coordinated expression of extracellular proteins markedly diminished the virulence. However, despite these data and the fact that a strain deficient in sspABC operon coding for serine (sspA) and cysteine (sspB) proteases was highly attenuated in virulence in the animal infection model, it was impossible to unambiguously demonstrate the importance of any particular protease as a virulence factor. Therefore, it can be assumed that the orchestrated expression and interaction of a variety of extracellular and cell surface proteins rather than any particular one is responsible for the staphylococcal pathogenicity and that the proteases apparently play an important role in this complex process. Such redundant mechanism is very well suited for promoting the survival of staphylococci under diverse environmental conditions encountered in the infected host.
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Affiliation(s)
- Grzegorz Dubin
- Institute of Molecular Biology and Biotechnology, Jagiellonian University, Kraków, Poland
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Hejazi M, Piotukh K, Mattow J, Deutzmann R, Volkmer-Engert R, Lockau W. Isoaspartyl dipeptidase activity of plant-type asparaginases. Biochem J 2002; 364:129-36. [PMID: 11988085 PMCID: PMC1222554 DOI: 10.1042/bj3640129] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recombinant plant-type asparaginases from the cyanobacteria Synechocystis sp. PCC (Pasteur culture collection) 6803 and Anabaena sp. PCC 7120, from Escherichia coli and from the plant Arabidopsis thaliana were expressed in E. coli with either an N-terminal or a C-terminal His tag, and purified. Although each of the four enzymes is encoded by a single gene, their mature forms consist of two protein subunits that are generated by autoproteolytic cleavage of the primary translation products at the Gly-Thr bond within the sequence GTI/VG. The enzymes not only deamidated asparagine but also hydrolysed a range of isoaspartyl dipeptides. As various isoaspartyl peptides are known to arise from proteolytic degradation of post-translationally altered proteins containing isoaspartyl residues, and from depolymerization of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartic acid (cyanophycin), plant-type asparaginases may not only function in asparagine catabolism but also in the final steps of protein and cyanophycin degradation. The properties of these enzymes are compared with those of the sequence-related glycosylasparaginases.
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Affiliation(s)
- Mahdi Hejazi
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestr. 117, D-10115 Berlin, Germany
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41
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Abstract
The product of the MDM2 gene interacts with and regulates a number of proteins, in particular the tumor suppressor p53. The MDM2 protein is likely to be extensively modified in vivo, and such modification may regulate its functions in cells. We identified a potential cyclin-dependent kinase (CDK) site in murine MDM2, and found the protein to be efficiently phosphorylated in vitro by cyclin A-containing complexes (cyclin A-CDK2 and cyclin A-CDK1), but MDM2 was either weakly or not phosphorylated by other cyclin-containing complexes. Moreover, a peptide containing a putative MDM2 cyclin recognition motif specifically inhibited phosphorylation by cyclin A-CDK2. The site of cyclin A-CDK2 phosphorylation was identified as Thr-216 by two-dimensional phosphopeptide mapping and mutational analysis. Phosphorylation of MDM2 at Thr-216 both weakens its interaction with p53 and modestly augments its binding to p19(ARF). Interestingly, an MDM2-specific monoclonal antibody, SMP14, cannot recognize MDM2 phosphorylated at Thr-216. Changes in SMP14 reactivity of MDM2 in staged cell extracts indicate that phosphorylation of MDM2 at Thr-216 in vivo is most prevalent at the onset of S phase when cyclin A first becomes detectable.
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Affiliation(s)
- T Zhang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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42
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Falk MM. Connexins/connexons. Cell-free expression. Methods Mol Biol 2001; 154:91-116. [PMID: 11218667 PMCID: PMC7121760 DOI: 10.1385/1-59259-043-8:91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
With a few exceptions, all secretory and plasma membrane proteins studied to date are synthesized in the endoplasmic reticulum (ER) membrane. Then, they are transported by successive vesicle budding and fusion from the ER through the Golgi stacks to the plasma membrane following the general intracellular transport route referred to as secretory pathway (originally reviewed in 1). Gap junction connexins have been shown to follow this pathway.
