1
|
Ivanov AS, Ershov PV, Poverennaya EV, Lisitsa AV, Archakov AI. [Protocols of proteins interactomics: molecular fishing on optical chips and magnetic nanoparticles]. BIOMEDITSINSKAIA KHIMIIA 2013; 59:171-182. [PMID: 23789344 DOI: 10.18097/pbmc20135902171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Now it is absolutely clear, that the majority of proteins in living systems function due to interaction with each other in stable or dynamic proteins complexes. Therefore necessity of deeper studies of proteins functions causes expansion of protein-protein interaction research. In the present review the brief description and comparative estimation of experimental methods and protocols of protein interactomics, based on technology of molecular fishing on an optical chips and paramagnetic nanoparticles is given.
Collapse
|
2
|
Madian AG, Rochelle NS, Regnier FE. Mass-linked immuno-selective assays in targeted proteomics. Anal Chem 2012; 85:737-48. [PMID: 22950521 DOI: 10.1021/ac302071k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ashraf G Madian
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | |
Collapse
|
3
|
Ershov P, Mezentsev Y, Gnedenko O, Mukha D, Yantsevich A, Britikov V, Kaluzhskiy L, Yablokov E, Molnar A, Ivanov A, Lisitsa A, Gilep A, Usanov S, Archakov A. Protein interactomics based on direct molecular fishing on paramagnetic particles: experimental simulation and SPR validation. Proteomics 2012; 12:3295-8. [PMID: 23001861 DOI: 10.1002/pmic.201200135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 07/04/2012] [Accepted: 08/14/2012] [Indexed: 11/10/2022]
Abstract
We describe an experimental approach for direct molecular fishing of prey protein on the surface of two types of paramagnetic particles (PMP) having different size and composition. Human microsomal cytochrome b(5) (b(5)) and its known partner human cytochrome P450 3A5 (CYP3A5) were used as bait and prey proteins, respectively. For assessing the level of unspecific binding of background proteins, α-fetoprotein (aFP) was used. SPR measurements were applied for quantitative analysis of trapped proteins (CYP3A5 and aFP) after fishing on PMP. It was shown that the described approach of molecular fishing on micro-PMP provides enough prey proteins for LC-MS/MS identification and SPR validation, so this approach can be used for discovery of new protein-protein interactions in the framework of Human Proteome Project.
Collapse
Affiliation(s)
- Pavel Ershov
- Orechovich Institute of Biomedical Chemistry of RAMS, Moscow, Russia
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Ivanov AS, Ershov PV, Mezentsev YV, Poverennaya EV, Lisitsa AV, Archakov AI. Protocols of protein interactomics: Molecular fishing on optical chips and magnetic nanoparticles. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2012. [DOI: 10.1134/s1990750812020072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
5
|
Ivanov AS, Zgoda VG, Archakov AI. Technologies of protein interactomics: A review. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:8-21. [DOI: 10.1134/s1068162011010092] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
6
|
Abstract
The combination of surface plasmon resonance (SPR) and mass spectrometry (MS) creates a comprehensive protein investigation approach wherein SPR is employed for protein quantification and MS is utilized to structurally characterize the proteins. In such, MS utterly complements the SPR detection and reveals intrinsic protein structural modifications that go unregistered via the SPR detection. Protein complexes and non-specific binding can also be delineated via the SPR-MS approach. Described here are the protocols and know-how for successful and reproducible integration of SPR and MS. The individual steps of the entire SPR-MS process are illustrated via an example showing analysis of myoglobin from human plasma.
