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Pharmaceutical Protein categories & taxonomy
Evolving Terminology for Emerging Technologies
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Last revised July 09, 2019

Biology term index:  Protein categories is a sub-category of Proteins,  Related glossaries include Protein informatics  Protein Structures    Protein Technologies   Proteomics and Proteomic categories

adaptor proteins: A class of proteins involved in the transport of molecules via TRANSPORT VESICLES. They perform functions such as binding to the cell membrane, capturing cargo molecules and promoting the assembly of CLATHRIN. The majority of adaptor proteins exist as multisubunit complexes, however monomeric varieties have also been found. MeSH 2003

antifreeze proteins: Proteins that bind to ice and modify the growth of ice crystals. They perform a cryoprotective role in a variety of organisms. MeSH, 2001

basic proteins: Alkaline proteins, pI approximately above 7.0-7.5 pH.

carrier proteins:  Transport proteins that carry specific substances in the blood or across cell membranes. MeSH, 1973  Narrower term: membrane transport proteins

checkpoint control proteins: Proteins that control passage through critical stages of the cell cycle, these might, for example, halt passage through the cell cycle in the case of DNA damage. 

chemokines: Class of pro-inflammatory cytokines that have the ability to attract and activate leukocytes. They can be divided into at least three structural branches: C; (CHEMOKINES, C); CC; (CHEMOKINES, CC); and CXC; (CHEMOKINES, CXC); according to variations in a shared cysteine motif. MeSH 1996  Related term: Drug targets GPCRs 

chromosomal proteins: Protein which is associated with chromosomal DNA, including histones, protamines and high mobility group proteins. UNI-PROT KnowledgeBase keywords   Swiss Institute of Bioinformatics, Geneva Switzerland, European Bioinformatics Institute, Hinxton, UK, PIR Protein Information Resource, 2011

chromosomal proteins, non-histone: Nucleoproteins which in contrast to histones are acid insoluble. They are involved in chromosomal functions; e.g. they bind selectively to DNA, stimulate transcription resulting in tissue- specific RNA synthesis and undergo specific changes in response to various hormones or phytomitogens. MeSH, 1977

chimera protein: Wikipedia 

complex proteins: Complex proteins usually have more than one folding domain, each involving a sequence of 100 to 300 amino acids. The entire folding architecture of a complex protein must be precisely constructed in order for protein functionality to exist. Science Week 1998

A protein that contains a simple protein and at least one molecule of another substance, as a glycoprotein, lipoprotein, nucleoprotein, or hemoglobin. Mosby's Medical Dictionary, 8th edition. © 2009, Elsevier.

Is there a precise definition of  complex proteins?  Ones with more than two disulfide bonds?  More than one folding domain?  The Nature issue with the human genome sequence noted that "Humans have an unusually high number of complex proteins that fit into more than one functional category".  Various sources describe categories of  "simple proteins" and "conjugated proteins" and "derived proteins" Enzymes are identified as complex proteins.  Not the same as protein complexes

constitutive proteins: Proteins produced in fixed amounts, regardless of the organism's need for them. Dorland's Illustrated Medical Dictionary  Related term? housekeeping proteins 

cytokines:  Non- antibody proteins secreted by inflammatory leukocytes and some non- leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of  tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner. MeSH, 1991

Not really different from hormones, but the term tends to be used as a convenient generic shorthand for interleukins, lymphokines and several related signalling molecules such as TNF [Tumor Necrosis Factor] and interferons … Rather an imprecise term, though in very common usage.  Lackie
Horst Ibelgauft's Cytokines Online Pathfinder Encyclopaedi
Related term: Drug discovery & development cytokine based therapeutics Narrower terms: interleukins, interferons, tumor necrosis factors, transforming growth factor-beta, hematopoietic growth factors, chemokines, chemotactic cytokines

designer proteins: Protein design is currently used for the creation of new proteins with desirable traits. In our lab, we focus on the synthesis of proteins with high essential amino acid content having potential applications in animal nutrition. One of the limitations we face in this endeavour is achieving stable proteins despite a highly biased amino acid content. We report here the synthesis and characterisation of two mutants derived from our MB-1 designer protein. Williams M, Gagnon MC, Doucet A, Beauregard M, "Design of high essential amino acid proteins: two design strategies for improving protease resistance of the nutritious MB-1 protein" Journal of Biotechnology 94(3): 245- 254, Apr. 11, 2002

Designer proteins can also refer to high- protein nutritional supplements.

