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Dixon JM, Egusa S. Limited Proteolysis and Gel Electrophoresis in the Presence of Metal Cations: Au(III)-binding Luminescent Domain in Serum Albumins. J Vis Exp 2021. [PMID: 33554961 DOI: 10.3791/61905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The purpose of the presented protocols is to determine the domain of Au(III) binding in BSA. The BSA-Au(III) compound exhibits ultraviolet (UV)-excitable red luminescence (λem = 640 nm), with unusual Stokes shifts compared to the innate UV/blue fluorescence arising from the aromatic residues. Red-luminescent complexes are formed in highly alkaline conditions above pH 10 and require a conformation change within the protein to occur. In addition, preservation of Cys-Cys disulfide bonds in BSA is necessary to obtain this red luminescence. In order to understand the mechanism of this luminescence, elucidation of the luminophore-forming Au(III) binding site is essential. A facile way to assess the luminophore-forming site would be to (1) predictably fragment the protein by enzymatic digestion, (2) react the obtained fragments with Au(III), then (3) perform gel electrophoresis to observe the well-separated fragment bands and analyze the in-gel red luminescence. However, due to the alkaline conditions and the reaction with metal cations, new limited proteolysis techniques and gel electrophoresis conditions must be applied. Particularly, the presence of metal cations in gel electrophoresis can make the band separations technically difficult. We describe this new protocol in steps to identify the red-luminophore-forming metal binding domain in BSA. This protocol can thus be applied for analyzing protein fragments that must remain in a non-denatured or a partially denatured state, in the presence of metal cations. Because the majority of proteins need metal cations to function, analyses of metal-bound proteins are often desired, which have relied on x-ray crystallography in the literature. This method, on the other hand, could be used in supplement to study the interactions of proteins with metal cations without requiring the protein crystallization and at a desired pH condition.
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Affiliation(s)
- Jacob M Dixon
- Department of Physics and Optical Science, Center for Biomedical Engineering & Science, The University of North Carolina
| | - Shunji Egusa
- Department of Physics and Optical Science, Center for Biomedical Engineering & Science, The University of North Carolina;
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Dixon JM, Tomida J, Egusa S. Identifying the Red-Luminophore-Forming Domain in Serum Albumin-Gold Complexes. J Phys Chem Lett 2020; 11:3345-3349. [PMID: 32294382 DOI: 10.1021/acs.jpclett.0c00805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Serum albumin-gold complexes exhibit UV-excitable red luminescence (λem = 640 nm) with unusual Stokes shifts compared with the innate UV/blue fluorescence arising from the aromatic residues. In order to understand the mechanism of this luminescence, we employed limited proteolysis and molecular cloning techniques and assessed the domain containing the red luminophore in bovine serum albumin (BSA) and human serum albumin (HSA). We identified that the luminophore is localized in a domain of serum albumin, residing within the N-terminus half.
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Zhang Y, Yu D, Dai J, Wang X, Zhu Z, Huang Y, Sun J, Chen Z, Jin L, Wang Y. A method for rapid and sensitive negative staining of proteins in SDS-PAGE using 2′,7′-dichlorofluorescein. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 04/24/2017] [Accepted: 04/27/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Yuan Zhang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Dongdong Yu
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Jiangbo Dai
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Xu Wang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Zhongxin Zhu
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Yewei Huang
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Jia Sun
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Zhiwei Chen
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
| | - Litai Jin
- School of Pharmaceutical Sciences; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
- Wenzhou Undersun Biotechnology Co. Ltd.; Wenzhou Zhejiang P. R. China
| | - Yang Wang
- Institute of neuroscience, Department of histology and embryology; Wenzhou Medical University; Wenzhou Zhejiang P. R. China
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Advanced negative detection method comparable to silver stain for SDS-PAGE separated proteins detection. Anal Biochem 2016; 510:21-25. [PMID: 27430933 DOI: 10.1016/j.ab.2016.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 11/20/2022]
Abstract
In order to achieve an easy, rapid and sensitive protocol to detect proteins in polyacrylamide gel, an advanced negative detection method comparable to silver stain is described. When a gel was incubated with Phloxine B and followed by the development in acidic solution, the zones where forming protein-dye complex were selectively transparent, unlike opaque gel background. Within 50 min after electrophoresis, down to 0.1-0.4 ng of gel-separated proteins (similar with silver stain) could be observed, without labor-intensive and time-consuming procedure. Comparing with the most common negative stain method, Imidazole-zinc stain, Phloxine B stain has been shown higher sensitivity and distinct contrast between the transparent protein bands/spots and opaque background than those; furthermore, it is no longer necessary to concern about retention time of observation. This technique may provide a sensitive and practical choice for proteomics researches.
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EGFP reporter protein: its immunogenicity in Leishmania-infected BALB/c mice. Appl Microbiol Biotechnol 2015; 100:3923-34. [PMID: 26685673 DOI: 10.1007/s00253-015-7201-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 02/06/2023]
Abstract
Optical reporter genes such as green fluorescent protein (GFP) and luciferase are efficiently and widely used in monitoring and studying the protective/therapeutic potential of candidate agents in leishmaniasis. But several observations and controversial reports have generated a main concern, whether enhanced GFP (EGFP) affects immune response. To address this issue, we studied the immunogenicity of EGFP in vivo by two lines of stably transfected parasites (Leishmania major (EGFP) or L. major (EGFP-LUC)) in BALB/c model and/or as a recombinant protein (rEGFP) produced in vitro by bacteria in parallel. Disease progression was followed by footpad swelling measurements and parasite burden in draining lymph nodes using microtitration assay and real-time PCR, and immune responses were also evaluated in spleen. EGFP-expressing parasites generated larger swellings in comparison with wild-type (L. major) while mice immunized with rEGFP and challenged with wild-type parasite were quite comparable in footpad swelling with control group without significant difference. However, both conventional and molecular approaches revealed no significant difference in parasite load between different groups. More importantly, no significant inflammatory responses were detected in groups with higher swelling size measured by interferon-γ (IFN-γ), interleukin (IL)-10, IL-5, and nitric oxide against frozen and thawed lysate of parasite as stimulator. Altogether, these results clearly revealed that EGFP protein expressed in prokaryotic and eukaryotic hosts is not an immunological reactive molecule and acts as a neutral protein without any side effects in mice. So, EGFP expressing Leishmania could be a safe and reliable substitution for wild-types that simplifies in situ follow-up and eliminates the animal scarification wherever needed during the study.
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Górnicka-Michalska E, Kowalski A, Pałyga J. Allelic isoforms of the chicken and duck histone H1.a. Cell Mol Biol Lett 2014; 19:116-25. [PMID: 24549575 PMCID: PMC6275575 DOI: 10.2478/s11658-014-0182-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 01/23/2014] [Indexed: 12/05/2022] Open
Abstract
Two isoforms of the erythrocyte histone H1.a were identified in two conservative flocks of Rhode Island Red chickens and six conservative flocks of ducks. The H1.a1 and H1.a2 isoforms formed three phenotypes (a1, a2 and a1a2) and were electrophoretically similar in the two species. The frequency of phenotype and histone H1.a allele occurrence varied within the genetic groups of birds, but the relatively rare allele a(2) was only detected in chicken and duck strains with colored feathers. Using mass spectrometry, we established that the difference between the measured masses of the duck H1.a isoforms was 156 Da. Since this value corresponds to the mass of the arginine residue alone or to the combined mass of the valine and glycine residues, we believe that the polymorphism of duck histone H1.a might have originated from sequence variation. A mass difference of 1 Da observed between chicken H1.a isoforms corresponded well to the previously detected Glu/Lys substitution (0.9414 Da) at position 117.
