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2D gel electrophoresis: A key technology for proteomics. Chromatography & electrophoresis antibody arrays: Microarrays & protein chips categories for studying regulation at the protein level antibody display: de Kruif J,, Boel E, Logtenberg T. Selection and application of human single chain Fv antibody fragments from a semi-synthetic phage antibody display library with designed CDR3 regions. J Mol Biol. 1995 Apr 21;248 (1): 97-105, April 1995 . aptamers: Technologies overview bacteriophage: Many phage have proved useful in the study of molecular biology and as vectors for the transfer of genetic information between cells … lambda bacteriophage can also undergo a lytic cycle or can enter a lysogenic cycle, in which the page DNA is incorporated into that of the host, awaiting a signal that initiates events leading to replication of the virus and lysis of the host cell. Glick The workhorse of phage display is the M13 bacteriophage virus. Related terms: phage, phage display bacteriophage, biopanning, phage; Labels, signaling & detection carbohydrate chips, carbohydrate microarrays: Microarrays & protein chips categories cDNA phage display: Display cloning: functional identification of natural product receptors using cDNA-phage display. Sche PP, McKenzie KM, White JD, Austin DJ. Chem Biol. 1999 Oct;6(10):707- 716 co-immunoprecipitation Used to determine protein- protein interactions. An antibody is used to precipitate a protein along with bound proteins. John Yates, “Mass spectrometry and the Age of the Proteome” Journal Mass Spectrometry 33: 16, 1998 combinatorial biology: Involves genetic manipulation of bacteria and fungi that produce complex natural products. This technology includes construction of large libraries of recombinant microbes capable of generating novel organic molecules and engineering secondary metabolite biosynthetic pathways to modify valuable biologically active microbial metabolites. [ASB [Am Soc. Biomechanics] Newsletter, June 1998] http://asb-biomech.org/newsletter/V11N1/guest.html Wikipedia http://en.wikipedia.org/wiki/Combinatorial_biology Related term: phage display co-precipitation: Method to identify interacting proteins by using antibodies to bind to the protein if immunoprecipitated under non- denaturing using conditions … (allow any other proteins bound to the protein known to be involved in a process) to precipitate rather than be washed away. depletion: Method of sample preparation which removes high abundance proteins (not of interest) from the sample. Related term: low- abundance proteins.
directed
evolution: an iterative process
scientists use to design biological molecules like enzymes. It requires
inducing some randomness in the target enzyme within an organism like
bacteria. The resulting mutated bacteria are screened to see which ones do
the intended job the best. The winners are then cultured, and from their
offspring, the best are selected, and then cultured, and so on.
https://www.vox.com/science-and-health/2018/10/3/17931612/nobel-prize-2018-chemistry-directed-evolution-enzymes-antibodies
DNA shuffling: Genomic technologies Can be used to evolve proteins. domain shuffling: Protein structure fluorescent
proteins: Using fluorescence is turning into one of the premier technologies
for drug discovery. To tap the full potential of these new and exciting
opportunities, many challenges still need to be addressed: How to increase the
stability of cell lines expressing fluorescent proteins; how to increase drug
screening by using better disease models utilizing FP’s in whole organisms;
how to develop better tools to enhance the high-throughput applications; and how
to improve effectiveness while lowering costs. Related terms: Labels
Signaling & Detection Fluorescence Recovery After Photobleaching FRAP, Fluorescence Resonance Energy Transfer FRET: Labels Signaling & Detection fusion proteins: A fusion protein is the product of joining two genes or two proteins / peptides together. Fusion proteins can happen naturally or it can be created artificially in a laboratory for research purposes. This is achieved through the creation of a fusion gene which is done through the removal of the stop codon from a DNA sequence of the first protein and then attaching the DNA sequence of the second protein in frame. The resulting DNA sequence will then be expressed by a cell as a single protein. International Society for Complexity, Information and Design http://www.iscid.org/encyclopedia/Fusion_Protein Wikipedia http://en.wikipedia.org/wiki/Fusion_protein fusion proteins, recombinant: Proteins that are the result of genetic engineering. A regulatory part or promoter of one or more genes is combined with a structural gene. The fusion protein is formed after transcription and translation of the fused gene. This type of fusion protein is used in the study of gene regulation or structure- activity relationships. They might also be used clinically as targeted toxins (immunotoxins). MeSH, 1987 Related term: cell fusion gene shuffling: Genomic technologies Can be used to evolve proteins. 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/toc/0900toc.html 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 Related/equivalent term?: interaction proteomics interactome, interactomics: Omes & omics intrabodies: Recent advances in antibody engineering have now allowed the genes encoding antibodies to be manipulated so that the antigen binding domain can be expressed intracellularly. The specific and high- affinity binding properties of antibodies, combined with their ability to be stably expressed in precise intracellular locations inside mammalian cells, has provided a powerful new family of molecules for gene therapy applications. These intracellular antibodies are termed 'intrabodies'. Wayne A. Marasco, "Intrabodies: turning the humoral immune system outside in for intracellular immunization" Gene Therapy 4 (1): 11- 15, Jan. 1997 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 lambda
