The proteomics revolution is in full swing in the international biomedical research community as a way to study and ultimately identify the protein molecules that confer health and disease in humans.
University of Wisconsin (Madison, WI) Chemistry Professor Song Jin, along with Ying Ge, Cory Alexander Nelson and Qingge Xu disclose improved methods and nanomaterials for isolating, purifying, and enriching the concentration of compounds having one or more phosphate groups and derivatives, including phosphorylated peptides and phosphorylated proteins in U.S. Patent Application 20100093102,
The Wisconsin research team developed nanostructured enrichment materials, such as metal oxide mesoporous materials, which selectively and reversibly bind with phosphorylated compounds with high specificity and are capable of controlled release of phosphorylated compounds bound to their active surfaces.
FIG. 1. Transmission electron microscope (TEM) micrograph for mesoporous HfO2 (a) with its corresponding small angle X-ray scattering (SAXS) diffraction pattern (b). TEM micrograph for mesoporous ZrO2 (c) with its corresponding SAXS pattern (d) and nitrogen adsorption-desorption isotherms (e).
FIG. 2. Flow diagram of a phosphopeptide enrichment procedure.
Mesoporous metal oxide nanomaterials effectively enrich phosphopeptides for mass spectrometry-based phosphoproteomics. Reversible protein phosphorylation is a ubiquitous post-translational modification that plays a vital role in the control of many biological processes such as cellular growth, division, and signaling. Aberrant phosphorylation is known to be one of the underlying mechanisms for many human diseases, most notably cancer.
Proteomics is becoming an indispensable research tool with the potential to broadly impact biological research and laboratory medicine. However, the unique characteristics of the proteome including high dynamic range in protein abundance, extreme complexity, and heterogeneity due to the various post-translational modifications, present tremendous challenges. The present invention provides methods and devices combining advances in mass spectrometry and nanotechnology, particularly for characterizing proteins with complex post-translational modifications as well as protein-protein and protein-small molecule interactions. Post-translational modifications, which usually occur in low abundance, are of critical importance for understanding the biological functions of proteins.
The researchers reveal nanoscale or nanostructured materials to enrich the low abundant proteins or peptides, which allow for more effective applications of mass spectrometric techniques for investigating important post-translational modifications, such as phosphorylation and glycosylation, and protein-protein or protein-small molecule interactions. Additionally, they disclose a method for enrichment of phosphopeptides using mesoporous nanomaterials, and results acquired using mass spectrometry confirm significant enrichment of phosphorylated peptide digests of standard purified proteins.
Proteins are involved in nearly every aspect of cellular function; therefore technologies for global protein characterization are necessary to virtually all areas of the biological sciences. Research in the field of proteomics has expanded tremendously over the last decade due to its potential to revolutionize biological and medical research, particularly for the development of new drugs, therapies and diagnostic methods. The term proteome is used to describe the entire set of proteins encoded by a genome. In a broader sense, however, the study of the proteome, referred to generally as the field of proteomics, involves the characterization of gene and cellular function by determining the identities, activities, interactions, localization and modifications of individual proteins and protein complexes present in a cell or tissue. Technology development has, and continues, to drive rapid evolution in this field.
Research has demonstrated that a proteome is typically characterized by very dynamic behavior. For example, the types of proteins expressed by a cell, as well as their abundances, post-translational modifications and subcellular locations, vary substantially with the physiological condition of a cell or tissue, including the onset and progression of disease. Accordingly, quantitative characterization of changes in protein content, composition and activity at the organ, tissue, and cellular levels provide information useful for identifying new biological targets for drug development and novel biomarkers for the diagnosis and early detection of disease. Furthermore, proteomics research is highly complementary to other functional approaches for understanding cellular and sub-cellular processes, such as microarray-based expression profiles, systems level genetics, and small molecule based arrays.
The complexity of proteomics, at least in part, is due to the large number of proteins and protein complexes corresponding to a genome. For example, the human proteome is expected to consist of between about 400,000 to about 1,000,000 proteins, which interact to form a huge number of protein-protein complexes important in regulating cellular behavior. The complexity of the human proteome is significantly compounded by the large dynamic range observed for protein expression, typically exceeding over six orders of magnitude, and by post-translational modifications that critically impact protein activity and function. To address this inherent complexity, a number of high throughput platforms for identifying and characterizing proteins have been developed, including two-dimensional gel electrophoresis (2D-GE) protein identification methods, genetic readout experiments, such as the yeast two-hybrid assay, micro-array and chip technologies, and mass spectrometry methods.
Research has demonstrated that a proteome is typically characterized by very dynamic behavior. For example, the types of proteins expressed by a cell, as well as their abundances, post-translational modifications and subcellular locations, vary substantially with the physiological condition of a cell or tissue, including the onset and progression of disease. Accordingly, quantitative characterization of changes in protein content, composition and activity at the organ, tissue, and cellular levels provide information useful for identifying new biological targets for drug development and novel biomarkers for the diagnosis and early detection of disease. Furthermore, proteomics research is highly complementary to other functional approaches for understanding cellular and sub-cellular processes, such as microarray-based expression profiles, systems level genetics, and small molecule based arrays.
The complexity of proteomics, at least in part, is due to the large number of proteins and protein complexes corresponding to a genome. For example, the human proteome is expected to consist of between about 400,000 to about 1,000,000 proteins, which interact to form a huge number of protein-protein complexes important in regulating cellular behavior. The complexity of the human proteome is significantly compounded by the large dynamic range observed for protein expression, typically exceeding over six orders of magnitude, and by post-translational modifications that critically impact protein activity and function. To address this inherent complexity, a number of high throughput platforms for identifying and characterizing proteins have been developed, including two-dimensional gel electrophoresis (2D-GE) protein identification methods, genetic readout experiments, such as the yeast two-hybrid assay, micro-array and chip technologies, and mass spectrometry methods.
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