1
|
Kitade Y, Miyabe Y, Yamamoto Y, Takeda H, Shimizu T, Yasui H, Kishimura H. Structural characteristics of phycobiliproteins from red alga Mazzaella japonica. J Food Biochem 2017. [DOI: 10.1111/jfbc.12436] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yumi Kitade
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| | - Yoshikatsu Miyabe
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| | - Yohei Yamamoto
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| | - Hirohumi Takeda
- Fisheries Research Department, Hokkaido Research Organization, Abashiri Fishries; Research Institute; Hokkaido Japan
| | - Takeshi Shimizu
- Department of Research and Development; Hokkaido Industrial Technology Center; Hakodate Hokkaido Japan
| | - Hajime Yasui
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| | - Hideki Kishimura
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido Japan
| |
Collapse
|
2
|
Miyabe Y, Furuta T, Takeda T, Kanno G, Shimizu T, Tanaka Y, Gai Z, Yasui H, Kishimura H. Structural Properties of Phycoerythrin from DulsePalmaria palmata. J Food Biochem 2016. [DOI: 10.1111/jfbc.12301] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yoshikatsu Miyabe
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| | - Tomoe Furuta
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| | - Tomoyuki Takeda
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| | - Gaku Kanno
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| | - Takeshi Shimizu
- Department of Research and Development; Hokkaido Industrial Technology Center; Hakodate Hokkaido 041-0801 Japan
| | - Yoshikazu Tanaka
- Laboratory of X-Ray Structural Biology, Faculty of Advanced Life Science; Hokkaido University; Sapporo 060-0810 Japan
- Japan Science and Technology Agency, PRESTO; Sapporo 060-0810 Japan
| | - Zuoqi Gai
- Laboratory of X-Ray Structural Biology, Faculty of Advanced Life Science; Hokkaido University; Sapporo 060-0810 Japan
| | - Hajime Yasui
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| | - Hideki Kishimura
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences; Hokkaido University; Hakodate Hokkaido 041-8611 Japan
| |
Collapse
|
3
|
Sheth BP, Thaker VS. Plant systems biology: insights, advances and challenges. PLANTA 2014; 240:33-54. [PMID: 24671625 DOI: 10.1007/s00425-014-2059-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/06/2014] [Indexed: 05/20/2023]
Abstract
Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.
Collapse
Affiliation(s)
- Bhavisha P Sheth
- Department of Biosciences, Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Saurashtra University, Rajkot, 360005, Gujarat, India,
| | | |
Collapse
|
4
|
Magdeldin S, Enany S, Yoshida Y, Xu B, Zhang Y, Zureena Z, Lokamani I, Yaoita E, Yamamoto T. Basics and recent advances of two dimensional- polyacrylamide gel electrophoresis. Clin Proteomics 2014; 11:16. [PMID: 24735559 PMCID: PMC3996944 DOI: 10.1186/1559-0275-11-16] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 03/20/2014] [Indexed: 12/19/2022] Open
Abstract
Gel- based proteomics is one of the most versatile methods for fractionating protein complexes. Among these methods, two dimensional- polyacrylamide gel electrophoresis (2-DE) represents a mainstay orthogonal approach, which is popularly used to simultaneously fractionate, identify, and quantify proteins when coupled with mass spectrometric identification or other immunological tests. Although 2-DE was first introduced more than three decades ago, several challenges and limitations to its utility still exist. This review discusses the principles of 2-DE as well as both recent methodological advances and new applications.
Collapse
Affiliation(s)
- Sameh Magdeldin
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-dori, Niigata, Japan.,Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Shymaa Enany
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-dori, Niigata, Japan.,Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Yutaka Yoshida
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-dori, Niigata, Japan
| | - Bo Xu
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-dori, Niigata, Japan
| | - Ying Zhang
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-dori, Niigata, Japan
| | | | | | - Eishin Yaoita
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-dori, Niigata, Japan
| | - Tadashi Yamamoto
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-dori, Niigata, Japan
| |
Collapse
|
5
|
Butterfield DA, Swomley AM, Sultana R. Amyloid β-peptide (1-42)-induced oxidative stress in Alzheimer disease: importance in disease pathogenesis and progression. Antioxid Redox Signal 2013; 19:823-35. [PMID: 23249141 PMCID: PMC3749710 DOI: 10.1089/ars.2012.5027] [Citation(s) in RCA: 365] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/05/2012] [Accepted: 12/17/2012] [Indexed: 12/14/2022]
Abstract
SIGNIFICANCE Alzheimer disease (AD) is an age-related neurodegenerative disease. AD is characterized by progressive cognitive impairment. One of the main histopathological hallmarks of AD brain is the presence of senile plaques (SPs) and another is elevated oxidative stress. The main component of SPs is amyloid beta-peptide (Aβ) that is derived from the proteolytic cleavage of amyloid precursor protein. RECENT ADVANCES Recent studies are consistent with the notion that methionine present at 35 position of Aβ is critical to Aβ-induced oxidative stress and neurotoxicity. Further, we also discuss the signatures of oxidatively modified brain proteins, identified using redox proteomics approaches, during the progression of AD. CRITICAL ISSUES The exact relationships of the specifically oxidatively modified proteins in AD pathogenesis require additional investigation. FUTURE DIRECTIONS Further studies are needed to address whether the therapies directed toward brain oxidative stress and oxidatively modified key brain proteins might help delay or prevent the progression of AD.
Collapse
Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, USA.
| | | | | |
Collapse
|
6
|
Jordan JD, Nyquist P. Biomarkers and vasospasm after aneurysmal subarachnoid hemorrhage. Neurosurg Clin N Am 2010; 21:381-91. [PMID: 20380977 DOI: 10.1016/j.nec.2009.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Subarachnoid hemorrhage from the rupture of a saccular aneurysm is a devastating neurological disease that has a high morbidity and mortality not only from the initial hemorrhage, but also from the delayed complications, such as cerebral vasospasm. Cerebral vasospasm can lead to delayed ischemic injury 1 to 2 weeks after the initial hemorrhage. Although the pathophysiology of vasospasm has been described for decades, the molecular basis remains poorly understood. With the many advances in the past decade in the development of sensitive molecular biological techniques, imaging, biochemical purification, and protein identification, new insights are beginning to reveal the etiology of vasospasm. These findings will not only help to identify markers of vasospasm and prognostic outcome, but will also yield potential therapeutic targets for the treatment of this disease. This review focuses on the methods available for the identification of biological markers of vasospasm and their limitations, the current understanding as to the utility and prognostic significance of identified biomarkers, the utility of these biomarkers in predicting vasospasm and outcome, and future directions of research in this field.