Collapse
|
7
|
Combination of a SAW-biosensor with MALDI mass spectrometric analysis. Biosens Bioelectron 2008; 23:1496-502. [DOI: 10.1016/j.bios.2008.01.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 01/03/2008] [Indexed: 11/21/2022]
|
8
|
Benesch JLP, Ruotolo BT, Simmons DA, Robinson CV. Protein complexes in the gas phase: technology for structural genomics and proteomics. Chem Rev 2007; 107:3544-67. [PMID: 17649985 DOI: 10.1021/cr068289b] [Citation(s) in RCA: 344] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Justin L P Benesch
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | | | |
Collapse
|
9
|
Nedelkov D. Mass spectrometry-based immunoassays for the next phase of clinical applications. Expert Rev Proteomics 2007; 3:631-40. [PMID: 17181477 DOI: 10.1586/14789450.3.6.631] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent applications of affinity mass spectrometry into clinical laboratories brought a renewed interest in immunoaffinity mass spectrometry as a more specific affinity method capable of selectively targeting and studying protein biomarkers. In mass spectrometry-based immunoassays, proteins are affinity retrieved from biological samples via surface-immobilized antibodies, and are then detected via mass spectrometric analysis. The assays benefit from dual specificity, which is brought about by the affinity of the antibody and the protein mass readout. The mass spectrometry aspect of the assays enables single-step detection of protein isoforms and their individual quantification. This review offers a comprehensive review of mass spectrometry-based immunoassays, from historical perspectives in the development of the immunoaffinity mass spectrometry, to current applications of the assays in clinical and population proteomic endeavors. Described in more detail are two types of mass spectrometry-based immunoassays, one of which incorporates surface plasmon resonance detection for protein quantification. All mass spectrometry-based immunoassays offer high-throughput targeted protein investigation, with clear implications in clinical research, encompassing biomarker discovery and validation, and in diagnostic settings as the next-generation immunoassays.
Collapse
Affiliation(s)
- Dobrin Nedelkov
- Intrinsic Bioprobes Inc., 2155 East Conference Drive, Suite 104, Tempe, AZ 85284, USA.
| |
Collapse
|
10
|
Catimel B, Rothacker J, Catimel J, Faux M, Ross J, Connolly L, Clippingdale A, Burgess AW, Nice E. Biosensor-Based Micro-Affinity Purification for the Proteomic Analysis of Protein Complexes. J Proteome Res 2005; 4:1646-56. [PMID: 16212417 DOI: 10.1021/pr050132x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A biosensor-based micro-affinity purification method to recover protein binding partners and their complexes for down stream proteomics analysis has been developed using the BIAcore 3000 fitted with a prototype Surface Prep Unit (SPU). The recombinant GST-intracellular domain of E-cadherin or the recombinant GST-beta-catenin binding domain of Adenomatous Polyposis Coli (APC) were immobilized onto the SPU and used to affinity purify binding partners from chromatographically enriched SW480 colon cancer cell lysates. A GST- immobilized surface was used as a control. Samples recovered from the SPU were subjected to SDS-PAGE with sensitive Coomassie staining followed by automated in-gel digestion and LC-MS/MS. The results obtained using the SPU were compared with similar experiments performed using Sepharose beads.
Collapse
Affiliation(s)
- B Catimel
- The Ludwig Institute for Cancer Research, Melbourne Tumor Biology Branch, PO Box 2008, Royal Melbourne Hospital, Victoria 3050, Melbourne, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Abstract
The rapid development of proteomic technologies, combined with the completion of the Human Genome Map, has enabled the compiling of an unprecedented inventory of cellular proteins. Functional proteomics is an emerging field that aims to utilize the enormous amount of information provided by these proteomic technologies to understand the functions of cellular proteins. The utility of functional proteomics has been recently exploited to elucidate cellular mechanisms in numerous fields, of particular salience in the area of signal transduction. This review presents a functional proteomic approach for the study of cardiac cell signaling. It illustrates the strategies by which the subproteome of a targeted signaling system is characterized in an unbiased fashion, the manner in which the biochemical functions of this subproteome are assessed using established molecular and protein chemistry methods, and the challenges associated with these studies.
Collapse
Affiliation(s)
- Peipei Ping
- Department of Physiology Medicine and the Division of Cardiology, David Geffen School of Medicine at UCLA, Los Angeles, Calif, USA.
| |
Collapse
|
12
|
Abstract
The combination of surface plasmon resonance (SPR) and mass spectrometry (MS) has created a unique approach to protein investigations. Surface plasmon resonance is used to quantify interactions between proteins and surface-immobilized ligands, and MS is used to determine the structural features of the bound proteins. Recent progress in SPR-MS includes improved methods and operations, increased limits of detection, multi-protein analysis and protein-complex delineation. With the subsequent design of SPR protein arrays, SPR-MS is expected to enter into the field of high-throughput protein interaction discovery and miniaturized diagnostics.
