PEP
Talk January 7-11, 2008 • Coronado, California
Applications
Map: Finding guide to terms in these glossaries Site
Map
Related glossaries include Proteomics
categories
Applications:
Functional genomics, Metabolic
engineering, Structural Genomics
Informatics Algorithms,
In
silico & Molecular
Modeling, Information Management &
Interpretation
Technologies: Chromatography
& electrophoresis, Mass
spectrometry, Microarrays &
protein chips, NMR
& x-ray crystallography
Biology:
Expression, Proteins,
Protein
Structure
2D gel electrophoresis:
A key technology for proteomics. Chromatography
& electrophoresis glossary
allosteric ribozymes (allozymes): Pharmaceutical
biology glossary
Potential for use in proteomics.
annotation- proteins:
The annotation of a protein sequence needs the following steps: protein
classification into defined groups according to its homology to well
characterized proteins, relevant literature is given by a link to Pub- Med,
protein assignment into at least one functional category. Complete genome
annotation, Munich Information Center for Protein Sequences MIPS, 2003 http://mips.gsf.de/projects/annotation
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
Narrower terms: annotation- proteomes, functional annotation - proteome
antibody arrays: Microarrays &
protein chips categories for studying
regulation at the protein level
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.
binary
interactions:
It is important to realize that there is
not a single, clear definition of a 'binary interaction'. In case of the MIPS
protein complexes, the matrix representation, in which each complex is
represented by the set of binary interactions corresponding to all pairs of
proteins from the complex, is almost exclusively. used. For complex pull-down
experiments, two different representations have been proposed: the matrix
representation and the spoke representation in which only bait- prey
interactions are included. Lars J. Jensen, Peer Bork, Quality analysis and
integration of large- scale molecular data sets. Drug Discovery Today: Targets,
3(2): 51-56.
biological atlas: Maps, genomic & genetic
glossary
cell expression profiles: Cell biology glossary
cell mapping: Maps
genomic & genetic
Can determine subcellular locations of proteins.
cellular pathways: Metabolic
engineering See under metabolic engineering
cellular proteome:
All of the proteins expressed in a cell.
Google = about 948 Oct.
25, 2006
chemoproteomics:
-Omes & -omics glossary
Google = about 503 Oct.
25, 2006
clinical proteomics: Molecular
Medicine glossary
Google = about 435 Sept. 18, 2002;
about 96,900 Oct. 25, 2006
combinatorial peptide libraries: Combinatorial
libraries & synthesis
complete proteome
sets: We consider as "complete"
genomes that have been fully closed and for which there are good gene prediction
models. ... For bacterial and archaeal genomes, whole-genome shotguns (WGS) and
draft sequences are not included in the UniProtKB complete proteome sets and are
not considered for manual annotation. ...For eukaryotic genomes, several
criteria apply to consider a proteome "complete". Some sequenced
genomes have submission/annotation problems that prevent the production of a
non-redundant protein set; others have problems regarding the gene model
predictions. UniProt, What are complete proteome sets? 2007 http://beta.uniprot.org/faq/15
DNA protein interactions: See protein- DNA interactions
degradomics: -Omes & -omics glossary
Google = about 59 Sept. 18, 2002'
about 641 Oct. 25, 2006
designer proteins: Protein
categories
Google = about 314 Sept. 18, 2002,
about 10,900 Oct. 25, 2006
differential labeling:
Labeling, signaling &
detection glossary
Used for comparing the proteomes of different cell states.
directed protein evolution:
http://cat.inist.fr/?aModele=afficheN&cpsidt=17092756
Google = about 902 Oct.
25, 2006
dissociator assays:
A collective term for yeast- one hybrid,
yeast- two
hybrid or yeast- three hybrid assays.
Google = about 25 Oct.
25, 2006
domain: Protein
structure glossary
evolutionary
genomics, evolutionary homology: Phylogenomics
glossary
Expressed Protein Tags EPTs:
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://www.current-drugs.com/CDD/CDD/CDDContents-August.htm
Related term: DNA glossary EST expressed sequence
tags
FlexGene repository: FLEX
Full- Length Expression http://www.hip.harvard.edu/flex_gene/index.htm
fragmentome:
-Omes & -omics glossary
functional protein microarrays: Microarrays
categories
functional
proteomics: Proteomics
categories
Google = about 3,160 Sept. 18, 2002;
about 152,000 Oct. 25, 2006
glycosylation: Proteins
glossary
guilt by association: Expression glossary
HUPO: SEE Human Proteome Project
Hidden Markov Models HMM: In
silico & Molecular
modeling glossary
high-density protein arrays: Microarrays
categories
high- throughput proteomics: Proteomics
categories
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, homology: Functional
Genomics
homology
modelling: Structural
genomics glossary
Human Plasma Proteome: See under Human
Proteome
Human Proteome: See
Plasma Proteome
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.. HUPO Human Proteome Organisation website: http://www.hupo.org/
Human Proteomics Initiative:
http://au.expasy.org/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.
immunoproteomics: -Omes
& -Omics glossary
interaction
proteomics: Proteomics
categories
Google = about 73 Sept. 18, 2002;
about 403 Feb. 17, 2005; about 697 Oct. 25, 2006
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]
Isotope Coded Infinity Tag ICAT:
These tags provide the ability
to both identify and quantify a broad range of proteins in a high- throughput
mode. Using ICAT reagents, researchers can compare the expression levels of
proteins from two samples, such as from normal and diseased cells. ICAT reagents
comprise a protein reactive group, an affinity tag (biotin), and an
isotopically labeled linker.
