1
|
da Silva NR, Ferreira LA, Teixeira JA, Uversky VN, Zaslavsky BY. Effects of sodium chloride and sodium perchlorate on properties and partition behavior of solutes in aqueous dextran-polyethylene glycol and polyethylene glycol-sodium sulfate two-phase systems. J Chromatogr A 2019; 1583:28-38. [DOI: 10.1016/j.chroma.2018.11.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 11/25/2022]
|
2
|
Quintana MDP, Ch’ng JH, Zandian A, Imam M, Hultenby K, Theisen M, Nilsson P, Qundos U, Moll K, Chan S, Wahlgren M. SURGE complex of Plasmodium falciparum in the rhoptry-neck (SURFIN4.2-RON4-GLURP) contributes to merozoite invasion. PLoS One 2018; 13:e0201669. [PMID: 30092030 PMCID: PMC6084945 DOI: 10.1371/journal.pone.0201669] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/19/2018] [Indexed: 12/25/2022] Open
Abstract
Plasmodium falciparum invasion into red blood cells (RBCs) is a complex process engaging proteins on the merozoite surface and those contained and sequentially released from the apical organelles (micronemes and rhoptries). Fundamental to invasion is the formation of a moving junction (MJ), a region of close apposition of the merozoite and the RBC plasma membranes, through which the merozoite draws itself before settling into a newly formed parasitophorous vacuole (PV). SURFIN4.2 was identified at the surface of the parasitized RBCs (pRBCs) but was also found apically associated with the merozoite. Using antibodies against the N-terminus of the protein we show the presence of SURFIN4.2 in the neck of the rhoptries, its secretion into the PV and shedding into the culture supernatant upon schizont rupture. Using immunoprecipitation followed by mass spectrometry we describe here a novel protein complex we have named SURGE where SURFIN4.2 forms interacts with the rhoptry neck protein 4 (RON4) and the Glutamate Rich Protein (GLURP). The N-terminal cysteine-rich-domain (CRD) of SURFIN4.2 mediates binding to the RBC membrane and its interaction with RON4 suggests its involvement in the contact between the merozoite apex and the RBC at the MJ. Supporting this suggestion, we also found that polyclonal antibodies to the extracellular domain (including the CRD) of SURFIN4.2 partially inhibit merozoite invasion. We propose that the formation of the SURGE complex participates in the establishment of parasite infection within the PV and the RBCs.
Collapse
Affiliation(s)
- Maria del Pilar Quintana
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Jun-Hong Ch’ng
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
| | - Arash Zandian
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH-Royal Institutet of Technology, Stockholm, Sweden
| | - Maryam Imam
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Kjell Hultenby
- Division of Clinical Research Centre, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Michael Theisen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Nilsson
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH-Royal Institutet of Technology, Stockholm, Sweden
| | - Ulrika Qundos
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH-Royal Institutet of Technology, Stockholm, Sweden
| | - Kirsten Moll
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Sherwin Chan
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
3
|
The solvent side of proteinaceous membrane-less organelles in light of aqueous two-phase systems. Int J Biol Macromol 2018; 117:1224-1251. [PMID: 29890250 DOI: 10.1016/j.ijbiomac.2018.06.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/07/2018] [Indexed: 12/29/2022]
Abstract
Water represents a common denominator for liquid-liquid phase transitions leading to the formation of the polymer-based aqueous two-phase systems (ATPSs) and a set of the proteinaceous membrane-less organelles (PMLOs). ATPSs have a broad range of biotechnological applications, whereas PMLOs play a number of crucial roles in cellular compartmentalization and often represent a cellular response to the stress. Since ATPSs and PMLOs contain high concentrations of polymers (such as polyethylene glycol (PEG), polypropylene glycol (PPG), Ucon, and polyvinylpyrrolidone (PVP), Dextran, or Ficoll) or biopolymers (peptides, proteins and nucleic acids), it is expected that the separated phases of these systems are characterized by the noticeable changes in the solvent properties of water. These changes in solvent properties can drive partitioning of various compounds (proteins, nucleic acids, organic low-molecular weight molecules, metal ions, etc.) between the phases of ATPSs or between the PMLOs and their surroundings. Although there is a sizable literature on the properties of the ATPS phases, much less is currently known about PMLOs. In this perspective article, we first represent liquid-liquid phase transitions in water, discuss different types of biphasic (or multiphasic) systems in water, and introduce various PMLOs and some of their properties. Then, some basic characteristics of polymer-based ATPSs are presented, with the major focus being on the current understanding of various properties of ATPS phases and solvent properties of water inside them. Finally, similarities and differences between the polymer-based ATPSs and biological PMLOs are discussed.
