1
|
Gao L, Chen L, Peng Y, Zhao Y, Dong J, Mao Z, Jia J, Zhou Y. Iridium tetrazolato complexes as efficient protein staining agents. Dalton Trans 2022; 51:16870-16875. [DOI: 10.1039/d2dt02564g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iridium tetrazolato complexes have been illustrated as one kind of efficient protein staining agent.
Collapse
Affiliation(s)
- Ling Gao
- Department of Immunology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
- The Laboratory Center for Basic Medicine Sciences, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
| | - Luyao Chen
- Department of Immunology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
| | - Yu Peng
- Department of Immunology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
- The Laboratory Center for Basic Medicine Sciences, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
| | - Yibo Zhao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, Jiangsu, P.R. China
| | - Jianhua Dong
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, Jiangsu, P.R. China
| | - Ziwang Mao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, Jiangsu, P.R. China
| | - Junli Jia
- Department of Immunology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, Jiangsu, P.R. China
| | - Yuyang Zhou
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, Jiangsu, P.R. China
| |
Collapse
|
2
|
Oyama H, Ishii K, Maruno T, Torisu T, Uchiyama S. Characterization of Adeno-Associated Virus Capsid Proteins with Two Types of VP3-Related Components by Capillary Gel Electrophoresis and Mass Spectrometry. Hum Gene Ther 2021; 32:1403-1416. [PMID: 34082578 PMCID: PMC10112878 DOI: 10.1089/hum.2021.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recombinant adeno-associated virus is a leading platform in human gene therapy. The adeno-associated virus (AAV) capsid is composed of three viral proteins (VPs): VP1, VP2, and VP3. To ensure the safety of AAV-based gene therapy products, the stoichiometry of VPs of AAV vector should be carefully monitored. In this study, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, capillary gel electrophoresis (CGE), and liquid chromatography-UV-mass spectrometry (LC-UV-MS) were performed to evaluate the VP components of AAV1, AAV2, and AAV6. Two types of VP3-related components, VP3 variant and VP3 fragment, were identified. The VP3 variant was the N-terminal shorter VP3, of which the translation started at M211, not at the conventional initiation codon, M203. The VP3 variant could be generated by leaky scanning of the first initiation codon of VP3. We also showed that the VP3 variant was identified in a minor peak before VP3 in CGE measurement. Meanwhile, the VP3 fragment was the C-terminal cleaved VP3, of which the sequence of VP3 ended at D590 or D626, indicating that cleavage occurred between D590 and P591, or D626 and G627. The cause of the cleavage of the DP or DG sequence was hydrolysis due to low pH of the mobile phase and high temperature of the column oven in the LC system, which was necessary to clearly separate the peak of VPs. VP3 fragments, detected only in LC-UV-MS in small amount account with less than 3% of total peak area, should be included in the quantification of VP3. Finally, the relationship of VP stoichiometry determined by the above three methods was discussed. From this study, we proposed that the VP components of AAV should be complementarily evaluated by CGE and LC-UV-MS.
Collapse
Affiliation(s)
- Hiroaki Oyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Kentaro Ishii
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Tetsuo Torisu
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Myodaiji-cho, Japan
| |
Collapse
|
3
|
Carreño A, Gacitúa M, Solis-Céspedes E, Páez-Hernández D, Swords WB, Meyer GJ, Preite MD, Chávez I, Vega A, Fuentes JA. New Cationic fac-[Re(CO) 3(deeb)B2] + Complex, Where B2 Is a Benzimidazole Derivative, as a Potential New Luminescent Dye for Proteins Separated by SDS-PAGE. Front Chem 2021; 9:647816. [PMID: 33842435 PMCID: PMC8027506 DOI: 10.3389/fchem.2021.647816] [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: 12/30/2020] [Accepted: 01/29/2021] [Indexed: 01/14/2023] Open
Abstract
Sodium-dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) can be used to separate proteins based mainly on their size such as in denaturing gels. Different staining methods have been reported to observe proteins in the gel matrix, where the most used dyes are generally anionic. Anionic dyes allow for interactions with protonated amino acids, retaining the dye in the proteins. Fluorescent staining is an alternative technique considered to be sensitive, safe, and versatile. Some anionic complexes based on d6 transition metals have been used for this purpose, where cationic dyes have been less explored in this context. In this work, we synthesized and characterized a new monocationic rhenium complex fac-[Re(CO)3(deeb)B2]+ (where deeb is 4,4′-bis(ethoxycarbonyl)-2,2′-bpy and B2 is 2,4-di-tert-butyl-6-(3H-imidazo[4,5-c]pyridine-2-yl)phenol). We carried out a structural characterization of this complex by MS+, FTIR, 1H NMR, D2O exchange, and HHCOSY. Moreover, we carried out UV-Vis, luminescence, and cyclic voltammetry experiments to understand the effect of ligands on the complex’s electronic structure. We also performed relativistic theoretical calculations using the B3LYP/TZ2P level of theory and R-TDDFT within a dielectric continuum model (COSMO) to better understand electronic transitions and optical properties. We finally assessed the potential of fac-[Re(CO)3(deeb)B2]+ (as well as the precursor fac-Re(CO)3(deeb)Br and the free ligand B2) to stain proteins separated by SDS-PAGE. We found that only fac-[Re(CO)3(deeb)B2]+ proved viable to be directly used as a luminescent dye for proteins, presumably due to its interaction with negatively charged residues in proteins and by weak interactions provided by B2. In addition, fac-[Re(CO)3(deeb)B2]+ seems to interact preferentially with proteins and not with the gel matrix despite the presence of sodium dodecyl sulfate (SDS). In future applications, these alternative cationic complexes might be used alone or in combination with more traditional anionic compounds to generate counterion dye stains to improve the process.
Collapse
Affiliation(s)
- Alexander Carreño
- Center of Applied NanoSciences (CANS), Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago, Chile
| | | | - Eduardo Solis-Céspedes
- Escuela de Bioingeniería Médica, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile.,Laboratorio de Bioinformática y Química Computacional, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Dayán Páez-Hernández
- Center of Applied NanoSciences (CANS), Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago, Chile
| | - Wesley B Swords
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Gerald J Meyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Marcelo D Preite
- Departamento de Química Orgánica, Facultad de Química y Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ivonne Chávez
- Departamento de Química Inorgánica, Facultad de Química y Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrés Vega
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Viña del Mar, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnología Cedenna, Santiago, Chile
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| |
Collapse
|
4
|
Wang Y, Nakajima E, Okamura Y, Wang D, Okumura N, Takao T. Metastable decomposition at the peptide C-terminus: Possible use in protein identification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8734. [PMID: 32031718 DOI: 10.1002/rcm.8734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 12/14/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE The b n-1 ion of a peptide, as well as a [b n-1 + 18] ion, can be observed not only as normal product ions, but also as prominent metastable ions in a reflectron-embedded matrix-assisted laser desorption ionization time-of-flight spectrometer. The m/z values for the peaks are slightly shifted compared with the ordinary product ions and appear as relatively broad peaks, which permits them to be discriminated from other ions. METHODS A standard protein mixture and gel-derived proteins digested with LysN protease, which cleaves peptide linkages in proteins at the N-terminal side of Lys residues, were examined. The collected data were used for protein identification using in-house software, iD-plus (http://coco.protein.osaka-u.ac.jp/id-plus/), which was developed for searching for proteins in the peptide database, based on enzyme specificity (N-terminal Lys in this study), peptide masses and C-terminal amino acids. RESULTS The b n-1 as well as [b n-1 + 18] ions were observed as broad ion peaks for all of the peptides (86 peptides) examined in this study. In silico calculations using the database of LysN digested peptides (11 969 470), created from 553 941 protein sequences (SwissProt: 2017_03), indicate that the use of no less than four peptides permits a protein to be identified without the need of any probability-based scoring. CONCLUSIONS The preference for b n-1 ion formation is probably due to the higher propensity of the C-terminal peptide bond to be cleaved than other internal bonds. The fact that such C-terminal fragmentation takes place for most of the peptides examined suggests that the use of an N-terminal specific enzyme would allow the C-terminal amino acids to be more reliably read out than other internal sequences, information that could be efficiently used for protein identification.