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Affiliation(s)
- Ewa Górnicka-Michalska
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, ul. Świętokrzyska 15, 25-406 Kielce, Poland
| | - Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, ul. Świętokrzyska 15, 25-406 Kielce, Poland
| | - Jan Pałyga
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, ul. Świętokrzyska 15, 25-406 Kielce, Poland
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Smejkal GB. The Coomassie chronicles: past, present and future perspectives in polyacrylamide gel staining. Expert Rev Proteomics 2014; 1:381-7. [PMID: 15966833 DOI: 10.1586/14789450.1.4.381] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Soltanieh S, Lapensée M, Dragon F. Nucleolar proteins Bfr2 and Enp2 interact with DEAD-box RNA helicase Dbp4 in two different complexes. Nucleic Acids Res 2013; 42:3194-206. [PMID: 24357410 PMCID: PMC3950691 DOI: 10.1093/nar/gkt1293] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Different pre-ribosomal complexes are formed during ribosome biogenesis, and the composition of these complexes is highly dynamic. Dbp4, a conserved DEAD-box RNA helicase implicated in ribosome biogenesis, interacts with nucleolar proteins Bfr2 and Enp2. We show that, like Dbp4, Bfr2 and Enp2 are required for the early processing steps leading to the production of 18S ribosomal RNA. We also found that Bfr2 and Enp2 associate with the U3 small nucleolar RNA (snoRNA), the U3-specific protein Mpp10 and various pre-18S ribosomal RNA species. Thus, we propose that Bfr2, Dbp4 and Enp2 are components of the small subunit (SSU) processome, a large complex of ∼80S. Sucrose gradient sedimentation analyses indicated that Dbp4, Bfr2 and Enp2 sediment in a peak of ∼50S and in a peak of ∼80S. Bfr2, Dbp4 and Enp2 associate together in the 50S complex, which does not include the U3 snoRNA; however, they associate with U3 snoRNA in the 80S complex (SSU processome). Immunoprecipitation experiments revealed that U14 snoRNA associates with Dbp4 in the 50S complex, but not with Bfr2 or Enp2. The assembly factor Tsr1 is not part of the '50S' complex, indicating this complex is not a pre-40S ribosome. A combination of experiments leads us to propose that Bfr2, Enp2 and Dbp4 are recruited at late steps during assembly of the SSU processome.
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Affiliation(s)
- Sahar Soltanieh
- Département des sciences biologiques and Centre de recherche BioMed, Université du Québec à Montréal, Montréal, Québec, Canada
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Ramos I, Fernández-Rivero N, Arranz R, Aloria K, Finn R, Arizmendi JM, Ausió J, Valpuesta JM, Muga A, Prado A. The intrinsically disordered distal face of nucleoplasmin recognizes distinct oligomerization states of histones. Nucleic Acids Res 2013; 42:1311-25. [PMID: 24121686 PMCID: PMC3902905 DOI: 10.1093/nar/gkt899] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The role of Nucleoplasmin (NP) as a H2A-H2B histone chaperone has been extensively characterized. To understand its putative interaction with other histone ligands, we have characterized its ability to bind H3-H4 and histone octamers. We find that the chaperone forms distinct complexes with histones, which differ in the number of molecules that build the assembly and in their spatial distribution. When complexed with H3-H4 tetramers or histone octamers, two NP pentamers form an ellipsoidal particle with the histones located at the center of the assembly, in stark contrast with the NP/H2A-H2B complex that contains up to five histone dimers bound to one chaperone pentamer. This particular assembly relies on the ability of H3-H4 to form tetramers either in solution or as part of the octamer, and it is not observed when a variant of H3 (H3C110E), unable to form stable tetramers, is used instead of the wild-type protein. Our data also suggest that the distal face of the chaperone is involved in the interaction with distinct types of histones, as supported by electron microscopy analysis of the different NP/histone complexes. The use of the same structural region to accommodate all type of histones could favor histone exchange and nucleosome dynamics.
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Affiliation(s)
- Isbaal Ramos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencia y Tecnología, Universidad del PaísVasco, P. O. Box 644, 48080 Bilbao, Spain, Unidad de Biofísica (Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea), Barrio Sarriena s/n, 48080 Leioa Spain, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain and Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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10
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Gauci VJ, Padula MP, Coorssen JR. Coomassie blue staining for high sensitivity gel-based proteomics. J Proteomics 2013; 90:96-106. [PMID: 23428344 DOI: 10.1016/j.jprot.2013.01.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/27/2013] [Indexed: 11/26/2022]
Abstract
Gel electrophoresis, particularly one- (1DE) and two-dimensional electrophoresis (2DE), remain among the most widely used top-down methods for resolving and analysing proteomes. Detection of the resulting protein maps relies on staining (i.e. colloidal coomassie blue (CCB) or SYPRO Ruby (SR), in addition to many others). Fluorescent in-gel protein stains are generally preferred for higher sensitivity, reduced background, and wider dynamic range. Although traditionally used for densitometry, CBB has fluorescent properties. Indeed, infrared detection of CCB stained protein was comparable to SR, with BioSafe (Bio-Rad) and the Neuhoff formulation (NCCB) identified as potentially superior to SR; a minor sensitivity issue encountered in gel-resolved proteomes; might have been due to the unified staining protocol used. Here the staining protocol for both CCB formulations was optimised, yielding improved selectivity without affecting sensitivity; the resulting linear dynamic range was similar for BioSafe and NCCB and somewhat better than SR. 2D gel-based analyses of mouse brain and Arabidopsis thaliana (leaf) proteomes indicated markedly superior spot detection using the NCCB formulation. Thus more sensitive, quantitative in-gel protein analyses can be achieved using NCCB, at a fraction of the cost.
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Affiliation(s)
- Victoria J Gauci
- Molecular Physiology, and the Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, Australia
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Wada K, Kimura K, Hasegawa A, Fukuyama K, Nagasaki K. Establishment of a bacterial expression system and immunoassay platform for the major capsid protein of HcRNAV, a dinoflagellate-infecting RNA virus. Microbes Environ 2012; 27:483-9. [PMID: 23047150 PMCID: PMC4103558 DOI: 10.1264/jsme2.me12046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HcRNAV is a small icosahedral virus that infects the shellfish-killing marine dinoflagellate Heterocapsa circularisquama, which harbors a dicistronic linear single-stranded RNA (ssRNA) genome ca. 4.4 kb in length. Its major capsid protein (MCP) gene sequence is not expressed by various strains of Escherichia coli, possibly because of a codon usage problem. To solve this problem, a chemically modified (i.e., de novo synthesized) gene was designed and cloned into the pCold-GST expression vector, and transformed into E. coli strain C41 (DE3), in which codon usage was universally optimized to efficiently express the polypeptide having the viral MCP amino acid sequence. The bacterially expressed protein, which was purified after a procedure involving denaturation and refolding, successfully formed virus-like particles that significantly resembled native HcRNAV particles. The purified, denatured protein was used as an antigen to immunize rabbits, and the resulting antiserum was shown to be strongly reactive to not only the bacterially expressed recombinant protein, but also to native HcRNAV MCP by Western blotting and dot immunoassays, respectively. These results indicate that an antiserum recognizing native HcRNAV MCP was successfully obtained using bacterially expressed HcRNAV MCP as the antigen.
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Affiliation(s)
- Kei Wada
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560–0043, Japan
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Mohit E, Bolhassani A, Zahedifard F, Taslimi Y, Rafati S. The contribution of NT-gp96 as an adjuvant for increasing HPV16 E7-specific immunity in C57BL /6 mouse model. Scand J Immunol 2012; 75:27-37. [PMID: 21916914 DOI: 10.1111/j.1365-3083.2011.02620.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To control cervical cancer, efficient vaccination against human papillomavirus (HPV) is highly required. Despite the advantages and safety of the protein vaccines, additional strategies to enhance their immunogenicity are needed. E7 is a transforming protein which represents a perfect target antigen for vaccines or immunotherapies. Heat shock proteins (HSPs) facilitate cellular immune responses to antigenic peptides or proteins bound to them. Regarding to previous studies, vaccination with purified HSP/antigen complexes efficiently elicit antigen-specific immune responses in mice model. The N-terminal of glycoprotein 96 (NT-gp96) has adjuvant effect and can induce effective cumulative immune response against clinical disorders, especially cancers. In this study, the recombinant HPV16 E7 and E7 linked to NT-gp96 (E7-NT-gp96) proteins were generated in prokaryotic expression system. Mice were vaccinated twice with this recombinant proteins and the immunogenicity of the fusion protein was determined. The preventive efficacy of E7-NT-gp96 fusion protein was also evaluated and compared to E7 protein after challenging with cancerous TC-1 cell line. In vitro re-stimulated splenocytes of mice vaccinated with rE7-NT-gp96 protein induced higher IFN-γ response in comparison with E7 protein immunization. Moreover, immunization with E7-NT-gp96 protein displayed low but stable humoral responses at post-challenge time. The data showed that vaccination with fused E7-NT-gp96 protein delayed the tumour occurrence and growth as compared to protein E7 alone. These results suggest that fused adjuvant-free E7-NT-gp96 protein vaccination could direct the immune responses towards Th1 immunity. Furthermore, the linkage of NT-gp96 to E7 could enhance protective anti-tumour immunity.