DNA-Binding proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single- stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases. MeSH, 1984

factitious protein: A product of genetic engineering; a protein designed for a specific purpose or for its expected properties. [Glick]   Factitious implies not natural or contrived.

fibrous proteins: Family of proteins which include collagen and keratin. Insoluble. 

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  

full-length proteins: Compare truncation

fusion protein:  defined as a multifunctional protein derived from a single nucleotide sequence which may contain 2 or more genes or portions of genes with or without amino acid linker sequences. The genes should originally code for separate proteins, both with pharmacological action (e.g., action and targeting).

gatekeeper protein: A protein that monitors transfer of a protein from the endoplasmic reticulum to the Golgi apparatus and prevents transfer of newly synthesized proteins with inappropriate conformations or with unpaired thiol groups. Glick

globular proteins: Water soluble proteins. Narrower term: enzymes

glycoproteins: Conjugated protein- carbohydrate compounds including mucins, mucoid, and amyloid glycoproteins. MeSH

Glycoproteins are complexes in which carbohydrates are attached covalently to asparagine (N-glycans) or serine/ threonine (O-glycans) residues of peptides. "Glycoproteins: How are glycoprotein sugar chains functioning within us", Glycoforum, Japan 2001

growth factors: This collective term originally referred to substances that promote cell growth. It is used rather loosely now, comprising molecules that function as growth stimulators (mitogens) but also as growth inhibitors (sometimes referred to as negative growth factors ), factors that stimulate cell migration (see: Motogenic cytokines ) or function as chemotactic agents (see also: Chemotaxis ) or inhibit cell migration or invasion of tumor cells, factors that modulate differentiated functions of cells, factors involved in apoptosis , or factors that promote survival of cells without influencing growth and differentiation. ... In many instances the term is used as a synonym for cytokines. Horst Ibelgauft's Cytokines Online Pathfinder Encyclopaedia   Narrower term IGF-1 Insulin like Growth Factor Compare cytokines

GTP-binding proteins: Regulatory proteins that act as molecular switches. They control a wide range of biological processes including: receptor signaling, intracellular signal transduction pathways, and protein synthesis. Their activity is regulated by factors that control their ability to bind to and hydrolyze GTP to GDP. EC 3.6.1 MeSH, 1997  Is this different from G- proteins?

heat shock proteins: Proteins which are synthesized in eukaryotic organisms and bacteria in response to hyperthermia and other environmental stresses. They increase thermal tolerance and perform functions essential to cell survival under these conditions. MeSH, 1984

housekeeping proteins: Highly expressed proteins > 10,000 copies per cell. Blackstock & Weir “Proteomics” Trends in Biotechnology: 121 Mar 1999 

Universal proteins.  Not the proteins of greatest interest, which are often of low abundance. Compare luxury proteins

hub proteins:  Most proteins interact with only a few other proteins while a small number of proteins (hubs) have many interaction partners. Hub proteins and non-hub proteins differ in several respects; however, understanding is not complete about what properties characterize the hubs and set them apart from proteins of low connectivity. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Diana Ekman, Sara Light, Åsa K Björklund and Arne Elofsson*  Genome Biology 2006, 7:R45  doi:10.1186/gb-2006-7-6-r45

hyperthermal proteins: Many microorganisms live in extreme environments such as hyperthermal vents, volcanoes, salty lakes, hot springs, and frozen glaciers. The objective of this program is to discover the structural and biochemical basis for understanding the unusual stabilities and biochemical properties of the proteins from these organisms, and to find their application for industrial and medical purposes. Rosalind Kim, Physical Biosciences Division, Lawrence Berkeley National Lab US 

hydrophobic proteins: Repel water. Related term membrane proteins.