Collapse
|
4
|
Ahmadi S, Winter D. Identification of Poly(ethylene glycol) and Poly(ethylene glycol)-Based Detergents Using Peptide Search Engines. Anal Chem 2018; 90:6594-6600. [DOI: 10.1021/acs.analchem.8b00365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shiva Ahmadi
- Institute for Biochemistry and Molecular Biology, University of Bonn, 53115 Bonn, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, University of Bonn, 53115 Bonn, Germany
| |
Collapse
|
5
|
Zaslavsky BY, Uversky VN. In Aqua Veritas: The Indispensable yet Mostly Ignored Role of Water in Phase Separation and Membrane-less Organelles. Biochemistry 2018; 57:2437-2451. [PMID: 29303563 DOI: 10.1021/acs.biochem.7b01215] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the common practice of presenting structures of biological molecules on an empty background and the assumption that interactions between biological macromolecules take place within the inert solvent, water represents an active component of various biological processes. This Perspective addresses indispensable, yet mostly ignored, roles of water in biological liquid-liquid phase transitions and in the biogenesis of various proteinaceous membrane-less organelles. We point out that changes in the structure of water reflected in the changes in its abilities to donate and/or accept hydrogen bonds and participate in dipole-dipole and dipole-induced dipole interactions in the presence of various solutes (ranging from small molecules to synthetic polymers and biological macromolecules) might represent a driving force for the liquid-liquid phase separation, define partitioning of various solutes in formed phases, and define the exceptional ability of intrinsically disordered proteins to be engaged in the formation of proteinaceous membrane-less organelles.
Collapse
Affiliation(s)
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , Florida 33612 , United States.,Laboratory of New Methods in Biology , Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
| |
Collapse
|
6
|
Streamlined Membrane Proteome Preparation for Shotgun Proteomics Analysis with Triton X-100 Cloud Point Extraction and Nanodiamond Solid Phase Extraction. MATERIALS 2016; 9:ma9050385. [PMID: 28773508 PMCID: PMC5503057 DOI: 10.3390/ma9050385] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/28/2016] [Accepted: 05/11/2016] [Indexed: 12/19/2022]
Abstract
While mass spectrometry (MS) plays a key role in proteomics research, characterization of membrane proteins (MP) by MS has been a challenging task because of the presence of a host of interfering chemicals in the hydrophobic protein extraction process, and the low protease digestion efficiency. We report a sample preparation protocol, two-phase separation with Triton X-100, induced by NaCl, with coomassie blue added for visualizing the detergent-rich phase, which streamlines MP preparation for SDS-PAGE analysis of intact MP and shot-gun proteomic analyses. MP solubilized in the detergent-rich milieu were then sequentially extracted and fractionated by surface-oxidized nanodiamond (ND) at three pHs. The high MP affinity of ND enabled extensive washes for removal of salts, detergents, lipids, and other impurities to ensure uncompromised ensuing purposes, notably enhanced proteolytic digestion and down-stream mass spectrometric (MS) analyses. Starting with a typical membranous cellular lysate fraction harvested with centrifugation/ultracentrifugation, MP purities of 70%, based on number (not weight) of proteins identified by MS, was achieved; the weight-based purity can be expected to be much higher.
Collapse
|
7
|
Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
Collapse
Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
| |
Collapse
|
8
|
Mansour FR, Zhou L, Danielson ND. Applications of Poly(Ethylene)Glycol (PEG) in Separation Science. Chromatographia 2015. [DOI: 10.1007/s10337-015-2983-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Yue L, He Z, Zhu Y, Shang Y, Liu H. Physicochemical Characterization of Novel Aqueous Two-Phase System: Gemini Surfactant 12-2-12/NaBr/H2O. Appl Biochem Biotechnol 2015; 175:3557-70. [DOI: 10.1007/s12010-015-1526-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/21/2015] [Indexed: 10/24/2022]
|
10
|
A new enabling proteomics methodology to investigate membrane associated proteins from parasitic nematodes: case study using ivermectin resistant and ivermectin susceptible isolates of Caenorhabditis elegans and Haemonchus contortus. Vet Parasitol 2014; 207:266-75. [PMID: 25537855 DOI: 10.1016/j.vetpar.2014.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 11/23/2014] [Accepted: 12/06/2014] [Indexed: 01/06/2023]
Abstract
The mechanisms involved in anthelmintic resistance (AR) are complex but a greater understanding of AR management is essential for effective and sustainable control of parasitic helminth worms in livestock. Current tests to measure AR are time consuming and can be technically problematic, gold standard diagnostics are therefore urgently required to assist in combatting the threat from drug resistant parasites. For anthelmintics such as ivermectin (IVM), target proteins may be present in the cellular membrane. As proteins usually act in complexes and not in isolation, AR may develop and be measurable in the target associated proteins present in the parasite membrane. The model nematode Caenorhabditis elegans was used to develop a sub-proteomic assay to measure protein expression differences, between IVM resistant and IVM susceptible isolates in the presence and absence of drug challenge. Evaluation of detergents including CHAPS, ASB-14, C7BzO, Triton ×100 and TBP (tributyl phosphine) determined optimal conditions for the resolution of membrane proteins in Two Dimensional Gel Electrophoresis (2DE). These sub-proteomic methodologies were then translated and evaluated using IVM-susceptible and IVM-resistant Haemonchus contortus; a pathogenic blood feeding parasitic nematode which is of global importance in livestock health, welfare and productivity. We have demonstrated the successful resolution of membrane associated proteins from both C. elegans and H. contortus isolates, using a combination of CHAPS and the zwitterionic amphiphilic surfactant ASB-14 to further support the detection of markers for AR.