Collapse
Affiliation(s)
- Yang Wang
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Etsuko Nakajima
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Yoshihito Okamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Danqing Wang
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Nobuaki Okumura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| | - Toshifumi Takao
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
| |
Collapse
|
5
|
Babak MV, Le Faouder P, Trivelli X, Venkatesan G, Bezzubov SI, Kajjout M, Gushchin AL, Hanif M, Poizat O, Vezin H, Rolando C. Heteroleptic Ruthenium(II) Complexes with Bathophenanthroline and Bathophenanthroline Disulfonate Disodium Salt as Fluorescent Dyes for In-Gel Protein Staining. Inorg Chem 2020; 59:4527-4535. [DOI: 10.1021/acs.inorgchem.9b03679] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria V. Babak
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse l’Analyse et la Protèomique, F-59 000 Lille, France
| | - Pauline Le Faouder
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse l’Analyse et la Protèomique, F-59 000 Lille, France
| | - Xavier Trivelli
- Univ. Lille, CNRS, INRA, Centrale Lille, ENSCL, Univ. Artois, FR 2638 – IMEC - Institut Michel-Eugène Chevreul, F-59000 Lille, France
| | - Gopalakrishnan Venkatesan
- Department of Pharmacy, National University of Singapore, Lower Kent Ridge Road, 18 Science Drive 2, Singapore 119260
| | - Stanislav I. Bezzubov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119991, Russia
| | - Mohammed Kajjout
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse l’Analyse et la Protèomique, F-59 000 Lille, France
| | - Artem L. Gushchin
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch of Russian Academy of Sciences, 3 Acad. Lavrentiev Avenue, Novosibirsk 630090, Russia
- Novosibirsk State University, 2 Pirogov Street, 630090 Novosibirsk, Russia
| | - Muhammad Hanif
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Olivier Poizat
- Univ. Lille, CNRS, UMR 8516 - LASIRe - Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l’Environnement, F-59000 Lille, France
| | - Hervé Vezin
- Univ. Lille, CNRS, UMR 8516 - LASIRe - Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l’Environnement, F-59000 Lille, France
| | - Christian Rolando
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse l’Analyse et la Protèomique, F-59 000 Lille, France
| |
Collapse
|
6
|
Fiorini V, Bergamini L, Monti N, Zacchini S, Plush SE, Massi M, Hochkoeppler A, Stefan A, Stagni S. Luminescent protein staining with Re(i) tetrazolato complexes. Dalton Trans 2018; 47:9400-9410. [DOI: 10.1039/c8dt02052c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Re(i) tricarbonyl diiimine complexes for the first time exploited as luminescent staining agents for SDS-PAGE.
Collapse
Affiliation(s)
- Valentina Fiorini
- Department of Industrial Chemistry “Toso Montanari”
- University of Bologna
- I-40136 Bologna
- Italy
| | - Linda Bergamini
- Department of Industrial Chemistry “Toso Montanari”
- University of Bologna
- I-40136 Bologna
- Italy
| | - Nicola Monti
- Department of Industrial Chemistry “Toso Montanari”
- University of Bologna
- I-40136 Bologna
- Italy
| | - Stefano Zacchini
- Department of Industrial Chemistry “Toso Montanari”
- University of Bologna
- I-40136 Bologna
- Italy
| | - Sally E. Plush
- School of Pharmacy and Medical Sciences and the Future Industries Institute University of South Australia
- Adelaide
- Australia
| | - Massimiliano Massi
- Curtin Institute for Functional Molecules and Interfaces
- School of Molecular and Life Science
- Curtin University
- Bentley 6102
- Australia
| | | | - Alessandra Stefan
- CSGI
- Department of Chemistry
- University of Florence
- I-50019 Sesto Fiorentino (FI)
- Italy
| | - Stefano Stagni
- Department of Industrial Chemistry “Toso Montanari”
- University of Bologna
- I-40136 Bologna
- Italy
| |
Collapse
|
7
|
Zhou Y, Jia J, Wang X, Guo W, Wu Z, Xu N. Protein Staining Agents from Cationic and Neutral Luminescent Iridium(III) Complexes. Chemistry 2016; 22:16796-16800. [DOI: 10.1002/chem.201603630] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Yuyang Zhou
- Jiangsu Key Laboratory of Environmental Functional Materials; School of Chemistry, Biology and Material Engineering; Suzhou University of Science and Technology, Suzhou; 215009 Jiangsu P. R. China
| | - Junli Jia
- Department of Immunology; Nanjing Medical University, Nanjing; 211166 Jiangsu P. R. China
| | - Xiaomei Wang
- Jiangsu Key Laboratory of Environmental Functional Materials; School of Chemistry, Biology and Material Engineering; Suzhou University of Science and Technology, Suzhou; 215009 Jiangsu P. R. China
| | - Weiqiang Guo
- Jiangsu Key Laboratory of Environmental Functional Materials; School of Chemistry, Biology and Material Engineering; Suzhou University of Science and Technology, Suzhou; 215009 Jiangsu P. R. China
| | - Zhengying Wu
- Jiangsu Key Laboratory of Environmental Functional Materials; School of Chemistry, Biology and Material Engineering; Suzhou University of Science and Technology, Suzhou; 215009 Jiangsu P. R. China
| | - Nan Xu
- Jiangsu Key Laboratory of Environmental Functional Materials; School of Chemistry, Biology and Material Engineering; Suzhou University of Science and Technology, Suzhou; 215009 Jiangsu P. R. China
| |
Collapse
|
8
|
Liu C, Huang D, Yang T, Cremer PS. Simultaneous Detection of Multiple Proteins that Bind to the Identical Ligand in Supported Lipid Bilayers. Anal Chem 2015; 87:7163-70. [DOI: 10.1021/acs.analchem.5b00999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Chunming Liu
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Da Huang
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Tinglu Yang
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Paul S. Cremer
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
9
|
Butt RH, Coorssen JR. Coomassie blue as a near-infrared fluorescent stain: a systematic comparison with Sypro Ruby for in-gel protein detection. Mol Cell Proteomics 2013; 12:3834-50. [PMID: 24043422 DOI: 10.1074/mcp.m112.021881] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Quantitative proteome analyses suggest that the well-established stain colloidal Coomassie Blue, when used as an infrared dye, may provide sensitive, post-electrophoretic in-gel protein detection that can rival even Sypro Ruby. Considering the central role of two-dimensional gel electrophoresis in top-down proteomic analyses, a more cost effective alternative such as Coomassie Blue could prove an important tool in ongoing refinements of this important analytical technique. To date, no systematic characterization of Coomassie Blue infrared fluorescence detection relative to detection with SR has been reported. Here, seven commercial Coomassie stain reagents and seven stain formulations described in the literature were systematically compared. The selectivity, threshold sensitivity, inter-protein variability, and linear-dynamic range of Coomassie Blue infrared fluorescence detection were assessed in parallel with Sypro Ruby. Notably, several of the Coomassie stain formulations provided infrared fluorescence detection sensitivity to <1 ng of protein in-gel, slightly exceeding the performance of Sypro Ruby. The linear dynamic range of Coomassie Blue infrared fluorescence detection was found to significantly exceed that of Sypro Ruby. However, in two-dimensional gel analyses, because of a blunted fluorescence response, Sypro Ruby was able to detect a few additional protein spots, amounting to 0.6% of the detected proteome. Thus, although both detection methods have their advantages and disadvantages, differences between the two appear to be small. Coomassie Blue infrared fluorescence detection is thus a viable alternative for gel-based proteomics, offering detection comparable to Sypro Ruby, and more reliable quantitative assessments, but at a fraction of the cost.