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Affiliation(s)
- E Mohit
- Molecular Immunology and Vaccine Research Laboratory, Pasteur Institute of Iran, Tehran, Iran
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14
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Virdi AS, Pareek A, Singh P. Evidence for the possible involvement of calmodulin in regulation of steady state levels of Hsp90 family members (Hsp87 and Hsp85) in response to heat shock in sorghum. PLANT SIGNALING & BEHAVIOR 2011; 6:393-9. [PMID: 21336025 PMCID: PMC3142421 DOI: 10.4161/psb.6.3.13867] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 09/17/2010] [Accepted: 10/05/2010] [Indexed: 05/09/2023]
Abstract
Pharmacological studies, using Ca(2+) channel blockers (LaCl 3 and verapamil) and calmodulin (CaM) antagonists (CPZ and W7), were carried out to understand the role of Ca(2+)/CaM in the regulation of heat shock-induced expression of Hsp90 (Hsp87 and Hsp85) and Hsp70 (Hsp75 and Hsp73) members in sorghum. It was observed that the expression of both Hsp87 and Hsp85 proteins was decreased in presence of Ca ( 2+) channel blockers and CaM antagonists, under both control and heat stress conditions, as contrary to the steady state levels of Hsp75 and Hsp73, which were not affected significantly under similar conditions. Further, the exposure of sorghum seedlings to geldanamycin, a specific inhibitor of Hsp90, resulted in induction of Hsp87 and Hsp85 in the absence of heat shock also. This study provides the first evidence suggesting that in plants, the in vivo expression of Hsp90 (Hsp87 and Hsp85) is likely to be modulated by Ca(2+)/CaM under normal and thermal stress conditions. The likely implications of these findings are discussed.
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Affiliation(s)
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory; School of Life Sciences; Jawaharlal Nehru University; New Delhi, India
| | - Prabhjeet Singh
- Department of Biotechnology; Guru Nanak Dev University; Amritsar, Punjab India
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Gauci VJ, Wright EP, Coorssen JR. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol 2011; 4:3-29. [PMID: 21686332 PMCID: PMC3022124 DOI: 10.1007/s12154-010-0043-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/02/2010] [Indexed: 11/28/2022] Open
Abstract
Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist.
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Affiliation(s)
- Victoria J. Gauci
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Elise P. Wright
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Jens R. Coorssen
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
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Wang X, Hwang SY, Cong WT, Jin LT, Choi JK. Promoted negative staining of proteins in SDS-PAGE using Eosin B compounded with magnesium chloride. Electrophoresis 2010; 31:3808-15. [DOI: 10.1002/elps.201000343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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di Clemente N, Jamin SP, Lugovskoy A, Carmillo P, Ehrenfels C, Picard JY, Whitty A, Josso N, Pepinsky RB, Cate RL. Processing of anti-mullerian hormone regulates receptor activation by a mechanism distinct from TGF-beta. Mol Endocrinol 2010; 24:2193-206. [PMID: 20861221 DOI: 10.1210/me.2010-0273] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
TGF-β family ligands are translated as prepropeptide precursors and are processed into mature C-terminal dimers that signal by assembling a serine/threonine kinase receptor complex containing type I and II components. Many TGF-β ligands are secreted in a latent form that cannot bind their receptor, due to the pro-region remaining associated with the mature ligand in a noncovalent complex after proteolytic cleavage. Here we show that anti-Müllerian hormone (AMH), a TGF-β family ligand involved in reproductive development, must be cleaved to bind its type II receptor (AMHRII), but dissociation of the pro-region from the mature C-terminal dimer is not required for this initial interaction. We provide direct evidence for this interaction by showing that the noncovalent complex binds to a soluble form of AMHRII in an ELISA format and to AMHRII immobilized on Sepharose. Binding of the noncovalent complex to Sepharose-coupled AMHRII induces dissociation of the pro-region from the mature C-terminal dimer, whereas no dissociation occurs after binding to immobilized AMH antibodies. The pro-region cannot be detected after binding of the AMH noncovalent complex to AMHRII expressed on COS cells, indicating that pro-region dissociation may occur as a natural consequence of receptor engagement on cells. Moreover, the mature C-terminal dimer is more active than the noncovalent complex in stimulating Sma- and Mad-related protein activation, suggesting that pro-region dissociation contributes to the assembly of the active receptor complex. AMH thus exemplifies a new mechanism for receptor engagement in which interaction with the type II receptor promotes pro-region dissociation to generate mature ligand.
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Affiliation(s)
- Nathalie di Clemente
- Institut National de la Santé et de la Recherche Médicale U782, 32 rue des Carnets, Clamart F-92140, France
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Cong WT, Hwang SY, Jin LT, He HZ, Choi JK. High-throughput negative detection of SDS-PAGE separated proteins and its application for proteomics. Electrophoresis 2010; 31:411-20. [DOI: 10.1002/elps.200900472] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Avanzo P, Sabotič J, Anžlovar S, Popovič T, Leonardi A, Pain RH, Kos J, Brzin J. Trypsin-specific inhibitors from the basidiomycete Clitocybe nebularis with regulatory and defensive functions. Microbiology (Reading) 2009; 155:3971-3981. [DOI: 10.1099/mic.0.032805-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We have isolated serine protease inhibitors from the basidiomycete Clitocybe nebularis, CnSPIs, using trypsin affinity chromatography. Full-length gene and cDNA sequences were determined for one of them, named cnispin, and the recombinant protein was expressed in Escherichia coli at high yield. The primary structure and biochemical properties of cnispin are very similar to those of the Lentinus edodes serine protease inhibitor, until now the only member of the I66 family of protease inhibitors in the MEROPS classification. Cnispin is highly specific towards trypsin, with K
i in the nanomolar range. It also exhibited weaker inhibition of chymotrypsin and very weak inhibition of subtilisin and kallikrein; other proteases were not inhibited. Inhibitory activity against endogenous proteases from C. nebularis revealed a possible regulatory role for CnSPIs in the endogenous proteolytic system. Another possible biological function in defence against predatory insects was indicated by the deleterious effect of CnSPIs on the development of larvae of Drosophila melanogaster. These findings, together with the biochemical and genetic characterization of cnispin, suggest a dual physiological role for this serine protease inhibitor of the I66 MEROPS family.
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Affiliation(s)
- Petra Avanzo
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Jerica Sabotič
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Sabina Anžlovar
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Tatjana Popovič
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Adrijana Leonardi
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Roger H. Pain
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Janko Kos
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Jože Brzin
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
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20
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Rabilloud T, Vaezzadeh AR, Potier N, Lelong C, Leize-Wagner E, Chevallet M. Power and limitations of electrophoretic separations in proteomics strategies. MASS SPECTROMETRY REVIEWS 2009; 28:816-843. [PMID: 19072760 DOI: 10.1002/mas.20204] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed.
