Proteomics Glossary

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  • Published: Jan 14, 2014
  • Channels: Proteomics & Genomics / Proteomics / Base Peak
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This glossary has been reproduced with the permission of
Cambridge Healthtech Institute

Suggestions? Comments? Questions?  mchitty@healthtech.com
Related glossaries include:  Protein StructuresStructural Genomics.

 

2D gel electrophoresis: A key technology for proteomics. Chromatography & electrophoresis glossary

activity based proteomics:  Identification and analysis of changes in active proteins in different cell types and under different conditions ... addressing the biochemical mechanisms of disease more directly than standard genomics and proteomics techniques. (ActivX website "About Precision Proteomics') http://www.activx.com/about.htm

allosteric ribozymes (allozymes): Pharmaceutical biology glossary Potential for use in proteomics. 

annotation- proteins:  In  SWISS- PROT, as in most other sequence databases, two classes of data can be distinguished: the core data and the annotation. For each sequence entry the core data consists of the sequence data, the citation information (bibliographical references), and the taxonomic data (description of the biological source of the protein), while the annotation consists of the description of the following items: Function(s) of the protein,  Post- translational modification(s). For example carbohydrates,  phosphorylation, acetylation, GPI- anchor, etc.,  Domains and sites. For example calcium binding regions, ATP- binding sites, zinc fingers, homeobox, kringle, etc.,  Secondary structure, Quaternary structure, Similarities to other proteins, Disease(s) associated with deficiencie(s) in the protein, Sequence conflicts, variants, etc. (Rolf Apweiler et. al " Protein Sequence Annotation in the Genome Era: The Annotation Concept of SWISS- PROT + TrEMBL" Intelligent Systems in Molecular Biology, 1997) http://www.ebi.ac.uk/swissprot/Publications/ismb97.html

applied proteomics:  Current applications of proteomics seem to be focusing on toxicology and drug  target identification  and  target validation

bait: The basic format of the  yeast-two hybrid system involves the creation of two hybrid molecules, one in which the "bait" protein is fused with a transcription factor, and one in which the "prey" protein is fused with a related  transcription factor. If the bait and prey proteins indeed interact then the two factors fused to these two proteins are also brought into proximity with each other. As a result a specific signal is produced, indicating an interaction has taken place. (CHI Proteomics) 

biological atlas: Maps, genomic & genetic glossary

cell mapping: Maps genomic & genetic

cell signalling proteomics: Using an  antibody- based detection system that is proprietary to Kinexus called Kinetworks, over 100 proteins can be selectively tracked on a single SDS-PAGE minigel with 250 µg of crude protein extract. Kinexus has developed several commercial screens for the specific analysis of panels of protein kinases, protein phosphatases, phosphoproteins, cell cycle proteins, heat shock/ stress proteins and apoptosis proteins. Many of these regulatory proteins are produced at low levels that they not detected by traditional 2D gel- based approaches. We have observed profound differences in the expression, phosphorylation states and subcellular locations of these regulatory proteins in hormone-, drug- and toxin-treated cultured cells and in tissue biopsies from animal and human patient samples. This information is being used to map novel cell signalling pathways through bioinformatic analyses. Dr. Steven Pelech, Kinexus Bioinformatics Corporation "Antibody-Based Cell Signaling Proteomics - Mapping Protein Phosphorylation Networks" Proteomics Europe: Proteins to Profits March 25- 27, 2002, Munich, Germany

cellular pathways: See under Expression glossary metabolic engineering

cellular proteome: All of the proteins expressed in a cell. 

chemical microarrays: Microarrays glossary

chemical proteomics: To link new proteins with known catalytic activities, proteome- scale screens for generic enzyme activities (e.g. protease and phosphatase) should be implemented ... Although it is impossible to screen for chemical reactions that are unknown, in theory, identifying small molecules that bind to the new proteins may elucidate clues to new activities. These ligands might be found by screening the new proteins against diverse chemical libraries using existing methods such as NMR spectroscopy, microcalorimetry, or microarrays. The general concept of ascribing function to new proteins by discovering small molecule ligands might be referred to as chemical proteomics. (Aled Edwards et al. "Proteomics: new tools for a new era" Modern Drug Discovery 3 (7): 35- 44 Sept. 2000) http://pubs.acs.org/journals/mdd/

Related terms Functional Genomics glossary biochemical genomics;  Drug discovery & development chemical genomics

clinical proteomics: Clinical genomics glossary

comparative proteomics:  The  C. elegans proteome was used as an alignment template to assist in novel human gene identification. Among the available 18,452  C. elegans  protein sequences, our results indicate that at least 83% had human homologous genes, with 7954 records of  C. elegans  proteins matching known human gene transcripts. (CH Lai et al "Identification of Novel Human Genes Evolutionarily Conserved in  Caenorhabditis elegans by Comparative Proteomics" Genome Research 10(5): 703-713 May 2000) 