Collapse
|
10
|
Konstantinidis S, Kong S, Titchener-Hooker N. Identifying analytics for high throughput bioprocess development studies. Biotechnol Bioeng 2013; 110:1924-35. [PMID: 23334907 DOI: 10.1002/bit.24850] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/01/2012] [Accepted: 01/07/2013] [Indexed: 12/31/2022]
Abstract
In recent years, high throughput screening (HTS) studies have been increasingly employed as an integral element of bioprocess development activities. These studies are often limited by an analytical bottleneck; they generate multiple samples for analysis and the available analytical methods cannot always cope with the added analytical burden. A potential solution to this challenge is offered by the deployment of appropriate analytics. This article outlines features of analytical methods that affect their fit to high throughput (HT) applications. These are discussed for a range of analytics frequently used in bioprocess development studies of monoclonal antibodies. It then outlines how these features need to be considered in order to classify analytical methods in terms of their particular application in high throughput scenarios.
Collapse
Affiliation(s)
- Spyridon Konstantinidis
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | | | | |
Collapse
|
11
|
Jia J, Fei H, Zhou M. Luminescent iridium(III) complexes as novel protein staining agents. Electrophoresis 2012; 33:1397-401. [DOI: 10.1002/elps.201100693] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Junli Jia
- Division of Nanobiomedicine,; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou; Jiangsu; P. R. China
| | - Hao Fei
- Division of Nanobiomedicine,; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou; Jiangsu; P. R. China
| | | |
Collapse
|
12
|
Lin JT, Chen PC, Goud TV, Huang BR, Lin TC, Biellmann JF, Chen CS. A sulfhydryl-reactive ruthenium (II) complex and its conjugation to protein G as a universal reagent for fluorescent immunoassays. PLoS One 2012; 7:e36086. [PMID: 22563441 PMCID: PMC3338566 DOI: 10.1371/journal.pone.0036086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 03/26/2012] [Indexed: 11/19/2022] Open
Abstract
To develop a fluorescent ruthenium complex for biosensing, we synthesized a novel sulfhydryl-reactive compound, 4-bromophenanthroline bis-2,2′-dipyridine Ruthenium bis (hexafluorophosphate). The synthesized Ru(II) complex was crosslinked with thiol-modified protein G to form a universal reagent for fluorescent immunoassays. The resulting Ru(II)-protein G conjugates were identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The emission peak wavelength of the Ru(II)-protein G conjugate was 602 nm at the excitation of 452 nm which is similar to the spectra of the Ru(II) complex, indicating that Ru(II)-protein G conjugates still remain the same fluorescence after conjugation. To test the usefulness of the conjugate for biosensing, immunoglobulin G (IgG) binding assay was conducted. The result showed that Ru(II)-protein G conjugates were capable of binding IgG and the more cross-linkers to modify protein G, the higher conjugation efficiency. To demonstrate the feasibility of Ru(II)-protein G conjugates for fluorescent immunoassays, the detection of recombinant histidine-tagged protein using the conjugates and anti-histidine antibody was developed. The results showed that the histidine-tagged protein was successfully detected with dose-response, indicating that Ru(II)-protein G conjugate is a useful universal fluorescent reagent for quantitative immunoassays.
Collapse
Affiliation(s)
- Jing-Tang Lin
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli City, Taoyuan Country, Taiwan
| | - Po-Chung Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli City, Taoyuan Country, Taiwan
| | | | - Bor-Rong Huang
- Department of Chemistry, National Central University, Jhongli City, Taoyuan Country, Taiwan
| | - Tzu-Chau Lin
- Department of Chemistry, National Central University, Jhongli City, Taoyuan Country, Taiwan
| | - Jean-François Biellmann
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli City, Taoyuan Country, Taiwan
- * E-mail: (JFB); (CSC)
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli City, Taoyuan Country, Taiwan
- * E-mail: (JFB); (CSC)
| |
Collapse
|
13
|
Wang X, Wang D, Wang D, Wang H, Chang L, Yi X, Peng M, Guo A. Systematic comparison of technical details in CBB methods and development of a sensitive GAP stain for comparative proteomic analysis. Electrophoresis 2012; 33:296-306. [DOI: 10.1002/elps.201100300] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xuchu Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Dongyang Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Dan Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Haiyan Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Lili Chang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Xiaoping Yi
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Ming Peng
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| | - Anping Guo
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan, P. R. China
| |
Collapse
|
14
|
Abstract
Proteins separated by two-dimensional gel electrophoresis can be visualized by in-gel detection using -different staining methods. Ideally, the dye should bind non-covalently to the protein following a linear response curve. Since protein concentrations in biological systems may vary by six or more orders of magnitude (Corthals GL et al., Electrophoresis 21(6):1104-1115, 2000), the staining should allow for a detection of very low protein amounts. At the same time, saturation effects have to be avoided because they impede normalized quantification.Most proteomics laboratories apply Coomassie, silver, or fluorescent stains. Using the colloidal properties of Coomassie dyes, detection limits at the lower nanogram level can meanwhile be achieved. Characteristics like ease of use, low cost, and compatibility with downstream characterization methods such as mass spectrometry, therefore, make colloidal Coomassie staining well suited for the in-gel detection method in quantitative proteomics.
Collapse
Affiliation(s)
- Nadine Dyballa
- Biological-Medical-Research Center, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | | |
Collapse
|
15
|
Van Damme P, Evjenth R, Foyn H, Demeyer K, De Bock PJ, Lillehaug JR, Vandekerckhove J, Arnesen T, Gevaert K. Proteome-derived peptide libraries allow detailed analysis of the substrate specificities of N(alpha)-acetyltransferases and point to hNaa10p as the post-translational actin N(alpha)-acetyltransferase. Mol Cell Proteomics 2011; 10:M110.004580. [PMID: 21383206 DOI: 10.1074/mcp.m110.004580] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The impact of N(α)-terminal acetylation on protein stability and protein function in general recently acquired renewed and increasing attention. Although the substrate specificity profile of the conserved enzymes responsible for N(α)-terminal acetylation in yeast has been well documented, the lack of higher eukaryotic models has hampered the specificity profile determination of N(α)-acetyltransferases (NATs) of higher eukaryotes. The fact that several types of protein N termini are acetylated by so far unknown NATs stresses the importance of developing tools for analyzing NAT specificities. Here, we report on a method that implies the use of natural, proteome-derived modified peptide libraries, which, when used in combination with two strong cation exchange separation steps, allows for the delineation of the in vitro specificity profiles of NATs. The human NatA complex, composed of the auxiliary hNaa15p (NATH/hNat1) subunit and the catalytic hNaa10p (hArd1) and hNaa50p (hNat5) subunits, cotranslationally acetylates protein N termini initiating with Ser, Ala, Thr, Val, and Gly following the removal of the initial Met. In our studies, purified hNaa50p preferred Met-Xaa starting N termini (Xaa mainly being a hydrophobic amino acid) in agreement with previous data. Surprisingly, purified hNaa10p preferred acidic N termini, representing a group of in vivo acetylated proteins for which there are currently no NAT(s) identified. The most prominent representatives of the group of acidic N termini are γ- and β-actin. Indeed, by using an independent quantitative assay, hNaa10p strongly acetylated peptides representing the N termini of both γ- and β-actin, and only to a lesser extent, its previously characterized substrate motifs. The immunoprecipitated NatA complex also acetylated the actin N termini efficiently, though displaying a strong shift in specificity toward its known Ser-starting type of substrates. Thus, complex formation of NatA might alter the substrate specificity profile as compared with its isolated catalytic subunits, and, furthermore, NatA or hNaa10p may function as a post-translational actin N(α)-acetyltransferase.
Collapse
Affiliation(s)
- Petra Van Damme
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Chiangjong W, Sinchaikul S, Chen ST, Thongboonkerd V. Calcium oxalate dihydrate crystal induced changes in glycoproteome of distal renal tubular epithelial cells. MOLECULAR BIOSYSTEMS 2011; 7:1917-25. [DOI: 10.1039/c1mb05052d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
17
|
Aude-Garcia C, Collin-Faure V, Luche S, Rabilloud T. Improvements and simplifications in in-gel fluorescent detection of proteins using ruthenium II tris-(bathophenanthroline disulfonate): the poor man's fluorescent detection method. Proteomics 2010; 11:324-8. [PMID: 21204259 DOI: 10.1002/pmic.201000370] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 09/10/2010] [Accepted: 10/14/2010] [Indexed: 11/09/2022]
Abstract
Fluorescent detection of proteins is a popular method of detection allying sensitivity, linearity and compatibility with mass spectrometry. Among the numerous methods described in the literature, staining with ruthenium II tris(bathophenanthroline disulfonate) is particularly cost-effective, but slightly cumbersome owing to difficulties in the preparation of the complex and complexity of staining protocols. We describe here the modifications on both aspects that allow to perform a higher contrast staining and offer a more robust method of complex preparation, thereby maximizing the advantages of the method.
