gene shuffling: Genomic technologies  Can be used to evolve proteins.

glycoarrays: Carbohydrate arrays (glycoarrays) have recently emerged as a high-throughput tool for studying carbohydrate-binding proteins and carbohydrate-processing enzymes. A number of sophisticated array platforms that allow for qualitative and quantitative analysis of carbohydrate binding and modification on the array surface have been developed, including analysis by fluorescence spectroscopy, mass spectrometry and surface plasmon resonance spectroscopy. Glycoarrays--tools for determining protein-carbohydrate interactions and glycoenzyme specificity. Laurent N1, Voglmeir J, Flitsch SL. Chem Commun (Camb). 2008 Oct 7;(37):4400-12. doi: 10.1039/b806983m. Epub 2008 Aug 5.  https://pubs.rsc.org/en/Content/ArticleLanding/CC/2008/B806699J#!divAbstract  https://www.ncbi.nlm.nih.gov/pubmed/18802573

glycoprotein microarrays:  We employ carbohydrate and glycoprotein microarrays to analyze glycan- dependent gp120- protein interactions. In concert with new linking chemistries and synthetic methods, the carbohydrate arrays combine the advantages of microarray technology with the flexibility and precision afforded by organic synthesis. With these microarrays, we individually and competitively determined the binding profiles of five gp120 binding proteins, established the carbohydrate structural requirements for these interactions, and identified a potential strategy for HIV vaccine development. EW Adams et. al., Oligosaccharide and glycoprotein microarrays as tools in HIV glycobiology; glycan- dependent gp120/ protein interactions, Chem Biol. 11(6): 875- 881, June 2004   Related terms: oligosaccharide chips; Glycosciences glossary

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

molecular evolution protein: Evolution of proteins is studied by comparing the sequences and structures of proteins from many organisms representing distinct evolutionary clades. If the sequences/structures of two proteins are similar indicating that the proteins diverged from a common origin, these proteins are called as homologous proteins. More specifically, homologous proteins that exist in two distinct species are called as orthologs. Whereas, homologous proteins encoded by the genome of a single species are called paralogs. Wikipedia accessed 2018 Nov 10 https://en.wikipedia.org/wiki/Molecular_evolution#Protein_evolution  

molecular protein evolution directed: 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. One of the most effective strategies in directed protein evolution is to gradually accumulate mutations, either sequentially or by recombination, while applying selective pressure. This is typically achieved by the generation of libraries of mutants followed by efficient screening of these libraries for targeted functions and subsequent repetition of the process using improved mutants from the previous screening. Here we review some of the successful strategies in creating protein diversity Yuan L, Kurek I, English J, Keenan R. Laboratory-Directed Protein Evolution. Microbiology and Molecular Biology Reviews. 2005;69(3):373-392. doi:10.1128/MMBR.69.3.373-392.2005.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1197809/

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  
Wikipedia http://en.wikipedia.org/wiki/Molecular_motors

oligosaccharide microarrays: Studies on glycans are indispensable to define complex life systems and cell communities because all living organisms consist of diverse cells, which are covered with an abundance of heterogeneous carbohydrates. Although studies on glycans are extremely difficult because of the lack of basic technologies common to DNAs and proteins, a few new aspects of glycotechnologies have now become realized in the form of 'bio- chips', which include 'oligosaccharide arrays' or 'glyco- chips'. Recently, Fukui et al. developed oligosaccharide microarrays for glycomic analysis of extensive carbohydrate- binding proteins. How and why such glyco- engineering projects have been made in the contexts of both pure and applied sciences is described. J. Hirabayashi, Oligosaccharide microarrays for glycomics, Trends in Biotechnology 21 (4): 141-143, Apr. 2003    Related terms: glycochip, glycoprotein arrays 

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 arrays:  Steve Fodor and colleagues at Affymax published several articles on these in the early 1990s.   Related terms protein arrays, protein chips, protein microarrays