Collapse
|
11
|
Patchornik G, Danino D, Kesselman E, Wachtel E, Friedman N, Sheves M. Purification of a membrane protein with conjugated engineered micelles. Bioconjug Chem 2013; 24:1270-5. [PMID: 23758098 DOI: 10.1021/bc400069w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A novel method for purifying membrane proteins is presented. The approach makes use of engineered micelles composed of a nonionic detergent, β-octylglucoside, and a hydrophobic metal chelator, bathophenanthroline. Via the chelators, the micelles are specifically conjugated, i.e., tethered, in the presence of Fe(2+) ions, thereby forming micellar aggregates which provide the environment for separation of lipid-soluble membrane proteins from water-soluble proteins. The micellar aggregates (here imaged by cryo-transmission electron microscopy) successfully purify the light driven proton pump, bacteriorhodopsin (bR), from E. coli lysate. Purification takes place within 15 min and can be performed both at room temperature and at 4 °C. More than 94% of the water-soluble macromolecules in the lysate are excluded, with recovery yields of the membrane protein ranging between 74% and 85%. Since this approach does not require precipitants, high concentrations of detergent to induce micellar aggregates, high temperature, or changes in pH, it is suggested that it may be applied to the purification of a wide variety of membrane proteins.
Collapse
Affiliation(s)
- Guy Patchornik
- Department of Biological Chemistry, Ariel University, 70400, Israel.
| | | | | | | | | | | |
Collapse
|
12
|
Vuckovic D, Dagley LF, Purcell AW, Emili A. Membrane proteomics by high performance liquid chromatography-tandem mass spectrometry: Analytical approaches and challenges. Proteomics 2013; 13:404-23. [DOI: 10.1002/pmic.201200340] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/24/2012] [Accepted: 10/09/2012] [Indexed: 01/01/2023]
Affiliation(s)
- Dajana Vuckovic
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto ON Canada
| | - Laura F. Dagley
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto ON Canada
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; University of Melbourne; Parkville Victoria Australia
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Victoria Australia
| | - Andrew Emili
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto ON Canada
- Department of Molecular Genetics; University of Toronto; Toronto ON Canada
| |
Collapse
|
13
|
Miteva YV, Budayeva HG, Cristea IM. Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem 2013; 85:749-68. [PMID: 23157382 PMCID: PMC3666915 DOI: 10.1021/ac3033257] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Ileana M. Cristea
- Corresponding author: Ileana M. Cristea 210 Lewis Thomas Laboratory Department of Molecular Biology Princeton University Princeton, NJ 08544 Tel: 6092589417 Fax: 6092584575
| |
Collapse
|
14
|
Liu Y, Wu Z, Zhang Y, Yuan H. Partitioning of biomolecules in aqueous two-phase systems of polyethylene glycol and nonionic surfactant. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.08.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
15
|
Abstract
The response to extracellular stimuli often alters the phosphorylation state of plasma membrane- associated proteins. In this regard, generation of a comprehensive membrane phosphoproteome can significantly enhance signal transduction and drug mechanism studies. However, analysis of this subproteome is regarded as technically challenging, given the low abundance and insolubility of integral membrane proteins, combined with difficulties in isolating, ionizing and fragmenting phosphopeptides. In this article, we highlight recent advances in membrane and phosphoprotein enrichment techniques resulting in improved identification of these elusive peptides. We also describe the use of alternative fragmentation techniques, and assess their current and future value to the field of membrane phosphoproteomics.