hypothetical proteins: protein whose existence has been predicted, but for which there is a lack of experimental evidence that it is expressed in vivo. Sequencing of several genomes has resulted in numerous predicted open reading frames to which functions cannot be readily assigned. These proteins, either orphan or conserved hypothetical proteins, make up ~ 20% to 40% of proteins encoded in each newly sequenced genome.[1] Even when there is enough evidence that the product of the gene is expressed, by techniques such as microarray and mass-spectrometry, it is difficult to assign a function to it given its lack of identity to protein sequences with annotated biochemical function. Nowadays, most protein sequences are inferred from computational analysis of genomic DNA sequence. Hypothetical proteins are created by gene prediction software during genome analysis. Wikipedia accessed 2018 Oct 16

immediate-early proteins: Proteins that are coded by immediate- early genes, in the absence of de novo protein synthesis. The term was originally used exclusively for viral regulatory proteins that were synthesized just after viral integration into the host cell. It is also used to describe cellular proteins which are synthesized immediately after the resting cell is stimulated by extracellular signals. MeSH, 1994

immunoglobulin Ig: A protein of the globulin- type found in serum or other body fluids that possesses antibody activity. An individual Ig molecule is built up from two light (L) and two heavy (H) polypeptide chains linked together by disulfide bonds. Igs are divided into five classes based on antigenic and structural differences in the H chains. IUPAC Compendium

Glycoproteins present in the blood (ANTIBODIES) and in other tissue. They are classified by structure and activity into five classes (IMMUNOGLOBULIN A; IMMUNOGLOBULIN D; IMMUNOGLOBULIN E; IMMUNOGLOBULIN G; IMMUNOGLOBULIN M).  MeSH, 1972  Related term: Gene categories immunoglobulin genes

Integral membrane proteins, also called intrinsic proteins, have one or more segments that are embedded in thephospholipid bilayer. Most integral proteins contain residues with hydrophobic side chains that interact with fatty acyl groups of the membrane phospholipids, thus anchoring the protein to the membrane. Most integral proteins span the entire phospholipid bilayer. These transmembrane proteins contain one or more membrane-spanning domains as well as domains, from four to several hundred residues long, extending into the aqueous medium on each side of the bilayer. In all the transmembrane proteins examined to date, the membrane-spanning domains are α helices or multiple β strands. In contrast, some integral proteins are anchored to one of the membrane leaflets by covalently bound fatty acids, as discussed later. In these proteins, the bound fatty acid is embedded in the membrane, but the polypeptide chain does not enter the phospholipid bilayer. Molecular Cell Biology 4th ed. Membrane Proteins

Wikipedia   See also under membrane proteins

interferons: A class of glycoproteins (with sugar groups attached at specific locations) important in immune function. They are able to inhibit the multiplication of viruses in cells. IUPAC Biotech, IUPAC Compendium

Proteins secreted by vertebrate cells in response to a wide variety of inducers. They confer resistance against many different viruses, inhibit proliferation of normal and malignant cells, impede multiplication of intracellular parasites, enhance macrophage and granulocyte phagocytosis, augment natural killer cell activity, and show several other immunomodulatory functions. MeSH, 1983

low-abundance proteins: Often the proteins of greatest interest, but difficult to detect because more abundant proteins predominate. 

luxury proteins:  When specialized differentiated cells are formed, another set of proteins is synthesized, which are commonly known as luxury proteins  Compare housekeeping proteins

membrane proteins:  Drug Targets

membrane transport proteins: Membrane proteins whose primary function is to facilitate the transport of molecules across a biological membrane. Included in this broad category are proteins involved in active transport (BIOLOGICAL TRANSPORT, ACTIVE), facilitated transport and ION CHANNELS.  MeSH 2002 

Classification, glossary of membrane transport proteins, IUBMB International Union of Biochemistry and Molecular Biology, 2002, 13 definitions 