Related terms Genomics glossary comparative genomics, evolutionary genomics.

computational proteomics:  Large- scale generation and analysis of 3D and 4D protein structural information and the application of structural knowledge across all life science disciplines. (Edward T. Maggio, Kal Ramnarayan "Recent developments in computational proteomics" Trends in Biotechnology 19 (7): 266- 272 July 2001) 

DNA protein interactions: See protein- DNA interactions

designer proteins: Proteins glossary in-depth

differential labeling: Assays, labeling, signaling & detection glossary

directed protein evolution:  We have developed an integrated program for the discovery and production of antibody mimetics that are screened for microarray applications. Using our proprietary directed protein evolution technology, PROfusion, stable binding proteins are rapidly produced with high affinity and specificity for their target antigens. Automation of the PROfusion system, coupled with an automated E. coli- based protein expression system, has allowed for the high- throughput generation of binders at low cost. Dr. Richard W. Wagner, Research, Phylos, Inc. "Development of an Automated Directed Protein Evolution Engine to Produce High- Affinity Binders for Protein Microarrays Protein Arrays: Technology and Applications: PepTalk January 7- 8, 2002 San Diego CA 

dissociator assays:  A collective term for  yeast- one hybridyeast- two hybrid or  yeast- three hybrid assays.

environmental proteomics: Many environmental chemicals interact directly with cellular proteins to modify protein functions and interactions. Environmental agents also may affect gene expression and presumably the levels of protein products of those genes. ... This new Core was developed to promote the integration of proteomics technologies into studies of the health effects of environmental agents. Investigators in the Environmental Proteomics Research Core use and adapt these technologies, particularly protein separations and mass spectrometry to investigate the interplay of environmental agents and the proteome. The overall goal of the Environmental Proteomics Research Core is to promote interdisciplinary, collaborative research into how environmental agents affect cellular proteomes. (Environmental Proteomics Research Core, Univ. of Arizona Southwest Environmental Health Sciences Center 2001) http://www.niehs.nih.gov/centers/res-core/az-res3.htm

evolutionary homology: Functional Genomics glossary

Expressed Protein Tags EPTs: Multi- cellular organisms have been evolving a system with which they can discriminate between cells of their own origin and other adventitious cells or cells which have been infected with intracellular pathogens. To achieve this goal, a family of receptors, known as multi- ligand receptors (MLR), have evolved to be remarkably promiscuous binders of peptide ligands. The MLR-bound ligands are derived from degradation intermediates of cellular proteins. Typically, these ligands are 8-12 amino acids in length and have been coined by CANVAS as "expressed protein tags" or EPTs. EPTs are of sufficient length to differentiate particular proteins and/ or individual genes. Each MLR has a single binding site and thus contains a single EPT copy. (Canvas Informatics, Inc, "Technology" 2001) http://www.canvas-informatics.com/

Represent the collection of proteins which are present in a cell. (Robert G. Urban "Proteomics: Making sense of the census" Current Drug Discovery, Aug. 2001) http://currentdrugdiscovery.com/CDDPDF/issue%205/Urban.pdf

Related term:  EST expressed sequence tags: Sequences, DNA & beyond

expression proteomics: Expression glossary

Fluorescence Resonance Energy Transfer FRET: Assays, labels, signaling & detection glossary

functional cloning: Functional Genomics glossary

functional glycomics:  At the present time approximately 110 glycogenes which encode glycosyltransferases and related genes have been cloned. Even though some of the biological functions of those genes have been elucidated, most of the actual functions of these genes continue to be obscure, and limited information is available in terms of their pathophysiolgical significance. Therefore in order to clarify the functional significance of these genes, one of the major strategies is focused on the identification of likely target molecules in vivo and the identification of their functional significance.  Knock out or  transgenic mice have already been reported for several glycogenes and currently available information indicate that some are lethal and some lead to interesting phenotypic changes. (Naoyuki Taniguchi "Beyond glycogenes" Glycoforum, Japan 2001) http://www.glycoforum.gr.jp/science/glycogenes/BG01/BG01E.html

functional protein microarrays: Microarrays glossary

functional proteomics: Relating function to  gene expression protein- protein interactions.  (CHI Proteomics) 

Is yielding large databases of interacting proteins and extensive pathways maps of these interactions are being scored and deciphered by novel high throughput technologies. However, traditional methods of screening have not been very successful in identifying  protein- protein interaction  inhibitors. (CHI Summit Proteomics) 