Collapse
Affiliation(s)
- Benjamin C Orsburn
- Drug Mechanism Group, Developmental Therapeutics Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - Luke H Stockwin
- Drug Mechanism Group, Developmental Therapeutics Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - Dianne L Newton
- Drug Mechanism Group, Developmental Therapeutics Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA
| |
Collapse
|
16
|
Vertommen A, Panis B, Swennen R, Carpentier SC. Challenges and solutions for the identification of membrane proteins in non-model plants. J Proteomics 2011; 74:1165-81. [PMID: 21354347 DOI: 10.1016/j.jprot.2011.02.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/04/2011] [Accepted: 02/16/2011] [Indexed: 01/27/2023]
Abstract
The workhorse for proteomics in non-model plants is classical two-dimensional electrophoresis, a combination of iso-electric focusing and SDS-PAGE. However, membrane proteins with multiple membrane spanning domains are hardly detected on classical 2-DE gels because of their low abundance and poor solubility in aqueous media. In the current review, solutions that have been proposed to handle these two problems in non-model plants are discussed. An overview of alternative techniques developed for membrane proteomics is provided together with a comparison of their strong and weak points. Subsequently, strengths and weaknesses of the different techniques and methods to evaluate the identification of membrane proteins are discussed. Finally, an overview of recent plant membrane proteome studies is provided with the used separation technique and the number of identified membrane proteins listed.
Collapse
Affiliation(s)
- A Vertommen
- Laboratory of Tropical Crop Improvement, Department of Biosystems, K.U. Leuven, Kasteelpark Arenberg 13, B-3001 Heverlee, Belgium
| | | | | | | |
Collapse
|
17
|
Tajima N, Takai M, Ishihara K. Significance of Antibody Orientation Unraveled: Well-Oriented Antibodies Recorded High Binding Affinity. Anal Chem 2011; 83:1969-76. [DOI: 10.1021/ac1026786] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Madoka Takai
- Department of Materials Engineering,
- Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kazuhiko Ishihara
- Department of Materials Engineering,
- Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| |
Collapse
|
18
|
Hu R, Feng X, Chen P, Fu M, Chen H, Guo L, Liu BF. Rapid, highly efficient extraction and purification of membrane proteins using a microfluidic continuous-flow based aqueous two-phase system. J Chromatogr A 2011; 1218:171-7. [PMID: 21112057 DOI: 10.1016/j.chroma.2010.10.090] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 10/22/2010] [Accepted: 10/25/2010] [Indexed: 10/18/2022]
|
19
|
Wasbrough ER, Dorus S, Hester S, Howard-Murkin J, Lilley K, Wilkin E, Polpitiya A, Petritis K, Karr TL. The Drosophila melanogaster sperm proteome-II (DmSP-II). J Proteomics 2010; 73:2171-85. [DOI: 10.1016/j.jprot.2010.09.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 09/07/2010] [Accepted: 09/07/2010] [Indexed: 01/07/2023]
|
20
|
|
21
|
Systematic cyanobacterial membrane proteome analysis by combining acid hydrolysis and digestive enzymes with nano-liquid chromatography–Fourier transform mass spectrometry. J Chromatogr A 2010; 1217:285-93. [DOI: 10.1016/j.chroma.2009.11.045] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 08/26/2009] [Accepted: 11/13/2009] [Indexed: 11/22/2022]
|
22
|
Ge B, Li W, Yin Y. Enrichment separation of recombinant human CCR3 using detergent/polymer two-phase system. Biotechnol Lett 2009; 32:393-7. [PMID: 19941034 DOI: 10.1007/s10529-009-0169-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 11/04/2009] [Accepted: 11/05/2009] [Indexed: 11/30/2022]
Abstract
Studies on the structure and functions of membrane proteins are impeded by their lability, hydrophobicity, difficulty in purification and low yields. Human chemokine receptor 3 (CCR3) is a G protein-coupled receptor related to allergic diseases. A Triton X-100/PEG20000 two-phase system was employed for enrichment separation of CCR3 over-expressed in E. coli. Optimal CCR3 partitioning with partition coefficient around 8 was obtained at pH 7.0, ionic strength of 0.3 mol/kg and 3 h equilibration time. Total recovery of CCR3 reached 102 +/- 15%, which was much higher than 32 +/- 5% of the normally used ultracentrifugation method. The recovered CCR3 was finally purified by two chromatography steps giving a final protein of 87 kDa.