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21
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Lin CY, Wang V, Shui HA, Juang RH, Hour AL, Chen PS, Huang HM, Wu SY, Lee JC, Tsai TL, Chen HM. A comprehensive evaluation of imidazole-zinc reverse stain for current proteomic researches. Proteomics 2009; 9:696-709. [PMID: 19137546 DOI: 10.1002/pmic.200700470] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this paper, we comprehensively evaluated the capability of imidazole-zinc reverse stain (ZN) in comparative proteomics. Three commonly used protein gel staining methods, including silver (SN), SYPRO Ruby (SR), and CB stain were investigated alongside for comparison purpose. A transparency scanning procedure, which may deliver more even and contrasting gel images, was found best for documenting ZN stained gels. Our results showed that ZN was more sensitive than SN, SR, and CB. It may reveal as few as 1.8 ng of proteins in a gel. Moreover, ZN was found to provide a linear dynamic range of staining for revealing proteins up to 140 ng, and show an insignificant staining preference. To analyze a ZN stained 2-D gel image that generally comprises an apparent but even background, the Melanie 4 software was found more suitable than others. Furthermore, ZN demonstrated an equivalent or better MS compatibility than the other three staining methods. Intense and comprehensive MS profiles were frequently observed for ZN stained gel spots. Approximate two-third of ZN stained gel spots were successfully identified for protein identities. Taken together, our results suggest that the prompt, cost effective and versatile ZN is well suited for current proteomic researches.
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Affiliation(s)
- Ching-Yu Lin
- Graduate Institute of Applied Science and Engineering, Catholic Fu-Jen University, Taipei, Taiwan, Republic of China
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22
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Kimura S, Shiraiwa Y, Suzuki I. Function of the N-terminal region of the phosphate-sensing histidine kinase, SphS, in Synechocystis sp. PCC 6803. MICROBIOLOGY-SGM 2009; 155:2256-2264. [PMID: 19389760 DOI: 10.1099/mic.0.028514-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In Synechocystis sp. PCC 6803 the histidine kinase SphS (sll0337) is involved in transcriptional activation of the phosphate (Pi)-acquisition system which includes alkaline phosphatase (AP). The N-terminal region of SphS contains both a hydrophobic region and a Per-Arnt-Sim (PAS) domain. The C-terminal region has a highly conserved transmitter domain. Immunological localization studies on heterologously expressed SphS in Escherichia coli indicate that the hydrophobic region is important for membrane localization. In order to evaluate the function of the N-terminal region of SphS, deletion mutants under the control of the native promoter were analysed for in vivo AP activity. Deletion of the N-terminal hydrophobic region resulted in loss of AP activity under both Pi-deficient and Pi-sufficient conditions. Substitution of the hydrophobic region of SphS with that from the Ni2+-sensing histidine kinase, NrsS, resulted in the same induction characteristics as SphS. Deletion of the PAS domain resulted in the constitutive induction of AP activity regardless of Pi availability. To characterize the PAS domain in more in detail, four amino acid residues conserved in the PAS domain were substituted with Ala. Among the mutants R121A constitutively expressed AP activity, suggesting that R121 is important for the function of the PAS domain. Our observations indicated that the presence of a transmembrane helix in the N-terminal region of SphS is critical for activity and that the PAS domain is involved in perception of Pi availability.
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Affiliation(s)
- Satoshi Kimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8572 Japan
| | - Yoshihiro Shiraiwa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8572 Japan
| | - Iwane Suzuki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8572 Japan
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23
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Hellman J. Stabilization of thin-layer agarose gels after isoelectric focusing with polyacrylamide enables reverse imidazole-zinc staining and facilitates two-dimensional gel electrophoresis. Anal Bioanal Chem 2008; 392:239-45. [DOI: 10.1007/s00216-008-2247-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 05/21/2008] [Accepted: 06/12/2008] [Indexed: 11/29/2022]
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24
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Wu SY, Chin LT, Chen LM, Chen HM. Direct visualization of fluorescent signals in protein gels using a backlit blue light plate. Proteomics 2008; 8:3382-8. [DOI: 10.1002/pmic.200701013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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25
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Rafati S, Zahedifard F, Azari MK, Taslimi Y, Taheri T. Leishmania infantum: Prime boost vaccination with C-terminal extension of cysteine proteinase type I displays both type 1 and 2 immune signatures in BALB/c mice. Exp Parasitol 2008; 118:393-401. [DOI: 10.1016/j.exppara.2007.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 09/27/2007] [Accepted: 10/02/2007] [Indexed: 10/22/2022]
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26
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Hellman J. Polyacrylamide lamination enables mass spectrometry compatible staining and in-gel digestion of proteins separated by agarose IEF. Proteomics 2007; 7:3441-4. [PMID: 17722206 DOI: 10.1002/pmic.200700299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Agarose IEF enables the separation of large proteins and protein complexes. A complication of agarose gels attached onto polyester support is the lack of sensitive protein staining methods compatible with protein analysis and identification protocols. In this study, agarose IEF gels were used to separate the proteins, followed by layering the agarose with polyacrylamide. The formed laminate gels were seamless and durable and they were readily detached from the polyester. The gels were amenable to MS compatible staining. The sensitivity obtained with the acidic silver staining method was 20-50 ng/band of myoglobin. Laminated agarose was a suitable matrix for in-gel digestion based generation of tryptic peptides for MALDI-MS.
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Affiliation(s)
- Jukka Hellman
- University of Turku, Department of Biochemistry and Food Chemistry/Biotechnology, Turku, Finland.
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27
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Chiou YY, Lin WJ, Fu SL, Lin CH. Direct mass-spectrometric identification of Arg296 and Arg299 as the methylation sites of hnRNP K protein for methyltransferase PRMT1. Protein J 2007; 26:87-93. [PMID: 17191129 DOI: 10.1007/s10930-006-9049-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein methylation is one of the most important post-translational modifications that contribute to the diversity and complexity of proteome. Here we report the study of in vitro methylation of heterogeneous nuclear ribonucleoprotein K (hnRNP K) with protein arginine methyltransferase 1 (PRMT1), as an enzyme, and S-adenosyl-L-methionine (SAM), as a methyl donor. The mass analysis of tryptic peptides of hnRNP K before and after methylation reveals the addition of four methyl groups in the residues 288-303. Tandem mass-spectrometric analysis of this peptide shows that both Arg296 and Arg299 are dimethylated. In addition, fragmentation analysis of such methylated arginines illustrate that they are both asymmetric dimethylarginines. Since Arg296 and Arg299 are located near the SH3-binding domains of hnRNP K, such methylation has the potential in regulating the interaction of hnRNP K with Src protein family. Our results provide crucial information for further functional study of hnRNP K methylation.
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Affiliation(s)
- Yi-Ying Chiou
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan
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28
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López-Castejón G, Sepulcre MP, Mulero I, Pelegrín P, Meseguer J, Mulero V. Molecular and functional characterization of gilthead seabream Sparus aurata caspase-1: the first identification of an inflammatory caspase in fish. Mol Immunol 2007; 45:49-57. [PMID: 17610954 DOI: 10.1016/j.molimm.2007.05.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 05/14/2007] [Accepted: 05/15/2007] [Indexed: 10/23/2022]
Abstract
Caspases are a family of cysteine proteases that fulfil critical roles in mammalian apoptosis and in the proteolytic activation of cytokines. In humans, the caspase family includes 13 members whose functions seem to correlate with their phylogenetic relationship. They are classified into two main groups, the cell death (apoptotic) and the inflammatory caspases. Caspase-1 is the best characterized inflammatory caspase and is responsible for the processing of interleukin-1beta (IL-1beta), IL-18 and IL-33. Despite the importance of caspase-1 in inflammation, no information is available on the presence and activity of this enzyme in fish. In this study, we cloned a caspase-1-like gene from the bony fish gilthead seabream (Sparus aurata L.) which shows a conserved N-terminal caspase-recruitment domain (CARD) and a C-terminal caspase catalytic domain. The seabream caspase-1 gene was expressed in 1 day post-hatching larvae and its mRNA levels increased throughout development. In adult fish, caspase-1 was found to be constitutively expressed in all immune tissues analyzed and, unexpectedly, infection of fish and stimulation of professional phagocytes in vitro decreased its mRNA levels. It was also demonstrated that the recombinant seabream caspase-1 ectopically expressed in HEK293 cells was able to cleave a caspase-1 specific substrate, this activity being enhanced upon activation of the rat P2X7 receptor with BzATP. Finally, seabream fibroblast cell line SAF-1 and primary leukocytes showed endogenous caspase-1 activity, which was almost completely inhibited by a caspase-1 specific inhibitor.