Are  there any transport proteins which are not membrane proteins?  Broader term: carrier proteins

mitochondrial proteins: Proteins encoded by the mitochondrial genome or proteins encoded by the nuclear genome that are imported to and resident in the MITOCHONDRIA. MeSH, 2002 
See also under Proteomic categories mitochondrial proteome

moonlighting proteins: A protein that has more than one independent function. Petsko, Gregory A.  2001.  Size doesn't matter. Genome Biology 2:1003.1-1003.2

mosaic proteins: Proteins with many (often repeated) domains are termed mosaic proteins. These domains or modules may be considered to be connected units which are independent in terms of their structure, function and folding behaviour. Principles of protein structure using the Internet, Dept. of Crystallography, Birkbeck College, Univ. of London, UK 1997-98
Mosaic proteins, Birkbeck College, Univ. of London

naked proteins: (informal, biochemistry) Any protein that normally exists combined with another entity (metalcarbohydrate or lipid etc), free from its normal attachment. Wiktionary
Related? term:  naked DNA  

nuclear proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus. MeSH, 1988

Any other way of characterizing?

nucleoproteins: Proteins conjugated with nucleic acids. MeSH

oncogene proteins: Proteins coded by oncogenes. They include proteins resulting from the fusion of an oncogene and another gene (ONCOGENE PROTEINS, FUSION). MeSH, 1993

orphan proteins: those proteins that do not have significant sequence identity(>10%) with other known proteins.  Bioinformatics.Org general forum

Proteins without sequence (and/or structural?) similarity to previously characterized proteins.

peripheral membrane proteins, or extrinsic proteins, do not interact with the hydrophobic core of the phospholipid bilayer. Instead they are usually bound to the membrane indirectly by interactions with integral membrane proteins or directly by interactions with lipid polar head groups. Peripheral proteins localized to the cytosolic face of the plasma membrane include the cytoskeletal proteins spectrin and actin in erythrocytes (Chapter 18) and the enzyme proteinkinase C. This enzyme shuttles between the cytosol and the cytosolic face of the plasma membrane and plays a role in signal transduction (Chapter 20). Other peripheral proteins, including certain proteins of the extracellular matrix, are localized to the outer (exoplasmic) surface of the plasma membrane. Molecular Cell Biology 4th ed. Membrane Proteins

polypeptides: Peptides containing ten or more amino acids. IUPAC Compendium

polyproteins: Proteins which are synthesized as a single polymer and then cleaved into several distinct proteins.  MeSH, 2000

probable protein (similarity): When a protein exhibits extensive sequence similarity to a characterised protein and/ or has the same conserved regions then the label ‘probable' is used in the DE line. "SWISS- PROT" in Introduction to Molecular Biology Databases, R. Apweiler, R. Lopez, B. Marx, 1999   Related term: putative protein

proteases: Enzymes that catalyse the hydrolysis of proteins. Usually several proteolytic enzymes are necessary for the complete breakdown of polypeptides to their amino acids. IUPAC Biotech, IUPAC Compendium

protein complex or multi protein complex:  a group of two or more associated polypeptide chains. Different polypeptide chains may have different functions. This is distinct from a multienzyme complex, in which multiple catalytic domains are found in a single polypeptide chain.[1]  Protein complexes are a form of quaternary structure. Proteins in a protein complex are linked by non-covalent protein–protein interactions, and different protein complexes have different degrees of stability over time. These complexes are a cornerstone of many (if not most) biological processes and together they form various types of molecular machinery that perform a vast array of biological functions. The cell is seen to be composed of modular supramolecular complexes, each of which performs an independent, discrete biological function.[2]    Wikipedia accessed 2018 Feb 20

putative proteins: Hypothetical and putative protein are predicted sequences, means the functional expression are not yet shown in experimental studies. Relatively, hypothetical proteins have weaker reliability than putative ones …Putative proteins are identified in similar manner [to hypothetical] [ but they share sequence similarity to an extent with characterized proteins. Usually, the similarity will be only in their conserved amino acid residues and no other significant region will be similar to annotated proteins. Unknown proteins are predicted and experimentally proven to exist but are not biochemically characterized or they cannot be linked to a known gene.  Related term probable protein (similarity)

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

regulatory proteins: Any protein that influences the regions of a DNA molecule that are transcribed by RNA polymerase during the process of transcription. These proteins, which include transcription factors, therefore help control the synthesis of proteins in cells.

repressor proteins: Proteins which are normally bound to the operator locus of an operon, thereby preventing transcription of the structural genes. In enzyme induction, the substrate of the inducible enzyme binds to the repressor protein, causing its release from the operator and freeing the structural genes for transcription. In enzyme repression, the end product of the enzyme sequence binds to the free repressor protein, the resulting complex then binds to the operator and prevents transcription of the structural genes. MeSH, 1991