Related term:
protein profiling
localization: SEE protein localization: Proteins glossary
localizome: Omes & omics glossary
localizome mapping: Maps, genomic &
genetic glossary
microfluidics: Nanoscience
& Miniaturization glossary
MudPIT Multidimensional Protein identification Technology:
Related term: Databases
& Software Directory SEQUEST [software]
NHLBI Proteomics Initiative:
ORFeome: Omes & omics glossary
ontologies - proteomics:
A
principal aim of post- genomic biology is elucidating the structures, functions
and biochemical properties of all gene products in a genome. However, to
adequately comprehend such a large amount of information we need new
descriptions of proteins that scale to the genomic level. In short, we need a
unified ontology for proteomics. Much progress has been made towards this end,
including a variety of approaches to systematic structural and functional
classification and initial work towards developing standardized, unified
descriptions for protein properties. In relation to function, there is a
particularly great diversity of approaches, involving placing a protein in
structured hierarchies or more- generalized networks and a recent approach based
on circumscribing a protein's function through systematic enumeration of
molecular interactions. N Lan, GT Montelione, M. Gerstein, Ontologies for
proteomics: towards a systematic definition of structure and function that
scales to the genome level, Current Opinion in Chemical Biology 7(1): 44- 54,
Feb. 2003
Peptalk:
The Protein Information Week January 7 - 11, 2008 • San Diego CA
peptide mapping, peptide maps: Maps, genomic & genetic
peptidomics: -Omes &
-omics glossary
Google = about 180 Sept. 18, 2002;
about 748 July 14, 2004
perturbagens:
Peptides or protein fragments that, when expressed in
cells, create desirable shifts in phenotype. These phenotypic probes
("perturbagens") can be used in turn to define their binding partners
using a variant of yeast two- hybrid methodology. Drs. Jon Karpilow, Giordano
Caponigro, Arcaris Inc. "Trans- FACS Analysis in Melanoma" CHI Gene
Functional Analysis, Mar. 2-3, 2000, San Francisco CA
Used in physics to determine the effects of a number of variables upon
a system.
phage display: Genetic
manipulation & disruption
phage display peptide libraries: Combinatorial
libraries & synthesis
pharmacoproteomics:
Pharmacogenomics
Google = about 195 Sept. 18, 2002,
about 488 July 14, 2004; about 12,200 Oct. 25, 2006
phosphoproteome,
phosphoproteomics : Proteomics
categories
glossary
phosphorylation: Proteins
glossary
phylogenetic profiles: Phylogenomics glossary
Can be used to hypothesize protein function.
plasma
proteome: Comprehensive, systematic characterization
of the plasma proteome in healthy and diseased states greatly facilitates the
development of biosignatures for early disease detection, clinical diagnosis,
and therapy. However, blood plasma is the most complex human-derived proteome
containing other tissue proteome subsets as well as a wide dynamic range of
protein concentrations. Mining
the Plasma Proteome: Discovering Biomarkers for Diagnostics/Prognostics and Drug
Discovery/ Development, January 7-9, 2008, San Diego, CA
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.healthtech.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: See under yeast two hybrid
protein: Proteins glossary
protein
analysis: http://www.indianacaps.com/index.php?option=com_content&task=view&id=24&Itemid=43
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 glossary; Genomics
glossary genome data; functional
genomics data Omes & omics
transcriptome, translatome
protein annotation - dictionary-driven
For
many years, computational methods seeking to automatically determine the
properties (functional, structural, physiochemical, etc.) of a protein directly
from sequence have been the focus of numerous research groups, including ours.