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Affiliation(s)
- Gloria López-Castejón
- Department of Cell Biology, Faculty of Biology, University of Murcia, 30100 Murcia, Spain
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29
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Castellanos-Serra L, Hardy E. Negative detection of biomolecules separated in polyacrylamide electrophoresis gels. Nat Protoc 2007; 1:1544-51. [PMID: 17406447 DOI: 10.1038/nprot.2006.233] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Here we describe the protocols for negative or reverse detection of proteins, nucleic acids and lipopolysaccharides separated in polyacrylamide electrophoresis gels. These protocols are based on the selective synthesis and precipitation of a white imidazole-zinc complex in the gel, which is absent from those zones where biomolecules are located. These methods are highly sensitive (1-10 ng of biomolecules per band), very cheap as they use inexpensive, common laboratory reagents (imidazole and a Zn II salt), rapid (less than 20 min after gel washing), robust and simple (two steps). Reverse-stained biomolecules are reversibly fixed in the gel. After brief incubation in a zinc chelating agent, biomolecules can be recovered from the gel with the same efficiency as from unstained gels. In consequence, they are procedures of choice for micropreparative applications. References covering typical applications are included.
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Affiliation(s)
- Lila Castellanos-Serra
- Division of Physical Chemistry, Center for Genetic Engineering and Biotechnology, Havana, Cuba
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30
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Khodak YA, Koroleva ON, Drutsa VL. A system for heterologous expression and isolation of Escherichia coli RNA polymerase and its components. BIOCHEMISTRY (MOSCOW) 2007; 72:178-87. [PMID: 17367295 DOI: 10.1134/s0006297907020071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A set of plasmid vectors for expression of all major Escherichia coli RNA polymerase subunits as fusion proteins with intein- and chitin-binding domains, allowing protein purification in accordance with IMPACT technology, was constructed. It is demonstrated that the fusion subunits alpha, beta or beta' in conjunction with the natural subunits alpha, beta, beta', and sigma can participate in RNA polymerase assembly in vivo, providing affinity-based isolation of the enzyme. Functional activity of the enzyme preparations was demonstrated in the experiments on in vitro transcription and promoter complex formation. With the use of IMPACT technology, sigma(70) subunit can be isolated as an individual protein without admixture of RNA polymerase.
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Affiliation(s)
- Yu A Khodak
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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31
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Rafati S, Gholami E, Hassani N, Ghaemimanesh F, Taslimi Y, Taheri T, Soong L. Leishmania major heat shock protein 70 (HSP70) is not protective in murine models of cutaneous leishmaniasis and stimulates strong humoral responses in cutaneous and visceral leishmaniasis patients. Vaccine 2007; 25:4159-69. [PMID: 17395340 DOI: 10.1016/j.vaccine.2007.03.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 02/28/2007] [Accepted: 03/05/2007] [Indexed: 11/17/2022]
Abstract
Heat shock proteins (HSP) are highly conserved molecules that play important roles in protein folding, assembly of protein complexes and translocation of proteins across cellular compartments, as well as in several immunological processes. In this study, we first immunized susceptible BALB/c and resistant C57BL/6 mice with the complete open-reading frame of Leishmania HSP-70 (pcDNA-HSP70) and boosted mice with rHSP-70 (amino acid 221-604 cloned in pQE-HSP70 and referred to as rHSP70) mixed with Montanide 720. When we evaluated the effects of HSP70 in both mouse strains, we found that the entire fragment (amino acids 221-604) and rCT-HSP70 (amino acids 491-604 cloned in pQE-CT), but not rNT-HSP70 (amino acids 221-291 cloned pQE-NT), contained the highest immunogenicity. However, after infectious challenge with Leishmania major, no efficient protective responses were observed in either mouse strain. The humoral immune responses against the different truncated forms of HSP70 suggested a mixed TH1/TH2 response in vivo. We then assessed infected susceptible and resistant mice for lymphoproliferative and cytokine responses against the truncated forms of HSP70. At 9-week post-infection, we observed no differences in those responses between vaccinated and control mice. Next, we initiated comparative studies in human patient samples, finding no significant proliferation against all three truncated forms of HSP70 in the cellular immune responses of 16 cured cutaneous leishmaniasis patients and 5 normal individuals. Sera from active cutaneous and visceral leishmaniasis patients, however, were reactive to all three forms of HSP70. This study demonstrates the potential of HSP70 in stimulating humoral responses in humans and mice and indicates there is a need to further explore and examine the value of this important molecule in the control of leishmaniasis.
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MESH Headings
- Adjuvants, Immunologic/pharmacology
- Animals
- Antibodies, Protozoan/blood
- Antigens, Protozoan/genetics
- Antigens, Protozoan/immunology
- Antigens, Protozoan/isolation & purification
- Cell Proliferation
- Cells, Cultured
- Cytokines/biosynthesis
- Disease Models, Animal
- Female
- HSP70 Heat-Shock Proteins/genetics
- HSP70 Heat-Shock Proteins/immunology
- HSP70 Heat-Shock Proteins/isolation & purification
- Humans
- Immunoglobulin G/blood
- Iran
- Leishmania major/immunology
- Leishmaniasis, Cutaneous/immunology
- Leishmaniasis, Cutaneous/prevention & control
- Leishmaniasis, Visceral/immunology
- Lymphocytes/cytology
- Mannitol/analogs & derivatives
- Mannitol/pharmacology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Oleic Acids/pharmacology
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/isolation & purification
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Affiliation(s)
- Sima Rafati
- Molecular Immunology and Vaccine Research Lab, Pasteur Institute of Iran, Tehran, Iran.
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32
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Vennestrøm J, Jensen PM. Ixodes ricinus: the potential of two-dimensional gel electrophoresis as a tool for studying host-vector-pathogen interactions. Exp Parasitol 2006; 115:53-8. [PMID: 16904668 DOI: 10.1016/j.exppara.2006.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 05/25/2006] [Accepted: 05/29/2006] [Indexed: 11/16/2022]
Abstract
Ixodes ricinus is a three-host tick, with three active instars. For moulting to occur the tick has to find a host where it can take a blood meal. Throughout feeding I. ricinus can be infected or infect the host with different pathogens, e.g., Tick-Borne Encephalitis virus or Borrelia burgdorferi. The host-vector-pathogen interaction is very complex, making a detailed study difficult. Here we analyse the potential of two-dimensional gel electrophoresis (2DE) to study the host-vector-pathogen interaction. We examined 20 nymphs, which as larvae parasitised either mouse or hen. After moulting, they were kept alive for up to 30 weeks, to analyse whether tick ageing influenced host determination, and for comparison of the 2D-gels. Even though the number of proteins in the gel decreased during ageing, some proteins of the host determination persisted for all 30 weeks. We also discovered persisting proteins in relation to nymphs. These findings showed that 2DE is suitable as a tool for studying host-vector-pathogen interactions.
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Affiliation(s)
- J Vennestrøm
- Department of Genetics and Microbiology, The Royal Veterinary and Agricultural University, Frederiksberg, Denmark.
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33
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Rafati S, Zahedifard F, Nazgouee F. Prime-boost vaccination using cysteine proteinases type I and II of Leishmania infantum confers protective immunity in murine visceral leishmaniasis. Vaccine 2005; 24:2169-75. [PMID: 16325969 DOI: 10.1016/j.vaccine.2005.11.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Accepted: 11/01/2005] [Indexed: 11/26/2022]
Abstract
Vaccination with a cocktail of DNA encoding cysteine proteinases has been previously shown to confer protection against experimental cutaneous leishmaniasis (CL). In the present study we test the efficacy of immunization against Leishmania infantum in a murine model of infection, using a prime-boost strategy. BALB/c mice were immunized twice, in a 3 weeks interval, with cocktail of plasmids DNA encoding type I (cpb) and II (cpa) cysteine proteinases. DNA immunization was then followed by a boost with rCPA/rCPB in addition to CpG ODN and Montanide720 as adjuvant. Analysis of the immune response showed that vaccination mainly elicited antigen-specific IgG2a antibodies, suggesting the induction of a Th1 immune response. This was further confirmed by the analysis of the splenic cytokine production: at all time points the ratio of IFN-gamma/IL-5 induced upon restimulation with rCPA and rCPB was always significantly higher in vaccinated group compared to both control groups.