The identification and measurement of changes in concentration of specific proteins that cells make as a result of their genetic response to specific toxicants and how these proteins are related (NIEHS, US "National Center for Toxicogenomics to Study Genetic Basis of Disease Caused by Environmental Pollution" Dec. 7, 2000) http://www.niehs.nih.gov/nct/pr07de00.htm

guilt by association: Expression glossary

Hidden Markov Models HMM: Molecular modeling glossary

high-density protein arrays: Microarrays glossary

high- throughput proteomics:  Following the publication of the draft of the human genome sequence, the critical question to address now is: how will this information be used for  drug target discovery and selection? It is becoming increasingly widely recognised that  mechanisms underpinning disease mechanisms involve only specific protein isoforms. Therefore, to design effective therapeutic intervention, the identification of all protein isoforms coded by a particular gene, as well as information on what their structure, function and expression patterns represents is required. Unfortunately current computational gene predictions give only limited and partially accurate views on  gene structure and  products. High throughput proteomics is the only possible way to unambiguously identify and map protein coding genes in the human genome. Dr. Andrew Lyall, Oxford GlycoSciences "High- Throughput Industrialised Proteomics Leverages the Genome to Facilitate Target Discovery" Genome Tri- Conference: Human Genome Discovery Feb. 25- 27, 2002 Santa Clara CA 

A bioinformatic approach was used to identify all  putative genes from human chromosome 21, and almost all of them have been expressed in a semi- automated process. The resulting proteins and peptides were used to create antibody reagents. Labeled antibodies have been used to carry out functional proteomic studies, with particular emphasis on expression localization. The use of tissue arrays has facilitated the throughput of these studies. Comparisons of protein expression results with gene expression data will also be discussed. Dr. Mathias Uhlen, Royal Institute of Technology and Affibody AB "High- Throughput Proteomics" Proteomics Europe: Proteins to Profits March 25- 27, 2002, Munich, Germany

homointeraction:  A lot of proteins interact with themselves. (Dr. Jong Paik, Bioinformatics/ Proteomics, Dunn Human Nutrition Unit, Medical Research Council, UK, 2001) http://www.mrc-dunn.cam.ac.uk/research/bioinformatics_proteomics.html

homolog, homologue: Functional Genomics

homology: Functional Genomics

homology modelling: Structural genomics glossary

Human Proteome Organisation HUPO:  The reason for creating HUPO is to assist in increasing the awareness of this discipline of science across society, particularly with regard to the Human Proteome Project and to engender a broader understanding of the importance of proteomics and the opportunities it offers in the diagnosis, prognosis and therapy of disease. As a global body it will also have the objective of fostering international cooperation across the proteomics community and of promoting scientific research in an on- going manner around the world.. Human Proteome Project: PepTalk Jan. 9-11 2002 San Diego CA 

HUPO Human Proteome Organisation website: http://www.hupo.org/

Human Proteomics Initiative: http://www.expasy.ch/sprot/hpi/ Swiss Institute of Bioinformatics' major project to annotate all known human sequences according to the quality standards of  SWISS- PROT. This means providing, for each known protein, a wealth of information that include the description of its function, its domain structure, subcellular location,  post- translational modifications, variants, similarities to other proteins, etc. 

in silico proteomics: Molecular modeling glossary

interaction proteomics:  Protein- protein interactions lie at the heart of most cellular processes. A complete understanding of cellular function depends on a full characterization of the complex network of cellular protein- protein associations. Alternative proteomics technologies are being developed to complement the two- hybrid system. These methods reveal direct protein- protein interactions by using protein  affinity chromatography. Protein affinity chromatography, as developed by Greenblatt, Alberts, and colleagues, has the disadvantage of requiring purified proteins as reagents, but it is superior to the two- hybrid approach because it generates fewer false positives and is more amenable to high- throughput screening. (Aled Edwards et al. "Proteomics: new tools for a new era" Modern Drug Discovery 3 (7): 35-44 Sept. 2000) http://pubs.acs.org/journals/mdd/

Related terms  protein- DNA interactions, protein- protein interactions, protein- RNA interactions, reverse two- hybrid, yeast one- hybrid, yeast- two hybrid; yeast three- hybrid, co- precipitation, co- immunoprecipitation; Maps genetic & genomic cell mapping, maps- protein, peptide mapping, protein interaction mapping, protein linkage maps; Omes & omics glossary interactome

interactome, interactomics: Omes & omics glossary

interologs:  Protein interaction maps have provided insight into the relationships among the predicted proteins of model organisms for which a genome sequence is available. These maps have been useful in generating potential interaction  networks, which have confirmed the existence of known complexes and  pathways  and have suggested the existence of new complexes and or crosstalk between previously unlinked pathways. However, the generation of such maps is costly and labor intensive. Here, we investigate the extent to which a protein interaction map generated in one species can be used to predict interactions in another species. (LR Matthews "Identification of potential interaction networks using sequence- based searches for conserved protein- protein interactions or "Interologs" Genome Research 11 (12): 2120- 2126, Dec. 2001) 

