What Is “Proteomics”? (Genetics & Inherited Conditions)
Historically, much of the focus in genetic research has been on genes and completion of the Human Genome Project. More recently, the focus has shifted to a new and related topic, the proteome. Proteins are known to perform most of the important functions of cells. Therefore, proteomics is, essentially, the study of proteins in an organism and, most important, their function. There are many aspects to the understanding of protein function, including where a particular protein is located in the cell, what modifications occur during its activity, what ligands may bind to it, and its activity. Researchers are seeking to identify all the proteins made in a given cell, tissue, or organism and determine how those proteins interact with metobolites, with themselves, and with nucleic acids. By studying proteomics, scientists hope to uncover underlying causes of disease at the cellular level, invent better methods of diagnosis, and discover new, more efficient medicines for the treatment of disease.
Proteomics has moved to the forefront of molecular research, especially in the area of drug research. Neither the structure nor the function of a protein can be predicted from the DNA sequence alone. Although genes code for proteins, there is a large difference between the number of messenger (mRNA) molecules transcribed from DNA and the number of proteins in a cell. In addition, two hundred known modifications occur during the...
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Methods of Proteomic Research (Genetics & Inherited Conditions)
In order to study the functions of a protein, it must be separated from other proteins or contaminants, purified, and structurally characterized. These are the major tasks facing researchers in the field.
In order to obtain a sufficient quantity of a particular protein for study, the coding plasmid can be injected into Escherichia coli bacteria and the cells will translate the protein multiple times. Alternatively, it must be extracted from biological tissues. The desired polypeptide must then be separated from cells or tissues that may contain thousands of unique proteins. This can be accomplished by homogenizing the tissue, extracting the proteins with solvents or by centrifugation, and further purifying the protein by various means, including high-pressure liquid chromatography (HPLC, separation by solubility differences) and two-dimensional (2-D) gel electrophoresis (separation of molecules by charge and molecular mass). A relatively recent development in laboratory technique research is three-dimensional (3-D) gel electrophoresis, allowing for further separation and identification of proteins.
Structural characterization begins with establishing the order of linked amino acids in the protein. This can be accomplished by the classical techniques of using proteases to fragment the protein chemically and then analyzing the fragments by separation and spectroscopic analysis. The molecular mass...
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Challenges and Limitations of Current Methods (Genetics & Inherited Conditions)
The amount of data being obtained by proteomics research poses a problem in organizing and processing the information obtained on proteins. The Human Proteome Organization (HUPO) and the European Bioinformatics Institute (EBI) are two organizations whose purposes include the management and organization of proteomics information and databases, and the facilitation of the advancement of this scientific endeavor.
Analyzing MS data from proteins and relating the complex array of proteins within a single cell to the linear genetic material of DNA present challenges to researchers that they are tackling through computer algorithms, programs, and databases. The SWISS-PROT database, for example, is an annotated protein-sequence database maintained by the Swiss Bioinformatics Institute.
Other obstacles to relating proteins to parent genes include the loss of quaternary structure during separation and the presence of post-translation processing, which can alter the amino acid sequence to the extent that it becomes almost unrecognizable from the parent gene. A lack of protein amplification methods—techniques that would produce more copies of a protein to aid in study—requires sensitive analysis methods and increasingly strong detectors. Currently new methods are being developed, but the limit of study is as large as 1 nanometer.
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DiseaseDiseasesprotein markers (Genetics & Inherited Conditions)
Proteins often act as markers for disease. As researchers study proteins, they have found that disease may be characterized by some proteins that are being overproduced, not being produced at all, or being produced at inappropriate times. As the correlation of proteins to disease becomes clearer, better diagnostic tests and drugs are being explored. For example, Alzheimer’s disease and Down syndrome are associated with a common protein fragment as the major extracellular protein component of senile plaques.
Researchers are investigating changes in protein expression in heart disease and heart failure, and several hundred cardiac proteins have already been identified. The study of proteomics in immunological diseases has revealed that there is a connection between the human neutrophil α-defensins (HNPs) and human immunodeficiency virus, HIV-1. HNPs are small, cysteine-rich, cationic antimicrobial proteins that are stored in the azurophilic granules of neutrophils and released during phagocytosis to kill ingested foreign microbes. To date, the three most abundant forms of the protein have been implicated in suppressing HIV-1 in vivo.