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Affiliation(s)
- Sima Rafati
- Molecular Immunology and Vaccine Research Lab., Pasteur Institute of Iran, P.O. Box 11365-6699, Tehran, Iran.
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34
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Takiya S, Ishikawa T, Ohtsuka K, Nishita Y, Suzuki Y. Fibroin-modulator-binding protein-1 (FMBP-1) contains a novel DNA-binding domain, repeats of the score and three amino acid peptide (STP), conserved from Caenorhabditis elegans to humans. Nucleic Acids Res 2005; 33:786-95. [PMID: 15687387 PMCID: PMC548367 DOI: 10.1093/nar/gki228] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 01/18/2004] [Accepted: 01/18/2004] [Indexed: 11/13/2022] Open
Abstract
The predicted transcriptional regulatory factor for the fibroin gene of the silkworm Bombyx mori, fibroin-modulator-binding protein-1 (FMBP-1), was purified by sequential DNA affinity column chromatography, and cDNA clones corresponding to FMBP-1 were isolated from a library. The N-terminal half of FMBP-1 has a weak similarity to the DNA-binding domain of several transcriptional regulatory factors in higher plants. The C-terminal half contains four tandem repeats of a novel 23 amino acid motif, which we named the score and three amino acid peptide (STP). Other genes containing STP repeats were found in Drosophila, Caenorhabditis elegans, mouse and human. Mutational analysis of FMBP-1 showed that the STP repeats form a novel DNA-binding domain. Sequences flanking STP repeats modulated DNA-binding activity. The FMBP-1 gene was expressed during the fourth to fifth instar. FMBP-1 activity appeared to be regulated at the transcriptional level and by the post-transcriptional modification.
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Affiliation(s)
- Shigeharu Takiya
- Center for Advanced Science and Technology and Hokkaido UniversityNorth 10, West 8, Kita-ku, Sapporo 060-0810, Japan
- Graduate School of Environmental Earth Science, Hokkaido UniversityNorth 10, West 8, Kita-ku, Sapporo 060-0810, Japan
| | - Tetsurou Ishikawa
- Graduate School of Environmental Earth Science, Hokkaido UniversityNorth 10, West 8, Kita-ku, Sapporo 060-0810, Japan
| | - Katsuya Ohtsuka
- Graduate School of Environmental Earth Science, Hokkaido UniversityNorth 10, West 8, Kita-ku, Sapporo 060-0810, Japan
| | - Yoshinori Nishita
- Center for Advanced Science and Technology and Hokkaido UniversityNorth 10, West 8, Kita-ku, Sapporo 060-0810, Japan
| | - Yoshiaki Suzuki
- National Institute for Basic BiologyNishigo-naka 38, Okazaki 444-8585, Japan
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35
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Hardy E, Castellanos-Serra LR. "Reverse-staining" of biomolecules in electrophoresis gels: analytical and micropreparative applications. Anal Biochem 2004; 328:1-13. [PMID: 15081901 DOI: 10.1016/j.ab.2004.02.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Negative or reverse staining using imidazole and zinc salts for protein detection in electrophoresis gels was originally introduced in 1990. The method is based on the selective precipitation of zinc imidazolate in the gel except in the zones where proteins are located. The method was later adapted to allow high-sensitivity negative detection of nucleic acids and bacterial lipopolysaccharides. It provides a practically quantitative recovery of intact biomolecules and is a method of choice for micropreparative applications of gel electrophoresis to proteomics and similar structural studies. Zinc-mediated protein fixation in the gel is fully reversible and the eluted biomolecules are neither chemically modified nor contaminated with organic dyes. Here we present a detailed compilation of practical methods for implementing these techniques with emphasis in their analytical or micropreparative applications.
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Affiliation(s)
- Eugenio Hardy
- Center for Genetic Engineering and Biotechnology, Division of Physical Chemistry, P.O. Box 6162, Havana City, Cuba
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36
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Zadeh-Vakili A, Taheri T, Taslimi Y, Doustdari F, Salmanian AH, Rafati S. Immunization with the hybrid protein vaccine, consisting of Leishmania major cysteine proteinases Type I (CPB) and Type II (CPA), partially protects against leishmaniasis. Vaccine 2004; 22:1930-40. [PMID: 15121305 DOI: 10.1016/j.vaccine.2003.11.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2003] [Accepted: 11/06/2003] [Indexed: 11/28/2022]
Abstract
Cysteine proteinases (CPs) are enzymes that belong to the papain superfamily, which are found in a number of organisms from prokaryotes to mammals. On the parasitic protozoan Leishmania, extensive studies have shown that CPs are involved in parasite survival, replication and the onset of disease, and have, therefore, been considered as attractive drugs and/or vaccine targets for the control of leishmaniasis. We have previously shown that cysteine proteinases, Type I (CPB) and Type II (CPA), in Leishmania major (L. major), delivered as recombinant proteins or in plasmid DNA, induce partial protection against infection with the parasite in BALB/c mice. We had shown that the level of protection was greater if a cocktail of cpa and cpb containing DNA constructs was used. Therefore, to reduce the costs associated with the production of these vaccine candidates, a construct was developed, whereby the cpa and cpb genes were fused together to give rise to a single hybrid protein. The genes were fused in tandem where the C-terminal extension (CTE), encoding region of CPB, was located at the 3' of the fused genes, and ultimately expressed in the bacterial expression construct pET-23a. The expression of the CPA/B hybrid protein (60 kDa) was verified using rabbit anti-CPA and anti-CPB antibodies by SDS-PAGE and immunoblotting. The protective potential of the CPA/B hybrid protein against the infection with Leishmania was then assessed in BALB/c mice. The animals were vaccinated with CPA/B, challenged with live L. major promastigotes, and the degree of protection was examined by measuring footpad lesion sizes. It was found that there was a delay in the expansion of lesions size compared to control groups. Furthermore, an immunological analysis of antibody isotypes, before and after infection, showed high levels of IgG2a compared to IgG1 (more than five-fold) in the CPA/B hybrid protein vaccinated group. In addition, a predominant Th1 immune response characterized by in vitro IFN-gamma production was observed, along with little, if any, IL-5 production. This finding indicates that the hybrid CPA/B is able to elicit a protective immune response against L. major in the mice model. In addition, 54% of individuals tested, who had recovered from cutaneous leishmaniasis, produced more than 50 pg/ml IFN-gamma, in response to the CPA/B hybrid protein in an in vitro assay, demonstrating the importance of cysteine proteinases as targets of immune response in humans.
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Affiliation(s)
- Azita Zadeh-Vakili
- Department of Immunology, Pasteur Institute of Iran, P.O. Box 11365-6699, Tehran, Iran
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Pelegrín P, Chaves-Pozo E, Mulero V, Meseguer J. Production and mechanism of secretion of interleukin-1beta from the marine fish gilthead seabream. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2004; 28:229-237. [PMID: 14642889 DOI: 10.1016/j.dci.2003.08.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Mammalian interleukin-1beta (IL-1beta) is a secretory cytokine lacking a signal peptide, which does not follow the classical endoplasmic reticulum to Golgi pathway of secretion. Its post-translational processing by IL-1beta-converting enzyme (ICE) and subsequent release from activated macrophages requires ATP acting on P2X7 receptors. Little information is available on the production and release of fish IL-1beta, but the IL-1beta gene sequences reported to date lack a conserved ICE recognition site. We show for the first time that lipopolysaccharide (LPS)/macrophage-activating factor/bacterial DNA (VaDNA)-primed immune cells of the marine fish gilthead seabream (Sparus aurata) accumulate intracellular IL-1beta as a approximately 30 kDa polypeptide (proIL-1beta). The combination of LPS and VaDNA was found to be synergistic, suggesting that each ligand is recognized by a different pattern recognition receptor. More importantly, addition of extracellular ATP does not promote IL-1beta secretion by immune cells and fails to induce phosphatidylserine flip. In contrast, gilthead seabream SAF-1 fibroblasts shed microvesicles containing a 22 kDa IL-1beta form within 30 min of activation with ATP. Notably, the post-translational processing of IL-1beta by SAF-1 cells is abrogated by a specific ICE inhibitor.