RING finger proteins:  Display a series of histidine and cysteine residues with a characteristic spacing that allows the coordination of two zinc ions. RING finger domains are found in many proteins and have been implicated in various cellular functions. RINGs presumably do not function as chemical catalysts but as molecular scaffolds that bring together other proteins such as E3 ubiquitin ligases with E2 ubiquitin conjugating enzymes and the corresponding substrate. Apoptopedia, Cell Death Encyclopedia, 2001

K.L. Lorick, J.P. Jensen, S.Y. Fang, A.M. Ong, S. Hatakeyama, A.M. Weissman, "RING fingers mediate ubiquitin- conjugating enzyme (E2)-dependent ubiquitination," PNAS Proceedings from the National Academy of Sciences, 96(20): 11364- 11369, Sept. 28, 1999

C.A.P. Joazeiro, S.S. Wing, H.K. Huang, J.D. Leverson, T. Hunter, Y.C. Liu, "The tyrosine kinase negative regulator c-Cbl as a RING- type, E2-dependent ubiquitin- protein ligase," Science, 286: 309- 312, Oct. 8, 1999

RING stands for really interesting new gene  

secreted proteins: Encoded (usually) by genes with signal sequences, and such proteins include potential therapeutic proteins such as hormones, cytokines, and growth factors

structural homology protein: The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN. MeSH 2003

structural proteins: 
Wikipedia   Contrast with nonstructural proteins. 

transport proteins: See membrane transport proteins.  Are  there any transport proteins which are not membrane proteins?

transcription factors: Sequences, DNA & beyond

truncation: Elimination of the N- or C-terminal portion of a protein by proteolysis or manipulation of the structural gene, or premature termination of protein elongation due to the presence of a termination codon in its structural gene as a result of a nonsense mutation. Genscript Glossary   Compare full length proteins

ubiquitins: A family of proteins that are structurally-related to Ubiquitin. Ubiquitins and ubiquitin- like proteins participate in diverse cellular functions, such as protein degradation and HEAT- SHOCK RESPONSE, by conjugation to other proteins. MeSH, 2002

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

wild-type proteins:  Native proteins, as found in the wild.  This seems analagous to wild- type [genes] Genetic variations. Are there any other implications? 

Zinc Finger Proteins ZFP: A domain, found in certain DNA- binding proteins, comprising a helix- loop structure in which a zinc ion is coordinated to 2- 4 cysteine sulfurs, the remaining ligands being histidines.  In many proteins of this type the domain is repeated several times. IUPAC Bioinorganic

ZFPs are naturally occurring, zinc- containing DNA- binding proteins that serve as transcription factors. Researchers have discovered the rules by which ZFPs recognize specific DNA sequences. This knowledge allows them to rapidly generate proteins that selectively regulate target genes of interest. Genetic constructs that code for these ZFPs can be transfected into cells in culture or into animals, resulting in the downregulation or upregulation of target genes. 

Proteins resources
IUPAC  International Union of Pure and Applied Chemistry, Compendium of Chemical Terminology: Recommendations, compiled by Alan D. McNaught and Andrew Wilkinson, Blackwell Science, 1997. "Gold Book" 6,500+ definitions.
IUPAC  International Union of Pure and Applied Chemistry, Glossary of Terms used in Bioinorganic Chemistry, Recommendations, 1997. 450+ definitions.
IUPAC  International Union of Pure and Applied Chemistry, Glossary for Chemists of terms used in biotechnology. Recommendations, Pure & Applied Chemistry 64 (1): 143-168, 1992. 200 + definitions.
Lackie, JM and JAT Dow, Dictionary of Cell & Molecular Biology, Academic Press, 3rd ed., 1999. 7,000+ definitions
Proteins" Kimball's Biology Pages, John W. Kimball
UNI-PROT KnowledgeBase keywords   Swiss Institute of Bioinformatics, Geneva Switzerland, European Bioinformatics Institute, Hinxton, UK, PIR Protein Information Resource, 2011, 800+ definitions.

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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