Collapse
Affiliation(s)
- J Dedrick Jordan
- Johns Hopkins School of Medicine, 600 North Wolfe Street, Meyer 8-140, Baltimore, MD 21287-7840, USA
| | | |
Collapse
|
7
|
Jones A, Wastling J, Hunt E. Proposal for a standard representation of two-dimensional gel electrophoresis data. Comp Funct Genomics 2010; 4:492-501. [PMID: 18628860 PMCID: PMC2447283 DOI: 10.1002/cfg.323] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The global analysis of proteins is now feasible due to improvements in techniques such as two-dimensional gel electrophoresis (2-DE), mass spectrometry, yeast two-hybrid
systems and the development of bioinformatics applications. The experiments form
the basis of proteomics, and present significant challenges in data analysis, storage and
querying. We argue that a standard format for proteome data is required to enable
the storage, exchange and subsequent re-analysis of large datasets. We describe the
criteria that must be met for the development of a standard for proteomics. We have
developed a model to represent data from 2-DE experiments, including difference
gel electrophoresis along with image analysis and statistical analysis across multiple
gels. This part of proteomics analysis is not represented in current proposals for
proteomics standards. We are working with the Proteomics Standards Initiative to
develop a model encompassing biological sample origin, experimental protocols, a
number of separation techniques and mass spectrometry. The standard format will
facilitate the development of central repositories of data, enabling results to be verified
or re-analysed, and the correlation of results produced by different research groups
using a variety of laboratory techniques.
Collapse
Affiliation(s)
- Andrew Jones
- Department of Computing Science, University of Glasgow, 17 Lilybank Gardens, Glasgow G12 8QQ, UK.
| | | | | |
Collapse
|
8
|
Rogowska-Wrzesinska A, Larsen PM, Blomberg A, Görg A, Roepstorff P, Norbeck J, Fey SJ. Comparison of the proteomes of three yeast wild type strains: CEN.PK2, FY1679 and W303. Comp Funct Genomics 2010; 2:207-25. [PMID: 18628919 PMCID: PMC2447217 DOI: 10.1002/cfg.94] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2001] [Accepted: 06/26/2001] [Indexed: 11/30/2022] Open
Abstract
Yeast deletion strains created during gene function analysis projects very often show
drastic phenotypic differences depending on the genetic background used. These results
indicate the existence of important molecular differences between the CEN.PK2, FY1679
and W303 wild type strains. To characterise these differences we have compared the
protein expression levels between CEN.PK2, FY1679 and W303 strains using twodimensional
gel electrophoresis and identified selected proteins by mass spectrometric
analysis. We have found that FY1679 and W303 strains are more similar to each other
than to the CEN.PK2 strain. This study identifies 62 proteins that are differentially
expressed between the strains and provides a valuable source of data for the interpretation
of yeast mutant phenotypes observed in CEN.PK2, FY1679 and W303 strains.
Collapse
Affiliation(s)
- A Rogowska-Wrzesinska
- Centre for Proteome Analysis in Life Sciences, University of Southern Denmark, International Science Park Odense, Forskerparken 10B, Odense M 5230, Denmark.
| | | | | | | | | | | | | |
Collapse
|
9
|
Maurer MH. Proteomics of brain extracellular fluid (ECF) and cerebrospinal fluid (CSF). MASS SPECTROMETRY REVIEWS 2010; 29:17-28. [PMID: 19116946 DOI: 10.1002/mas.20213] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mass spectrometry has become the gold standard for the identification of proteins in proteomics. In this review, I will discuss the available literature on proteomic experiments that analyze human cerebrospinal fluid (CSF) and brain extracellular fluid (ECF), mostly obtained by cerebral microdialysis. Both materials are of high diagnostic value in clinical neurology, for example, in cerebrovascular disorders like stroke, neurodegenerative diseases like Alzheimer's Disease, Parkinson's Disease, amyotrophic lateral sclerosis (ALS), traumatic brain injury and cerebral infectious and inflammatory disease, such as multiple sclerosis. Moreover, there are standard procedures for sampling. In a number of studies in recent years, biomarkers have been proposed in CSF and ECF for improved diagnosis or to control therapy, based on proteomics and mass spectrometry. I will also discuss the needs for a transition of research-based experimental screening with mass spectrometry to fast and reliable diagnostic instrumentation for clinical use.
Collapse
Affiliation(s)
- Martin H Maurer
- Department of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany.
| |
Collapse
|
10
|
Zheng G, Li H, Wang C, Sheng Q, Fan H, Yang S, Liu B, Dai J, Zeng R, Xie L. A platform to standardize, store, and visualize proteomics experimental data. Acta Biochim Biophys Sin (Shanghai) 2009; 41:273-9. [PMID: 19352541 DOI: 10.1093/abbs/gmp010] [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: 11/14/2022] Open
Abstract
With the development of functional genomics research, large-scale proteomics studies are now widespread, presenting significant challenges for data storage, exchange, and analysis. Here we present the Integrated Proteomics Exploring Database (IPED) as a platform for managing proteomics experimental data (both process and result data). IPED is based on the schema of the Proteome Experimental Data Repository (PEDRo), and complies with the General Proteomics Standard (GPS) drafted by the Proteomics Standards Committee of the Human Proteome Organization. In our work, we developed three components for the IPED platform: the IPED client editor, IPED server software, and IPED web interface. The client editor collects experimental data and generates an extensible markup language (XML) data file compliant with PEDRo and GPS; the server software parses the XML data file and loads information into a core database; and the web interface displays experimental results, to provide a convenient graphic representation of data. Given software convenience and data abundance, IPED is a powerful platform for data exchange and presents an important resource for the proteomics community. In its current release, IPED is available at http://www.biosino.org/iped2.
Collapse
Affiliation(s)
- Guangyong Zheng
- Bioinformation Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Göppert TM, Müller RH. Polysorbate-stabilized solid lipid nanoparticles as colloidal carriers for intravenous targeting of drugs to the brain: Comparison of plasma protein adsorption patterns. J Drug Target 2008; 13:179-87. [PMID: 16036306 DOI: 10.1080/10611860500071292] [Citation(s) in RCA: 201] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Plasma proteins enriched on the surface of drug-delivery-purpose nanoparticles are regarded as key factors for determination of in vivo organ distribution after intravenous injection. Polysorbate 80-coated polybutylcyanoacrylate (PBCA) nanoparticles, preferentially adsorbing apolipoprotein E (apoE) on their surface, have previously been considered to deliver various drugs to the brain. In the present study, in vivo well tolerable solid lipid nanoparticles (SLN) using different types of polysorbates as stabilizers were produced. The influence of the different surfactants on in vitro adsorption of human plasma proteins was investigated using two-dimensional polyacrylamide gel electrophoresis (2-DE). Possible correlations of different amounts of adsorbed apoE to the hydrophilic-lipophilic balance (HLB) of the polysorbates are shown and discussed. Apolipoprotein C-II, albumin and immunoglobulin G, which are also decisive plasma proteins with regard to site-specific drug delivery of intravenously injected carriers to the brain, are compared with regard to adsorption. Moreover, certain similarities to the plasma protein adsorption patterns of previously analysed brain-specific PBCA nanoparticles could be detected. Despite some differences in adsorption behavior of proteins on the surface of polysorbate-stabilized SLN and PBCA nanoparticles, we conclude that in both cases polysorbate 80 might have the highest potential to deliver drugs to the brain.