phage: See under bacteriophage molecular motors:
Protein based machines that are involved in or
cause movement such as the rotary devices (flagellar motor and the F1 ATPase) or
the devices whose movement is directed along cytoskeletal filaments (myosin,
kinesin and dynein motor families). MeSH, 1999
peptide aptamers: Engineered protein molecules selected from combinatorial libraries, [used] to dissect the function of specific genes and alleles, and to trace genetic pathways. Roger Brent "Peptide aptamers" Molecular Sciences Institute, 1999 Broader term: aptamers Peptide Mass Fingerprinting PMF: A means of protein identification, using mass spectrometry peptide sequencing: How is this different from protein sequencing (except that peptides are shorter than proteins)? phage: A virus for which the natural host is a bacterial cell. DOE Used as a vector for cloning segments of DNA. Schlindwein Related terms: bacteriophage, phage display.
prefractionation: Sample preparation method, capable of being automated. protein arrays: Microarrays & protein chips protein capture
reagents: The Common Fund’s Protein Capture Reagents
program is developing new resources and tools to understand the critical role
the multitude of cellular proteins play in normal development and health as well
as in disease. These resources will support a wide-range of research and
clinical applications that will enable the isolation and tracking of proteins of
interest and permit their use as diagnostic biomarkers of disease onset and
progression. NIH Common Fund http://commonfund.nih.gov/proteincapture/ protein engineering: A technique used to produce proteins with altered or novel amino acid sequences. The methods used are: 1. Transcription and translation systems from synthesized lengths of DNA or RNA with novel sequences. 2. Chemical modification of 'normal' proteins. 3. Solid- state polypeptide synthesis to form proteins. IUPAC Compendium Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes. MeSH 2003 Procedures by which nonrandom single- site changes are introduced into structural genes (site- specific mutagenesis) in order to produce mutant genes which can be coupled to promoters that direct the synthesis of a specifically altered protein, which is then analyzed for structural and functional properties and then compared with the predicted and sought- after properties. The design of the protein may be assisted by computer graphic technology and other advanced molecular modeling techniques. MeSH, 1989 the process of developing useful or valuable proteins. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles. It is also a product and services market, with an estimated value of $168 billion by 2017.[1] There are two general strategies for protein engineering: rational protein design and directed evolution. These methods are not mutually exclusive; researchers will often apply both. In the future, more detailed knowledge of protein structure and function, and advances in high-throughput screening, may greatly expand the abilities of protein engineering. Wikipedia accessed 2018 Oct 18 http://en.wikipedia.org/wiki/Protein_engineering protein expression profiling: Expression genes & proteins protein inhibition: An alternative approach to [gene expression] downregulation, but in this case, the protein, not the gene, is the target. As with downregulation of gene expression, protein inhibition is a powerful target validation tool. The major approach to protein inhibition is based on phage libraries, which are used to select antibodies against targets of interest. protein knockouts: protein localization: There is an ever- increasing number of genes that have been sequenced but are of completely unknown function. The ability to determine the location of such gene products within the cell, either by the use of antibodies or by the production of chimeras with green fluorescent protein, is a vital step towards understanding what they do. This is one major reason why fluorescence microscopy is enjoying a revival. Protein Localization by Fluorescence Microscopy: A Practical Approach Edited by VICTORIA J. ALLAN, Oxford University Press, 2000 Narrower terms: subcellular localization, tissue specific localization; Related terms Cell biology: subcellular fractionation; Gene definitions: gene localization; Omes & omics localizome
protein microarrays: Microarrays