Collapse
Affiliation(s)
- Catherine Aude-Garcia
- CEA-DSV/iRTSV/LBBSI, Biophysique et Biochimie des Systèmes Intégrés, CEA-Grenoble, Grenoble, France
| | | | | | | |
Collapse
|
18
|
Fränzel B, Trötschel C, Rückert C, Kalinowski J, Poetsch A, Wolters DA. Adaptation of Corynebacterium glutamicum to salt-stress conditions. Proteomics 2010; 10:445-57. [PMID: 19950167 DOI: 10.1002/pmic.200900482] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Corynebacterium glutamicum is one of the biotechnologically most important microorganisms because of its ability to enrich amino acids extracellularly. Hence, C. glutamicum requires effective adaptation strategies against both hypo- and hyperosmotic stress. We give a comprehensive and coherent outline about the quantitative dynamics of C. glutamicum during adaptation to hyperosmotic stress at the transcript and protein levels. The osmolyte carrier ProP, playing a pivotal role in hyperosmotic stress defence, exhibits the strongest up-regulation of all proteins. A conspicuously regulated group comprises proteins involved in lipid biosynthesis of the cell envelope. This is in accordance with our observation of a more viscous and stickier cell envelope, which is supported by the findings of an altered lipid composition. Together with our results, showing that several transporters were down-regulated, this membrane adaptation appears to be one of C. glutamicum's major protection strategies against hyperosmotic stress. In addition, we demonstrate that no oxidative stress and no iron limitation occur during salt stress contrary to former postulations. Ultimately, it is remarkable that various proteins with divergent mRNA-protein dynamics and regulation have been observed. This leads to the assumption that there are still unknown mechanisms in between the bacterial transcription, translation and post-translation and that these are waiting to be unravelled.
Collapse
Affiliation(s)
- Benjamin Fränzel
- Department of Analytical Chemistry, University of Bochum, Bochum, Germany
| | | | | | | | | | | |
Collapse
|
19
|
Lopez MM, Atherton AA, Tong WG. Ultrasensitive detection of proteins and antibodies by absorption-based laser wave-mixing detection using a chromophore label. Anal Biochem 2010; 399:147-51. [PMID: 20026295 DOI: 10.1016/j.ab.2009.12.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Revised: 12/09/2009] [Accepted: 12/11/2009] [Indexed: 11/26/2022]
Abstract
Nonlinear laser wave mixing is presented as an ultrasensitive absorption-based method for the detection of proteins and antibodies using a nonfluorescing chromophore label, Coomassie Brilliant Blue (CBB). The complexes are flowed through a 150-microm (i.d.) capillary cell and detected using a low-power He-Ne laser. The wave-mixing signal is detected after 10 min of room temperature incubation for the antibody complex and after 18 min for the protein complex. All solutions are prepared in an aqueous buffer without the addition of organic modifiers. Concentration detection limits of 3.4 x 10(-19) and 6.4 x 10(-14) M (signal-to-noise ratio [S/N] = 2) are determined for bovine serum albumin (BSA) and human papillomavirus (HPV) antibody, respectively. Based on the small laser probe volume used (i.e., overlap volume of the two input beams), mass detection limits of 1.7 x 10(-22) and 2.6 x 10(-17) mol are determined for BSA and HPV antibody, respectively.
Collapse
Affiliation(s)
- Mirna M Lopez
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA
| | | | | |
Collapse
|
20
|
A comparative study of different dyes for the detection of proteomes derived from Escherichia coli and MDCK cells: Sensitivity and selectivity. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1433-9. [DOI: 10.1016/j.jchromb.2009.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 02/28/2009] [Accepted: 03/09/2009] [Indexed: 11/22/2022]
|
21
|
|
22
|
Wang Z, Liu X, Baeyens WRG, Delanghe JR, Ouyang J. Copper(II)−Alizarin Red S Complex as an Efficient Chemiluminescent Probe for the Detection of Human Serum Proteins after Polyacrylamide Gel Electrophoresis. J Proteome Res 2008; 7:5075-81. [DOI: 10.1021/pr800365n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhenzhen Wang
- College of Chemistry, Beijing Normal University, Beijing, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent, Belgium
| | - Xia Liu
- College of Chemistry, Beijing Normal University, Beijing, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent, Belgium
| | - Willy R. G. Baeyens
- College of Chemistry, Beijing Normal University, Beijing, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent, Belgium
| | - Joris R. Delanghe
- College of Chemistry, Beijing Normal University, Beijing, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent, Belgium
| | - Jin Ouyang
- College of Chemistry, Beijing Normal University, Beijing, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent, Belgium
| |
Collapse
|
23
|
Zellner M, Babeluk R, Diestinger M, Pirchegger P, Skeledzic S, Oehler R. Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples. Electrophoresis 2008; 29:3621-7. [DOI: 10.1002/elps.200700935] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
24
|
Riederer BM. Non-covalent and covalent protein labeling in two-dimensional gel electrophoresis. J Proteomics 2008; 71:231-44. [DOI: 10.1016/j.jprot.2008.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Revised: 05/03/2008] [Accepted: 05/06/2008] [Indexed: 12/16/2022]
|
25
|
Romero-Puertas MC, Campostrini N, Mattè A, Righetti PG, Perazzolli M, Zolla L, Roepstorff P, Delledonne M. Proteomic analysis of S-nitrosylated proteins in Arabidopsis thaliana undergoing hypersensitive response. Proteomics 2008; 8:1459-69. [PMID: 18297659 DOI: 10.1002/pmic.200700536] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nitric oxide (NO) has a fundamental role in the plant hypersensitive disease resistance response (HR), and S-nitrosylation is emerging as an important mechanism for the transduction of its bioactivity. A key step toward elucidating the mechanisms by which NO functions during the HR is the identification of the proteins that are subjected to this PTM. By using a proteomic approach involving 2-DE and MS we characterized, for the first time, changes in S-nitrosylated proteins in Arabidopsis thaliana undergoing HR. The 16 S-nitrosylated proteins identified are mostly enzymes serving intermediary metabolism, signaling and antioxidant defense. The study of the effects of S-nitrosylation on the activity of the identified proteins and its role during the execution of the disease resistance response will help to understand S-nitrosylation function and significance in plants.
Collapse
|
26
|
van den Broeck HC, America AHP, Smulders MJM, Gilissen LJWJ, van der Meer IM. Staining efficiency of specific proteins depends on the staining method: Wheat gluten proteins. Proteomics 2008; 8:1880-4. [DOI: 10.1002/pmic.200700956] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
27
|
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.
Collapse
Affiliation(s)
- Jukka Hellman
- University of Turku, Department of Biochemistry and Food Chemistry/Biotechnology, Turku, Finland.
| |
Collapse
|
28
|
Wang X, Li X, Li Y. A modified Coomassie Brilliant Blue staining method at nanogram sensitivity compatible with proteomic analysis. Biotechnol Lett 2007; 29:1599-603. [PMID: 17563857 DOI: 10.1007/s10529-007-9425-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 05/03/2007] [Accepted: 05/15/2007] [Indexed: 10/23/2022]
Abstract
A more sensitive and convenient Coomassie Brilliant Blue (CBB) staining method for visualizing proteins was developed. Compared with the modifications include the supplement of 10% (v/v) methanol into the fixing solution, an increase of an additional sensitization step and CBB raised from 0.1 to 0.125%. The improved method can detect proteins at nanogram level. The improved method is more sensitive than Blue Silver and more convenient than the Silver protocol. Mass spectrometry results confirmed that it is suitable for subsequent proteomic research.