Collapse
Affiliation(s)
- Torsten M Göppert
- Department of Pharmaceutics, Biopharmaceutics and Quality Management, Institute of Pharmacy, The Free University of Berlin, Berlin, Germany
| | | |
Collapse
|
12
|
Sultana R, Butterfield DA. Redox Proteomics Analysis of Oxidative Modified Brain Proteins in Alzheimer's Disease and Mild Cognitive Impairment: Insights into the Progression of This Dementing Disorder. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
|
13
|
Muela A, Seco C, Camafeita E, Arana I, Orruño M, López JA, Barcina I. Changes in Escherichia coli outer membrane subproteome under environmental conditions inducing the viable but nonculturable state. FEMS Microbiol Ecol 2008; 64:28-36. [DOI: 10.1111/j.1574-6941.2008.00453.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
14
|
Local pixel value collection algorithm for spot segmentation in two-dimensional gel electrophoresis research. Comp Funct Genomics 2008:89596. [PMID: 18274608 PMCID: PMC2216074 DOI: 10.1155/2007/89596] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 06/14/2007] [Indexed: 12/02/2022] Open
Abstract
Two-dimensional gel-electrophoresis (2-DE) images show the expression levels of
several hundreds of proteins where each protein is represented as a blob-shaped spot of
grey level values. The spot detection, that is, the segmentation process has to be efficient as
it is the first step in the gel processing. Such extraction of information is a very complex
task. In this paper, we propose a novel spot detector that is basically a morphology-based
method with the use of a seeded region growing as a central paradigm and
which relies on the spot correlation information. The method is tested on our synthetic
as well as on real gels with human samples from SWISS-2DPAGE (two-dimensional
polyacrylamide gel electrophoresis) database. A comparison of results is done with a
method called pixel value collection (PVC). Since our algorithm efficiently uses local
spot information, segments the spot by collecting pixel values and its affinity with
PVC, we named it local pixel value collection (LPVC). The results show that LPVC
achieves similar segmentation results as PVC, but is much faster than PVC.
Collapse
|
15
|
Warda M, Han J. Retracted: Mitochondria, the missing link between body and soul: Proteomic prospective evidence. Proteomics 2008. [DOI: 10.1002/pmic.200700695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
16
|
Butterfield DA, Reed T, Newman SF, Sultana R. Roles of amyloid beta-peptide-associated oxidative stress and brain protein modifications in the pathogenesis of Alzheimer's disease and mild cognitive impairment. Free Radic Biol Med 2007; 43:658-77. [PMID: 17664130 PMCID: PMC2031860 DOI: 10.1016/j.freeradbiomed.2007.05.037] [Citation(s) in RCA: 423] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2007] [Revised: 05/20/2007] [Accepted: 05/25/2007] [Indexed: 12/17/2022]
Abstract
Oxidative stress has been implicated to play a crucial role in the pathogenesis of a number of diseases, including neurodegenerative disorders, cancer, and ischemia, just to name a few. Alzheimer disease (AD) is an age-related neurodegenerative disorder that is recognized as the most common form of dementia. AD is histopathologically characterized by the presence of extracellular amyloid plaques, intracellular neurofibrillary tangles, the presence of oligomers of amyloid beta-peptide (Abeta), and synapse loss. In this review we discuss the role of Abeta in the pathogenesis of AD and also the use of redox proteomics to identify oxidatively modified brain proteins in AD and mild cognitive impairment. In addition, redox proteomics studies in in vivo models of AD centered around human Abeta(1-42) are discussed.
Collapse
|
17
|
Butterfield DA, Perluigi M, Sultana R. Oxidative stress in Alzheimer's disease brain: New insights from redox proteomics. Eur J Pharmacol 2006; 545:39-50. [PMID: 16860790 DOI: 10.1016/j.ejphar.2006.06.026] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Revised: 11/28/2005] [Accepted: 06/13/2006] [Indexed: 12/20/2022]
Abstract
Alzheimer's disease, an age-related neurodegenerative disorder, is characterized clinically by a progressive loss of memory and cognitive functions. Neuropathologically, Alzheimer's disease is defined by the accumulation of extracellular amyloid protein deposited senile plaques and intracellular neurofibrillary tangles made of abnormal and hyperphosphorylated tau protein, regionalized neuronal death, and loss of synaptic connections within selective brain regions. Evidence has suggested a critical role for amyloid-beta peptide metabolism and oxidative stress in Alzheimer's disease pathogenesis and progression. Among the other indices of oxidative stress in Alzheimer's disease brain are protein carbonyls and 3-nitrotyrosine, which are the markers of protein oxidation. Thus, in this review, we discuss the application of redox proteomics for the identification of oxidatively modified proteins in Alzheimer's disease brain and also discuss the functions associated with the identified oxidized proteins in relation to Alzheimer's disease pathology. The information obtained from proteomics may be helpful in understanding the molecular mechanisms involved in the development and progression of Alzheimer's disease as well as of other neurodegenerative disorders. Further, redox proteomics may provide potential targets for drug therapy in Alzheimer's disease.
Collapse
|
18
|
Butterfield DA, Abdul HM, Newman S, Reed T. Redox proteomics in some age-related neurodegenerative disorders or models thereof. NeuroRx 2006; 3:344-57. [PMID: 16815218 PMCID: PMC3593385 DOI: 10.1016/j.nurx.2006.05.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Neurodegenerative diseases cause memory loss and cognitive impairment. Results from basic and clinical scientific research suggest a complex network of mechanisms involved in the process of neurodegeneration. Progress in treatment of such disorders requires researchers to better understand the functions of proteins involved in neurodegenerative diseases, to characterize their role in pathogenic disease mechanisms, and to explore their roles in the diagnosis, treatment, and prevention of neurodegenerative diseases. A variety of conditions of neurodegenerative diseases often lead to post-translational modifications of proteins, including oxidation and nitration, which might be involved in the pathogenesis of neurodegenerative diseases. Redox proteomics, a subset of proteomics, has made possible the identification of specifically oxidized proteins in neurodegenerative disorders, providing insight into a multitude of pathways that govern behavior and cognition and the response of the nervous system to injury and disease. Proteomic analyses are particularly suitable to elucidate post-translational modifications, expression levels, and protein-protein interactions of thousands of proteins at a time. Complementing the valuable information generated through the integrative knowledge of protein expression and function should enable the development of more efficient diagnostic tools and therapeutic modalities. Here we review redox proteomic studies of some neurodegenerative diseases.
Collapse
Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, University of Kentucky, Lexington, 40506, USA.
| | | | | | | |
Collapse
|
19
|
Göppert TM, Müller RH. Adsorption kinetics of plasma proteins on solid lipid nanoparticles for drug targeting. Int J Pharm 2005; 302:172-86. [PMID: 16098695 DOI: 10.1016/j.ijpharm.2005.06.025] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 06/06/2005] [Accepted: 06/14/2005] [Indexed: 11/22/2022]
Abstract
The interactions of intravenously injected carriers with plasma proteins are the determining factor for the in vivo fate of the particles. In this study the adsorption kinetics on solid lipid nanoparticles (SLN) were investigated and compared to the adsorption kinetics on previously analyzed polymeric model particles and O/W-emulsions. The adsorbed proteins were determined using two-dimensional polyacrylamide gel electrophoresis (2-DE). Employing diluted human plasma, a transient adsorption of fibrinogen was observed on the surface of SLN stabilized with the surfactant Tego Care 450, which in plasma of higher concentrations was displaced by apolipoproteins. This was in agreement with the "Vroman-effect" previously determined on solid surfaces. It says that in the early stages of adsorption, more plentiful proteins with low affinity are displaced by less plentiful with higher affinity to the surface. Over a period of time (0.5 min to 4 h) more interesting for the organ distribution of long circulating carriers, no relevant changes in the composition of the adsorption patterns of SLN, surface-modified with poloxamine 908 and poloxamer 407, respectively, were detected. This is in contrast to the chemically similar surface-modified polymeric particles but well in agreement with the surface-modified O/W-emulsions. As there is no competitive displacement of apolipoproteins on these modified SLN, the stable adsorption patterns may be better exploited for drug targeting than particles with an adsorption pattern being very dependent on contact time with plasma.