Collapse
Affiliation(s)
- Baosheng Ge
- Center for Bioengineering and Biotechnology, China University of Petroleum, 266555, Qingdao, Shandong, People's Republic of China.
| | | | | |
Collapse
|
23
|
Premsler T, Zahedi RP, Lewandrowski U, Sickmann A. Recent advances in yeast organelle and membrane proteomics. Proteomics 2009; 9:4731-43. [DOI: 10.1002/pmic.200900201] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
24
|
Lundbäck AK, Müller SA, Engel A, Hebert H. Assembly of Kch, a putative potassium channel from Escherichia coli. J Struct Biol 2009; 168:288-93. [PMID: 19631752 DOI: 10.1016/j.jsb.2009.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 07/16/2009] [Accepted: 07/21/2009] [Indexed: 11/30/2022]
Abstract
Attempts to explore the structure and function of Kch, a putative potassium channel of Escherichia coli have yielded varying results; potassium-associated functions have been found in vivo but not in vitro. Here the kch gene is shown to produce two proteins, full-length Kch and the large C-terminal cytosolic domain (the RCK domain). Further, these two proteins are associated at the initial stages of purification. Previous structural studies of full-length Kch claim that the isolated protein forms large aggregates that are not suitable for analysis. The results presented here show that the purified protein sample, although heterogeneous, has one major population with a mass of about 400kDa, implying the presence of two Kch tetramers in a complex form. A three dimensional reconstruction at 25A based on electron microscopy data from negatively stained particles, revealed a 210A long and 95A wide complex in which the two tetrameric Kch units are linked by their RCK domains, giving rise to a large central ring of density. The formation of this dimer of tetramers on expression or during purification, may explain why attempts to reconstitute Kch into liposomes for activity measurements have failed.
Collapse
Affiliation(s)
- Anna-Karin Lundbäck
- Karolinska Institutet, Department of Biosciences and Nutrition and Royal Institute of Technology, Novum, Huddinge, Sweden
| | | | | | | |
Collapse
|
25
|
Lefort N, Yi Z, Bowen B, Glancy B, De Filippis EA, Mapes R, Hwang H, Flynn CR, Willis WT, Civitarese A, Højlund K, Mandarino LJ. Proteome profile of functional mitochondria from human skeletal muscle using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS. J Proteomics 2009; 72:1046-60. [PMID: 19567276 DOI: 10.1016/j.jprot.2009.06.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 06/12/2009] [Accepted: 06/20/2009] [Indexed: 10/20/2022]
Abstract
Mitochondria can be isolated from skeletal muscle in a manner that preserves tightly coupled bioenergetic function in vitro. The purpose of this study was to characterize the composition of such preparations using a proteomics approach. Mitochondria isolated from human vastus lateralis biopsies were functional as evidenced by their response to carbohydrate and fat-derived fuels. Using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS, 823 unique proteins were detected, and 487 of these were assigned to the mitochondrion, including the newly characterized SIRT5, MitoNEET and RDH13. Proteins detected included 9 of the 13 mitochondrial DNA-encoded proteins and 86 of 104 electron transport chain (ETC) and ETC-related proteins. In addition, 59 of 78 proteins of the 55S mitoribosome, several TIM and TOM proteins and cell death proteins were present. This study presents an efficient method for future qualitative assessments of proteins from functional isolated mitochondria from small samples of healthy and diseased skeletal muscle.
Collapse
Affiliation(s)
- Natalie Lefort
- Center for Metabolic Biology, Arizona State University, Tempe, AZ, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Extraction of yeast mitochondrial membrane proteins by solubilization and detergent/polymer aqueous two-phase partitioning. Methods Mol Biol 2009. [PMID: 19153685 DOI: 10.1007/978-1-60327-310-7_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Identification and characterization of membrane proteins is of increasing importance in modern proteomic studies. It is of central interest to have access to methods that combine efficient solubilization with enrichment of proteins and intact protein complexes. Separation methods have been developed based on nondenaturing detergent extraction of yeast mitochondrial membrane proteins followed by enrichment of hydrophobic proteins in aqueous two-phase system. Combining the zwitterionic detergent Zwittergent 3-10 and the nonionic detergent Triton X-114 results in a complementary solubilization of proteins, which is similar to that of the anionic detergent sodium dodecyl sulfate (SDS) but with the important advantage of being nondenaturing. Detergent/polymer two-phase system partitioning offers removal of soluble proteins, which can be further improved by manipulation of the driving forces governing protein distribution between the phases. Integral and peripheral membrane protein subunits from intact membrane protein complexes partition to the detergent phase while soluble proteins are found in the polymer phase. A protocol is presented which combines nondenaturing solubilization of membrane proteins with extraction in detergent/polymer two-phase system for application in proteomic studies as a mild and efficient method for enrichment of membrane proteins and membrane protein complexes.