Collapse
Affiliation(s)
- Xuchu Wang
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, P.R. China
| | | | | |
Collapse
|
29
|
Schriebl K, Trummer E, Weik R, Lattenmayer C, Müller D, Kunert R, Katinger H, Vorauer-Uhl K. Applicability of different fluorescent dyes for isoform quantification on linear IPG gels. Electrophoresis 2007; 28:2100-7. [PMID: 17523139 DOI: 10.1002/elps.200600695] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
For biotechnological research, development, and production various analytical methods are required to determine the quality of the target product. In this context, the determination of isoforms is state-of-the-art; however, the majority of applied techniques are more qualitative than quantitative. To address this fact, we evaluated different post- and pre-electrophoretic staining dyes for their applicability on linear IPG gels using recombinant human erythropoietin as a model protein. Each evaluated dyes was able to detect all isoforms reproducibly, but CyDyes were found to be the most promising. Using CyDyes, up to three samples can be focused on the same lane under identical electrophoretic conditions, thus, a fast, reproducible, sensitive and quantitative isoform determination can be performed. To illustrate the practical relevance, quantitative CyDye technique was used for the characterization of our model protein, recombinant human Epo-Fc. This method makes it possible to determine the isoform pattern of nonpurified supernatants as well as purified proteins. We conclude that quantitative pre-electrophoretic staining IEF using CyDyes is a fast, simple, accurate method to determine isoforms, which can be used in research, development, and manufacturing for product quality analysis, e.g., clone screening, process optimization, and purification monitoring.
Collapse
|
30
|
Pluder F, Beck-Sickinger AG. One-step procedure for staining of proteins with ruthenium II tris (bathophenanthroline disulfonate). Anal Biochem 2007; 361:299-301. [PMID: 17196542 DOI: 10.1016/j.ab.2006.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Revised: 10/31/2006] [Accepted: 11/01/2006] [Indexed: 10/23/2022]
Affiliation(s)
- Franka Pluder
- Institute of Biochemistry, Faculty of Bioscience, Pharmacy and Psychology, University of Leipzig, D-04103 Leipzig, Germany
| | | |
Collapse
|
31
|
Kleffmann T, von Zychlinski A, Russenberger D, Hirsch-Hoffmann M, Gehrig P, Gruissem W, Baginsky S. Proteome dynamics during plastid differentiation in rice. PLANT PHYSIOLOGY 2007; 143:912-23. [PMID: 17189339 PMCID: PMC1803725 DOI: 10.1104/pp.106.090738] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We have analyzed proteome dynamics during light-induced development of rice (Oryza sativa) chloroplasts from etioplasts using quantitative two-dimensional gel electrophoresis and tandem mass spectrometry protein identification. In the dark, the etioplast allocates the main proportion of total protein mass to carbohydrate and amino acid metabolism and a surprisingly high number of proteins to the regulation and expression of plastid genes. Chaperones, proteins for photosynthetic energy metabolism, and enzymes of the tetrapyrrole pathway were identified among the most abundant etioplast proteins. The detection of 13 N-terminal acetylated peptides allowed us to map the exact localization of the transit peptide cleavage site, demonstrating good agreement with the prediction for most proteins. Based on the quantitative etioplast proteome map, we examined early light-induced changes during chloroplast development. The transition from heterotrophic metabolism to photosynthesis-supported autotrophic metabolism was already detectable 2 h after illumination and affected most essential metabolic modules. Enzymes in carbohydrate metabolism, photosynthesis, and gene expression were up-regulated, whereas enzymes in amino acid and fatty acid metabolism were significantly decreased in relative abundance. Enzymes involved in nucleotide metabolism, tetrapyrrole biosynthesis, and redox regulation remained unchanged. Phosphoprotein-specific staining at different time points during chloroplast development revealed light-induced phosphorylation of a nuclear-encoded plastid RNA-binding protein, consistent with changes in plastid RNA metabolism. Quantitative information about all identified proteins and their regulation by light is available in plprot, the plastid proteome database (http://www.plprot.ethz.ch).
Collapse
Affiliation(s)
- Torsten Kleffmann
- Institute of Plant Sciences, Eidgenössische Technische Hochschule Zurich, 8092 Zurich, Switzerland
| | | | | | | | | | | | | |
Collapse
|
32
|
Tokarski C, Cren-Olivé C, Fillet M, Rolando C. High-sensitivity staining of proteins for one- and two-dimensional gel electrophoresis using post migration covalent staining with a ruthenium fluorophore. Electrophoresis 2006; 27:1407-16. [PMID: 16502460 DOI: 10.1002/elps.200500426] [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: 11/09/2022]
Abstract
This paper describes the use of a ruthenium complex ((bis(2,2'-bipyridine)-4'-methyl-4-carboxybipyridine-ruthenium-N-succidimyl ester-bis(hexafluorophosphate), abbreviated below as ASCQ_Ru) commercially available and chemically pure. This new ruthenium complex ASCQ_Ru brings an activated ester, allowing the selective acylation of amino acid side chain amines for the post migration staining of proteins separated in 1-DE and 2-DE. The protocol used is a simple three-step protocol fixing the proteins in the gel, staining and then washing, as no lengthy destaining step is required. First the critical staining step was optimized. Although in solution the best described pH for acylating proteins with this reagent is phosphate buffer at pH 7.0, we found that best medium for in-gel staining is unbuffered ACN/water solution (20/80 v/v). The two other steps are less critical and classical conditions are satisfactory: fixing with 7% acetic acid/10% ethanol solution and washing four times for 10 min with water. Sensitivity tests were performed using 1-DE on protein molecular weight markers. We obtained a higher sensitivity than SYPRO Ruby with a detection limit of 80 pg of protein per well. However, contrary to SYPRO Ruby, ASCQ_Ru exhibits a logarithmic dependency on the amount of protein. The dynamic range is similar to SYPRO Ruby and is estimated between three and four orders of magnitude. Finally, the efficiency of the post migration ASCQ_Ru staining for 2-D gel separation is demonstrated on the whole protein extract from human colon carcinoma cells lines HCT 116. ASCQ_Ru gave the highest number of spot detected compared to other common stains Colloidal CBB, SYPRO Ruby and Deep Purple.
Collapse
Affiliation(s)
- Caroline Tokarski
- Laboratory of Organic and Macromolecular Chemistry, UMR CNRS 8009 and Proteomics, Post-Translational Modifications and Glycobiology, IFR 118, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq, France
| | | | | | | |
Collapse
|
33
|
Gil-Agusti MT, Campostrini N, Zolla L, Ciambella C, Invernizzi C, Righetti PG. Two-dimensional mapping as a tool for classification of green coffee bean species. Proteomics 2005; 5:710-8. [PMID: 15669003 DOI: 10.1002/pmic.200401014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Two species of the genus Coffea, Coffea arabica (Colombia) and Coffea canephora (Indiano Robusta) were analysed by two-dimensional (2-D) maps in order to obtain fingerprints of the expressed polypeptide chains and to determine which ones would characterize the two species. Green beans were milled under liquid nitrogen. A dry powder was produced by three different extraction protocols aimed at eliminating interfering substances (polyphenols). A reduced powder was produced by two successive extractions performed in acetone. Trichloroacetic acid (TCA; 10% w/v) and beta-mercaptoethanol (0.07% v/v) in acetone were used for the first extraction (a) and 10% w/v TCA in acetone was used for the second extraction (b). Proteins were then solubilized in a solution (40 microL per 1 mg powder) containing 7 M urea, 2 M thiourea, 3% w/v 3-(3-cholamidopropyldimethyl-amino)-1-propanesulfate, 1% v/v carrier ampholytes, 40 mM Tris, 5 mM tributylphosphine and 10 mM acrylamide as alkylating agent. Following incubation at room temperature for 1 hour and centrifugation (7000 rpm for 20 minutes), the supernatant was used for 2-D electrophoresis. The proteins were revealed by Sypro Ruby staining. Master maps of the five replicas of each species were compared by PDQuest analysis. The results of this differential proteome analysis were: sixteen proteins were expressed solely in C. canephora (var. Indiano Robusta) and five proteins were only found in C. arabica (var. Colombia). Another eight proteins were up-regulated in C. canephora (var. Indiano Robusta) in comparison to C. arabica (var. Colombia) and one was down-regulated in the same comparison. A number of these polypeptide chains were further characterized by mass spectrometry in the matrix-assisted laser desorption/ionisation-time of flight mode. Additionally, considering the low number of protein sequences of Coffea present in the databases we also investigated some spots with a more powerful tool, reversed phase-high-performance liquid chromatography-electrospray ionisation-tandem mass spectrometry, thus obtaining an internal peptide sequence. The general properties of the identified proteins are presented and discussed.