By general admission, this is a difficult problem and the methods that have been
proposed over the years typically concentrated on the analysis of individual
genes. With the advent of advanced sequencing methods and systems, the number of
amino acid sequences and fragments being deposited in the public databases has
been increasing steadily. This in turn generated a renewed demand for automated
approaches that can quickly, exhaustively and objectively annotate individual
sequences as well as complete genomes. In this paper, we present one such
approach. The approach is centered around and exploits the Bio- Dictionary, an
exhaustive collection of amino acid patterns (referred to as seqlets)
that completely covers the natural sequence space of proteins to the extent that
this space is sampled by the currently available public databases. Isidore Rigoutsos,
Tien Huynh, Laxmi P. Parida, Daniel E. Platt, Aris Floratos, Dictionary
Driven Protein Annotation, Nucleic Acids Research, 30 (no 17) 3901- 3916,
2002
protein arrays: Microarrays & protein chips glossary
Google = about 2,050 Sept. 18, 2002;
about 10,200 July 14, 2004; about 194,000 June 11, 2007
protein biomarkers: Biomarkers
glossary
protein
capture/proteome tools: The Proteome is the
complete set of proteins in the body. Efforts in this area would support
developing and making available to the scientific community high quality probes
specific to every protein in the human and in desired animal models. This would
allow the ability to characterize protein function in health and disease and to
monitor the markers of a disease in order to deploy early prevention efforts and
to identify potential therapeutic targets. New Roadmap
Emphasis areas for 2008, NIH Roadmap, http://nihroadmap.nih.gov/2008initiatives.asp
protein- carbohydrate interactions:
The overarching goal of the [Consortium for Functional
Glycomics] program is to:
Define paradigms by which protein-carbohydrate interactions mediate cell
communication. Consortium for Functional Glycomics, funded by NIGMS,
US http://web.mit.edu/glycomics/consortium/organization/program/program.shtml
protein chips: Microarrays & protein chips glossary
Google = about 2,450 Sept. 18, 2002;
about 7.450 July 14, 2004; about 113,000 Nov 10, 2006
protein complexes: http://en.wikipedia.org/wiki/Protein_complex
Google = about 23,900 Sept. 18, 2002;
about 151,000 July 14, 2004; about 806,000 Nov 10, 2006
Related terms: complexome: -Omes &
-omics glossary;
Metabolic engineering 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: Proteomics
categories interaction proteomics
protein databases:
Protein location can be determined by such genome-
wide techniques as green fluorescent protein (GFP) tagging, and protein-
protein interactions can be determined by affinity chromatography,
immunoprecipitation and yeast two- hybrid experiments. Databases resulting from
these methods are beginning to emerge, but they are of uncertain accuracy.
Defining the Mandate of Proteomics in the Post- Genomics Era, Board on
International Scientific Organizations, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html
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 terms: protein identification, protein localization; Expression
glossary expression profiling
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.
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
Google = about 5,800 Sept. 18, 2002;
about 18,200 July 14, 2004; about 295,000 Nov 10, 2006
protein expression:
Is variable, not all encoded proteins are
expressed at all times. More ... Expression glossary
Google = about 68,000 Sept. 18, 2002;
about 544,000 July 14, 2004; about 1,410,000 Nov 10, 2006
protein expression mapping: Maps, genetic
& genomic glossary
protein expression profiling: Expression glossary
protein folding
disorders: Molecular medicine glossary
protein function:
Function is not a fixed property for many, if not
most proteins. There are many ways that gene products can be altered to elicit
modified or completely new functions. For example there are exist - alternative
splicing - which may affect as many as ¼ or more of the genes in a higher
eukaryote and can alter biochemical function either drastically or subtly,
producing truncated proteins and proteins with different compositions - post-
translational modification, such as phosphorylation and glycosidation
(which can occur on numerous sites on the same protein) - pre-enzymes made for
secretion and pro- enzymes that are activated by cleavage - acylation and
ubiquitination - non- enzymatic modifications like oxidation, so a given protein
exists in the cell in different oxidized states. Defining the Mandate of
Proteomics in the Post- Genomics Era, Board on International Scientific
Organizations, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html
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 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
[subscription required for access]
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.
[Walter Blackstock & Malcolm Weir "Proteomics" Trends in Biotechnology: 121-134 Mar 1999]
Google = about 27,400 Sept. 18, 2002
about 58,400 Aug. 18, 2003, about 133,000 July 14, 2004; about 766,000 Nov 10,
2006
Related terms: Protein
categories 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 Genome Link
14.1 http://www.healthtech.com/newsarticles/issue14_1.asp
Google = about 8,460 Sept. 18, 2002
about 15,000 Aug. 18, 2003, about 32,000 July 14, 2004; about 494,000 Nov 10,
2006
Related term: protein databases
protein informatics:
The Protein Informatics Group currently consists of a collaboration between
researchers at the Oak Ridge National Laboratory, the University of Missouri,
and the University of Georgia. Our common interests are in development of
computational tools for solving problems from molecular biology. Our work ranges
from construction of mathematical/statistical models to development of
algorithms to code implementation on various platforms to applications of
computational tools to solve various bio-data analysis problems. Protein Informatics Group, Computational Biology, Oak Ridge
National Lab, US http://compbio.ornl.gov/structure/