Collapse
|
27
|
Yang L, Zhang H, Bruce JE. Optimizing the detergent concentration conditions for immunoprecipitation (IP) coupled with LC-MS/MS identification of interacting proteins. Analyst 2009; 134:755-62. [PMID: 19305927 DOI: 10.1039/b813335b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Immunoprecipitation (IP) coupled with LC-MS/MS is a widely used method in proteomics research to identify proteins and to study protein-protein interactions. IP techniques allow purification of proteins of interest and reduce sample complexity before introduction to the mass spectrometer. The effectiveness of IP experiments is an important factor for identification of proteins and protein-protein interactions. In this paper, a variety of IP conditions were studied systematically to improve IP-based protein interaction identification capabilities. Low concentration detergent (around 0.05% NP40/PBS) was found to improve IP effectiveness by decreasing non-specific binding. However, higher concentration detergent (e.g. 1% NP40/PBS) was detrimental. Furthermore, with lower protein concentrations, the IP system showed lower tolerance to detergent. For example, with a detergent concentration higher than 0.05% NP40/PBS, IP experiments were unsuccessful with low protein concentration (e.g. 0.28 microM ADH). In some cases the observed results were even worse than the results obtained without detergent. However, when the protein concentration was high (e.g. 1.12 microM ADH), this effect was not obvious and the high detergent (higher than 0.1%) experimental results were similar to those from low detergent concentration experiments (around 0.05%). Another application of this strategy to a more general system based on FLAG-Bacterial Alkaline Phosphatase (BAP) and anti-FLAG antibody was also performed. These results also suggested that low detergent concentration (0.05% NP40) is helpful for IP experiments, especially for the experiments with low protein concentrations. Considering that in most real applications, the proteins of interest are usually present in low abundance, a low amount of detergent is recommended to be used. The optimized detergent concentration was determined to be 0.05% in these studies. However, the key result presented here illustrates that both detergent and protein concentrations should be carefully considered when one is trying to optimize IP prior to mass spectrometry experiments.
Collapse
Affiliation(s)
- Li Yang
- Department of Genome Sciences, The University of Washington, Seattle, WA 98195-5065, USA
| | | | | |
Collapse
|
28
|
González de la Vara LE, Lino Alfaro B. Separation of membrane proteins according to their hydropathy by serial phase partitioning with Triton X-114. Anal Biochem 2009; 387:280-6. [PMID: 19454227 DOI: 10.1016/j.ab.2009.01.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 01/21/2009] [Accepted: 01/23/2009] [Indexed: 10/21/2022]
Abstract
The detergent Triton X-114, because of its convenient cloud point temperature (22 degrees C), has been used extensively to extract membrane proteins and to separate them in two phases according to their hydropathy. The upper detergent-poor phase contains mostly hydrophilic proteins, whereas hydrophobic ones are found mainly in the lower detergent-rich phase. In this work, we developed a method to fractionate membrane proteins and estimate their hydropathy based on a series of cloud point partitions with Triton X-114. With this method, beetroot plasma membrane proteins were separated in different fractions according to their hydropathy, following the binomial distribution law as expected. This method revealed the presence of both hydrophilic and hydrophobic Ca(2+)-dependent protein kinases in those membranes. At least five distinct Ca(2+)-dependent kinases were observed in in-gel kinase activity assays. This separation procedure was also used as the first step in the purification of a hydrophobic 60-kDa kinase.
Collapse
Affiliation(s)
- Luis E González de la Vara
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Gto. 36821, Mexico.
| | | |
Collapse
|
29
|
|
30
|
Li Y, Yu J, Wang Y, Griffin NM, Long F, Shore S, Oh P, Schnitzer JE. Enhancing identifications of lipid-embedded proteins by mass spectrometry for improved mapping of endothelial plasma membranes in vivo. Mol Cell Proteomics 2009; 8:1219-35. [PMID: 19155209 DOI: 10.1074/mcp.m800215-mcp200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lipid membranes structurally define the outer surface and internal organelles of cells. The multitude of proteins embedded in lipid bilayers are clearly functionally important, yet they remain poorly defined. Even today, integral membrane proteins represent a special challenge for current large scale shotgun proteomics methods. Here we used endothelial cell plasma membranes isolated directly from lung tissue to test the effectiveness of four different mass spectrometry-based methods, each with multiple replicate measurements, to identify membrane proteins. In doing so, we substantially expanded this membranome to 1,833 proteins, including >500 lipid-embedded proteins. The best method combined SDS-PAGE prefractionation with trypsin digestion of gel slices to generate peptides for seamless and continuous two-dimensional LC/MS/MS analysis. This three-dimensional separation method outperformed current widely used two-dimensional methods by significantly enhancing protein identifications including single and multiple pass transmembrane proteins; >30% are lipid-embedded proteins. It also profoundly improved protein coverage, sensitivity, and dynamic range of detection and substantially reduced the amount of sample and the number of replicate mass spectrometry measurements required to achieve 95% analytical completeness. Such expansion in comprehensiveness requires a trade-off in heavy instrument time but bodes well for future advancements in truly defining the ever important membranome with its potential in network-based systems analysis and the discovery of disease biomarkers and therapeutic targets. This analytical strategy can be applied to other subcellular fractions and should extend the comprehensiveness of many future organellar proteomics pursuits.