localizome: Omes & omics glossary

localizome mapping: Maps, genomic & genetic glossary

membrane proteins: Protein structure glossary 

microbial proteomics:  Bacterial genomes encode all possible virulence determinants, vaccine candidates, and potential drug targets. Further, a completed genomic sequence establishes a basis for high throughput analysis of the proteins expressed (i.e., the proteome). Respiratory pathogens have been among the first to have their genomes entirely sequenced. 

Mycoplasma pneumoniae harbors the second smallest genome of any self-replicating life form and encodes 679 putative proteins. These genome- predicted proteins will be correlated with those actually present, detecting any biological event that generates a protein of different molecular composition than that predicted. These include sequence or reading frame errors, imprecise bioinformatics, co- or post- translational modifications, and mutational or proteolytic strategies for antigenic variation. (Neil Kelleher "Enzymology and Proteomics" Dept. of Biochemistry, Univ. of Illinois - Urbana Champaign, US, 2000) http://www.scs.uiuc.edu/~bioch/kelleher.html

Related term: Omes & omics glossary microbiome

MudPIT Multidimensional Protein identification Technology: We will describe a largely unbiased method for rapid and large- scale proteome analysis via multidimensional  liquid chromatography, tandem mass spectrometry, and database searching via the SEQUEST algorithm named multidimensional protein identification technology (MudPIT). The method has been applied to the analysis of yeast total cell lysates. Categorization of the proteins identified demonstrated this technology's ability to detect and identify proteins rarely seen in proteome analysis including integral membrane proteins from several cellular compartments and low abundance proteins like transcription factors  and protein kinases. Of particular interest was our identification of 131 proteins with three or more predicted transmembrane domains. Dr. John Yates, Scripps Research Institute, "Large- Scale Analysis of Proteomes Using Mass Spectrometry" Proteomics June 21- San Francisco, CA

Related term: Databases & Software Directory SEQUEST (software)

ORFeome: Omes & omics glossary

peptide mapping: Maps, genomic & genetic

peptidomics: Omes & omics glossary

perturbagens: Peptides, which disrupt key  protein-protein interactions. (CHI Proteomics) 

Used in physics to determine the effects of a number of variables upon a system. 

phage display: Functional genomics glossary

pharmacoproteomics: Pharmacogenomics glossary

phylogenetic profiles:  Functional genomics glossary

phyloproteomics:  Identification of unknown bacterial isolates based on similarities within protein  biomarker databases. (Gregory C. Conway et. al. "Phyloproteomics: Species Identification of  Enterobacteriaceae Using Matrix- Assisted Laser Desorption/ Ionization Time- of- Flight Mass Spectrometry" J. Mol. Micro. Biotechnol. 3: 103-112, 2001) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11200222&dopt=Abstract

physiological proteomics:  Proteomics relying on two- dimensional (2-D) gel electrophoresis of proteins followed by spot identification with mass spectrometry is an excellent experimental tool for physiological studies opening a new perspective for understanding overall cell physiology. This is the intriguing outcome of a method introduced by Klose and O'Farrell independently 25 years ago. Physiological proteomics requires a 2-D reference map on which most of the main proteins were identified. ... A big challenge for future studies is to provide an experimental protocol covering the fraction of intrinsic membrane proteins that almost totally escaped detection by the experimental procedure used in this study. (K. Buttner et. al. A comprehensive two- dimensional map of cytosolic proteins of  Bacillus subtilis  Electrophoresis. 22(14):2908-2935, 2001 Aug.) 

post-proteomics:  Companies are taking position at the end stages of drug discovery in the hopes that industry- wide efforts in  gene expression, protein expression, protein- protein interaction  and other proteomic studies will yield many disease targets that must have their function verified. But to become a marketable solution for the industry, they must significantly increase the scale of functional experiments such as animal models and cell assays that, historically, have not been easily scaled. ("The Current State of Proteomic Technology" CHI's GenomeLink 3.1) http://www.chiresource.com/newsarticles/issue3_1.ASP

post- translational modification identification:  ExPASy Proteomics Tools http://www.expasy.ch/tools/#ptm list a number of tools for prediction of post- translational modification, as do other websites. Identification of these modifications may provide important structural- functional information. 