Collapse
|
34
|
David DC, Hoerndli F, Götz J. Functional Genomics meets neurodegenerative disorders. Prog Neurobiol 2005; 76:153-68. [PMID: 16168556 DOI: 10.1016/j.pneurobio.2005.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Revised: 07/14/2005] [Accepted: 07/19/2005] [Indexed: 11/22/2022]
Abstract
Transcriptomics and proteomics are increasingly applied to gain a mechanistic insight into neurodegenerative disorders. These techniques not only identify distinct, differentially expressed mRNAs and proteins but are also employed to dissect signaling pathways and reveal networks by using an integrated approach. In part I of this back-to-back review, technical aspects are discussed: in the transcriptomics section, which includes enrichment by laser microcapture dissection, we comment on qRT-PCR, SAGE, subtractive hybridization, differential display and microarrays, including software packages. In the proteomics section we discuss two-dimensional (2D) gel electrophoresis, liquid chromatography, methods to label and enrich specific proteins or peptides, and different types of mass spectrometers. These tools have been applied to a range of neurodegenerative disorders and are discussed and integrated in part II (Functional Genomics meets neurodegenerative disorders. Part II: application and data integration).
Collapse
Affiliation(s)
- Della C David
- Brain and Mind Research Institute, University of Sydney, 100 Mallett St., Camperdown, NSW 2050, Australia
| | | | | |
Collapse
|
35
|
Kashino Y. Separation methods in the analysis of protein membrane complexes. J Chromatogr B Analyt Technol Biomed Life Sci 2004; 797:191-216. [PMID: 14630150 DOI: 10.1016/s1570-0232(03)00428-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The separation of membrane protein complexes can be divided into two categories. One category, which is operated on a relatively large scale, aims to purify the membrane protein complex from membrane fractions while retaining its native form, mainly to characterize its nature. The other category aims to analyze the constituents of the membrane protein complex, usually on a small scale. Both of these face the difficulty of isolating the membrane protein complex without interference originating from the hydrophobic nature of membrane proteins or from the close association with membrane lipids. To overcome this difficulty, many methods have been employed. Crystallized membrane protein complexes are the most successful example of the former category. In these purification methods, special efforts are made in the steps prior to the column chromatography to enrich the target membrane protein complexes. Although there are specific aspects for each complex, the most popular method for isolating these membrane protein complexes is anion-exchange column chromatography, especially using weak anion-exchange columns. Another remarkable trend is metal affinity column chromatography, which purifies the membrane protein complex as an intact complex in one step. Such protein complexes contain subunit proteins which are genetically engineered so as to include multiple-histidine tags at carboxyl- or amino-termini. The key to these successes for multi-subunit complex isolation is the idea of keeping the expression at its physiological level, rather than overexpression. On the other hand, affinity purification using the Fv fragment, in which a Strep tag is genetically introduced, is ideal because this method does not introduce any change to the target protein. These purification methods supported by affinity interaction can be applied to minor membrane protein complexes in the membrane system. Isoelectric focusing (IEF) and blue native (BN) electrophoresis have also been employed to prepare membrane protein complexes. Generally, a combination of two or more chromatographic and/or electrophoretic methods is conducted to separate membrane protein complexes. IEF or BN electrophoresis followed by 2nd dimension electrophoresis serve as useful tools for analytical demand. However, some problems still exist in the 2D electrophoresis using IEF. To resolve such problems, many attempts have been made, e.g. introduction of new chaotropes, surfactants, reductants or supporting matrices. This review will focus in particular on two topics: the preparative methods that achieved purification of membrane protein complexes in the native (intact) form, and the analytical methods oriented to resolve the membrane proteins. The characteristics of these purification and analytical methods will be discussed along with plausible future developments taking into account the nature of membrane protein complexes.
Collapse
Affiliation(s)
- Yasuhiro Kashino
- Faculty of Science, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Hyogo 678-1297, Japan.
| |
Collapse
|
36
|
Hirsch J, Hansen KC, Burlingame AL, Matthay MA. Proteomics: current techniques and potential applications to lung disease. Am J Physiol Lung Cell Mol Physiol 2004; 287:L1-23. [PMID: 15187006 DOI: 10.1152/ajplung.00301.2003] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Proteomics aims to study the whole protein content of a biological sample in one set of experiments. Such an approach has the potential value to acquire an understanding of the complex responses of an organism to a stimulus. The large vascular and air space surface area of the lung expose it to a multitude of stimuli that can trigger a variety of responses by many different cell types. This complexity makes the lung a promising, but also challenging, target for proteomics. Important steps made in the last decade have increased the potential value of the results of proteomics studies for the clinical scientist. Advances in protein separation and staining techniques have improved protein identification to include the least abundant proteins. The evolution in mass spectrometry has led to the identification of a large part of the proteins of interest rather than just describing changes in patterns of protein spots. Protein profiling techniques allow the rapid comparison of complex samples and the direct investigation of tissue specimens. In addition, proteomics has been complemented by the analysis of posttranslational modifications and techniques for the quantitative comparison of different proteomes. These methodologies have made the application of proteomics on the study of specific diseases or biological processes under clinically relevant conditions possible. The quantity of data that is acquired with these new techniques places new challenges on data processing and analysis. This article provides a brief review of the most promising proteomics methods and some of their applications to pulmonary research.
Collapse
Affiliation(s)
- Jan Hirsch
- Cardiovascular Research Institute, University of California, San Francisco, 505 Parnassus Ave. HSW 825, San Francisco, CA 94143-0130, USA.
| | | | | | | |
Collapse
|
37
|
Chevalier F, Rofidal V, Vanova P, Bergoin A, Rossignol M. Proteomic capacity of recent fluorescent dyes for protein staining. PHYTOCHEMISTRY 2004; 65:1499-1506. [PMID: 15276447 DOI: 10.1016/j.phytochem.2004.04.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Accepted: 04/16/2004] [Indexed: 05/24/2023]
Abstract
Staining of two-dimensional gel constitutes a crucial step in comparative proteome analysis with respect to both the number of proteins analysed, the accuracy of spot quantification and reproducibility. In this work, we compared the efficiency of recent fluorophores to stain Arabidopsis total protein extract: Sypro Ruby (SR), Deep Purple (DP) and 5-hexadecanoylamino-fluorescein (C16-F). In addition, classical visible dyes, colloidal Coomassie blue (CCB) and silver nitrate (SN), were also included. High quality images were obtained for the three fluorescent dyes, DP giving the cleaner background, whereas spikes were observed with SR and a rough background with C16-F. On the other hand, saturation occurred for abundant spots with SR and DP. For a same protein load the number of detected spots ranged between 250 for CCB and 800 for SR in the sequence SR > DP approximately SN > C16-F > CCB. These differences were shown to rely mainly on the sensitivity between dyes leading to the detection of additional spots belonging to classes of lower abundance. Analysis of the distribution of variation coefficients for spots from replicates showed differences in the staining reproducibility between dyes that ranged in the order SR > C16-F > DP > SN > CCB. The implications of these results for the selection of a convenient stain are discussed according to specific objectives as well as practical aspects.