Collapse
Affiliation(s)
- Yan Li
- Sidney Kimmel Cancer Center, San Diego, California 92121, USA
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Distler AM, Kerner J, Hoppel CL. Proteomics of mitochondrial inner and outer membranes. Proteomics 2009; 8:4066-82. [PMID: 18763707 DOI: 10.1002/pmic.200800102] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
For the proteomic study of mitochondrial membranes, documented high quality mitochondrial preparations are a necessity to ensure proper localization. Despite the state-of-the-art technologies currently in use, there is no single technique that can be used for all studies of mitochondrial membrane proteins. Herein, we use examples to highlight solubilization techniques, different chromatographic methods, and developments in gel electrophoresis for proteomic analysis of mitochondrial membrane proteins. Blue-native gel electrophoresis has been successful not only for dissection of the inner membrane oxidative phosphorylation system, but also for the components of the outer membrane such as those involved in protein import. Identification of PTMs such as phosphorylation, acetylation, and nitration of mitochondrial membrane proteins has been greatly improved by the use of affinity techniques. However, understanding of the biological effect of these modifications is an area for further exploration. The rapid development of proteomic methods for both identification and quantitation, especially for modifications, will greatly impact the understanding of the mitochondrial membrane proteome.
Collapse
Affiliation(s)
- Anne M Distler
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | |
Collapse
|
32
|
Recorbet G, Rogniaux H, Gianinazzi-Pearson V, DumasGaudot E. Fungal proteins in the extra-radical phase of arbuscular mycorrhiza: a shotgun proteomic picture. THE NEW PHYTOLOGIST 2009; 181:248-260. [PMID: 19121027 DOI: 10.1111/j.1469-8137.2008.02659.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Ghislaine Recorbet
- Unité Mixte de Recherche Plante-Microbe-Environnement INRA 1088/CNRS 5184/Université de Bourgogne. INRA-CMSE. BP 86510. 21065 Dijon Cedex, France;Unité de Recherche 1268 Biopolymères- Interactions-Assemblages, Spectrométrie de Masse, INRA, rue de la Géraudière. BP 71627, 44316 Nantes Cedex 3, France
| | - Hélène Rogniaux
- Unité Mixte de Recherche Plante-Microbe-Environnement INRA 1088/CNRS 5184/Université de Bourgogne. INRA-CMSE. BP 86510. 21065 Dijon Cedex, France;Unité de Recherche 1268 Biopolymères- Interactions-Assemblages, Spectrométrie de Masse, INRA, rue de la Géraudière. BP 71627, 44316 Nantes Cedex 3, France
| | - Vivienne Gianinazzi-Pearson
- Unité Mixte de Recherche Plante-Microbe-Environnement INRA 1088/CNRS 5184/Université de Bourgogne. INRA-CMSE. BP 86510. 21065 Dijon Cedex, France;Unité de Recherche 1268 Biopolymères- Interactions-Assemblages, Spectrométrie de Masse, INRA, rue de la Géraudière. BP 71627, 44316 Nantes Cedex 3, France
| | - Eliane DumasGaudot
- Unité Mixte de Recherche Plante-Microbe-Environnement INRA 1088/CNRS 5184/Université de Bourgogne. INRA-CMSE. BP 86510. 21065 Dijon Cedex, France;Unité de Recherche 1268 Biopolymères- Interactions-Assemblages, Spectrométrie de Masse, INRA, rue de la Géraudière. BP 71627, 44316 Nantes Cedex 3, France
| |
Collapse
|
33
|
|
34
|
Dormeyer W, van Hoof D, Mummery CL, Krijgsveld J, Heck AJR. A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells. Proteomics 2008; 8:4036-53. [DOI: 10.1002/pmic.200800143] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
35
|
Gong Y, Wang N, Wu F, Cass CE, Damaraju S, Mackey JR, Li L. Proteome Profile of Human Breast Cancer Tissue Generated by LC−ESI−MS/MS Combined with Sequential Protein Precipitation and Solubilization. J Proteome Res 2008; 7:3583-90. [DOI: 10.1021/pr800229j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Yan Gong
- PolyomX Program, Cross Cancer Institute, Alberta Cancer Board, and Departments of Chemistry, Oncology, and Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Nan Wang
- PolyomX Program, Cross Cancer Institute, Alberta Cancer Board, and Departments of Chemistry, Oncology, and Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Fang Wu
- PolyomX Program, Cross Cancer Institute, Alberta Cancer Board, and Departments of Chemistry, Oncology, and Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Carol E. Cass
- PolyomX Program, Cross Cancer Institute, Alberta Cancer Board, and Departments of Chemistry, Oncology, and Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sambasivarao Damaraju
- PolyomX Program, Cross Cancer Institute, Alberta Cancer Board, and Departments of Chemistry, Oncology, and Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - John R. Mackey