post-translational modifications: Proteins glossary

prey:  Interacting proteins captured in protein complexes using a  bait.  (MDS Proteomics, Glossary, 2002) http://www.mdsproteomics.com/default.asp?qType=Article&qID=23

protein: Proteins glossary

protein activity: Unraveling the mystery of protein activity is one of the largest challenges in scientific research and a key driver in the development of tools that enable the quick identification of high- quality  targets. Current  proteomics technologies can only identify already known proteins or proteins predicted from genomic data. MDS Proteomics uses PepSea to go one step beyond, enabling the identification of unknown proteins with no prediction necessary. PepSea also can, in seconds, determine the location and identity of human genes that encode the proteins. Because of the error tolerance inherent in the PepSea algorithm, proteins can even be identified regardless of intervening sequences, which make up the majority of human DNA. Dr. Matthias Mann, MDS Proteomics, "Proteomics Technology for Easier Mining of Novel Genes and Expressed Proteins" Proteomics Europe: Proteins to Profits March 25- 27, 2002, Munich, Germany

protein and mRNA data: Although the relationship between mRNA and protein levels is vague for individual genes, some of the statistics for broad categories of protein properties are much more robust... In contrast to the differences between mRNA and protein data for individual genes, the broad categories show that the  transcriptome and  translatome  populations are remarkably similar; both contain roughly the same proportions of secondary structure and functional categories. Moreover, this contrasts the difference with the genome, which appears to have a distinctly different composition of functional categories. This illustrates that we get a more consistent picture when we average across the population, i.e. there is broad similarity between the characteristics of highly expressed mRNA and highly abundant proteins. (Dov Greenbaum, Mark Gerstein et. al. "Interrelating Different Types of Genomic Data" Dept. of Biochemistry and Molecular Biology, Yale Univ. 2001) http://bioinfo.mbb.yale.edu/e-print/omes-genomeres/text.pdf

Related terms Expression glossaryGenomics glossary genome data; functional genomics data

protein arrays: Microarrays glossary

protein- carbohydrate interactions: Are now recognized to be important mediators of cell communication. In the last decade many novel carbohydrate binding proteins (CBPs) have been described, and several have been documented to play critical roles in cell trafficking and cell signaling. Despite these advances, the rate of generating new information has been slow, and the biological roles of most mammalian CBPs remain poorly understood. While the importance of this field has attracted many outstanding laboratories, a major barrier to rapid progress has been the structural complexity and heterogeneity of the carbohydrates themselves, and the analytical and synthetic challenges this poses. A further complexity arises from the fact that carbohydrate ligands are post- translational modifications of proteins and lipids whose synthesis is directed by the coordinated expression of multiple genes in a manner that is not  template driven. (Consortium for Functional Glycomics, "Overview of the Program" US, 2001) http://glycomics.scripps.edu/program.html

protein chips: Microarrays glossary

protein complexes:  To date scientists have studied proteins largely as discrete entities, yet most proteins operate collectively as part of protein complexes or  pathways. A deeper understanding of protein interactions will assist in validating novel drug  targets and may extend the usefulness of existing drug targets. At Cellzome we have implemented a  high- throughput use of  Tandem Affinity Purification (TAP) for effective isolation of complexes involved in human disease that is very robust, and is providing novel insights into  cellular pathways. Dr. Walter Blackstock, Cellzome UK, "The Large- scale Study of Protein Complexes for Target Validation" Proteomics Europe: Proteins to Profits March 25- 27, 2002, Munich, Germany

Related term:  complexome: Omes & omics glossary

protein-DNA interactions:  Can be detected by  DNA footprinting, gel shift analysis,  yeast one hybrid assays or Southwestern blots. (John A Wagner "The logic of molecular approaches to biological problems" Cornell University Medical College) http://www-users.med.cornell.edu/~jawagne/logic_&_experimental_desig.html

Can also be analyzed by genetic analysis and X-ray crystallography (John Little Biochemistry Fall 2000, University of Arizona) 

Related terms  interaction proteomics

protein databases:  Dr. Stanley Fields, Professor of Genetics and Medicine at the Univ. of Washington and developer of the yeast two hybrid system writes that protein databases "will need to become much more sophisticated if they are to help scientists make sense of the staggering number of experimental measurements that will soon emerge. ... protein data will need to be integrated with results from expression profiling, genome- wide mutation or antisense analyses, and polymorphism detection. As proteomic data accumulate, we will become better at triangulating from multiple disparate bits of information to gain a bearing on what a protein does in the cell. (S. Fields "Proteomics in Genomeland" Science 291: 1221-1224 Feb. 16, 2001) Related term  protein identification

Protein databases Databases & software directory

protein dynamics: Certain parts of a particular protein will be rigid, but others may be flexible and change their shape, even when bound. ... NMR has the unique ability to characterize protein fluctuations quantitatively, much more so than crystallography can. (CHI Structural proteomics) 