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: Antibody Display  May 4-5, 2020 • Boston, MA Program | cornerstone conference of the PEGS Summit and convenes leaders in the field year after year. This year’s meeting 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; Proteomics directed protein evolution  

photoaptamers: 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: Protein arrays are poised to become a central proteomics technology allowing for the global observation of biochemical activities on an unprecedented scale. Hundreds or thousands of proteins can be simultaneously screened for protein-protein, protein-nucleic acid, and small molecule interactions. The value of multiplexed protein measurement is being established in applications including: comprehensive proteomic surveys, studies of protein networks and pathways, validation of genomic discoveries, and clinical biomarker development. This technology holds great potential for basic molecular biology research, serum profiling, protein abundance determination, disease biomarker identification, immune and toxicological response profiling, and pharmaceutical target screening.  Related terms: antibody arrays, protein chips, protein microarrays Narrower terms: high- density protein arrays, protein- protein interaction chips, proteome chip

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 chips:  The protein chip is not going to replace certain discovery methods (such as 2D gel electrophoresis), which are very good at identifying novel proteins in a complex mixture. Perhaps the greatest limitation of methods based on electrophoresis is that they are relatively expensive to perform in terms of the cost per data point, and can be quite laborious. The trend, however, may continue toward reduced costs and ease of use. Another limitation of conventional proteomic methods is that they may not be versatile enough to rapidly gather biological information - changes in protein expression, protein- protein interactions, response to various conditions.

Ciphergen trademarked ProteinChip™ which is now owned by BioRad. Some chips can operate with both nucleic acids and proteins. Analogous to DNA chips, these are used for studying protein expression or protein- protein interactions.   Related terms: antibody arrays, carbohydrate chips, carbohydrate arrays, protein arrays, protein microarrays; Narrower terms: high- density protein microarrays, protein-protein interaction chips,  proteome chip

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

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. Eventually, even unnatural amino acids may be included, via newer methods, such as expanded genetic code, that allow encoding novel amino acids in genetic code. Wikipedia accessed 2018 Sept 5 Wikipedia http://en.wikipedia.org/wiki/Protein_engineering 

PEGS: the essential protein engineering summit  May 4-5, 2020 • Boston, MA Program | 

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: deGradFP (degrade Green Fluorescent Protein), an easy-to-implement protein knockout method applicable in any eukaryotic genetic system. Depleting a protein in order to study its function in a living organism is usually achieved at the gene level (genetic mutations) or at the RNA level (RNA interference and morpholinos). However, any system that acts upstream of the proteic level depends on the turnover rate of the existing target protein, which can be extremely slow. In contrast, deGradFP is a fast method that directly depletes GFP fusion proteins. In particular, deGradFP is able to counteract maternal effects in embryos and causes early and fast onset loss-of-function phenotypes of maternally contributed proteins. Protein Knockouts in Living Eukaryotes Using deGradFP and Green Fluorescent Protein Fusion Targets Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 73(73):30.2.1-30.2.13 · September 2013 DOI: 10.1002/0471140864.ps3002s7  https://www.ncbi.nlm.nih.gov/pubmed/24510595

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: These arrays can consist of proteins themselves (e.g., for studies of protein/ protein interactions or protein/ small- molecule binding) or of probes for capturing proteins (so that protein levels in a sample can be gauged).  Protein microarrays will permit researchers to scan thousands of proteins in a variety of proteomic experiments, including differential expression, response to drugs, protein- protein interactions and identification of disease biomarkers. So far, they have proven to be very quantitative and, by virtue of their addressable arrays, much easier to compare results between experiments than 2D gels. Commercialization of protein arrays also promises rapid development toward real applications in clinical and point- of- care diagnostics, which would be impossible with more complex proteomic technologies that require electrophoresis or chromatography. One disadvantage of the microarray approach is that generally it is a "closed" system - you can only measure proteins for which you have a capturing agent (such as an antibody).  Related terms: antibody microarrays, protein arrays, protein chips, protein profiling chips; Narrower terms:  electrospray- fabricated protein microarrays, functional protein microarrays, protein-protein interaction chips, proteome chip  
Wikipedia http://en.wikipedia.org/wiki/Protein_microarray 

protein purification: John Wagner's Logic of Molecular Approaches to Biological Problems (Cornell Univ. Graduate School of Medical Science, US ) has a section on the value of protein purification. http://www-users.med.cornell.edu/~jawagne/proteins_%26_purification.html

proteolysis: Wikipedia http://en.wikipedia.org/wiki/Proteolysis  Research and diagnostic applications

proteolytic processing: Related terms proteolysis Broader term post- translational modification

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.