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Affiliation(s)
- M M Falk
- Department of Cell Biology, Scripps Research Institute, La Jolla, CA, USA
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43
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Haensler M, Wissmann HD, Wehofsky N. Enzymatic formation of Glu-Xaa and Asp-Xaa bonds using Glu/Asp-specific endopeptidase from Bacillus licheniformis in frozen aqueous systems. J Pept Sci 2000; 6:366-71. [PMID: 10969865 DOI: 10.1002/1099-1387(200008)6:8<366::aid-psc262>3.0.co;2-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The capability of Glu/Asp-specific endopeptidase from Bacillus licheniformis to form Glu/Asp-Xaa bonds in frozen aqueous systems was investigated. Under frozen state conditions, the enzyme was able to catalyse peptide bond formation more effectively than in liquid reaction mixtures. The acceptance of amino components which were completely inefficient nucleophiles at room temperature indicates a changed specificity of Glu/Asp-specific endopeptidase under frozen state conditions. Protease-catalysed coupling of two acidic amino acids was demonstrated for the first time. The utilization of Glu/Asp-specific endopeptidase from Bacillus licheniformis in frozen aqueous systems offers new possibilities in enzyme-catalysed peptide synthesis.
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Affiliation(s)
- M Haensler
- Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, Leipzig University, Germany.
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Priolo N, Morcelle del Valle S, Arribére MC, López L, Caffini N. Isolation and characterization of a cysteine protease from the latex of Araujia hortorum fruits. JOURNAL OF PROTEIN CHEMISTRY 2000; 19:39-49. [PMID: 10882171 DOI: 10.1023/a:1007042825783] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A new protease (araujiain h I) was purified to mass spectroscopy homogeneity from the latex of Araujia hortorum Fourn. (Asclepiadaceae) fruits by ultracentrifugation and ion exchange chromatography. The enzyme has a molecular mass of 24,031 (mass spectrometry) and an iso-electric point higher than 9.3. The optimum pH range for casein hydrolysis was 8.0-9.5. The enzyme showed remarkable caseinolytic activity at high temperatures, although its thermal stability decayed rapidly. The proteinase was activated by thiol compounds and inhibited by common thiol-blocking reagents, particularly E-64 and HgCl2, suggesting the enzyme belongs to the cysteine protease family. The concentration of active sites as determined by titration with E-64 was 3.3 microM. When assayed on N-alpha-CBZ-amino acid-p-nitrophenyl esters, the enzyme showed higher preference for the glutamine derivative, followed by those of alanine, asparagine, glycine, and leucine, in decreasing order. Partial homology (36-48%) with other plant cysteine proteinases was observed in an internal fragment obtained by Protease V8 treatment.
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Affiliation(s)
- N Priolo
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Argentina.
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45
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Hamilton R, Walker B, Walker BJ. Synthesis and proteinase inhibitory properties of diphenyl phosphonate analogues of aspartic and glutamic acids. Bioorg Med Chem Lett 1998; 8:1655-60. [PMID: 9873408 DOI: 10.1016/s0960-894x(98)00272-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The synthesis of diphenyl phosphonate analogues of aspartic and glutamic acid, and their inhibitory activity against S. aureus V8 protease and granzyme B, is described. The study has revealed difficulties with protecting group compatibility in the synthesis of these analogues. Two analogues, Acetyl. AspP (OPh)2 and Acetyl.GluP (OPh)2 were found to function as irreversible inactivators of V8 proteinase, yet exhibit no activity against granzyme B.
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Affiliation(s)
- R Hamilton
- School of Chemistry, Queen's University of Belfast, Northern Ireland
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46
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Lipari F, Herscovics A. Role of the cysteine residues in the alpha1,2-mannosidase involved in N-glycan biosynthesis in Saccharomyces cerevisiae. The conserved Cys340 and Cys385 residues form an essential disulfide bond. J Biol Chem 1996; 271:27615-22. [PMID: 8910350 DOI: 10.1074/jbc.271.44.27615] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The Saccharomyces cerevisiae alpha1,2-mannosidase, which removes one specific mannose residue from Man9GlcNAc2 to form Man8GlcNAc2, is a member of a family of alpha1,2-mannosidases with similar amino acid sequences. The yeast alpha1,2-mannosidase contains five cysteine residues, three of which are conserved. Recombinant yeast alpha1, 2-mannosidase, produced as the soluble catalytic domain, was shown to contain two disulfide bonds and one free thiol group using 2-nitro-5-thiosulfobenzoate and 5,5'-dithiobis(2-nitrobenzoate), respectively. Cys485 contains the free thiol group, as demonstrated by sequencing of labeled peptides following modification with [3H]ICH2COOH and by high performance liquid chromatography/mass spectrometry tryptic peptide mapping. A Cys340-Cys385 disulfide was demonstrated by sequencing a purified peptide containing this disulfide and by tryptic peptide mapping. Cys468 and Cys471 were not labeled with [3H]ICH2COOH and a peptide containing these two residues was identified in the tryptic peptide map, showing that Cys468 and Cys471 form the second disulfide bond. The alpha1, 2-mannosidase loses its activity in the presence of dithiothreitol with first order kinetics, suggesting that at least one disulfide bond is essential for activity. Mutagenesis of each cysteine residue to serine showed that Cys340 and Cys385 are essential for production of recombinant enzyme, whereas Cys468, Cys471, and Cys485 are not required for production and enzyme activity. These results indicate that the sensitivity to dithiothreitol is due to reduction of the Cys340-Cys385 disulfide. Since Cys340 and Cys385 are conserved residues, it is likely that this disulfide bond is important to maintain the correct structure in the other members of the alpha1, 2-mannosidase family.