Understanding the function of a protein is fundamental for gaining insight into many biological processes. Proteins are stable mechanical constructs that allow certain internal motions to enable their biological function. Structural properties of a protein can be obtained with X-ray crystallography or NMR acquisition techniques. Molecular dynamics (MD) simulations at pico/ nano- second time scales output one or more trajectory files which describe the coordinates of each individual atom over time. The main problem with animating these trajectories is one of temporal scale. Taking large time steps will destroy the impression of smooth motion, while small time steps will result in the camouflage of interesting motions. (Henk Huitema, Robert van Liere " Interactive Visualization of Protein Dynamics" ERCIM (European Research Consortium for Computers and Informatics) News No. 44 - January 2001) http://www.ercim.org/publication/Ercim_News/enw44/van_liere.html

protein expression:  Is variable, not all encoded proteins are expressed at all times. Expression glossary

protein expression mapping: Maps, genomic & genetic glossary

protein expression profiling: Expression glossary

protein function: More systematic attempts have been made to place proteins within a hierarchy of standard functional categories or to connect them in overlapping networks of varying types of associations. These networks can obviously include  protein- protein interactions ... More broadly, they can include pathways, regulatory systems and signaling cascades... Perhaps, in the future, the systematic combination of networks may provide for a truly rigorous definition of protein function. (Mark Gerstein, et. al "Integrating Interactomes" Science 295 (5553): 284, Jan. 2002) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11786630&dopt=Abstract

A biologically useful definition of the function of a protein requires a description at several different levels. To the biochemist, function means the biochemical role of an individual protein: if it is an enzyme, function refers to the reaction catalyzed; if it is a signaling protein, function refers to the interactions that the protein makes. To the geneticist or cell biologist, function includes these roles but will also encompass the cellular roles of the protein, such as the phenotype of its deletion, the pathway in which it operates, among others. A physiologist or developmental biologist may have an even broader view of function, including tissue specificity and expression during the life cycle of the organism. (Gregory A Petsko, Dagmar Ringe "Overview: The Structural Basis of Protein Function" from Chapter 2 of Protein Structure and Function: New Science Press, 1991-2001) http://www.biomedcentral.com/nspprimers/proteinfunction/full

In the expanded view of protein function, a protein is defined as an element in the  network of its interactions. Various terms have been coined for this expanded notion of function, such as 'contextual function' or 'cellular function'.  Whatever the term, the idea is that each protein in living matter functions as part of an extended web of interacting molecules. Often it is possible to understand the cellular functions of uncharacterized proteins through their linkages to characterized proteins. In broader terms, the networks of linkages offer a new view of the meaning of protein function, and in time should offer a deepened understanding of the function of cells. (David Eisenberg et al "Protein function in the post- genomic era" Nature 405: 823-826, 15 June 2000) 

The principal problem facing the post- genome era. (Blackstock & Weir "Proteomics" Trends in Biotechnology: 121-134 Mar 1999) 

Related terms  interaction proteomics; Functional genomics glossary gene function, Gene OntologyTM ; Maps  cell mapping

protein identification:  The analytical method used most commonly to visualize and identify large numbers of proteins is  2D-gel electrophoresis. One can theoretically visualize changes in protein production, both qualitatively and quantitatively, from two individual samples (e.g., a control preparation and a treated preparation). Furthermore, one can potentially accomplish protein identification by "picking" proteins from the 2D- gel and subjecting the highly purified protein to MALDI- TOF mass spectrometry. ("High - Throughput Genomics, CHI GenomeLink 14.1) http://www.chiresource.com/newsarticles/issue14_1.asp

Related term protein databases

protein informatics: Includes bioinformatics technology to cross reference protein informatics with genomic databases, sequence data of protein fragments by mass spectrometry and identification of these fragments using more remote relationships; construction and management of international protein structural databases; protein profiling and characterization data handling; data that elucidates the relationship between structures and functions of biological macromolecules by X-ray crystallography, large scale molecular simulation and structural bioinformatics, protein structure data handling and storage, structural bioinformatics covering molecular modeling and design; protein array and chip data handling; development of new algorithms and software for large scale simulation calculations by parallel computers; protein- protein interaction data and libraries; protein structure data determination by X-ray crystallography and development of automatic analysis systems; protein expression databases; automated technology for high- throughput protein function assignment and annotationProtein Informatics November 12-13, 2001, San Diego, CA 