Collapse
Affiliation(s)
- Dobrin Nedelkov
- Intrinsic Bioprobes, 625 South Smith Rd, Suite 22, Tempe, AZ 85281, USA.
| | | |
Collapse
|
13
|
Nedelkov D, Nelson RW, Kiernan UA, Niederkofler EE, Tubbs KA. Detection of bound and free IGF-1 and IGF-2 in human plasma via biomolecular interaction analysis mass spectrometry. FEBS Lett 2003; 536:130-4. [PMID: 12586351 DOI: 10.1016/s0014-5793(03)00042-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Insulin like growth factor (IGF)-1 and IGF-2 were assayed from human plasma via biomolecular interaction analysis mass spectrometry, utilizing antibodies as ligands for affinity retrieval. Detection of both targeted and non-targeted IGFs in the mass spectra indicated possible protein complex retrieval by the individual antibodies. A series of control experiments eliminated the possibility of analyte cross-walking between flow cells, significant antibodies cross-reactivity, and direct IGF interactions. To disrupt the putative protein complex and release its constituent proteins, plasma samples were treated with detergents. An SDS-treated plasma yielded IGF signals in a different ratio than the one observed in the mass spectra from the non-treated plasma, suggesting disruption of the protein complex, and its retrieval from non-treated plasma. Novel truncated IGF-2 variant, missing its N-terminal Alanine, was detected in all mass spectra.
Collapse
Affiliation(s)
- Dobrin Nedelkov
- Intrinsic Bioprobes Inc., 625 S. Smith Rd. Suite 22, Tempe, AZ 85281, USA.
| | | | | | | | | |
Collapse
|
14
|
Nedelkov D, Nelson RW. Design and use of multi-affinity surfaces in biomolecular interaction analysis-mass spectrometry (BIA/MS): a step toward the design of SPR/MS arrays. J Mol Recognit 2003; 16:15-9. [PMID: 12557234 DOI: 10.1002/jmr.601] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The feasibility of multi-affinity ligand surfaces in biomolecular interaction analysis-mass spectrometry (BIA/MS) was explored in this work. Multi-protein affinity surfaces were constructed by utilizing antibodies to beta-2-microglobulin, cystatin C, retinol binding protein, transthyretin, serum amyloid P and C-reactive protein. In the initial experiments, all six antibodies were immobilized on a single site (flow cell) on the sensor chip surface, followed by verification of the surface activity via separate injections of purified proteins. After an injection of diluted human plasma aliquot over the antibodies-derivatized surfaces, and subsequent MALDI-TOF MS analysis, signals representing five out of the six targeted proteins were observed in the mass spectra. Further, to avoid the complexity of the spectra, the six proteins were divided into two groups (according to their molecular weight) and immobilized on two separate surfaces on a single sensor chip, followed by an injection of human plasma aliquot. The resulting mass spectra showed signals from all proteins. Also, the convolution resulting from the multiply charged ion species was eliminated. The ability to create such multi-affinity surfaces indicates that smaller-size ligand areas/spots can be employed in the BIA/MS protein interaction screening experiments, and opens up the possibilities for construction of novel multi-arrayed SPR-MS platforms and methods for high-throughput parallel protein interaction investigations.
Collapse
Affiliation(s)
- Dobrin Nedelkov
- Intrinsic Bioprobes Inc, 625 S. Smith Rd, Suite 22, Tempe, AZ 85281, USA.