Collapse
Affiliation(s)
- François Chevalier
- Laboratoire de Protéomique, INRA, UR 1199, 2 place Viala, 34060 Montpellier Cedex 1, France
| | | | | | | | | |
Collapse
|
38
|
Mooney BP, Krishnan HB, Thelen JJ. High-throughput peptide mass fingerprinting of soybean seed proteins: automated workflow and utility of UniGene expressed sequence tag databases for protein identification. PHYTOCHEMISTRY 2004; 65:1733-44. [PMID: 15276434 DOI: 10.1016/j.phytochem.2004.04.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 04/01/2004] [Indexed: 05/24/2023]
Abstract
Identification of anonymous proteins from two-dimensional (2-D) gels by peptide mass fingerprinting is one area of proteomics that can greatly benefit from a simple, automated workflow to minimize sample contamination and facilitate high-throughput sample processing. In this investigation we outline a workflow employing robotic automation at each step subsequent to 2-D gel electrophoresis. As proof-of-concept, 96 protein spots from a 2-D gel were analyzed using this approach. Whole protein (1 mg) from mature, dry soybean (Glycine max [L.] Merr.) cv. Jefferson seed was resolved by high resolution 2-D gel electrophoresis. Approximately 150 proteins were observed after staining with Coomassie Blue. The rather low number of detected proteins was due to the fact that the dynamic range of protein expression was greater than 100-fold. The most abundant proteins were seed storage proteins which in total represented over 60% of soybean seed protein. Using peptide mass fingerprinting 44 protein spots were identified. Identification of soybean proteins was greatly aided by the use of annotated, contiguous Expressed Sequence Tag (EST) databases which are available for public access (UniGene, ftp.ncbi.nih.gov/repository/UniGene/). Searches were orders of magnitude faster when compared to searches of unannotated EST databases and resulted in a higher frequency of valid, high-scoring matches. Some abundant, non seed storage proteins identified in this investigation include an isoelectric series of sucrose binding proteins, alcohol dehydrogenase and seed maturation proteins. This survey of anonymous seed proteins will serve as the basis for future comparative analysis of seed-filling in soybean as well as comparisons with other soybean varieties.
Collapse
Affiliation(s)
- Brian P Mooney
- Department of Biochemistry and Proteomics Center, University of Missouri-Columbia, 125 Chemistry, Columbia, MO 65211, USA
| | | | | |
Collapse
|
39
|
Choi NS, Yoo KH, Yoon KS, Maeng PJ, Kim SH. Nano-scale Proteomics Approach Using Two-dimensional Fibrin Zymography Combined with Fluorescent SYPRO Ruby Dye. BMB Rep 2004; 37:298-303. [PMID: 15469710 DOI: 10.5483/bmbrep.2004.37.3.298] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In general, a SYPRO Ruby dye is well known as a sensitive fluorescence-based method for detecting proteins by one-or two-dimensional SDS-PAGE (1-DE or 2-DE). Based on the SYPRO Ruby dye system, the combined two-dimensional fibrin zymography (2-D FZ) with SYPRO Ruby staining was newly developed to identify the Bacillus sp. proteases. Namely, complex protein mixtures from Bacillus sp. DJ-4, which were screened from Doen-Jang (Korean traditional fermented food), showed activity on the zymogram gel. The gel spots on the SYPRO Ruby gel, which corresponded to the active spots showing on the 2-D FZ gel, were analyzed by a matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometric analysis. Five intracellular fibrinolytic enzymes of Bacillus sp. DJ-4 were detected through 2-D FZ. The gel spots on the SYPRO Ruby dye stained 2-D gel corresponding to 2-D FZ were then analyzed by MALID-TOF MS. Three of the five gel spots proved to be quite similar to the ATP-dependent protease, extracellular neutral metalloprotease, and protease of Bacillus subtilis. Also, the extracellular proteases of Bacillus sp. DJ-4 employing this combined system were identified on three gels (e.g., casein, fibrin, and gelatin) and the proteolytic maps were established. This combined system of 2-D zymography and SYPRO Ruby dye should be useful for searching the specific protease from complex protein mixtures of many other sources (e.g., yeast and cancer cell lines).
Collapse
Affiliation(s)
- Nack-Shick Choi
- Proteome Research Laboratory, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Korea
| | | | | | | | | |
Collapse
|
40
|
Berggren KN, Schulenberg B, Lopez MF, Steinberg TH, Bogdanova A, Smejkal G, Wang A, Patton WF. An improved formulation of SYPRO Ruby protein gel stain: comparison with the original formulation and with a ruthenium II tris (bathophenanthroline disulfonate) formulation. Proteomics 2002; 2:486-98. [PMID: 11987123 DOI: 10.1002/1615-9861(200205)2:5<486::aid-prot486>3.0.co;2-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SYPRO Ruby protein gel stain is compatible with a variety of imaging platforms since it absorbs maximally in the ultraviolet (280 nm) and visible (470 nm) regions of the spectrum. Dye localization is achieved by noncovalent, electrostatic and hydrophobic binding to proteins, with signal being detected at 610 nm. Since proteins are not covalently modified by the dye, compatibility with downstream proteomics techniques such as matrix-assisted laser desorption/ionisation-time of flight mass spectrometry is assured. The principal limitation of the original formulation of SYPRO Ruby protein gel stain, is that it was only compatible with a limited number of gel fixation procedures. Too aggressive a fixation protocol led to diminished signal intensity and poor detection sensitivity. This is particularly apparent when post-staining gels subjected to labeling with other fluorophores such as Schiff's base staining of glycoproteins with fluorescent hydrazides. Consequently, we have developed an improved formulation of SYPRO Ruby protein gel stain that is fully compatible with commonly implemented protein fixation procedures and is suitable for post-staining gels after detection of glycoproteins using the green fluorescent Pro-Q Emerald 300 glycoprotein stain or detection of beta-glucuronidase using the green fluorescent ELF 97 beta-D-glucuronide. The new stain formulation is brighter, making it easier to manually excise spots for peptide mass profiling. An additional benefit of the improved formulation is that it permits staining of proteins in isoelectric focusing gels, without the requirement for caustic acids.
Collapse
Affiliation(s)
- Kiera N Berggren
- Proteomics Section, Molecular Probes, Inc., Eugene, OR 97402, USA
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Patton WF, Beechem JM. Rainbow's end: the quest for multiplexed fluorescence quantitative analysis in proteomics. Curr Opin Chem Biol 2002; 6:63-9. [PMID: 11827825 DOI: 10.1016/s1367-5931(01)00284-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
During the past two years, the performance of fluorescence-based protein detection methods has demonstrably eclipsed conventional technologies such as colloidal Coomassie Blue and silver staining with respect to detection sensitivity, quantitative accuracy and compatibility with modern protein identification and characterization procedures. At this point, fluorescence-based methods are poised to offer unprecedented new capabilities in proteomics investigations through the performance of multi-parameter quantitative measurements. The feasibility of such measurements has already been demonstrated through the specific detection of antibiotic-binding proteins, drug-metabolizing enzymes or post-translationally glycosylated proteins, along with the total protein expression profile from electrophoretically separated, complex biological specimens.
Collapse
Affiliation(s)
- Wayne F Patton
- Proteomics Section, Molecular Probes, Inc., 4849 Pitchford Avenue, Eugene, Oregon 97402, USA.
| | | |
Collapse
|
42
|
Affiliation(s)
- T J Griffin
- Institute for Systems Biology, Seattle, Washington 98105, USA.
| | | |
Collapse
|
43
|
Vogel JS, Grant PG, Buchholz BA, Dingley K, Turteltaub KW. Attomole quantitation of protein separations with accelerator mass spectrometry. Electrophoresis 2001; 22:2037-45. [PMID: 11465504 DOI: 10.1002/1522-2683(200106)22:10<2037::aid-elps2037>3.0.co;2-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Quantification of specific proteins depends on separation by chromatography or electrophoresis followed by chemical detection schemes such as staining and fluorophore adhesion. Chemical exchange of short-lived isotopes, particularly sulfur, is also prevalent despite the inconveniences of counting radioactivity. Physical methods based on isotopic and elemental analyses offer highly sensitive protein quantitation that has linear response over wide dynamic ranges and is independent of protein conformation. Accelerator mass spectrometry quantifies long-lived isotopes such as 14C to subattomole sensitivity. We quantified protein interactions with small molecules such as toxins, vitamins, and natural biochemicals at precisions of 1-5%. Micro-proton-induced X-ray emission quantifies elemental abundances in separated metalloprotein samples to nanogram amounts and is capable of quantifying phopsphorylated loci in gels. Accelerator-based quantitation is a possible tool for quantifying the genome translation into proteome.