Although mining of  protein structure homology data is a relatively small field now, it is likely to experience dramatic growth and to become pivotal in the ultimate exploitation of genomic data and tools. (CHI Target Validation)

protein interactions: Networks of protein interactions control the lives of cells, yet we are only beginning to appreciate the nature and  complexity  of these networks. We have taken two approaches to the study of  protein networks. The first is to infer functional interactions between proteins from genome sequences and correlated  mRNA expression. The second approach is to reconstruct networks from published experimental studies in the scientific literature. This Database of Interacting Proteins (http://dip.doe-mbi.ucla.edu/) DIP for short, has now grown to thousands of interactions and provides a second type of network of cellular protein interactions. Dr. David Eisenberg, UCLA, "Discovering Protein Interactions, Networks of Functionally Linked Proteins" Gene Functional Analysis Feb. 28 - Mar. 1, 2002 Santa Clara CA 

While proteomics is defined as a comprehensive study of  proteins expressed by an organism, it is often limited to expression profiling and sequence analysis. In reality, of course, proteins are not important simply because they are present but because they have unique functions. Most proteins function at least partly through their interactions with other proteins, and this information is not apparent from 2D PAGE expression analysis or amino acid sequencing. A comprehensive analysis of protein interactions is thus critical to proteomics as functional analysis cannot otherwise be considered complete. Protein interactions may be studied via expression in yeast two- hybrid complementation systems. But the tremendous quantity of data necessary for comprehensive analysis requires utilization of modern automated sample- handling instrumentation and data- handling software. AxCell Biosciences has developed true high- throughput, in vitro  protein interaction analysis. This process involves highly parallel peptide synthesis and protein expression, as well as custom HTS solutions. With InforMax, AxCell is also developing sophisticated tools for facile visualization and experimental manipulation of the complex patterns and pathways of protein interaction important for intracellular signaling processes. Dr. J. Mark Carter, AxCell Biosciences "High- Throughput in Vitro Protein Interaction Analysis" Proteomics Europe: Proteins to Profits March 25- 27, 2002, Munich, Germany

Narrower terms: annotation- proteins, interaction proteomics, protein- DNA interactions, protein- protein interactions, protein- RNA interactions.

protein interaction mapping: Maps genomic & genetic

protein knockouts: Our proteomics efforts are focused largely on developing new techniques to probe protein- protein interactions and to construct devices that allow one to monitor the levels and post- translational modification states of hundreds or even thousands of proteins simultaneously. A third major goal is to develop "protein knockout" methods that would allow researchers to rapidly develop  reagents to block one or more functions of a newly discovered protein to facilitate studies of its role in cellular metabolism. (Thomas J. Kodadek, Internal Medicine and Molecular Biology, Univ. of Texas Southwestern Graduate Biomedical School, 2001) http://www2.utsouthwestern.edu/gradschool/webrib/kodadek.htm

protein linkage maps: Maps genomic & genetic

protein localization: Proteins glossary

protein microarrays: Microarrays glossary

protein networks:  Yeast two- hybrid screens have provided a wealth of information describing potential protein- protein interactions in cells. This talk will discuss large- scale two- hybrid screening in  Saccharomyces cerevisiae using "living"  protein arrays consisting of ordered grids of protein fusions that are expressed in growing  yeast cells. Potential  protein interactions identified from these screens can be compiled into graphical maps of protein networks. The development of other novel high- throughput technologies for assaying protein function will also be discussed. Dr. Chandra L. Tucker, University of Washington "Protein Interactions, Protein Networks, and Beyond: Yeast as a Tool for Functional Genomic Analyses" Gene Functional Analysis Feb. 28 - Mar. 1, 2002 Santa Clara CA

protein profiling: Expression glossary

protein- protein interactions: Correlated changes in  protein expression (such as co- regulation or  sequential regulation) provide a hint that two proteins may be interacting with each other. (CHI Proteomics) 

A central phenomenon determining the biological  pathways found in living systems. They are the focus of many  proteomic technologies being developed today to decipher an intricate  network of interactions. (CHI Summit Proteomics) 

Can be detected by  yeast two- hybrids, phage display or  immunoprecipitation assays. (John A Wagner "The logic of molecular approaches to biological problems" Cornell University Medical College) http://www-users.med.cornell.edu/~jawagne/logic_&_experimental_desig.html

Play a major role in almost all relevant physiological processes occurring in living organisms, including DNA replication and  transcription, RNA splicing, protein biosynthesis, and  signal transduction

Related terms  interaction proteomicsyeast two-hybrid.