| | | |
Collapse
|
15
|
Nedelkov D, Nelson RW. Delineating protein-protein interactions via biomolecular interaction analysis-mass spectrometry. J Mol Recognit 2003; 16:9-14. [PMID: 12557233 DOI: 10.1002/jmr.600] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The utility of biomolecular interaction analysis-mass spectrometry (BIA/MS) in screening for protein-protein interactions was explored in this work. Experiments were performed in which proteins served as ligands for screening of possible interactions with other proteins from human plasma and urine. The proteins utilized were beta-2-microglobulin, cystatin C (cysC), retinol binding protein (RBP), transthyretin (TTR), alpha-1-microglobulin, C-reactive protein, transferrin and papain. The immobilization of functionally active proteins was confirmed via interactions with antibodies to the corresponding proteins. Various dilutions of human urine and plasma were injected over the protein-derivatized surfaces. It was observed that the urine injections generally yielded smaller SPR responses than those observed after the plasma injections. The BIA/MS experiments did not reveal novel protein-protein interactions, although several established interactions (such as those between RBP and TTR, and cysC and papain) were validated. Few protein ligand deficiencies (such as truncations) leading to false negative and false positive BIA/MS results were also discovered.
Collapse
Affiliation(s)
- Dobrin Nedelkov
- Intrinsic Bioprobes Inc, 625 S Smith Rd, Suite 22, Tempe, AZ 85281, USA.
| | | |
Collapse
|
16
|
Van Regenmortel MHV. A paradigm shift is needed in proteomics: 'structure determines function' should be replaced by 'binding determines function'. J Mol Recognit 2002; 15:349-51. [PMID: 12501156 DOI: 10.1002/jmr.603] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
17
|
Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
Collapse
Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
| | | |
Collapse
|
18
|
Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 2002; 1:845-67. [PMID: 12488461 DOI: 10.1074/mcp.r200007-mcp200] [Citation(s) in RCA: 3132] [Impact Index Per Article: 142.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The human plasma proteome holds the promise of a revolution in disease diagnosis and therapeutic monitoring provided that major challenges in proteomics and related disciplines can be addressed. Plasma is not only the primary clinical specimen but also represents the largest and deepest version of the human proteome present in any sample: in addition to the classical "plasma proteins," it contains all tissue proteins (as leakage markers) plus very numerous distinct immunoglobulin sequences, and it has an extraordinary dynamic range in that more than 10 orders of magnitude in concentration separate albumin and the rarest proteins now measured clinically. Although the restricted dynamic range of conventional proteomic technology (two-dimensional gels and mass spectrometry) has limited its contribution to the list of 289 proteins (tabulated here) that have been reported in plasma to date, very recent advances in multidimensional survey techniques promise at least double this number in the near future. Abundant scientific evidence, from proteomics and other disciplines, suggests that among these are proteins whose abundances and structures change in ways indicative of many, if not most, human diseases. Nevertheless, only a handful of proteins are currently used in routine clinical diagnosis, and the rate of introduction of new protein tests approved by the United States Food and Drug Administration (FDA) has paradoxically declined over the last decade to less than one new protein diagnostic marker per year. We speculate on the reasons behind this large discrepancy between the expectations arising from proteomics and the realities of clinical diagnostics and suggest approaches by which protein-disease associations may be more effectively translated into diagnostic tools in the future.
Collapse
|
19
|
Vondriska TM, Ping P. Functional proteomics to study protection of the ischaemic myocardium. Expert Opin Ther Targets 2002; 6:563-70. [PMID: 12387680 DOI: 10.1517/14728222.6.5.563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mechanisms to reduce the deleterious effects of myocardial ischaemia are of particular clinical importance and have been the focus of intense research for a number of years. Among novel approaches to studying the ischaemic heart, proteomics, or the analysis of all cellular proteins, presents as a powerful method to deconstruct the mechanisms of disease and protection. Specifically, the field of functional proteomics is an emerging application of proteomics that melds aspects of classical proteomics, biochemistry, molecular biology and physiology into an approach that facilitates an understanding of how proteins and protein interactions engender phenotype. This review highlights different types of proteomic applications and provides a prospectus for functional proteomics as a robust vehicle driving drug discovery and design.
Collapse
Affiliation(s)
- Thomas M Vondriska
- Department of Physiology, Division of Cardiology, University of California, Los Angeles, CA 90095, USA
| | | |
Collapse
|
20
|
Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:443-453. [PMID: 11948851 DOI: 10.1002/jms.251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
|
21
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2447281 DOI: 10.1002/cfg.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|