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 report]
Google = about 561 Sept. 18, 2002,
about 888 Aug. 18, 2003, about 1,810 July 14, 2004; about 16,200 Nov 10, 2006
Related
terms: proteoinformatics; Algorithms glossary;
Bioinformatics
glossary protein bioinformatics; In Silico & molecular modeling glossary, Structural
genomics glossary
protein interactions:
See protein DNA interactions, protein protein interactions, protein RNA
interactions
Google = about 59,900 Sept. 18, 2002;
about 141,000 Aug. 18, 2003, about 271,000 July 14, 2004; about 1.170,000 Nov
10, 2006
Narrower terms: annotation- proteins, binary
interaction, interaction proteomics, protein- DNA
interactions, protein- protein
interactions, protein- RNA interactions; Related terms: protein networks; -Omes
& -omics glossary interactome
protein interaction mapping: Maps genomic
& genetic
protein knockouts: Genetic
manipulation & disruption
Google = about
63, July 14, 2004; about 179 Nov 10, 2006
protein linkage maps: Maps genomic &
genetic
protein localization: Proteins glossary
protein microarrays: Microarrays
& protein chips glossary
Google = about 1,410 Sept. 18, 2002;
about 4,380 Aug. 18, 2003' about 11,000 July 14, 2004; about 198,000 Nov 10,
2006
protein networks:
The individual steps in signal
transduction pathways involve protein interactions with target molecules that
may be other proteins, small molecules or DNA. Identifying all of the proteins
that take part in a given class of interactions, on a genome-wide scale, remains
an extremely challenging task. We propose to apply mRNA display (1,
2) technology to this problem, with the goal of developing
databases of protein-ligand interactions that will add value to the existing and
growing sequence databases. PI Jack Szostak, Definition of Protein Networks
using mRNA display, ParaBioSYs, MGH, HMS, BU http://pga.mgh.harvard.edu/Parabiosys/projects/protein_networks_rna_display.php
Google = about 1,160 Sept. 18, 2002;
about 2,530 Aug. 18, 2003; about 6,170 July 14, 2004; about 138,000 Nov 10, 2006
Related term: protein interactions
protein profiling: Expression glossary
Google = about 1,290 Sept. 18, 2002;
about 2,820 Aug. 18, 2003, about 6,700 July 14, 2004; about 192,000 Nov 10, 2006
protein- protein interactions:
Protein-protein interactions (PPI) play a key role in many
biological processes, making them promising targets for drug discovery. Though
inhibition of protein-protein interactions has been challenging due to
binding-site characteristics at the protein-protein interface, there has been
considerable success in recent years. Drug
Discovery Chemistry Protein- Protein Interactions as Drug Targets April 29-30
2008 • La Jolla, CA As
the level of general knowledge of proteins and protein interaction networks
advances, the common understanding of a PPI [protein- protein interaction]
becomes complex. It is currently possible to define this term in a number
of different ways ... At the simplest level, two discrete proteins A and B
physically associate with each other in a stable complex ... Alternatively, two
associating proteins might retain unaltered individual functions ... Another
possibility is that a PPI may result in a loss of activity, or destruction for
component A or B, or both ... Alternatively, an interaction may serve a
regulatory function ... Alternatively, the interaction of A+ B may exclude A or
B from interaction with another potential partner molecule. [Erica A. Golemis,
Kenneth D. Tew, Disha Dadke "Protein Interaction - Targeted Drug
Discovery" Biotechniques 32 (3): 636- 647, 2002]
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
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. Correlated changes in protein expression
(such as co- regulation or sequential regulation) provide
a hint that two proteins may be interacting with each other.
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 proteomics, yeast two-hybrid.
Protein interaction databases Databases & software
directory.
protein-protein interaction inhibitors: See under Proteomics
categories 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] http://www-users.med.cornell.edu/~jawagne/logic_&_experimental_desig.html
Involved in gene expression and protein
synthesis.
Related terms: interaction
proteomics; Omes & omics glossary riboproteomics;
Cell biology glossary ribosome
Related term:
proteomimetics - small molecule
protein
therapeutics: Molecular Medicine glossary
proteoinformatics:
http://dir.niehs.nih.gov/proteomics/informtx.htm
Google = about 11 Sept. 18, 2002;
about 48 Aug, 18, 2003; about 244 July 14, 2004; about 200 Nov 10, 2006
Related term: protein informatics
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 Bioinformatics/ Cheminformatics to mine and analyze
data, New tools in proteomic analysis, Studies on proteomics with an impact on the understanding of disease, diagnosis and
medicine. Scope note, Journal of Proteome Research, American Chemical Society http://pubs.acs.org/journals/jprobs/
The importance of post- transcriptional and
post- translational regulation is recognized by placing emphasis on direct
knowledge of proteins and their higher- order associations in contrast to less
direct inferences about proteome composition drawn from RNA measurements. Molecular
Machines of Life, DOE Genomes to Life, US http://www.doegenomestolife.org/program/goal1.html
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 http://arep.med.harvard.edu/
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. Marc Wilkins and Denis 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
The dynamic nature of the proteome calls for
methods to monitor, for any organism, the entire proteome's conditional state
accurately and sensitively from thousands of samples. This will require greater
completeness, resolution, and sensitivity than has been possible in the past
using conventional imaging and gel-based technologies. Also, new tools
characterizing these complexes must be developed to bridge the current size and
resolution gap between single proteins suitable for high-resolution X-ray
crystallographic study and the very large protein assemblies and cellular
ultrastructures amenable to electron microscopy.