- PolyomX Program, Cross Cancer Institute, Alberta Cancer Board, and Departments of Chemistry, Oncology, and Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- PolyomX Program, Cross Cancer Institute, Alberta Cancer Board, and Departments of Chemistry, Oncology, and Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
36
|
Everberg H, Gustavasson N, Tjerned F. Enrichment of membrane proteins by partitioning in detergent/polymer aqueous two-phase systems. Methods Mol Biol 2008; 424:403-412. [PMID: 18369878 DOI: 10.1007/978-1-60327-064-9_31] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Methods that combine efficient solubilization with enrichment of proteins and intact protein complexes are of central interest in current membrane proteomics. We have developed methods based on nondenaturing detergent extraction of yeast mitochondrial membrane proteins followed by enrichment of hydrophobic proteins in aqueous two-phase system. Combining the zwitterionic detergent Zwittergent 3-10 and the nonionic detergent Triton X-114 results in a complementary solubilization of proteins, which is similar to that of the anionic detergent sodium dodecyl sulfate (SDS) but with the important advantage of being nondenaturing. Detergent/polymer two-phase system partitioning offers removal of soluble proteins that can be further improved by manipulation of the driving forces governing protein distribution between the phases. Integral and peripheral membrane protein subunits from intact membrane protein complexes partition to the detergent phase while soluble proteins are found in the polymer phase. An optimized solubilization protocol is presented in combination with detergent/polymer two-phase partitioning as a mild and efficient method for initial enrichment of membrane proteins and membrane protein complexes in proteomic studies.
Collapse
|
37
|
Liquid–liquid extraction of commercial and biosynthesized nisin by aqueous two-phase micellar systems. Enzyme Microb Technol 2008; 42:107-12. [DOI: 10.1016/j.enzmictec.2007.08.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 08/15/2007] [Accepted: 08/15/2007] [Indexed: 01/20/2023]
|
38
|
Arnold T, Linke D. Phase separation in the isolation and purification of membrane proteins. Biotechniques 2007; 43:427-30, 432, 434 passim. [DOI: 10.2144/000112566] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Phase separation is a simple, efficient, and cheap method to purify and concentrate detergent-solubilized membrane proteins. In spite of this, phase separation is not widely used or even known among membrane protein scientists, and ready-to-use protocols are available for only relatively few detergent/membrane protein combinations. Here, we summarize the physical and chemical parameters that influence the phase separation behavior of detergents commonly used for membrane protein studies. Examples for the successful purification of membrane proteins using this method with different classes of detergents are provided. As the choice of the detergent is critical in many downstream applications (e.g., membrane protein crystallization or functional assays), we discuss how new phase separation protocols can be developed for a given detergent buffer system.
Collapse
Affiliation(s)
- Thomas Arnold
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dirk Linke
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| |
Collapse
|
39
|
Affiliation(s)
- Anna E Speers
- Department of Pharmacology, University of Colorado School of Medicine, P.O. Box 6511, MS 8303, Aurora, Colorado 80045, USA
| | | |
Collapse
|
40
|
Cañas B, Piñeiro C, Calvo E, López-Ferrer D, Gallardo JM. Trends in sample preparation for classical and second generation proteomics. J Chromatogr A 2007; 1153:235-58. [PMID: 17276441 DOI: 10.1016/j.chroma.2007.01.045] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 12/18/2006] [Accepted: 01/12/2007] [Indexed: 11/16/2022]
Abstract
Sample preparation is a fundamental step in the proteomics workflow. However, it is not easy to find compiled information updating this subject. In this paper, the strategies and protocols for protein extraction and identification, following either classical or second generation proteomics methodologies, are reviewed. Procedures for: tissue disruption, cell lysis, sample pre-fractionation, protein separation by 2-DE, protein digestion, mass spectrometry analysis, multidimensional peptide separations and quantification of protein expression level are described.
Collapse
Affiliation(s)
- Benito Cañas
- Dept. Química Analítica, Facultad de CC, Químicas, UCM, Av.Complutense s/n, Madrid 28040, Spain.
| | | | | | | | | |
Collapse
|