Collapse
Affiliation(s)
- J S Vogel
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, CA 94551, USA.
| | | | | | | | | |
Collapse
|
44
|
Castellanos-Serra L, Vallin A, Proenza W, Le Caer JP, Rossier J. An optimized procedure for detection of proteins on carrier ampholyte isoelectric focusing and immobilized pH gradient gels with imidazole and zinc salts: its application to the identification of isoelectric focusing separated isoforms by in-gel proteolysis and mass spectrometry analysis. Electrophoresis 2001; 22:1677-85. [PMID: 11425223 DOI: 10.1002/1522-2683(200105)22:9<1677::aid-elps1677>3.0.co;2-h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A method for the characterization of proteins separated by isoelectric focusing in carrier ampholytes (CA-IEF) or immobilized pH gradient (IPG) gels by in-gel digestion and mass spectrometry is described. Proteins are detected by an improved imidazole-Sodium dodecyl sulfate (SDS)-zinc staining adapted for IEF and IPG gels. Sensitivity is close to that of mass spectrometry-compatible silver staining, but simpler and faster. Proteins were digested in imidazole-SDS-zinc stained CA-IEF and IPG gels in the presence of a zinc-chelating agent. Mass spectra were clearly interpretable as carrier ampholytes which were efficiently removed before digestion; high-sequence coverage that allowed isoform characterization was obtained by analyzing both the aqueous and the organic phase extracts.
Collapse
Affiliation(s)
- L Castellanos-Serra
- Division of Physical Chemistry, Center for Genetic Engineering and Biotechnology, Havana, Cuba.
| | | | | | | | | |
Collapse
|
45
|
Lamer S, Jungblut PR. Matrix-assisted laser desorption-ionization mass spectrometry peptide mass fingerprinting for proteome analysis: identification efficiency after on-blot or in-gel digestion with and without desalting procedures. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2001; 752:311-22. [PMID: 11270870 DOI: 10.1016/s0378-4347(00)00446-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In theory, peptide mass fingerprinting by matrix assisted laser desorption-ionization mass spectrometry (MALDI-MS) has the potential to identify all of the proteins detected by silver staining on gels. In practice, if the genome of the organism investigated is completely sequenced, using current techniques, all proteins stained by Coomassie Brilliant Blue can be identified. This loss of identification sensitivity of ten to hundred-fold is caused by loss of peptides by surface contacts. Therefore, we performed digestion and transfer of peptides in the lower microl range and reduced the number of steps. The peptide mix obtained from in-gel or on-blot digestion was analyzed directly after digestion or after concentration on POROS R2 beads. Eight protein spots of a 2-DE gel from Mycobacterium bovis BCG were identified using these four preparation procedures for MALDI-MS. Overall, on-blot digestion was as effective as in-gel digestion. Whereas higher signal intensities resulted after concentration, hydrophilic peptides are better detected by direct measurement of the peptide mix without POROS R2 concentration.
Collapse
Affiliation(s)
- S Lamer
- Max-Planck-Institute for Infection Biology, Central Support Unit Biochemistry, Berlin, Germany
| | | |
Collapse
|
46
|
Kemper C, Steinberg TH, Jones L, Patton WF. Simultaneous, two-color fluorescence detection of total protein profiles and beta-glucuronidase activity in polyacrylamide gel. Electrophoresis 2001; 22:970-6. [PMID: 11332766 DOI: 10.1002/1522-2683()22:5<970::aid-elps970>3.0.co;2-5] [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 dichromatic method for measuring the specific activity of beta-glucuronidase from complex cell homogenates or partially purified protein fractions is presented. Dual fluorescence is achieved by using the green emitting fluorogenic substrate ELF 97 beta-D-glucuronide to detect beta-glucuronidase activity, followed by the red emitting SYPRO Ruby protein gel stain or SYPRO Ruby IEF gel stain to detect the remaining proteins in the electrophoretic profile. Both ELF 97 alcohol, the highly fluorescent hydrolytic product generated from the enzyme substrate, and the SYPRO Ruby total protein stains are maximally excited by ultraviolet illumination. ELF 97 alcohol emits maximally at 525 nm while the SYPRO Ruby dyes emit maximally at 610 nm. Since ELF 97 beta-glucuronide is a precipitating substrate, it allows precise localization of beta-glucuronidase activity with minimal band diffusion. The staining method is simple and direct, without the requirement for ancillary coupling reactions. Dichromatic protein detection is demonstrated after sodium dodecyl sulfate(SDS)-polyacrylamide gel electrophoresis, carrier ampholyte-mediated isoelectric focusing or two-dimensional gel electrophoresis.
Collapse
Affiliation(s)
- C Kemper
- Molecular Probes, Inc, Eugene, OR 97402, USA
| | | | | | | |
Collapse
|
47
|
Abstract
The Dark Reader optical system (Clare Chemical Research, Denver, CO, USA) uses relatively low intensity broad-band visible blue light in combination with broad-band optical filters to detect fluorescence with a level of sensitivity that often surpasses that of UV transilluminators and can rival that of laser-based scanners. Applications of DR (Clare Chemical Research) devices include the detection of DNA and SYBR-stained protein samples following, and also during, electrophoresis. Unlike laser-based imaging systems, the fluorescence is directly visible to the user as well as being fully compatible with charge-coupled device (CCD) and Polaroid camera-based detection and imaging. Additionally, the DR optical system functions well in multicolor fluorophor environments. Because the Dark Reader does not emit any UV light, the extent of DNA damage incurred when visualizing DNA samples is drastically reduced compared to the damage produced by a UV device and this can have a significant benefit on downstream cloning protocols. Furthermore, dye photobleaching is minimal, extending the length of time that a fluorescent sample is visible. The inherent flexibility of the DR optical system allows many different configurations of the Dark Reader to be constructed such as transilluminators, hand lamps and integrated transilluminator-electrophoresis units.
Collapse
Affiliation(s)
- M Seville
- Clare Chemical Research, Inc, Denver, CO 80206, USA.
| |
Collapse
|
48
|
Lopez MF, Berggren K, Chernokalskaya E, Lazarev A, Robinson M, Patton WF. A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling. Electrophoresis 2000; 21:3673-83. [PMID: 11271486 DOI: 10.1002/1522-2683(200011)21:17<3673::aid-elps3673>3.0.co;2-m] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Proteomic projects are often focused on the discovery of differentially expressed proteins between control and experimental samples. Most laboratories choose the approach of running two-dimensional (2-D) gels, analyzing them and identifying the differentially expressed proteins by in-gel digestion and mass spectrometry. To date, the available stains for visualizing proteins on 2-D gels have been less than ideal for these projects because of poor detection sensitivity (Coomassie blue stain) or poor peptide recovery from in-gel digests and mass spectrometry (silver stain), unless extra destaining and washing steps are included in the protocol. In addition, the limited dynamic range of these stains has made it difficult to rigorously and reliably determine subtle differences in protein quantities. SYPRO Ruby Protein Gel Stain is a novel, ruthenium-based fluorescent dye for the detection of proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels that has properties making it well suited to high-throughput proteomics projects. The advantages of SYPRO Ruby Protein Gel Stain relative to silver stain demonstrated in this study include a broad linear dynamic range and enhanced recovery of peptides from in-gel digests for matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry.
Collapse
Affiliation(s)
- M F Lopez
- Proteome Systems, Inc., Woburn, MA 01824, USA.
| | | | | | | | | | | |
Collapse
|
49
|
Abstract
The goal of molecular ophthalmology is the early detection and therapeutic treatment of eye disease. Genomic technologies have profoundly enhanced the discovery of ocular disease candidate genes. Proteomics, the protein cognate of genomic technology, offers a means to monitor changes in the expression of a given ocular protein(s) and its post-translational modification, identify novel therapeutic targets and evaluate pharmacological effects on a given metabolic pathway. Using both tissue and cultured cells, numerous laboratories have begun to catalogue changes in ocular protein expression in normal, diseased and ageing subjects. Herein, we review published proteomic literature in the broad context of ophthalmic diseases involving various tissues of the eye.
Collapse
Affiliation(s)
- H T Steely
- Alcon Research Ltd, Fort Worth, TX 76134, USA.
| | | |
Collapse
|