Wikipedia http://en.wikipedia.org/wiki/Proteome
Proteome Society:
http://www.proteome.org/
Proteome Society glossary http://www.proteome.org/4Resources/glossary.htm
Google = about 74,600
July 11, 2002; about 83,500 Sept. 18, 2002;
about 159,000 Aug. 18, 2003, about 263,000 Jun 7, 2004, about 268,000 July 14, 2004, about 813,000 Aug. 15, 2005,
about 7.720,000 Oct. 25, 2006
Broader terms: Genomics glossary
genome; -Omes & -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 & protein chips glossary
Google = about 76 Sept. 18, 2002;
about 120 Aug. 18, 2003, about 208 July 14, 2004; about 1,620 Nov 10, 2006
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. Current Projects and
People, ExPASy, Swiss Institute of Bioinformatics http://au.expasy.org/people/pig/
Google = about 261 Sept. 18, 2002;
about 453 Aug. 18, 2003; about 708 July 14, 2004; about 10,700 Nov 10, 2006
proteome map: Maps, genomic & genetic
glossary
Google = about 149 Sept. 18, 2002;
about 319 Aug. 18, 2003; about 746 June 21, 2004; about 18,300 Nov 10,
2006
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
Google = about 68 Sept. 18, 2002;
about 156 Aug. 18, 2003; about 276 June 21, 2004; about 951 Nov 10, 2006
Related term: proteome database mining:
proteomic analysis:
Systematic and
quantitative analysis of the properties that define protein activity and
functions within a defined context, essential for biology and medicine. Ruedi
Aebersold quoted in Defining the Mandate of Proteomics in the Post- Genomics
Era, National Academies Press, 2002 http://www.nap.edu/books/NI000479/html/R1.html A
systematic analysis of proteins for their identify quantity and function. J Peng
and Steven Gygi, Proteomics: the move to mixtures, Journal of Mass Spectrometry
35: 1083- 1091, 2001
proteomic analysis - cells and tissue: Cell
biology glossary
proteomic
diagnostics: Using proteomics as a tool to
diagnose diseases early on is becoming a very established way of identifying
disease biomarkers. It is important to look beyond the gene expression into the
interaction and functional relationships of expressed proteins and to use this
information for developing new strategies for the prediction and diagnoses of
diseases and their potential treatments.
Proteomic
tools for diagnostics
May 20-21, 2008 • Boston, MA
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/...
Related term: RNA glossary alternative RNA splicing
Proteomic
Standards Initiative PSI: PSI currently develops
standards for two key areas of proteomics, mass spectrometry and protein-protein
interaction data, as well as a standardised general proteomics format.
Proteomic Standards Initiative, HUPO, 2005 http://psidev.sourceforge.net/
proteomics:
Proteomics is a rapidly
evolving field that is rife with commercial opportunities as the technology
achieves ever higher throughput at lower cost and greater sensitivity. Provides
insights into Strengths and weaknesses of the leading technologies for protein
separation, detection, and quantification - with an emphasis on high-throughput
approaches The fundamental challenge posed by the vast dynamic range among
protein concentrations, and the potential solutions in development and entering
the market. Recent applications of proteomics to discover biomarkers for
preeclampsia, and for neonatal ureteropelvic junction, and to differentiate
between diagnosis of ALS and Parkinson’s disease. Technologies such as mass
spectrometry, antibody-bearing chips, and solution array multiplexing to address
the challenge of detecting low-abundance proteins. Insight Pharma Reports, Proteomics:
Current State and Future Directions, 2006
The most useful definition of proteomics is
likely to be the broadest: proteomics represents the effort to establish the
identities, quantities, structures and biochemical and cellular functions of all
proteins in an organism, organ, or organelle, and how these properties vary in
space, time and physiological state. .. A much broader field than would be apparent from early
efforts, which have focused on cataloging levels of protein expression.
Ideally it should encompass efforts to obtain complete functional descriptions
for the gene products in a cell or organism. Defining the Mandate of
Proteomics in the Post- Genomics Era, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html
The systematic study
of the complete complement of proteins (PROTEOME) of organisms. MeSH 2003
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
[yeast] two- 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
At present, the aggregate of activities called proteomics has three distinct
technical subsets: protein profiling, protein- protein interaction and
structural biology. ... [producing] voluminous amounts of data ... substantial
attention is now being applied to annotation methods by which the resulting
information, e.g., source protein, types of modifications, subcellular
organelle, cell expression profiles, known protein interaction, protein domain
organization, atom- by- atom structural coordinates, etc. can be archived in a
manner amenable by computer query and in silico cross references. Robert
G. Urban, ZYCOS, Inc. "Proteomics: Making sense of the census" Current
Drugs 5, Aug. 2001 http://www.current-drugs.com/CDD/CDD/CDDContents-August.htm
The use of quantitative protein- level measurements of gene expression to
characterize biological processes (e.g. disease processes and drug effects) and
decipher the mechanisms of gene expression control. As such, proteomics focuses
on the dynamic description of gene regulation and, by doing so, offers
something much more powerful than a protein equivalent of DNA databases: the
concept of molecular recognition as a systematic science. For this reason,
proteomics emphasizes quantitation and the assembly of large bodies of
experimental observations in numerical databases N. Leigh Anderson, Norman G.