& protein protein pulldowns: High- throughput analyses afforded by mass spectroscopy require sample preparation processes that can keep pace. Standardization and automation of protein “pulldowns”, and related reagents are being developed. The processes are designed to provide a straightforward material flow in high- throughput format for the pulldown of protein complexes from the Rhodopseudomonas palustris and Shewanella oneidensis genomes. Existing techniques are well developed; however, some processes in clone library, antibody, and protein complex production have never been automated and few established protocols are available. P.R. Hoyt, Automation of Protein Complex Analyses in Rhodopseudomonas palustris and Shewanella oneidensis, DOE, Genomes to Life, 2003 http://doegenomestolife.org/pubs/2003abstracts/html/GTL.htm protein shuffling: We also constructed a computational method to determine the locations of crossovers that lead to functional hybrid proteins during in vitro recombination. Borrowing a concept from the schema theory of genetic algorithms, our approach assumes that crossovers resulting in functional proteins are those that least disrupt structural integrity. ... This method can be used to predict sites for protein shuffling and to screen sequence databases to determine optimal sets of starting sequences for in vitro evolution by recombination. Stephen L. Mayo, Computational Protein Design, Cal Tech, Howard Hughes Medical Institute http://www.hhmi.org/research/investigators/mayo.html proteolysis: Wikipedia http://en.wikipedia.org/wiki/Proteolysis Research and diagnostic applications proteolytic processing: Related terms proteolysis Broader term post- translational modification proteome arrays, proteome chips: Microarrays & protein chips 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 quantitative proteomics: Wikipedia http://en.wikipedia.org/wiki/Quantitative_proteomics involves the
identification and quantitation of protein components in various biological
systems. Stable isotope labelling technology, by both metabolic and chemical
methods, has been the most commonly used approach for global proteome-wide
profiling. Recently, its capability has been extended from labelled pairs to
multiple labels, allowing for the simultaneous quantification of multiplex
samples. The ion intensity-based quantitative approach has progressively gained
more popularity as mass spectrometry performance has improved significantly.
Although some success has been reported, it remains difficult comprehensively to
characterise the global proteome, due to its enormous complexity and dynamic
range. The use of sub-proteome fractionation techniques permits a simplification
of the proteome and provides a practical step towards the ultimate dissection of
the entire proteome. Further development of the technology for targeting
sub-proteomes on a functional basis - such as selecting proteins with
differential expression profiles from mass spectrometric analyses, for further
mass spectrometric sequencing in an intelligent manner--is expected in the near
future.
Institute for Systems Biology, self-assembling biomolecular materials: Examples of self- assembly include protein folding, the formation of liposomes, and the alignment of liquid crystals. While this type of equilibrium self- assembly is the central focus of this report, it is important to emphasize that much biological assembly is also driven by energy sources such as adenosine triphosphate (ATP), which power biomotors Biomolecular self- assembling materials, National Academy of Sciences 1996 http://www.nas.edu/bpa/reports/bmm/bmm.html#PBMM Broader term: self-assembly shotgun
proteomics:
Instrumentation aside, algorithms for matching mass spectra to proteins are at
the heart of shotgun proteomics. How do these algorithms work, what can we
expect of them and why is it so difficult to find protein modifications? Shotgun proteomics is a
remarkably powerful technology for identifying proteins, whether individually or
in samples as complex as cell lysates. How
do shotgun proteomics algorithms identify proteins? Edward M. Marcotte Nature Biotechnology
25, 755 - 757 (2007)
doi:10.1038/nbt0707-755 http://www.nature.com/nbt/journal/v25/n7/full/nbt0707-755.html subcellular proteomics: See under subproteomics subproteomics: Advances in the field of proteomics have made it possible to search for differences in protein expression between AM [alveolar macrophages] and their precursor monocytes. Proteome features of each cell type provide new clues into understanding mononuclear phagocyte biology. In-depth analyses using subproteomics and subcellular proteomics offer additional information by providing greater protein resolution and detection sensitivity. HM Wu, M Jin, CB Marsh, Toward functional proteomics of alveolar macrophages, Am J Physiol Lung Cell Mol Physiol. 288(4): L585- 595, April 2005 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15757951&query_hl=42 Subproteomics, utilising up to 40 two-dimensional gels per sample will become a powerful tool for near- to- total proteome analysis in the postgenome era. Furthermore, this new approach can direct biological focus towards molecules of specific interest within complex cells and thus simplify efforts in discovery- based proteome research. SJ Cordwell, AS Nouwens, NM Verrills, DJ Basseal, BJ Walsh, Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite two- dimensional electrophoresis gels, Electrophoresis, 21(6): 1094- 103, April 2000 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10786883&query_hl=42 targeted proteomics: Biochemical approaches to proteomics, particularly using mass spectrometry translation: Sequences, DNA & beyond Another approach to downregulating gene expression See also Genetic Manipulation & Disruption RNAi; Pharmaceutical biology antisense; RNA ribozymes. yeast display: See phage display
Proteomics resources IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry. |
