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Protein Technologies glossary & taxonomy
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions? 
Mary Chitty
Last revised July 10, 2019

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Related glossaries include Bioprocessing & manufacturing  Labels Signaling & Detection  Mass Spectrometry   NMR & x-ray crystallography   Proteomics

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]    Wikipedia   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.

a method used in protein engineering that mimics the process of natural selection to evolve proteins or nucleic acids toward a user-defined goal.[1] It consists of subjecting a gene to iterative rounds of mutagenesis (creating a library of  variants), selection (expressing the variants and isolating members with the desired function), and amplification (generating a template for the next round). It can be performed in vivo (in living cells), or in vitro (free in solution or microdroplet). Directed evolution is used both for protein engineering as an alternative to rationally designing modified proteins, as well as studies of fundamental evolutionary principles in a controlled, laboratory environment. Wikipedia accessed Sept 3 2018

directed protein evolution:  Systematic approaches to directed evolution of proteins have been documented since the 1970s. The ability to recruit new protein functions arises from the considerable substrate ambiguity of many proteins. The substrate ambiguity of a protein can be interpreted as the evolutionary potential that allows a protein to acquire new specificities through mutation or to regain function via mutations that differ from the original protein sequence. All organisms have evolutionarily exploited this substrate ambiguity. When exploited in a laboratory under controlled mutagenesis and selection, it enables a protein to "evolve" in desired directions.  Related term: phage display 

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     Wikipedia

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]  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 display: See under phage display
molecular evolution: Technologies overview

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 

PEGS: the essential protein engineering summit
PEGS: the essential protein engineering summit  April 8-12, 2019 • Boston, MA Program | Conference programs include protein and antibody engineering, cancer immunotherapy, oncology, and emerging therapeutics.

PEGS EuropeProtein Engineering  PEGS Europe  2018 Nov 12-16 Lisbon Portugal  Conference programs include Engineering, Oncology, Analytical, Immunotherapy, Expression and Bispecifics.


PepTalk  January 8-12, 2019 • San Diego, CA Program |  Conference programs include Protein Engineering and Development, Innovations in Discovery and Development, Antibody Therapeutics,  Formulation and Stability, Analytics & Impurities, Process Technologies & Purification, Biotherapeutic expression & production, Alternative expression & products.

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. 

phage display: Display of Antibodies April 8-9, 2019 • Boston, MA Program | showcases innovation in discovery, design and engineering of biologics through molecular evolution using phage, yeast and other display methodologies. The proliferation of novel constructs is possible through methods to improve library design, pharmacological and biophysical properties to create drug molecules with greater potency, modes of action, target specificity and activity than previously achievable.

Use of genetically engineered phage to present peptides as segments of their native surface proteins. Peptide libraries may be produced by populations of phage with different gene sequences. IUPAC Combinatorial Chemistry 
Broader term: display technologies  Related terms:  bacteriophage, biopanning, phage;  Labels, signaling & detection

Aptamers that incorporate a brominated deoxyuridine (BrdU) in place of the thymidine (T) normally found in DNA. A photoaptamer recognizes both the complex shape and charge distribution of its protein target and the presence of specific amino acid residues at specific sites. Related term: spiegelmer; Broader term: aptamers

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 

protein delivery: Drug discovery & development

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 

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 profiling: Expression 

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

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

proteolysis: Wikipedia  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

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

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,

recombinant proteins:  Proteins prepared by recombinant DNA technology.  MeSH, 1986  Related term: genetic recombination  

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  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

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

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  

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
NFCR Center for Therapeutic Antibody Engineering Glossary, National Foundation for Cancer Research, Dana Farber Cancer Institute 

How to look for other unfamiliar  terms

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.