Protein interaction databases see Databases & software directory.

protein-protein interaction inhibitors: See under functional proteomics

protein-RNA interactions:  Can be detected by the  yeast three- hybrid assay. (John A Wagner "The logic of molecular approaches to biological problems" Cornell University Medical College) Related term  interaction proteomics http://www-users.med.cornell.edu/~jawagne/logic_&_experimental_desig.html

Involved in  gene expression and protein synthesis

Related terms: Omes & omics glossary riboproteomics; Cell biology glossary In-depth ribosome 

proteome: The scope note for the  Journal of Proteome Research (Jan.2002) states that "primary topics will include: New approaches to  sample preparation, including  2- D gels and chromatographic techniques, Advancements in high- throughput protein identification and analysis, Array- based measurements, Structural genomics data related to protein function, Research on quantitative and structural analysis of proteins and their post- translational modifications, Metabolic and signal pathway analysis, including metabolomics and peptidomics, Protein- protein, protein- DNA, and protein- small molecule interactions, Computational approaches to predict protein function, Use of BioinformaticsCheminformatics to mine and analyze data, New tools in proteomic analysis, Studies on proteomics with an impact on the understanding of disease, diagnosis and medicine. http://pubs.acs.org/journals/jprobs/

Comprehensive quantitative data on the proteins of an organism under a variety of conditions (ideally including post synthetic modifications and interactions with other molecules). To achieve this, purification each protein (including modified versions and interacting antibodies) will be an important related project (George Church Lab, Harvard- Lipper Center for Computational Genomics, 2001) 

The concept of the proteome is fundamentally different to that of the genome: while the genome is virtually static and can be well defined for an organism, the proteome continually changes in response to external and internal events. (Wilkins and Hockstrasser "Thinking Big Proteome Studies in a Post- Genome Era" ABRF News Dec 1996) http://www.abrf.org/ABRFNews/1996/December1996/Proteome.html

Marc Wilkins is credited with coining the word in 1994 at the Conference on Genome and Protein Maps in Siena, Italy. PROTEin complement expressed by a genOME. (Wilkins et al "Progress with gene product mapping of the Mollicutes" Electrophoresis 16:1090-1094, July 1995) 

Broader terms: Genomics glossary genomeOmes & omics glossary ORFeome  Related terms Omes & omics glossary translatome.  See  translatome for a discussion of the ambiguities in competing definitions of  proteome

proteome chip: Microarrays glossary

proteome database mining: the identification of intrinsic patterns and relationships in translational expression data generated by large- scale  proteomics experiments. Improvements in genomegene expression and proteome  database mining algorithms will enable the prediction of protein function in the context of higher order processes such as the  regulation of gene expression,  metabolic pathways  and signalling cascades. Thus, the final objective of such higher- level functional analysis will be the elucidation of high-resolution structural and  functional maps of the human genome. (John L. Houle et. al., White Paper: Database Mining in the Human Genome Initiative, AMITA Corp. 2000) http://www.biodatabases.com/whitepaper01.html

Related terms:  proteome mining; Expression glossary gene expression database mining; Genomics glossary: genome database mining Narrower terms: cellular proteome, HUPO Human Proteome Organization, proteome chip, proteome informatics, proteome map, whole proteome

proteome informatics:  Peer Bork and David Eisenberg, "Genome and proteome informatics" Current Opinion in Structural Biology 10 (3): 341-342, 2000 

Proteome Informatics group is part of the Swiss Institute of Bioinformatics (SIB). It is in charge of research and development in the fields of bioinformatics, molecular imaging and the use of Internet for biomedical applications. (ExPASy, Swiss Institute of Bioinformatics) http://www.expasy.ch/people/PI_group.html

proteome map: Maps, genomic & genetic glossary

proteome mining: Timothy AJ Haystead "Proteome Mining: Exploiting serendipity in drug discovery" Current Drug Discovery, March 2001) http://www.current-drugs.com/CDD/CDD/CDDPDF/HAYSTEAD.pdf

Related term:  proteome database mining:

proteomic diversity: Alternative RNA splicing generates extreme proteomic diversity in the mammalian nervous system, where hundreds of thousands of distinct proteins are generated from approximately 30,000 genes. These protein counterparts play important roles in learning and memory, cell communication, and neural development. (Paula Grabowski, Dept. of Biological Sciences, Univ. of Pittsburgh, US, 2001) http://www.pitt.edu/AFShome/b/i/biohome/public/html/Dept/Frame/Faculty/grabowski.htm

proteomics: The analysis of complete complements of proteins. Proteomics includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, activities, and, ultimately, their function. Initially encompassing just two- dimensional  (2D) gel electrophoresis for protein separation and identification, proteomics now refers to any procedure that characterizes large sets of proteins. The explosive growth of this field is driven by multiple forces - genomics and its revelation of more and more new proteins; powerful protein technologies, such as newly developed mass spectrometry approaches, global (yeasttwo- hybrid techniques, and spin- offs from  DNA arrays; and innovative computational tools and methods to process, analyze, and interpret prodigious amounts of data. (Stanley Fields "Proteomics in Genomeland" Science 291: 1221-1224 Feb. 16, 2001) 

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