Similarly, cancer is being studied to find a roster of proteins that are present in cancerous cells but not in normal cells. The Clinical Proteomics Program, a joint effort of the National Cancer Institute and the Food and Drug Administration is searching for the...
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Possible Future Directions (Genetics & Inherited Conditions)
Although proteomics is a relatively new area of genetic research, there are three fields that are gaining attention, glycomics, metabolomics, and metabonomics. Glycomics addresses the importance of the sugar coatings of proteins and cells and is gaining attention. This area of study has arisen because of the many roles of sugar coatings in important cellular functions, including the immunological recognition sites, barriers, and sites for attack by pathogens. Metabolomics is the study of the proteins left behind as the cell performs its processes. This field primarily looks at small proteins produced as by-products. Metabonomics is often used interchangeably with metabolomics but differs in that it examines the change that proteins produce when the cell responds to stresses, such as disease.
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Further Reading (Genetics & Inherited Conditions)
Hopker, Hans-Rudolf, et al. Proteomics in Practice: Guide for Successful Research Design, 2d ed. Weinham, Germany: Wiley-VCH Verlag GmbH, 2008. A combination textbook and lab manual geared toward academic and industry researchers.
Liebler, David G. Introduction to Proteomics: Tools for the New Biology. Totowa, N.J.: Humana Press, 2001. Basics of protein and proteome analysis, key concepts of proteomics, workings of the analytical instrumentation, overview of software tools, and applications of protein and peptide separation techniques, mass spectrometry, and more.
Link, Andrew J., ed. 2-D Proteome Analysis Protocols. Totowa, N.J.: Humana Press, 1999. Practical proteomics, presenting techniques with step-by-step instructions for laboratory researchers. Fifty-five chapters prepared by more than seventy specialists.
Modern Drug Discovery (October, 2002). The entire issue is devoted to proteomics, with many interesting articles on methods of research, Web sites, and computer-assisted methods of data analysis.
Twyman, Richard M. Principles of Proteomics. Oxon, England: Garland Science/BIOS Scientific, 2009. This book is designed for students in advanced-level courses.
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Web Sites of Interest (Genetics & Inherited Conditions)
Biotechnology News and Information Portal. http://www.bioexchange.com/news/proteomics.html. Provides information about new developments in the biotechnology business.
Cambridge Healthtech Institute. http://www.genomicglossaries.com/content/proteomics.asp. Provides a useful glossary of technical terms used in proteomics, as well as many links to related sites.
Clinical Proteomics Program. http://home.ccr.cancer.gov/ncifdaproteomics. Serves as an entrance to information on the joint program between the National Cancer Institute of the National Institutes of Health and the U.S. Food and Drug Administration to support the development of proteomics-based technologies.
Human Proteomics Organization. http://www.hupo.org. HUPO works to consolidate regional proteome organizations into a worldwide group, conduct scientific and educational activities, and disseminate knowledge about both the human proteome and model organisms.
Introduction to Proteomics. http://web1.tch.harvard.edu/cfapps/research/data_admin/Site602/mainpageS602P0.html A Web site was developed by the Proteomics Center at Children’s Hospital, Boston. Has an interactive component, which serves as an excellent basic educational tool for understanding proteomics.
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Methodologies (Magill’s Medical Guide, Sixth Edition)
Proteomics focuses on developing a proteome profile for any given cell, tissue, or disease through three main perspectives. Functional (quantitative) proteomics aims to identify, quantify, and localize proteins within proteomes. Structural proteomics aims to develop a precise three-dimensional structure of each protein in normal and abnormal states, which is vital to clinical diagnostics and drug discovery. Mapping protein-protein interactions aims to understand how proteins interact with one another in complexes, forming networks and pathways of biological activity to understand how diseases originate and progress.
Proteome size, complexity, and dynamics are the current biggest challenges to proteomics. For this reason, this field is closely tied to technological advances. The use of robotic techniques has led to processing hundreds of thousands of extremely small samples every day, which is called high-throughput. To profile proteomes, they must first be isolated, their proteins separated and then purified through large-scale two-dimensional polyacrylamide gel electrophoresis and/or mass spectrometry. Protein structural information is then determined using protein sequencing, mass spectrometry, and/or X-ray crystallography. Assigning protein function within a proteome involves protein and/or antibody microarray analyses to determine biochemical pathway involvement and any protein-protein interactions. Typically, laboratories...