Collapse
Affiliation(s)
- T M Göppert
- The Free University of Berlin, Institute of Pharmacy, Department of Pharmaceutical Technology, Biotechnology and Quality Management, Kelchstr. 31, 12169 Berlin, Germany
| | | |
Collapse
|
20
|
Komatsu S. Rice proteome database: a step toward functional analysis of the rice genome. PLANT MOLECULAR BIOLOGY 2005; 59:179-90. [PMID: 16217611 DOI: 10.1007/s11103-005-2160-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Accepted: 02/11/2005] [Indexed: 05/04/2023]
Abstract
The technique of proteome analysis using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) has the power to monitor global changes that occur in the protein complement of tissues and subcellular compartments. In this study, the proteins of rice were cataloged, a rice proteome database was constructed, and a functional characterization of some of the identified proteins was undertaken. Proteins extracted from various tissues and subcellular compartments in rice were separated by 2D-PAGE and an image analyzer was used to construct a display of the proteins. The Rice Proteome Database contains 23 reference maps based on 2D-PAGE of proteins from various rice tissues and subcellular compartments. These reference maps comprise 13129 identified proteins, and the amino acid sequences of 5092 proteins are entered in the database. Major proteins involved in growth or stress responses were identified using the proteome approach. Some of these proteins, including a beta-tubulin, calreticulin, and ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice, have unexpected functions. The information obtained from the Rice Proteome Database will aid in cloning the genes for and predicting the function of unknown proteins.
Collapse
Affiliation(s)
- Setsuko Komatsu
- Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
| |
Collapse
|
21
|
Schneider M, Bairoch A, Wu CH, Apweiler R. Plant protein annotation in the UniProt Knowledgebase. PLANT PHYSIOLOGY 2005; 138:59-66. [PMID: 15888679 PMCID: PMC1104161 DOI: 10.1104/pp.104.058933] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The Swiss-Prot, TrEMBL, Protein Information Resource (PIR), and DNA Data Bank of Japan (DDBJ) protein database activities have united to form the Universal Protein Resource (UniProt) Consortium. UniProt presents three database layers: the UniProt Archive, the UniProt Knowledgebase (UniProtKB), and the UniProt Reference Clusters. The UniProtKB consists of two sections: UniProtKB/Swiss-Prot (fully manually curated entries) and UniProtKB/TrEMBL (automated annotation, classification and extensive cross-references). New releases are published fortnightly. A specific Plant Proteome Annotation Program (http://www.expasy.org/sprot/ppap/) was initiated to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Through UniProt, our aim is to provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information that will allow the plant community to fully explore and utilize the wealth of information available for both plant and non-plant model organisms.
Collapse
Affiliation(s)
- Michel Schneider
- Swiss Institute of Bioinformatics, Centre Medical Universitaire, University of Geneva, 1211 Geneva 4, Switzerland.
| | | | | | | |
Collapse
|
22
|
Komatsu S, Tanaka N. Rice proteome analysis: A step toward functional analysis of the rice genome. Proteomics 2005; 5:938-49. [PMID: 15627974 DOI: 10.1002/pmic.200401040] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The technique of proteome analysis using 2-DE has the power to monitor global changes that occur in the protein complement of tissues and subcellular compartments. In this review, we describe construction of the rice proteome database, the cataloging of rice proteins, and the functional characterization of some of the proteins identified. Initially, proteins extracted from various tissues and organelles were separated by 2-DE and an image analyzer was used to construct a display or reference map of the proteins. The rice proteome database currently contains 23 reference maps based on 2-DE of proteins from different rice tissues and subcellular compartments. These reference maps comprise 13 129 rice proteins, and the amino acid sequences of 5092 of these proteins are entered in the database. Major proteins involved in growth or stress responses have been identified by using a proteomics approach and some of these proteins have unique functions. Furthermore, initial work has also begun on analyzing the phosphoproteome and protein-protein interactions in rice. The information obtained from the rice proteome database will aid in the molecular cloning of rice genes and in predicting the function of unknown proteins.
Collapse
Affiliation(s)
- Setsuko Komatsu
- Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba, Japan.
| | | |
Collapse
|
23
|
Schneider M, Tognolli M, Bairoch A. The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2004; 42:1013-21. [PMID: 15707838 DOI: 10.1016/j.plaphy.2004.10.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Accepted: 10/01/2004] [Indexed: 05/01/2023]
Abstract
The Swiss-Prot protein knowledgebase provides manually annotated entries for all species, but concentrates on the annotation of entries from model organisms to ensure the presence of high quality annotation of representative members of all protein families. A specific Plant Protein Annotation Program (PPAP) was started to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Its main goal is the annotation of proteins from the model plant organism Arabidopsis thaliana. In addition to bibliographic references, experimental results, computed features and sometimes even contradictory conclusions, direct links to specialized databases connect amino acid sequences with the current knowledge in plant sciences. As protein families and groups of plant-specific proteins are regularly reviewed to keep up with current scientific findings, we hope that the wealth of information of Arabidopsis origin accumulated in our knowledgebase, and the numerous software tools provided on the Expert Protein Analysis System (ExPASy) web site might help to identify and reveal the function of proteins originating from other plants. Recently, a single, centralized, authoritative resource for protein sequences and functional information, UniProt, was created by joining the information contained in Swiss-Prot, Translation of the EMBL nucleotide sequence (TrEMBL), and the Protein Information Resource-Protein Sequence Database (PIR-PSD). A rising problem is that an increasing number of nucleotide sequences are not being submitted to the public databases, and thus the proteins inferred from such sequences will have difficulties finding their way to the Swiss-Prot or TrEMBL databases.