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Affiliation(s)
- F Lipari
- McGill Cancer Centre, McGill University, Montréal, Québec, Canada H3G 1Y6.
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47
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Cohen SL, Ferré-D'Amaré AR, Burley SK, Chait BT. Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Sci 1995; 4:1088-99. [PMID: 7549873 PMCID: PMC2143150 DOI: 10.1002/pro.5560040607] [Citation(s) in RCA: 138] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A simple biochemical method that combines enzymatic proteolysis and matrix-assisted laser desorption ionization mass spectrometry was developed to probe the solution structure of DNA-binding proteins. The method is based on inferring structural information from determinations of protection against enzymatic proteolysis, as governed by solvent accessibility and protein flexibility. This approach was applied to the study of the transcription factor Max--a member of the basic/helix-loop-helix/zipper family of DNA-binding proteins. In the absence of DNA and at low ionic strengths, Max is rapidly digested by each of six endoproteases selected for the study, results consistent with an open and flexible structure of the protein. At physiological salt levels, the rates of digestion are moderately slowed; this and the patterns of cleavage are consistent with homodimerization of the protein through a predominantly hydrophobic interface. In the presence of Max-specific DNA, the protein becomes dramatically protected against proteolysis, exhibiting up to a 100-fold reduction in cleavage rates. Over a 2-day period, both complete and partial proteolysis of the Max-DNA complex is observed. The partial proteolytic fragmentation patterns reflect a very high degree of protection in the N-terminal and helix-loop-helix regions of the protein, correlating with those expected of a stable dimer bound to DNA at its basic N-terminals. Less protection is seen at the C-terminal where a slow, sequential proteolytic cleavage occurs, correlating to the presence of a leucine zipper. The results also indicate a high affinity of Max for its target DNA that remains high even when the leucine zipper is proteolytically removed. In addition to the study of the helix-loop-helix protein Max, the present method appears well suited for a range of other structural biological applications.
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Affiliation(s)
- S L Cohen
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, New York, New York 10021, USA
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48
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Campbell RM, Bongers J, Felix AM. Rational design, synthesis, and biological evaluation of novel growth hormone releasing factor analogues. Biopolymers 1995; 37:67-88. [PMID: 7893948 DOI: 10.1002/bip.360370204] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Since its initial discovery in 1982, growth hormone-releasing factor (GRF) has been the subject of intense investigation. This interest was prompted by the potential application of GRF for stimulating growth in dwarf humans and for performance enhancement in livestock. Substantial research has been focused upon the development of potent, long-acting analogs as therapeutics. Herein is described a summary of the cumulative efforts of various laboratories endeavoring in this quest. The rationale utilized in GRF analog development is discussed: 1) determination of bioactive core, 2) evaluation of secondary structure, and 3) elucidation of degradation pathways (chemical and enzymatic). Using this information, several series of linear (unnatural and natural sequence) and cyclic GRF analogs were designed, synthesized, and evaluated. Stimulated by the constraints of commercial production, innovative, alternative methods of synthesis were explored: solid-phase, solution-phase, enzymatic, and recombinant. To date, the most promising candidate for drug development is [His1, Val2, Gln8, Ala15, Leu27]-hGRF(1-32)-OH. This natural sequence analog, consisting of rodent and human sequences, incorporates the bioactive core, preferred secondary structure, resistance to chemical and enzymatic degradation; with the added benefit of amenability to large-scale recombinant synthesis.