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Medicine and Proteomics (Magill’s Medical Guide, Sixth Edition)
Most diseases create alterations in cellular function. Complex diseases such as cancer, heart disease, and diabetes cannot be treated effectively if the underlying cause and proteins responsible remain unknown. However, the current practice of biomedical research is unable to identify these changes or determine how they relate to disease processes quickly enough to develop the needed diagnostics and treatment. Identifying proteomic components that are specific for a disease (biomarkers) is a major effort of proteomic research. The aim is to develop diagnostic kits that detect the very early phase of a disease. Within populations, the diagnosis, prognosis, treatment, origins, and progression of a disease are public health issues overseen by epidemiologists. Genetic epidemiology is a new discipline that is closely following proteomic progress to develop better public health policies and planning. Proteomics is also expected to identify targets for new drugs.
In the early stages of development, proteome profiling has already shown that the human cardiac proteome is reproducibly and uniquely altered for different heart diseases and disorders. Biomarkers specific to prostate and breast cancer have been identified. These first studies encouraged proteomic researchers to turn to disease proteomic profiling. Because most diseases create protein alterations in blood plasma long before symptoms appear, proteomic serum and...
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Perspective and Prospects (Magill’s Medical Guide, Sixth Edition)
The origins of proteomics can be traced to the technique of separating complex mixtures of proteins by two-dimensional polyacrylamide gel electrophoresis in the mid-1970’s. Refinement of the technique and the addition of protein sequencing methods enabled identification of the separated proteins. In the 1990’s, advances in mass spectrometry provided a highly accurate, sensitive analysis of proteins capable of handling thousands of samples.
The final impetus for proteomic research was a direct outcome of the technological advancements of the Human Genome Project, including microarray analyses, the concept of high-throughput, and a paradigm shift in biological science research. Paramount was the recognition that the protein products of a gene, not the gene itself, are responsible for cellular processes. It became clear that the function of proteins in cellular pathways and processes could not be deduced from the deoxyribonucleic acid (DNA) sequence alone. Efforts quickly turned to studying all proteins and their functions in the context of genetics and diseases. As an emerging discipline, proteomics represents a new research form that is more global and integrative than traditional protein research in the past, which concentrated on the study of single proteins.
Currently, the concern among researchers is the sequestering of data generated in proteomic research for private company use or through aggressive...
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For Further Information: (Magill’s Medical Guide, Sixth Edition)
Berman, Helen M., David S. Goodsell, and Philip E. Bourne. “Protein Structures: From Famine to Feast.” American Scientist 90, no. 4 (July/August, 2002): 350-351.
Campbell, A. Malcolm, and Laurie J. Heyer. Discovering Genomics, Proteomics, and Bioinformatics. 2d ed. San Francisco: Pearson/Benjamin Cummings, 2007.
Dreger, Mathias. “Proteome Analysis at the Level of Subcellular Structures.” European Journal of Biochemistry 270, no. 4 (February, 2003): 589-599.
Ezzell, Carol. “Proteins Rule.” Scientific American 286, no. 4 (April, 2002): 40-47.
Hanash, Sam. “Disease Proteomics.” Nature 422, no. 6928 (March 13, 2003): 226-232.
Merrill, Stephen A., and Anne-Marie Mazza, eds. Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health. Washington, D.C.: National Academies Press, 2006.
Patterson, Scott D., and Ruedi H. Aebersold. “Proteomics: The First Decade and Beyond.” Nature Genetics, supp. 33 (March, 2003): 311-323.
Sali, Andrej, et al. “From Words to Literature in Structural Proteomics.” Nature 422, no. 6928 (March 13, 2003): 216-225.
Sellers, Thomas A., and John R. Yates. “Review of Proteomics with Applications to Genetic Epidemiology.” Genetic Epidemiology 24, no. 2 (February, 2003): 83-98.
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Proteomics (World of Microbiology and Immunology)
Proteomics is a discipline of microbiology and molecular biology that has arisen from the gene sequencing efforts that culminated in the sequencing of the human genome in the last years of the twentieth century. In addition to the human genome, sequences of disease-causing bacteria are being deduced. Although fundamental, knowledge of the sequence of nucleotides that comprise deoxyribonucleic acid reveals only a portion of the protein structure encoded by the DNA. Because proteins are an essential element of bacterial structure and function (e.g., role in causing infection), the knowledge of the three-dimensional structure and associations of proteins is vital. Proteomics is an approach to unravel the structure and function of proteins.