Collapse
Affiliation(s)
- Michel Schneider
- Swiss Institute of Bioinformatics, CMU, 1, Rue Michel Servet, 1211 Geneva-4, Switzerland.
| | | | | |
Collapse
|
24
|
Mikkat S, Koy C, Ulbrich M, Ringel B, Glocker MO. Mass spectrometric protein structure characterization reveals cause of migration differences of haptoglobin ? chains in two-dimensional gel electrophoresis. Proteomics 2004; 4:3921-32. [PMID: 15378693 DOI: 10.1002/pmic.200400825] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Haptoglobin belongs to the major constituents of plasma and acts as hemoglobin-binding and acute-phase protein. Due to the occurrence of three major allelic variants and further structural modifications, the alpha chains of haptoglobin form varying spot patterns in two-dimensional gel electrophoresis (2-DE) gels, which is generally observed in differential proteome analyses using plasma or related body fluids of humans. In the present study plasma samples from 10 donors of initially unknown haptoglobin phenotype were separated by 2-DE and tryptic digests of excised haptoglobin alpha chain spots were analyzed by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and MALDI-quadrupole ion trap TOF-MS. Haptoglobin alpha1S, alpha1F, as well as alpha2 chains were found to occur each with at least three structurally differing protein species: (i) the unmodified form, which corresponds to the sequence database entries; (ii) derivatives, in which asparagine at position five is deamidated to aspartic acid; and (iii) derivatives with an additional C-terminal arginine residue. These structural variants account for the most commonly observed spot patterns of haptoglobin alpha chains in Coomassie-stained gels. Additionally, a minor derivative of the haptoglobin alpha2 chain carrying both modifications, deamidation at position five and the C-terminal arginine residue, was identified. Theoretical pI values of the characterized structural variants are, consistent with their observed migration in the 2-DE gels.
Collapse
Affiliation(s)
- Stefan Mikkat
- Proteome Center Rostock, University of Rostock, Germany
| | | | | | | | | |
Collapse
|
25
|
Garwood K, McLaughlin T, Garwood C, Joens S, Morrison N, Taylor CF, Carroll K, Evans C, Whetton AD, Hart S, Stead D, Yin Z, Brown AJP, Hesketh A, Chater K, Hansson L, Mewissen M, Ghazal P, Howard J, Lilley KS, Gaskell SJ, Brass A, Hubbard SJ, Oliver SG, Paton NW. PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics 2004; 5:68. [PMID: 15377392 PMCID: PMC521486 DOI: 10.1186/1471-2164-5-68] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2004] [Accepted: 09/17/2004] [Indexed: 11/10/2022] Open
Abstract
Background Proteomics is rapidly evolving into a high-throughput technology, in which substantial and systematic studies are conducted on samples from a wide range of physiological, developmental, or pathological conditions. Reference maps from 2D gels are widely circulated. However, there is, as yet, no formally accepted standard representation to support the sharing of proteomics data, and little systematic dissemination of comprehensive proteomic data sets. Results This paper describes the design, implementation and use of a Proteome Experimental Data Repository (PEDRo), which makes comprehensive proteomics data sets available for browsing, searching and downloading. It is also serves to extend the debate on the level of detail at which proteomics data should be captured, the sorts of facilities that should be provided by proteome data management systems, and the techniques by which such facilities can be made available. Conclusions The PEDRo database provides access to a collection of comprehensive descriptions of experimental data sets in proteomics. Not only are these data sets interesting in and of themselves, they also provide a useful early validation of the PEDRo data model, which has served as a starting point for the ongoing standardisation activity through the Proteome Standards Initiative of the Human Proteome Organisation.
Collapse
Affiliation(s)
- Kevin Garwood
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Thomas McLaughlin
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Chris Garwood
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Scott Joens
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Norman Morrison
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
- School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Christopher F Taylor
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Kathleen Carroll
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Caroline Evans
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Anthony D Whetton
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Sarah Hart
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - David Stead
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Zhikang Yin
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Alistair JP Brown
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Andrew Hesketh
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Keith Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Lena Hansson
- Scottish Centre for Genomic Technology & Informatics, University of Edinburgh Medical School, The Chancellor's Building, Little France Crescent, Edinburgh, EH16 4S, UK
| | - Muriel Mewissen
- Scottish Centre for Genomic Technology & Informatics, University of Edinburgh Medical School, The Chancellor's Building, Little France Crescent, Edinburgh, EH16 4S, UK
| | - Peter Ghazal
- Scottish Centre for Genomic Technology & Informatics, University of Edinburgh Medical School, The Chancellor's Building, Little France Crescent, Edinburgh, EH16 4S, UK
| | - Julie Howard
- University of Cambridge, Department of Biochemistry, Downing Site, Cambridge, CB2 1QW, UK
| | - Kathryn S Lilley
- University of Cambridge, Department of Biochemistry, Downing Site, Cambridge, CB2 1QW, UK
| | - Simon J Gaskell
- Department of Chemistry, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Andy Brass
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
- School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Simon J Hubbard
- School of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Stephen G Oliver
- School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Norman W Paton
- Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| |
Collapse
|
26
|
Aertsen A, Vanoirbeek K, De Spiegeleer P, Sermon J, Hauben K, Farewell A, Nyström T, Michiels CW. Heat shock protein-mediated resistance to high hydrostatic pressure in Escherichia coli. Appl Environ Microbiol 2004; 70:2660-6. [PMID: 15128516 PMCID: PMC404417 DOI: 10.1128/aem.70.5.2660-2666.2004] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A random library of Escherichia coli MG1655 genomic fragments fused to a promoterless green fluorescent protein (GFP) gene was constructed and screened by differential fluorescence induction for promoters that are induced after exposure to a sublethal high hydrostatic pressure stress. This screening yielded three promoters of genes belonging to the heat shock regulon (dnaK, lon, clpPX), suggesting a role for heat shock proteins in protection against, and/or repair of, damage caused by high pressure. Several further observations provide additional support for this hypothesis: (i). the expression of rpoH, encoding the heat shock-specific sigma factor sigma(32), was also induced by high pressure; (ii). heat shock rendered E. coli significantly more resistant to subsequent high-pressure inactivation, and this heat shock-induced pressure resistance followed the same time course as the induction of heat shock genes; (iii). basal expression levels of GFP from heat shock promoters, and expression of several heat shock proteins as determined by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteins extracted from pulse-labeled cells, was increased in three previously isolated pressure-resistant mutants of E. coli compared to wild-type levels.
Collapse
Affiliation(s)
- Abram Aertsen
- Laboratory of Food Microbiology, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Butterfield DA. Proteomics: a new approach to investigate oxidative stress in Alzheimer's disease brain. Brain Res 2004; 1000:1-7. [PMID: 15053946 DOI: 10.1016/j.brainres.2003.12.012] [Citation(s) in RCA: 165] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2003] [Indexed: 11/23/2022]
Abstract
In Alzheimer's disease (AD) brain oxidative stress is observed indexed by several markers, among which are protein carbonyls and 3-nitrotyrosine, markers for protein oxidation. We hypothesized that identity of these oxidatively modified proteins would lead to greater understanding of some of the potential molecular mechanisms involved in neurodegeneration in this dementing disorder. Proteomics is an emerging method for identification of proteins, and its application to neurodegenerative disorders, especially AD, is just beginning. Posttranslational modification of brain proteins, particularly that due of oxidation of proteins, provides an effective means of screening a subset of proteins within the brain proteome that likely reflects the extensive oxidative stress under which the AD brain exists, and this new methodology provides insights into mechanisms of neurodegeneration in and new therapeutic targets for AD. In this review, the use of proteomics to identify specifically oxidized proteins in AD brain is presented, from which new insights into mechanisms of neurodegeneration and synapse loss in this dementing disorder that is associated with oxidative stress have emerged.