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Affiliation(s)
- Pablo Pelegrín
- Department of Cell Biology, Faculty of Biology, University of Murcia, Campus Universitario de Espinardo, 30100, Murcia, Spain
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Nakhaee A, Taheri T, Taghikhani M, Mohebali M, Salmanian AH, Fasel N, Rafati S. Humoral and cellular immune responses against Type I cysteine proteinase of Leishmania infantum are higher in asymptomatic than symptomatic dogs selected from a naturally infected population. Vet Parasitol 2004; 119:107-23. [PMID: 14746971 DOI: 10.1016/j.vetpar.2003.11.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Canids are natural reservoirs of Leishmania infantum and have been promoted as experimental hosts to decipher the pathogenesis of human visceral leishmaniasis (VL). In this study, the presence of IgG antibodies as well as the presence of mononuclear leukocytes reactive to different cysteine proteinases (CPs) were examined in 13 L. infantum-infected dogs (six with symptoms, seven asymptomatic). Cysteine proteinases which belong to papain-like enzymes known as clan CA are the most studied CPs of parasite protozoa. These molecules are expressed by the intracellular stages of the parasite and could be immunogenic. We studied Type II CP (CPA) and Type I CP (CPB) with its long C-terminal extension (CTE) which could be highly immunogenic. We showed that the level of antibodies reactive to rCPA is low in both symptomatic and asymptomatic dogs. In contrast, when CPB and CTE were used as antigens, the level of total IgG (with IgG2 superior to IgG1) reached higher values in asymptomatic dogs than in dogs with VL. While the peripheral blood mononuclear cell (PBMC) reactivity was significant when cultured in the presence of freezed/thawed (F/T) lysate, it remained low in presence of CP although always higher for PBMC recovered from asymptomatic dogs. We showed the importance of CPB and CTE in particular as a target of immune response and their potential use for serodiagnosis in asymptomatic dogs.
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Affiliation(s)
- Alireza Nakhaee
- Department of Clinical Biochemistry, School of Medical Sciences, Tarbiat Modarres University, Tehran, Iran
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Mádi A, Pusztahelyi T, Punyiczki M, Fésüs L. The biology of the post-genomic era: the proteomics. ACTA BIOLOGICA HUNGARICA 2003; 54:1-14. [PMID: 12705317 DOI: 10.1556/abiol.54.2003.1.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The complete identification of coding sequences in a number of species has led to announce the beginning of the post-genomic era, new tools have become available to study complex phenomena in biological systems. Rapid advances in genomic sequencing and bioinformatics have established the field of genomics to investigate thousands genes' activity through mRNA display. However, recent studies have demonstrated a lack of correlation between the transcriptional profiles and the actual protein levels in cells, so investigation of the expressed part of the genome is also required to link genomic data to biological function. It is possible that evolutional development occured by increasing complexity of regulation processes at the level of RNA and protein molecules instead of simple increase in gene number, so investigation of proteins and protein complexes became important fields of our post-genomic era. High-resolution two-dimensional gels combined with sensitive mass spectrometry can reveal virtually all proteins present in cells opening new insights into functions of cells, tissues and whole organisms.
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Affiliation(s)
- A Mádi
- Signal Transduction and Apoptosis Research Group of the Hungarian Academy of Sciences, University of Debrecen, Nagyerdei krt. 98, H-4012 Debrecen, Hungary
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Rafati S, Nakhaee A, Taheri T, Ghashghaii A, Salmanian AH, Jimenez M, Mohebali M, Masina S, Fasel N. Expression of cysteine proteinase type I and II of Leishmania infantum and their recognition by sera during canine and human visceral leishmaniasis. Exp Parasitol 2003; 103:143-51. [PMID: 12880591 DOI: 10.1016/s0014-4894(03)00097-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this study, the mature domains of type I (CPB) and type II (CPA) cysteine proteinases (CPs) of Leishmania infantum were expressed and their immunogenic properties defined using sera from active and recovered cases of human visceral leishmaniasis and sera from infected dogs. Immunoblotting and ELISA analysis indicated that a freeze/thaw extract of parasite antigens showed similar and intensive recognition in both active cases of human and dog sera but lower recognition in recovered human individuals. The total IgG of actively infected human sera was higher than in recovered cases when rCPs were used as antigen. In contrast to dog sera, both active and recovered human cases have higher recognition toward rCPB than rCPA. Furthermore, the asymptomatic dogs in contrast to the symptomatic cases exhibited specific lymphocyte proliferation to both crude antigens and rCPs.
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Affiliation(s)
- Sima Rafati
- Department of Immunology, Pasteur Institute of Iran, Tehran, Iran.
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Shimamoto N. Assay for Movements of RNA Polymerase along DNA. Methods Enzymol 2003; 371:50-70. [PMID: 14712691 DOI: 10.1016/s0076-6879(03)71004-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Nobuo Shimamoto
- National Institute of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, 411-8540 Japan
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Abstract
Common strategies employed for general protein detection include organic dye, silver stain, radiolabeling, reverse stain, fluorescent stain, chemiluminescent stain and mass spectrometry-based approaches. Fluorescence-based protein detection methods have recently surpassed conventional technologies such as colloidal Coomassie blue and silver staining in terms of quantitative accuracy, detection sensitivity, and compatibility with modern downstream protein identification and characterization procedures, such as mass spectrometry. Additionally, specific detection methods suitable for revealing protein post-translational modifications have been devised over the years. These include methods for the detection of glycoproteins, phosphoproteins, proteolytic modifications, S-nitrosylation, arginine methylation and ADP-ribosylation. Methods for the detection of a range of reporter enzymes and epitope tags are now available as well, including those for visualizing beta-glucuronidase, beta-galactosidase, oligohistidine tags and green fluorescent protein. Fluorescence-based and mass spectrometry-based methodologies are just beginning to offer unparalleled new capabilities in the field of proteomics through the performance of multiplexed quantitative analysis. The primary objective of differential display proteomics is to increase the information content and throughput of proteomics studies through multiplexed analysis. Currently, three principal approaches to differential display proteomics are being actively pursued, difference gel electrophoresis (DIGE), multiplexed proteomics (MP) and isotope-coded affinity tagging (ICAT). New multiplexing capabilities should greatly enhance the applicability of the two-dimensional gel electrophoresis technique with respect to addressing fundamental questions related to proteome-wide changes in protein expression and post-translational modification.
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Affiliation(s)
- Wayne F Patton
- Proteomics Section, Biosciences Department, Molecular Probes, Inc., 4849 Pitchford Avenue, Eugene, OR 97402-9165, USA.
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Padmanabhan S, Elías-Arnanz M, Carpio E, Aparicio P, Murillo FJ. Domain architecture of a high mobility group A-type bacterial transcriptional factor. J Biol Chem 2001; 276:41566-75. [PMID: 11533063 DOI: 10.1074/jbc.m106352200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Myxococcus xanthus transcriptional factor CarD participates in carotenogenesis and fruiting body formation. It is the only reported prokaryotic protein having adjacent "AT-hook" DNA-binding and acidic regions characteristic of eukaryotic high mobility group A (HMGA) proteins. The latter are small, unstructured, nonhistone nuclear proteins that function as architectural factors to remodel DNA and chromatin structure and modulate various DNA binding activities. We find CarD to be predominantly dimeric with two stable domains: (a) an N-terminal domain of defined secondary and tertiary structure which is absent in eukaryotic HMGA proteins; (b) a C-terminal domain formed by the acidic and AT-hook segments and lacking defined structure. CarD, like HMGA proteins, binds specifically to the minor-groove of AT-rich DNA present in two appropriately spaced tracts. As in HMGA proteins, casein kinase II can phosphorylate the CarD acidic region, and this dramatically decreases the DNA binding affinity of CarD. The acidic region, in addition to modulating DNA binding, confers structural stability to CarD. We discuss how the structural and functional plasticity arising from domain organization in CarD could be linked to its role as a general transcriptional factor in M. xanthus.