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Affiliation(s)
- R M Campbell
- Hoffmann-La Roche, Inc., Roche Research Center, Nutley, New Jersey 07110
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49
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Morris NJ, Bushfield M, Lavan BE, Houslay MD. Multi-site phosphorylation of the inhibitory guanine nucleotide regulatory protein Gi-2 occurs in intact rat hepatocytes. Biochem J 1994; 301 ( Pt 3):693-702. [PMID: 8053895 PMCID: PMC1137044 DOI: 10.1042/bj3010693] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A phosphorylated form of alpha-Gi-2 (the alpha-subunit of Gi-2), immunoprecipitated from hepatocytes under basal conditions, migrated as a single species of pI approximately 5.7, the labelling of which increased approximately 2-fold in cells challenged with either vasopressin or phorbol 12-myristate 13-acetate (PMA); agents which activate protein kinase C. In contrast, treatment of hepatocytes with 8-bromo-cyclic AMP produced a more acidic species of phosphorylated alpha-Gi-2 having a pI of approximately 5.4 and whose labelling was increased approximately 3-fold. Trypsin digestion of labelled alpha-Gi-2 isolated from hepatocytes under basal conditions identified, on two-dimensional peptide analyses, three positively charged phosphoserine-containing peptides (C1, C2 and C3), with only peptides C1 and C2 being evident upon less extensive digestion with trypsin. These are suggested to reflect a single site of phosphorylation, with proteolysis by trypsin being incomplete, and where C2 is larger than C1, which is larger than C3. An identical pattern of tryptic phosphopeptides was seen in hepatocytes treated with either vasopressin or PMA, although labelling of this group of peptides was increased by approximately 2-fold compared with the basal state. In contrast, treatment of hepatocytes with glucagon, 8-bromo-cyclic AMP or forskolin not only resulted in increased labelling of the 'basal' sites approximately 3-fold, but identified a novel positively charged tryptic phosphoserine-containing peptide (AN). All four tryptic peptides were susceptible to proteolysis by V8 protease. Treatment of labelled alpha-Gi-2 from basal and PMA-treated cells produced a pattern of peptides which was identical with those found when the tryptic phosphopeptide was treated with V8 protease. We tentatively suggest that, on alpha-Gi-2, Ser144 is phosphorylated through the action of protein kinase C and Ser207 is phosphorylated upon elevation of the intracellular concentrations of cyclic AMP.
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Affiliation(s)
- N J Morris
- Department of Biochemistry, University of Glasgow, Scotland, U.K
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50
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Sára M, Pum D, Küpcü S, Messner P, Sleytr UB. Isolation of two physiologically induced variant strains of Bacillus stearothermophilus NRS 2004/3a and characterization of their S-layer lattices. J Bacteriol 1994; 176:848-60. [PMID: 8300538 PMCID: PMC205123 DOI: 10.1128/jb.176.3.848-860.1994] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
During growth of Bacillus stearothermophilus NRS 2004/3a in continuous culture on complex medium, the chemical properties of the S-layer glycoprotein and the characteristic oblique lattice were maintained only if glucose was used as the sole carbon source. With increased aeration, amino acids were also metabolized, accompanied by liberation of ammonium and by changes in the S-layer protein. Depending on the stage of fermentation at which oxygen limitation was relieved, two different variants, one with a more delicate oblique S-layer lattice (variant 3a/V1) and one with a square S-layer lattice (variant 3a/V2), were isolated. During the switch from the wild-type strain to a variant or from variant 3a/V2 to variant 3a/V1, monolayers of two types of S-layer lattices could be demonstrated on the surfaces of single cells. S-layer proteins from variants had different molecular sizes and a significantly lower carbohydrate content than S-layer proteins from the wild-type strain did. Although the S-layer lattices from the wild-type and variant strains showed quite different protein mass distributions in two- and three-dimensional reconstructions, neither the amino acid composition nor the pore size, as determined by permeability studies, was significantly changed. Peptide mapping and N-terminal sequencing results strongly indicated that the three S-layer proteins are encoded by different genes and are not derived from a universal precursor form.
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Affiliation(s)
- M Sára
- Zentrum für Ultrastrukturforschung und Ludwig Boltzmann-Institut für Molekulare Nanotechnologie, Universität für Bodenkultur, Vienna, Austria
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