Collapse
Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506-0055, USA.
| |
Collapse
|
28
|
Binz PA, Müller M, Hoogland C, Zimmermann C, Pasquarello C, Corthals G, Sanchez JC, Hochstrasser DF, Appel RD. The molecular scanner: concept and developments. Curr Opin Biotechnol 2004; 15:17-23. [PMID: 15102461 DOI: 10.1016/j.copbio.2003.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Approaches aimed at deciphering the proteome have illustrated the need for relatively complex and highly sensitive methodologies. The major elements of proteome analysis, such as powerful protein separation and enzymatic processing, mass spectrometry and dedicated bioinformatics have been assembled in the development of the molecular scanner. This highly flexible and data-rich approach has combined the power of electrophoretic protein separation, the simultaneous digestion and transfer of proteins through an enzymatic membrane, the immediate use of the MALDI mass spectrometer to scan a collecting membrane, and the development of dedicated bioinformatics tools to perform protein identification and molecular imaging of the proteome. Clinical applications of the molecular scanner have also started to be developed for disease diagnosis in biological material.
Collapse
MESH Headings
- Animals
- Biotechnology/instrumentation
- Biotechnology/methods
- Biotechnology/trends
- Electrophoresis, Gel, Two-Dimensional/instrumentation
- Electrophoresis, Gel, Two-Dimensional/methods
- Equipment Design
- Gene Expression Profiling/instrumentation
- Gene Expression Profiling/methods
- Gene Expression Profiling/trends
- Humans
- Proteins/analysis
- Proteins/chemistry
- Proteomics/instrumentation
- Proteomics/methods
- Proteomics/trends
- Sequence Analysis, Protein/instrumentation
- Sequence Analysis, Protein/methods
- Sequence Analysis, Protein/trends
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/trends
- Systems Integration
- User-Computer Interface
Collapse
Affiliation(s)
- Pierre-Alain Binz
- Swiss Institute of Bioinformatics, Proteome Informatics Group, CMU, Michel Servet 1, 1211 Geneva, Switzerland.
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Komatsu S, Kojima K, Suzuki K, Ozaki K, Higo K. Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003. Nucleic Acids Res 2004; 32:D388-92. [PMID: 14681440 PMCID: PMC308755 DOI: 10.1093/nar/gkh020] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified proteins showing tissue and subcellular localization, corresponding to 4180 separate protein entries in the database. The Rice Proteome Database contains the calculated properties of each protein such as molecular weight, isoelectric point and expression; experimentally determined properties such as amino acid sequences obtained using protein sequencers and mass spectrometry; and the results of database searches such as sequence homologies. The database is searchable by keyword, accession number, protein name, isoelectric point, molecular weight and amino acid sequence, or by selection of a spot on one of the 2D-PAGE reference maps. Cross-references are provided to tools for proteomics and to other 2D-PAGE databases, which in turn provide many links to other molecular databases. The information in the Rice Proteome Database is updated weekly, and is available on the World Wide Web at http://gene64.dna.affrc.go.jp/RPD/.
Collapse
Affiliation(s)
- Setsuko Komatsu
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
| | | | | | | | | |
Collapse
|
30
|
Babnigg G, Giometti CS. GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes. Nucleic Acids Res 2004; 32:D582-5. [PMID: 14681486 PMCID: PMC308823 DOI: 10.1093/nar/gkh089] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
GELBANK is a publicly available database of two-dimensional gel electrophoresis (2DE) gel patterns of proteomes from organisms with known genome information (available at http://gelbank.anl.gov and ftp://bioinformatics.anl.gov/gelbank/). Currently it includes 131 completed, mostly microbial proteomes available from the National Center for Biotechnology Information. A web interface allows the upload of 2D gel patterns and their annotation for registered users. The images are organized by species, tissue type, separation method, sample type and staining method. The database can be queried based on protein or 2DE-pattern attributes. A web interface allows registered users to assign molecular weight and pH gradient profiles to their own 2D gel patterns as well as to link protein identifications to a given spot on the pattern. The website presents all of the submitted 2D gel patterns where the end-user can dynamically display the images or parts of images along with molecular weight, pH profile information and linked protein identification. A collection of images can be selected for the creation of animations from which the user can select sub-regions of interest and unlimited 2D gel patterns for visualization. The website currently presents 233 identifications for 81 gel patterns for Homo sapiens, Methanococcus jannaschii, Pyro coccus furiosus, Shewanella oneidensis, Escherichia coli and Deinococcus radiodurans.
Collapse
Affiliation(s)
- György Babnigg
- Protein Mapping Group, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | | |
Collapse
|
31
|
Chapter 15 Electrophoresis of proteins and peptides. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0301-4770(04)80028-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
32
|
Butterfield DA, Boyd-Kimball D, Castegna A. Proteomics in Alzheimer's disease: insights into potential mechanisms of neurodegeneration. J Neurochem 2003; 86:1313-27. [PMID: 12950441 DOI: 10.1046/j.1471-4159.2003.01948.x] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Proteomics involves the identification of unknown proteins following their separation, often using two-dimensional electrophoresis, digestion of particular proteins of interest by trypsin, determination of the molecular weight of the resulting peptides, and database searching to make the identification of the proteins. Application of proteomics to Alzheimer's disease (AD), the major dementing disorder of the elderly, has just begun. Differences in protein expression and post-translational modification (mostly oxidative modification) of proteins from AD brain and peripheral tissue, as well as in brain from rodent models of AD, have yielded insights into potential molecular mechanisms of neurodegeneration in this dementing disorder. This review surveys the proteomics studies relevant to AD, from which new understandings of the pathology, biochemistry, and physiology of AD are beginning to emerge.
Collapse
Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, University of Kentucky, Lexington, Kentucky 40506-0055, USA.
| | | | | |
Collapse
|
33
|
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003; 31:3784-8. [PMID: 12824418 PMCID: PMC168970 DOI: 10.1093/nar/gkg563] [Citation(s) in RCA: 3386] [Impact Index Per Article: 161.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.
Collapse
Affiliation(s)
- Elisabeth Gasteiger
- Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 Rue Michel Servet, 1211 Geneva 4, Switzerland.
| | | | | | | | | | | |
Collapse
|
34
|
Apweiler R, Martin MJ, O'Donovan C, Pruess M. Managing core resources for genomics and proteomics. Pharmacogenomics 2003; 4:343-50. [PMID: 12718724 DOI: 10.1517/phgs.4.3.343.22689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Recent years have seen an explosive growth in biological data, which is often not published in a conventional sense but rather deposited in a database. This trend and the need for computational analyses of the data make databases essential tools for biological research. Data from a variety of sources, covering a wide range of biological information, are stored in different, often quite specialized, databases. The provision of such databases as useful resources for the scientific community is a demanding task since the data not only have to be stored in a consistent way, but also have to be easily accessible and highly integrated with other databases. Furthermore, it is necessary to provide users with effective tools to search the databases and to analyze the data. At the European Bioinformatics Institute (EBI), we develop and maintain a number of biological databases and provide a variety of bioinformatics tools to facilitate database and similarity searches and data analysis. In this review, we will provide examples of the core resources maintained at the EBI and summarize important issues of database management of such resources.