Anderson "Proteome and proteomics; New technologies, new concepts, and new
words" Electrophoresis 19 (11): 1853- 1861 August 1998
Industrial scale analysis of many proteins and their interactions, over time, ultimately tying this into physiological processes and biological
pathways and networks.
The earliest
PubMed reference I've found to proteomics is P James' "Protein
identification in the post- genome era: the rapid rise of proteomics"
Quarterly Review of Biophysics 30(4): 279- 331, Nov. 1997. References to proteomic
are just a little earlier (Ian Humphery- Smith and Walter Blackstock "Proteome
analysis: genomics via the output rather than the input code" Journal of
Protein Chemistry16(5): 537- 544, July 1997). Perhaps earlier references can be
found in the chemical and/ or biophysics literature.
Wikipedia http://en.wikipedia.org/wiki/Proteomics
Harvard Institute of Proteomics:
http://www.hip.harvard.edu/
Variant spellings without (as far as I can tell) truly
variant meanings seem to distinguish proteinomics and
proteonics. I would welcome any thoughts or comments on these words.
Related term proteonomics (Or is this just another variant
spelling?)
Google proteomics = about 138,000
July 11, 2002; about 162,000 Sept. 18, 2002;
about 357,000 Aug. 18, 2003; about 776,000 June 7, 2004, about 842,000 July 14, 2004; about 4,680,000 Aug. 15, 2005,
about 10,900,000 Oct. 25, 2006
Narrower terms: Proteomics categories activity based proteomics, applied proteomics,
bottom up proteomics, cell
signalling proteomics, chemical proteomics, clinical proteomics, comparative
proteomics, computational proteomics, differential proteomics, discovery based
proteomics, drug proteomics, environmental proteomics, expression
proteomics, functional proteomics, high- throughput proteomics, Human Proteomics
Initiative, in silico proteomics, interaction proteomics, microbial
proteomics, phyloproteomics, physiological proteomics, post- proteomics,
proteomic technologies, reverse proteomics, riboproteomics, shotgun proteomics,
structural proteomics, targeted proteomics, tissue proteomics, topological
proteomics, toxicoproteomics proteomics - commercialization:
Covers key areas in
proteomics today, including new approaches to protein expression, evolving
methods of studying protein function, new technologies such as protein
chips,
and advances in protein informatics. Focuses on how researchers are applying new
proteomic approaches to drug discovery and
development, and how these
technologies can be used most effectively and in a high- throughput capacity.
Case studies analyzing particular applications of proteomic technologies to
specific disease- related research are provided, and future trends and
developments are forecast.
proteomics technologies:
Major types include protein separation, ultrafiltration, 1D and 2D gel
electrophoresis, liquid chromatography, capillary
electrophoresis, mass spectrometry, protein informatics,
protein arrays, protein quantification, protein localization, and
protein- protein interactions.
The application of
proteomics technologies to clinical research and public health in general is an
immediate goal of proteomics. A distantly related goal is the eventual
application of proteomics to environmental, agricultural and veterinary
research, research areas that are far less developed than clinical applications.
Defining the Mandate of Proteomics in the Post- Genomics Era, Board on
International Scientific Organizations, National Academy of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html
For a field so laden with razzmatazz
methods, it is striking that the number one need in proteomics may be new
technology. There are simply not enough assays that are sufficiently streamlined
to allow the automation necessary to perform them on a genome's worth of
proteins. Those currently available barely scratch the surface of the thousands
of specialized analyses biologists use every day on their favorite proteins.
What we need are experimental strategies that could be termed cell biological
genomics, biophysical genomics, physiological genomics, and so on, to provide
clues to function. In addition, a protein contains so many types of information
that each of its properties needs to be assayed on a proteome- wide scale,
ideally in a quantitative manner. Stanley Fields "Proteomics in Genomeland"
Science 291: 1221-1224 Feb. 16, 2001
proteomimetics--
small molecule: The interaction between proteins
is fundamental to many receptor- ligand, enzyme- substrate, and protein- protein
interactions that have been linked to human disease states. Given the large
number of novel protein targets emerging from the genome and the dearth of small
molecules known to bind to and antagonize these targets, the challenge presented
to the pharmaceutical industry is in the identification of novel agents
effecting these novel targets. Traditional screening methods can be augmented by
directed discovery efforts that seek to capture the essence of a protein's
binding epitope in the context of a small molecule. Folding@home
glossary, Stanford Univ. http://www.stanford.edu/group/pandegroup/folding/education/P.html Related term:
protein small molecule interactions
Google = about 43
July 14, 2004, about 327 Oct. 25, 2006
Related
term: protein small molecule interactions
proteonomics:
Expression systems that can rapidly produce high levels
of recombinant proteins are a critical link between the discovery of new genes
and the identification of targets and molecules for drug development. Advances
in the baculovirus expression technology makes it the system of choice in the
emerging field of proteonomics where rapid production and high yields of
biologically active complex proteins are essential in the discovery of new drug
targets, vaccines, and biotherapeutics. Folding@home
glossary, Stanford Univ. http://www.stanford.edu/group/pandegroup/folding/education/P.html
Google = about 593 Sept. 18, 2002;
about 805 Aug 18, 2003; about 3,530 July 14, 2004; about 10,200 Nov. 5, 2005;
about 17,300 Nov 10, 2006
Related term: proteomics
quantitation - proteins:
It is likely that in the
near future, researchers will continue to use comprehensive gene arrays at the
start of their work, to generate hypotheses and narrow their research questions.