The word proteomics is derived from PROTEin complement to a genOME. Essentially, this is the spectrum of proteins that are produced from the template of an organism's genetic material under a given set of conditions. Proteomics compares the protein profiles of proteomes under different conditions in order to unravel biological processes.
The origin of proteomics dates back to the identification of the double-stranded structure of DNA by Watson and Crick in 1953. More recently, the development of the techniques of protein sequencing and gel electrophoresis in the 1960s and 1970s provided the technical means to probe protein structure. In 1986, the first protein sequence database was created (SWISS-PROT, located at the University of Geneva). By the mid-1990s, the concept of the proteome and the discipline of proteomics were well established. The power of proteomics was manifest in March 2000, when the complete proteome of a whole organism was published, that of the bacterium Mycoplasma genitalium
Proteomics research often involves the comparison of the proteins produced by a bacterium (example, Escherichia coli) grown at different temperatures, or in the presence of different food sources, or a population grown in the lab versus a population recovered from an infection. Escherichia coli responds to changing environments by altering the proteins it produces. However, the full extent of the various alterations and their molecular bases are largely unknown. Proteomics research essentially attempts to provide a molecular explanation for bacterial behavior.
Proteomics can be widely applied to research of diverse microbes. For example, the yeast Saccharomyces cerevisiae is being studied to reveal the proteins produced and their functional associations with one another.
The task of sorting out all the proteins that can be produced by a bacterium or yeast cell is formidable. Targeting of the research effort is essential. For example, the comparison of the protein profile of a bacterium obtained directly from an infection (in vivo) with populations of the same microbe grown under defined conditions in the lab (in vitro) could identify proteins that are unique to the infection. Some of these could become targets for diagnosis, therapy, or for prevention of the infection.
The study of proteins is difficult. The amount of protein cannot be amplified as easily as can the amount of DNA, making the detection of minute amounts of protein challenging. The structure of proteins must be maintained, which can be difficult. For example, enzymes, heat, light, or the energy of mixing can break down some proteins.
With the advent of the so-called DNA chips, the expression of thousands of genes can be monitored simultaneously. But DNA is static. It exists and is either expressed or not. Moreover, the expression of a protein does not necessarily mean that the protein is active. Also, proteins can be modified after being produced. Proteins can adopt different shapes, which can determine different functions and levels of activity after they have been produced. These functions provide the structural and operational framework for the life of the bacterium. Proteomics represents the next step after gene expression analysis
Proteomics utilizes various techniques to probe protein expression and structure. The migration of proteins can depend on their net charge and on the size of the protein molecule. When these migrations are in two dimensions, as in 2-D polyacrylamide gel electrophoresis, thousands of proteins can be distinguished in a single experiment. A technique called mass spectrometry analyzes a trait of proteins known as the mass-to-charge ratio, which essentially enables the sequence of amino acids comprising the protein to be determined. Techniques exist that detect modifications after protein manufacture, such as the addition of phosphate groups. Analogous to DNA chips, so-called protein microarrays have been developed. In these, a solid support holds various molecules (antibodies and receptors, as two examples) that will specifically bind protein. The binding pattern of proteins to the support can help determine what proteins are being made and when they are synthesized.
Proteomics typically operates in tandem with bioinformatics, which is an integration of mathematical, statistical, and computational methods to unravel biological data. The vast amount of protein information emerging from a single experiment would be impossible to analyze by manual computation or analysis. Accordingly, comparison of the data with other databases and the use of computer modeling programs, such as those that calculate three-dimensional structures, are invaluable in proteomics.
The knowledge of protein expression and structure, and the potential changes in structure and function under different conditions, could allow the tailoring of treatment strategies. For example, in the lungs of those afflicted with cystic fibrosis, the bacterium Pseudomonas aeuruginosa forms adherent populations on the surface of the lung tissue. These populations, which are enclosed in a glycocalyx that the bacteri produce, are very resistant to treatments and directly and indirectly damage the lung tissue to a lethal extent. Presently, it is known that the bacteria change their genetic expression as they become more firmly associated with the surface. Through proteomics, more details of the proteins involved in the initial approach to the surface and the subsequent, irreversible surface adhesion could be revealed. Once the targets are known, it is conceivable that they can be blocked. Thus, biofilms would not form and the bacteria could be more expeditiously eliminated from the lungs.
See also Biotechnology; Molecular biology and molecular genetics