Collapse
Affiliation(s)
- Rolf Apweiler
- The EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | | | | | | |
Collapse
|
35
|
Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, Kell DB, Lilley KS, Roepstorff P, Yates JR, Brass A, Brown AJP, Cash P, Gaskell SJ, Hubbard SJ, Oliver SG. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol 2003; 21:247-54. [PMID: 12610571 DOI: 10.1038/nbt0303-247] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2003] [Accepted: 01/27/2003] [Indexed: 11/08/2022]
Abstract
Both the generation and the analysis of proteome data are becoming increasingly widespread, and the field of proteomics is moving incrementally toward high-throughput approaches. Techniques are also increasing in complexity as the relevant technologies evolve. A standard representation of both the methods used and the data generated in proteomics experiments, analogous to that of the MIAME (minimum information about a microarray experiment) guidelines for transcriptomics, and the associated MAGE (microarray gene expression) object model and XML (extensible markup language) implementation, has yet to emerge. This hinders the handling, exchange, and dissemination of proteomics data. Here, we present a UML (unified modeling language) approach to proteomics experimental data, describe XML and SQL (structured query language) implementations of that model, and discuss capture, storage, and dissemination strategies. These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository.
Collapse
Affiliation(s)
- Chris F Taylor
- School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Champion MM, Campbell CS, Siegele DA, Russell DH, Hu JC. Proteome analysis of Escherichia coli K-12 by two-dimensional native-state chromatography and MALDI-MS. Mol Microbiol 2003; 47:383-96. [PMID: 12519190 DOI: 10.1046/j.1365-2958.2003.03294.x] [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: 11/20/2022]
Abstract
To identify proteins expressed in Escherichia coli K-12 MG1655 during exponential growth in defined medium, we separated soluble proteins of E. coli over two dimensions of native-state high-performance liquid chromatography, and examined the components of the protein mixtures in each of 380 fractions by peptide mass fingerprinting. To date, we have identified the products of 310 genes covering a wide range of cellular functions. Validation of protein assignments was made by comparing the assignments of proteins to specific first-dimension fractions to proteins visualized by two-dimensional gel electrophoresis. Co-fractionation of proteins suggests the possible identities of components of multiprotein complexes. This approach yields high-throughput gel-independent identification of proteins. It can also be used to assign identities to spots visualized by two-dimensional gels, and should be useful to evaluate differences in expressed proteome content and protein complexes among strains or between different physiological states.
Collapse
Affiliation(s)
- Matthew M Champion
- Department of Biochemistry, Texas A & M University, College Station TX 77843-2128, USA
| | | | | | | | | |
Collapse
|
37
|
Pruess M, Apweiler R. Bioinformatics Resources for In Silico Proteome Analysis. J Biomed Biotechnol 2003; 2003:231-236. [PMID: 14615630 PMCID: PMC514268 DOI: 10.1155/s1110724303209219] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2002] [Accepted: 12/10/2002] [Indexed: 11/17/2022] Open
Abstract
In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data. To utilise this data for healthcare and drug development, first the characteristics of proteomes of entire species-mainly the human-have to be understood, before secondly differentiation between individuals can be surveyed. Specialised databases about nucleic acid sequences, protein sequences, protein tertiary structure, genome analysis, and proteome analysis represent useful resources for analysis, characterisation, and classification of protein sequences. Different from most proteomics tools focusing on similarity searches, structure analysis and prediction, detection of specific regions, alignments, data mining, 2D PAGE analysis, or protein modelling, respectively, comprehensive databases like the proteome analysis database benefit from the information stored in different databases and make use of different protein analysis tools to provide computational analysis of whole proteomes.
Collapse
Affiliation(s)
- Manuela Pruess
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rolf Apweiler
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| |
Collapse
|
38
|
Müller M, Gras R, Appel RD, Bienvenut WV, Hochstrasser DF. Visualization and analysis of molecular scanner peptide mass spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:221-231. [PMID: 11908802 DOI: 10.1016/s1044-0305(01)00358-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The molecular scanner combines protein separation using gel electrophoresis with peptide mass fingerprinting (PMF) techniques to identify proteins in a highly automated manner. Proteins separated in a 2-dimensional polyacrylamide gel (2-D PAGE) are digested in parallel and transferred onto a membrane keeping their relative positions. The membrane is then sprayed with a matrix and inserted into a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometer, which measures a peptide mass fingerprint at each site on the scanned grid. First, visualization of PMF data allows surveying all fingerprints at once and provides very useful information on the presence of chemical noise. Chemical noise is shown to be a potential source for erroneous identifications and is therefore purged from the mass fingerprints. Then, the correlation between neighboring spectra is used to recalibrate the peptide masses. Finally, a method that clusters peptide masses according to the similarity of the spatial distributions of their signal intensities is presented. This method allows discarding many of the false positives that usually go along with PMF identifications and allows identifying many weakly expressed proteins present in the gel.
Collapse
|
39
|
Vuadens F, Gasparini D, Déon C, Sanchez JC, Hochstrasser DF, Schneider P, Tissot JD. Identification of specific proteins in different lymphocyte populations by proteomic tools. Proteomics 2002. [DOI: 10.1002/1615-9861(200201)2:1<105::aid-prot105>3.0.co;2-f] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
40
|
Schaffer S, Weil B, Nguyen VD, Dongmann G, Günther K, Nickolaus M, Hermann T, Bott M. A high-resolution reference map for cytoplasmic and membrane-associated proteins of Corynebacterium glutamicum. Electrophoresis 2001; 22:4404-22. [PMID: 11824608 DOI: 10.1002/1522-2683(200112)22:20<4404::aid-elps4404>3.0.co;2-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We present a high-resolution reference map for soluble proteins obtained from Corynebacterium glutamicum cells grown in glucose minimal medium. The analysis window covers the pl range from 4-6 and the molecular mass range from 5-100 kDa. Using overlapping narrow immobilized pH gradients for isoelectric focusing, 970 protein spots were detected after second-dimensional separation on SDS-polyacrylamide gels and colloidal Coomassie-staining. By tryptic peptide mass fingerprinting 169 protein spots were identified, representing 152 different proteins including many enzymes involved in central metabolism (18), amino acid biosynthesis (24) and nucleotide biosynthesis (11). Thirty-five of the identified proteins have no known function. A comparison of the observed and the expected physicochemical properties of the identified proteins indicated that nine proteins were covalently modified, since variants with apparently identical molecular mass, but differing pl were detected. The N-termini of eight proteins were determined by post-source decay (PSD) analysis of selected peptides. In addition to the soluble proteins, a map of the membrane-bound proteins within the pl range 4-7 is presented, which contains 660 protein spots, 22 of which were identified, representing 13 different proteins.
Collapse
Affiliation(s)
- S Schaffer
- Institut für Biotechnologie 1, Forschungszentrum Jülich, Germany
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Lind K, Kresse M, Müller RH. Comparison of protein adsorption patterns onto differently charged hydrophilic superparamagnetic iron oxide particles obtained in vitro and ex vivo. Electrophoresis 2001; 22:3514-21. [PMID: 11669535 DOI: 10.1002/1522-2683(200109)22:16<3514::aid-elps3514>3.0.co;2-q] [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: 11/11/2022]
Abstract
Protein adsorption patterns of superparamagnetic iron oxides (SPIO) were evaluated by two-dimensional electrophoresis (2-DE) after in vitro incubation of the particles in plasma or serum. SPIO particles having positive (MKK 1211), negative (MKA 1211), or neutral (MKG 1411) charge were used. Protein adsorption patterns of different charged SPIO particles acquired in vitro and recollected 5 min after intravenous injection into rats (ex vivo) were compared. For the uncharged MKG 1411 particles, the differences of protein adsorption patterns were negligible and only minor differences were found for the negatively charged MKA 1211 and positively charged MKK 1211 particles. A good correlation between in vitro and ex vivo data could be shown. For the evaluation of protein adsorption patterns of SPIO particles determining organ distribution and allowing estimation of site-specific delivery (drug targeting), the currently used protocol for 2-DE analysis could be confirmed.
