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Proteomics and genomics
Proteomics and genomics Editorial overview John Yates III and Michael Snyder Current Opinion in Chemical Biology 2004, 8:1–2 This review comes from a themed issue on Proteomics and genomics Edited by John Yates III and Michael Snyder 1367-5931/$ – see front matter ß 2003 Elsevier Ltd. All rights reserved. DOI 10.1016/j.cbpa.2003.12.011
John Yates III 10550 North Torrey Pines Road, Department of Cell Biology, SR11, The Scripps Research Institute, LaJolla, CA 92037, USA e-mail: [email protected]
Michael Snyder Department of MCDB/KBT 926, Yale University, PO Box 208103, New Haven, CT 06620-8103, USA e-mail: [email protected]
Attention is turning to the study of proteins as genome projects continue to churn out genome sequences. Harvesting knowledge from genomic sequence data requires systematic and large-scale studies of proteins. Traditional studies of proteins examined only the isolated protein, but new higher-throughput strategies have made feasible a broader scope to studies to examine the properties of proteins in a broader context. This issue reviews current research in a broad selection of research areas in proteomics. Once a genome sequence is complete, bioinformatics defines open reading frames (ORFs) by using computer algorithms to identify likely coding regions of the genome. Efforts are under way to comprehensively clone the ORFs of an organism. This will create a set of reagents that facilitate studies of the ORFs and to address the more fundamental question of which ORFs are real. Reagents produced in such endeavors can be used to create protein microarrays. A microarray format for the display of proteins permits a variety of large-scale experiments to identify protein–protein interactions, protein–ligand interactions and identification of proteins with specific types of functions (e.g. kinase activity). Computational approaches to define the structures of proteins a priori have improved significantly over the past few years as a result of more sophisticated algorithms and the rise of the computing cluster. Complex and time-consuming calculations can be performed very quickly on computing clusters, leading to more accurate predictions. Predicting structures and folds is a difficult undertaking; thus, increasing the number of known protein structures provides valuable information for those modeling or predicting structures. Large-scale studies to collect a representative set of structures are progressing. Recent research to collect in a high-throughput manner structures of representative proteins and folds for all proteins is reviewed in this issue. Determining the functions of proteins integrates several analytical and chemical technologies with protein biochemistry. Profiling protein expression identifies proteins expressed (or not) as a function of diseases or perturbations of some type. A new form of profiling identifies proteins of specific enzymatic classes on the basis of their activity. Thus, proteins that are active in the cell are recovered and identified. This information increases the specificity of the description of cellular functions and activity potential. Frequently, protein activities or functions are regulated through covalent modifications to proteins. High-throughput methods to identify protein modifications remain a significant challenge, though progress is being made. Increasingly large-scale studies can add clearer perspective on what proteins might be doing in the cell. Where proteins localize provides valuable information as to where and what they might be
www.sciencedirect.com
Current Opinion in Chemical Biology 2004, 8:1–2
2 Proteomics and genomics
doing in the cell. Proteins often function in the context of complexes and thus large-scale studies of protein–protein interactions have led to a more global understanding of the complexity of cellular processes and eventually will lead to a greater understanding of how physiological processes are controlled and regulated.
Current Opinion in Chemical Biology 2004, 8:1–2
The rush to understand the proteome has resulted in a flurry of activity that is yielding new insights into biology. We fully expect this trend to continue with new and improved methods increasing the scale, completeness and accuracy of measurements, which will lead to a greater understanding of the amazing complexity of life.
www.sciencedirect.com
John Yates III 10550 North Torrey Pines Road, Department of Cell Biology, SR11, The Scripps Research Institute, LaJolla, CA 92037, USA e-mail: [email protected]
Michael Snyder Department of MCDB/KBT 926, Yale University, PO Box 208103, New Haven, CT 06620-8103, USA e-mail: [email protected]
Attention is turning to the study of proteins as genome projects continue to churn out genome sequences. Harvesting knowledge from genomic sequence data requires systematic and large-scale studies of proteins. Traditional studies of proteins examined only the isolated protein, but new higher-throughput strategies have made feasible a broader scope to studies to examine the properties of proteins in a broader context. This issue reviews current research in a broad selection of research areas in proteomics. Once a genome sequence is complete, bioinformatics defines open reading frames (ORFs) by using computer algorithms to identify likely coding regions of the genome. Efforts are under way to comprehensively clone the ORFs of an organism. This will create a set of reagents that facilitate studies of the ORFs and to address the more fundamental question of which ORFs are real. Reagents produced in such endeavors can be used to create protein microarrays. A microarray format for the display of proteins permits a variety of large-scale experiments to identify protein–protein interactions, protein–ligand interactions and identification of proteins with specific types of functions (e.g. kinase activity). Computational approaches to define the structures of proteins a priori have improved significantly over the past few years as a result of more sophisticated algorithms and the rise of the computing cluster. Complex and time-consuming calculations can be performed very quickly on computing clusters, leading to more accurate predictions. Predicting structures and folds is a difficult undertaking; thus, increasing the number of known protein structures provides valuable information for those modeling or predicting structures. Large-scale studies to collect a representative set of structures are progressing. Recent research to collect in a high-throughput manner structures of representative proteins and folds for all proteins is reviewed in this issue. Determining the functions of proteins integrates several analytical and chemical technologies with protein biochemistry. Profiling protein expression identifies proteins expressed (or not) as a function of diseases or perturbations of some type. A new form of profiling identifies proteins of specific enzymatic classes on the basis of their activity. Thus, proteins that are active in the cell are recovered and identified. This information increases the specificity of the description of cellular functions and activity potential. Frequently, protein activities or functions are regulated through covalent modifications to proteins. High-throughput methods to identify protein modifications remain a significant challenge, though progress is being made. Increasingly large-scale studies can add clearer perspective on what proteins might be doing in the cell. Where proteins localize provides valuable information as to where and what they might be
www.sciencedirect.com
Current Opinion in Chemical Biology 2004, 8:1–2
2 Proteomics and genomics
doing in the cell. Proteins often function in the context of complexes and thus large-scale studies of protein–protein interactions have led to a more global understanding of the complexity of cellular processes and eventually will lead to a greater understanding of how physiological processes are controlled and regulated.
Current Opinion in Chemical Biology 2004, 8:1–2
The rush to understand the proteome has resulted in a flurry of activity that is yielding new insights into biology. We fully expect this trend to continue with new and improved methods increasing the scale, completeness and accuracy of measurements, which will lead to a greater understanding of the amazing complexity of life.
www.sciencedirect.com