Then, they might delve deeper into these questions by using non-array- based
gene expression studies (to get better quantitation and true relative
expression) or go to a focused protein array that covers most of proteins that
are indicated based on the gene array experiments. "Proteomewide
chips - not so fast" CHI's
GenomeLink 21.2
regulatory homology:
Quantitative analysis of protein expression data
obtained by high - throughput methods has led us to define the concept of
"regulatory homology" and use it to begin to elucidate the basic
structure of gene expression control in vivo. [N. Leigh Anderson, Norman
G. Anderson "Proteome and proteomics; New technologies, new concepts, and
new words" Electrophoresis 19(11):1853-61 August 1998]
Google = about 22 Sept. 18, 2002;
about 38 Aug. 18, 2003; about 49 July 14, 2004; about 144 Nov 10, 2006
reverse-two hybrid:
A variation of the yeast two hybrid
system, in which protein- protein interactions increase the transcription
of a toxic counterselectable marker, resulting in growth inhibition. The
availability of a counterselectable marker significantly extends the possibilities
of the two- hybrid system. Most importantly, dissociation of protein- protein
interactions can be selected for, and thus protein- protein interactions
can be characterized and manipulated genetically. [Marc Vidal et al. "The
reverse two- hybrid system and several of its applications "Yeast Genetics
and Molecular Biology, Madison, WI August 1996] http://genome-www.stanford.edu/Saccharomyces/yeast96/f3041.html
Google = about 197 Sept. 18, 2002;
about 399 Aug. 18, 2003; about 607 July 14, 2004; about 15,700 Nov 10, 2006
riboproteomics: RNA
glossary
Rosetta stone method: A way of looking at the correlation of
protein
domains across species. Some proteins have homologs that are fused
in other species, yielding clues as to the proteins with which they might
interact. In addition, proteins that have been identified in particular
complexes and pathways hint at the location and function of their homologs
in other species. [S. Spengler “Bioinformatics in the information age”
Science 287 (5451): 221- 223 Feb. 18, 2000]
Related term: Phylogenomics glossary phylogenetic profiles
SPR Surface Plasmon Resonance: Assays,
labels, signaling & detection glossary
SWISS- PROT: Databases &
software directory
sample prep: Drug discovery &
development glossary
shotgun proteomics: Proteomics
categories
Google = about 39 Sept. 18, 2002;
about 206 Aug. 18, 2003; about 491 July 14, 2004; about 28,500 Nov 10, 2006
single cell proteomics: Ultrasensitivity
glossary
Google = about 25 Sept. 18, 2002;
about 84 Aug. 18, 2003; about 97 July 14, 2004; about 617 Nov 10, 2006
subcellular localization: Proteins
glossary
subproteomes: The separation of a
complex mixture of proteins is often insufficient and many protein mixtures are
dominated by a few major proteins. This makes the detection of many low
abundance proteins difficult or even impossible. Therefore, covering a proteome
as complete as possible often requires its separation into several subproteomes.
These "functional proteomics" approaches are especially useful when
looking for answers to well defined biological questions. Affinity purification
of proteins, separation of organelles or multiprotein complexes that take part
in certain cellular functions are good examples of these approaches. [Satu,
Lehesranta, Introduction to Proteomics, Dept. Biochemistry, Univ. of Kuopio,
Finland, 2001] Proteins
found in a specific tissue, cell type or body fluid (may incorporate a temporal
aspect as well.
Google = about 35 Sept. 18, 2002;
about 76 Aug. 18, 2003; about 217 July 14, 2004; about 9,840 Nov 10, 2006
systems
biology: Genetic manipulation
& disruption glossary
top-down mass
spectrometry: Mass spectrometry glossary
toxicoproteomics: Pharmacogenomics glossary
Google = about 96 Sept. 18, 2002;
about 261 Aug. 18, 2003; about 634 July 14, 2004; about 16,400 Nov 10, 2006
two-D gel electrophoresis: See 2D gel electrophoresis
two hybrid: See yeast two hybrid
two hybrid system techniques:
Screening techniques used to identify
genes encoding interacting proteins. Variations are used to evaluate complex interplay between proteins and other molecules.