Collapse
Affiliation(s)
- K Lind
- Department of Pharmaceutical Technology, The Free University of Berlin, Germany
| | | | | |
Collapse
|
42
|
Schwartz R, Ting CS, King J. Whole Proteome pI Values Correlate with Subcellular Localizations of Proteins for Organisms within the Three Domains of Life. Genome Res 2001. [DOI: 10.1101/gr.158701] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Isoelectric point (pI) values have long been a standard measure for distinguishing between proteins. This article analyzes distributions of pI values estimated computationally for all predicted ORFs in a selection of fully sequenced genomes. Histograms of pI values confirm the bimodality that has been observed previously for bacterial and archaeal genomes (Van Bogelen et al. 1999) and reveal a trimodality in eukaryotic genomes. A similar analysis on subsets of a nonredundant protein sequence database generated from the full database by selecting on subcellular localization shows that sequences annotated as corresponding to cytosolic and integral membrane proteins have pI distributions that appear to correspond with the two observed modes of bacteria and archaea. Furthermore, nuclear proteins have a broader distribution that may account for the third mode observed in eukaryotes. On the basis of this association between pI and subcellular localization, we conclude that the bimodal character of whole proteome pI values in bacteria and archaea and the trimodal character in eukaryotes are likely to be general properties of proteomes and are associated with the need for different pI values depending on subcellular localization. Our analyses also suggest that the proportions of proteomes consisting of membrane-associated proteins may be currently underestimated.
Collapse
|
43
|
Poirier F, Imam N, Pontet M, Joubert-Caron R, Caron M. The BPP (protein biochemistry and proteomics) two-dimensional electrophoresis database. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2001; 753:23-8. [PMID: 11302443 DOI: 10.1016/s0378-4347(00)00459-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The BPP (protein biochemistry and proteomics) two-dimensional electrophoresis (2-DE) database (http://www-smbh.univ-paris13.fr/lbtp/Biochemistry/Biochimie/bque.htm) was established in 1998. The current release contains 11 reference maps from human hematopoietic and lymphoid cell line samples. These reference maps have now 255 identified spots, corresponding to 84 protein entries. The World Wide Web (WWW) presentation is designed to allow public access to the available 2-DE data together with logical connections to databases providing complementary information.
Collapse
Affiliation(s)
- F Poirier
- Biochimie des Protéines et Protéomique, Biochimie Cellulaire des Hémopathies Lymphoïdes (EA 1625), UFR SMBH Léonard de Vinci, Université Paris 13, Bobigny, France
| | | | | | | | | |
Collapse
|
44
|
Poutanen M, Salusjärvi L, Ruohonen L, Penttilä M, Kalkkinen N. Use of matrix-assisted laser desorption/ionization time-of-flight mass mapping and nanospray liquid chromatography/electrospray ionization tandem mass spectrometry sequence tag analysis for high sensitivity identification of yeast proteins separated by two-dimensional gel electrophoresis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2001; 15:1685-1692. [PMID: 11555867 DOI: 10.1002/rcm.424] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Current analytical techniques in protein identification by mass spectrometry are based on the generation of peptide mass maps or sequence tags that are idiotypic for the protein sequence. This work reports on the development of the use of mass spectrometric methods for protein identification in research on metabolic pathways of a genetically modified strain of the baker's yeast Saccharomyces cerevisiae. This study describes the use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass mapping and liquid chromatography/quadrupole time-of-flight electrospray ionization tandem mass spectrometry (LC/Q-TOF-ESI-MS/MS) sequence tag analysis in identification of yeast proteins separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). The spots were selected for analysis in order to collect information for future studies, to cover the whole pI range from 3 to 10, and to evaluate information from spots of different intensities. Mass mapping as a rapid, high-throughput method was in most cases sensitive enough for identification. LC/MS/MS was found to be more sensitive and to provide more accurate data, and was very useful when analyzing small amounts of sample. Even one sequence tag acquired by this method could be enough for unambiguous identification, and, in the present case, successfully identified a point mutation.
Collapse
Affiliation(s)
- M Poutanen
- Institute of Biotechnology, P.O. Box 56 (Viikinkaari 9), FIN-00014 University of Helsinki, Finland.
| | | | | | | | | |
Collapse
|
45
|
Affiliation(s)
- J Godovac-Zimmermann
- Center for Molecular Medicine, Department of Medicine, University College London, 5 University Street, London WC1E 6JJ, United Kingdom.
| | | |
Collapse
|
46
|
Chapter 14 Two-dimensional maps. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0301-4770(01)80046-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
47
|
Abstract
Proteome research aims to unravel the biological complexity encoded by the genome. Due to the complexity of higher eukaryotic cells, single-step characterization of a proteome is likely to be difficult to achieve. However, advantage can be taken of the macromolecular architecture of a cell, e.g., subcellular compartments, organelles, macromolecular structures and multiprotein complexes, to establish subcellular proteomes. This review highlights recent developments in this area of proteomics, namely the establishment of two-dimensional electrophoresis (2-DE) reference maps of subcellular compartments and organelles as well as the characterization of macromolecular structures and multiprotein complexes using a proteomics approach.
Collapse
Affiliation(s)
- E Jung
- Central Clinical Chemistry Laboratory, Geneva University Hospital, Switzerland.
| | | | | | | |
Collapse
|
48
|
Jung E, Hoogland C, Chiappe D, Sanchez JC, Hochstrasser DF. The establishment of a human liver nuclei two-dimensional electrophoresis reference map. Electrophoresis 2000; 21:3483-7. [PMID: 11079567 DOI: 10.1002/1522-2683(20001001)21:16<3483::aid-elps3483>3.0.co;2-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This short communication describes the establishment of a two-dimensional electrophoresis (2-DE) reference map of nuclear proteins isolated from human liver. The human liver nuclei 2-DE reference map contains 1497 spots. In an initial identification study using peptide mass fingerprinting as a means of protein identification we were able to identify 26 spots corresponding to 15 different proteins. The human liver nuclei 2-DE reference map is now included in the SWISS-2DPAGE database, which can be accessed through the ExPASy server (http://www.expasy.ch/ch2d/).
Collapse
Affiliation(s)
- E Jung
- Central Clinical Chemistry Laboratory, Geneva University Hospital, Switzerland.
| | | | | | | | | |
Collapse
|
49
|
Crawford ME, Cusick ME, Garrels JI. Databases and knowledge resources for proteomics research. Trends Biotechnol 2000. [DOI: 10.1016/s0167-7799(00)00012-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|