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Affiliation(s)
- S Padmanabhan
- Departamento de Genética y Microbiologia and Area de Inmunologia, Universidad de Murcia, 30071 Murcia, Spain.
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Fehring V, Wandschneider S, Löhr M. Physical markers for landmarking fluorescently stained gels that facilitate automated spot-picking. Electrophoresis 2001; 22:2903-7. [PMID: 11565786 DOI: 10.1002/1522-2683(200108)22:14<2903::aid-elps2903>3.0.co;2-f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The quantitative comparison of spot patterns relies heavily on protein stains that do provide an appropriate dynamic range. Unfortunately most spot picking robot devices are still limited to nonfluorescent protein stains and the appropriate equipment is still quite expensive. These problems are solved by the application of a newly developed "GelMarker" that combines a spot picking robot device and a UV scanner. The "GelMarkers" are detectable in both the visible and UV range of light and permit the comparison of gel pictures taken by such different devices. The application of these "GelMarkers" together with the transformation of spot coordinates by using a "spot matching" procedure allows the automated excision of selected protein spots. The obtained picking accuracies are as good as those obtainable from visible stained gels due to the shape stability of the gels even over a longer time period.
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Affiliation(s)
- V Fehring
- Proteome Centre Rostock, University of Rostock, Germany
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Castellanos-Serra L, Hardy E. Detection of biomolecules in electrophoresis gels with salts of imidazole and zinc II: a decade of research. Electrophoresis 2001; 22:864-73. [PMID: 11332754 DOI: 10.1002/1522-2683()22:5<864::aid-elps864>3.0.co;2-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The proven ability of gel electrophoresis to simultaneously resolve, in a single experiment, many components from complex biological samples, has determined its preference over a variety of well-established chromatographic methods. Therefore, procedures placed at the interface between gel separation and microanalysis have earned increasing significance with respect to the overall success of the microanalytical strategy. The first of these procedures is the detection technique. The most important requirement for compatibility with further analysis or bioapplications is that the staining method does not compromise the chemical integrity and the biological properties of micropurified biomolecules. Procedures for negative detection of proteins with metal salts that have been proven to comply with this condition have been known for about 15 years. Only recently have these procedures been extended to the field of nucleic acids and lipopolysaccharides. The focus of this review is to chronicle the development and current status of the negative or reverse stain procedure based on the in-gel reaction of imidazole with zinc salts and its applications forthe micropurification and analysis of unmodified proteins, nucleic acids and bacterial lipopolysaccharides. We highlight the common aspects in the detection of the three types of biomolecules, and their applications to structural and biological analyses. Emphasis is given on the mechanism underlying imidazole-zinc staining, as it contributes to a deeper understanding of a general detection mechanism with metal salts. Finally, we discuss the latest applications of the techniques in proteomics and their possible impact on the characterization of gel-separated single components from complex lipopolysaccharides.
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Valdes I, Pitarch A, Gil C, Bermúdez A, Llorente M, Nombela C, Méndez E. Novel procedure for the identification of proteins by mass fingerprinting combining two-dimensional electrophoresis with fluorescent SYPRO red staining. JOURNAL OF MASS SPECTROMETRY : JMS 2000; 35:672-682. [PMID: 10862118 DOI: 10.1002/1096-9888(200006)35:6<672::aid-jms993>3.0.co;2-k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The fluorescent sensitive SYPRO Red dye was successfully employed to stain proteins in two-dimensional gels for protein identification by peptide mass fingerprinting. Proteins which are not chemically modified during the SYPRO Red staining process are well digested enzymatically in the gel and hence the resulting peptides can be efficiently eluted and analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A SYPRO Red two-dimensional gel of a complex protein extract from Candida albicans was analysed by MALDI-TOF MS. The validity of SYPRO Red staining was demonstrated by identifying, via peptide mass fingerprinting, 10 different C. albicans proteins from a total of 31 selected protein spots. The peptide mass signal intensity, the number of matched peptides and the percentage of coverage of protein sequences from SYPRO Red-stained proteins were similar to or greater than those obtained in parallel with the modified silver protein gel staining. This work demonstrates that fluorescent SYPRO Red staining is compatible with the identification of proteins separated on polyacrylamide gel and that it can be used as an alternative to silver staining. As far as we know, this is the first report in which C. albicans proteins separated using 2-D gels have been identified by peptide mass fingerprinting. The improved technique described here should be very useful for carrying out proteomic studies.
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Affiliation(s)
- I Valdes
- Unidad de Análisis Estructural de Proteínas, Centro Nacional de Biotecnología, E-28049 Madrid, Spain
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McGinley MD, Davis MT, Robinson JH, Spahr CS, Bures EJ, Beierle J, Mort J, Patterson SD. A simplified device for protein identification by microcapillary gradient liquid chromatography-tandem mass spectrometry. Electrophoresis 2000; 21:1678-84. [PMID: 10870954 DOI: 10.1002/(sici)1522-2683(20000501)21:9<1678::aid-elps1678>3.0.co;2-c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A simplified device and procedure have been developed for microcapillary gradient liquid chromatography-tandem mass spectrometry (LC-MS/MS). This procedure has proved useful in identifying low level quantities of proteins from sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel bands. Microelectrospray needles are packed with reversed-phase resin and function both as a high performance liquid chromatography (HPLC) column and a nanospray mass spectrometer tip when interfaced between an HPLC and ion trap mass spectrometer. Variable submicroliter flow rates are generated by flow splitting between the microelectrospray capillary and an HPLC system. A manual injector is used to inject a protein digest mixture that binds to the column and is then washed at a high flow rate (2 microL/min post split). Gradient elution of bound peptides was initiated by the injection of a filled loop of 70% v/v methanol (5 microL) concomitant with a reduction of flow rate (0.1 microL/min post split). This forms a diffusion-dependent gradient of variable length (typically 15-30 min in length) depending upon the final flow rate. Chromatographic separations of a standard solution digest demonstrate that this diffusion-dependent gradient provides reasonable separations such that multiple peptide identifications by MS/MS can be obtained. Application of this methodology to the analysis of several in-gel-digested gel-separated proteins is presented to demonstrate its utility.
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48
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Patton WF. A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 2000; 21:1123-44. [PMID: 10786886 DOI: 10.1002/(sici)1522-2683(20000401)21:6<1123::aid-elps1123>3.0.co;2-e] [Citation(s) in RCA: 198] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
As proteomics evolves into a high-throughput technology for the study of global protein regulation, new demands are continually being placed upon protein visualization and quantitation methods. Chief among these are increased detection sensitivity, broad linear dynamic range and compatibility with modern methods of microchemical analyses. The limitations of conventional protein staining techniques are increasingly being encountered as high sensitivity electrophoresis methods are interfaced with automated gel stainers, image analysis workstations, robotic spot excision instruments, protein digestion work stations, and mass spectrometers. Three approaches to fluorescence detection of proteins in two-dimensional (2-D) gels are currently practiced: covalent derivatization of proteins with fluorophores, intercalation of fluorophores into the sodium dodecyl sulfate (SDS) micelle, and direct electrostatic interaction with proteins by a Coomassie Brilliant Blue-type mechanism. This review discusses problems encountered in the analysis of proteins visualized with conventional stains and addresses advances in fluorescence protein detection, including immunoblotting, as well as the use of charge-coupled device (CCD) camera-based and laser-scanner-based image acquisition devices in proteomics.
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Affiliation(s)
- W F Patton
- Molecular Probes, Inc., Eugene, OR 97402, USA.
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49
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Patton WF. A thousand points of light: The application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 2000. [DOI: 10.1002/(sici)1522-2683(20000401)21:6%3c1123::aid-elps1123%3e3.0.co;2-e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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50
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Rabilloud T, Charmont S. Detection of Proteins on Two-Dimensional Electrophoresis Gels. ACTA ACUST UNITED AC 2000. [DOI: 10.1007/978-3-642-57105-3_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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