MeSH, 2000
whole proteome:
Proteome analysis has become indispensable and complementary to genomic analysis. With access to whole genome sequences from various organisms and with the imminent completion of many more, the
SWISS- PROT group at EBI has developed a research- oriented initiative that utilises many of the existing resources and provides comparative analysis of the
predicted protein coding sequences of all complete genomes. [Rolf Apweiler
"Whole Proteome Analysis: The role of InterPro and CluSTr" Plant &
Animal Genome IX, San Diego CA Jan. 13-17, 2001] http://www.intl-pag.org/pag/9/abstracts/W22_01.html
Google = about 259 Sept. 18, 2002;
about 586 Aug. 18, 2003; about 1,610 July 14, 2004; about 30,600 Nov 10, 2006
whole proteome interaction mining:
A
major post- genomic scientific and technological pursuit is to describe the
functions performed by the proteins encoded by the genome. One strategy is to
first identify the protein- protein interactions in a proteome, then determine
pathways and overall structure relating these interactions, and finally to
statistically infer functional roles of individual proteins. Although huge
amounts of genomic data are at hand, current experimental protein interaction
assays must overcome technical problems to scale- up for high- throughput
analysis. In the meantime, bioinformatics approaches may help bridge the
information gap required for inference of protein function. JR Bock, DA Gough, Whole-
proteome interaction mining, Bioinformatics 19(1) :125- 134, Jan. 2003
yeast localizome: See under Proteins
glossary protein localization
yeast one hybrid:
A variant of the yeast two- hybrid
system, which identifies DNA- binding proteins from cDNA libraries
or known gene sequences.
Google = about 542 Sept. 18, 2002;
about 1,290 Aug. 18, 2003; about 2,260 July 14, 2004; about 45,800 Nov 10, 2006
Related term: protein- DNA interactions
yeast three hybrid:
The three-hybrid system enables the detection of RNA- protein interactions in
yeast using simple phenotypic assays. It was developed in collaboration with Stan
Fields laboratory (University of Washington- Seattle).
Original publication of the method [D. SenGupta, B. Zhang, B. Kraemer, P.
Prochart, S. Fields and M. Wickens. 1996. A three- hybrid system for detecting
RNA- protein interactions. Proc. Natl. Acad. Sci.
93, 8496- 8501] http://www.biochem.wisc.edu/wickens/3H/3HybrdSys_SenGupta.pdf
[Marvin Wickens, Dept. of Biochemistry,. Univ. of Wisconsin] http://www.biochem.wisc.edu/wickens/3H/
Modification of yeast two hybrid system.
The third hybrid may be a first one with an RNA or with a small molecule
that is a cell permeable chemical inducer of dimerization.
Google = about 192 Sept. 18, 2002;
about 603 Aug. 18, 2003, about 812 July 14, 2004; about 24,000 Nov 10, 2006
Related term protein- RNA interactions. yeast two hybrid:
An
approach to studying protein- protein interactions. The basic format
involves the creation of two hybrid molecules, one in which a "bait"
protein is fused with a transcription factor, and one in which a "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. A system first developed in 1989 (by Stan Fields
and colleagues) to identify proteins (and their genes) that interact with
known proteins. Google = about 11,700 Sept. 18,
2002; about 36,400 Aug. 18, 2003, about 81,700 July 14, 2004; about 836,000 Nov
10, 2006 Interaction Trap at Work, Ilya Serebriiski,
Fox Chase Cancer Center, US http://www.fccc.edu/research/labs/golemis/InteractionTrapInWork.html Related terms: dissociator assays, reverse two
hybrid, two hybrid system techniques, bait, prey
Bibliography
Insight Pharma Proteomics:
Current State and Future Directions, 2006
CHI Proteins:
Strategies for Optimizing Drug Discovery report, 2004
Folding@home
glossary, Stanford Univ. Tug Sezen, Vijay Pande, 2002, 200+ definitions http://www.stanford.edu/group/pandegroup/folding/education/glossary.html
National Academy of
Sciences, Defining the Mandate of
Proteomics in the Post- Genomics Era, 2002 http://www.nap.edu/books/NI000479/html/R1.html
National Academy
of Sciences, Technology, Science and Economic Policy Board, Workshop on
Exploring Patent and Licensing Policy for Proteomics, June 2004 http://www7.nationalacademies.org/step/Proteomics_June_transcript.pdf
Nature, “Post-Genomics Gateway” http://www.nature.com/genomics/post-genomics/index.html
Nature Proteomics, Mar
2003 http://www.nature.com/nature/insights/6928.html
Nature, "Proteomics in action" http://www.nature.com/genomics/post-genomics/action.html
Nature Reviews
Proteomics, 2005 http://www.nature.com/reviews/focus/proteomics/index.html
UNI-PROT KnowledgeBase keywords, Swiss
Institute of Bioinformatics, Geneva Switzerland, European Bioinformatics
Institute, Hinxton, UK, PIR Protein Information Resource, 2007 http://beta.uniprot.org/keywords/
Alpha
glossary index
How
to look for other unfamiliar terms
IUPAC definitions are reprinted with the
permission of the International Union of Pure and Applied Chemistry.
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