Automatically knowledge-mined and generated summary of the topic Protein from from all articles contained in Wikipedia
 

Protein 

• The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code.

• Quaternary structure: the structure formed by several protein molecules (polypeptide chains), usually called protein subunits in this context, which function as a single protein complex.

• A useful technique for assessing cellular localization uses genetic engineering to express in a cell a fusion protein or chimera consisting of the natural protein of interest linked to a "reporter" such as green fluorescent protein (GFP).

• Cryoelectron microscopy is used to produce lower-resolution structural information about very large protein complexes, including assembled viruses; a variant known as electron crystallography can also produce high-resolution information in some cases, especially for two-dimensional crystals of membrane proteins.

• Solved structures are usually deposited in the Protein Data Bank (PDB), a freely available resource from which structural data about thousands of proteins can be obtained in the form of Cartesian coordinates for each atom in the protein.

• Protein structure prediction methods attempt to provide a means of generating a plausible structure for proteins whose structures have not been experimentally determined.

• Distributed computing is a relatively new tool researchers are using to examine the infamously complex interactions that govern protein folding; the statistical analysis techniques employed to calculate a protein's probable tertiary structure from its amino acid sequence (primary structure) are well-suited for the distributed computing environment, which has made this otherwise prohibitively expensive and time consuming problem significantly more manageable.

• Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein.

Protein G 

• Protein G is an immunoglobulin-binding protein expressed in group C and G Streptococcal bacteria much like Protein A but with differing specificities.

• It is a 65-kDa (G148 protein G) and a 58 kDa (C40 protein G) cell surface protein that has found application in purifying antibodies through its binding to the Fc region.

• The native molecule also binds albumin, however, because serum albumin is a major contaminant of antibody sources, the albumin binding site has been removed from recombinant forms of Protein G.

• Charge at that pH is 1.11022302462516e-16) In addition to Protein G, other immunoglobulin-binding bacterial proteins such as Protein A, Protein A/G and Protein L are all commonly used to purify, immobilize or detect immunoglobulins.

• http://www.jbc.org/cgi/reprint/266/1/399 Sjobring U, Bjorck L, Kastern W, Streptococcal protein G. Gene structure and protein binding properties, J Biol Chem.

• An ab initio simulation of the protein G B1 domain demonstrates that, as earlier results suggested, this protein initiates folding via a nucleation event in the hydrophobic core residues followed by small adjustments.

• The folding events are as follows: The protein G B1 domain is (aka. GB1) often used as part of a fusion protein to keep other domains in solution during experiments in solution (e.g. NMR).

Protein L 

• Protein L was first isolated from the surface of bacterial species Peptostreptococcus magnus and was found to bind Ig through L chain interaction, from which the name was suggested.

• The molecular weight of Protein L purified from the cell walls of Peptostreptoccus magnus was first estimated as 95kD by SDS-PAGE in the presence of reducing agent 2-mercaptoethanol, while the molecular weight was determined to 76kD by gel chromotography in the presence of 6 M guanidine HCl.

• Protein L does not contain any interchain disulfide loops, nor does it consist of disulfide-linked subunits.

• Unlike Protein A and Protein G, which bind to the Fc region of immunoglobilins (antibodies), Protein L binds antibodies through light chain interactions.

• Protein L binding is restricted to those antibodies that contain kappa light chains.

• Protein L is only effective in binding certain subtypes of kappa light chains.

• Since no part of the heavy chain is involved in the binding interaction, Protein L binds a wider range of antibody classes than Protein A or G. Protein L binds to representatives of all antibody classes, including IgG, IgM, IgA, IgE and IgD.

• Single chain variable fragments (ScFv) and Fab fragments also bind to Protein L. Despite this wide binding range, Protein L is not a universal antibody-binding protein.

• Given these specific requirements for effective binding, the main application for immobilized Protein L is purification of monoclonal antibodies from ascites or cell culture supernatant that are known to have the kappa light chain.

• Also, Protein L does not interfere with the antigen-binding site of the antibody, making it useful for immunoprecipitation assays, even using IgM.

• In addition to Protein L, other immunoglobulin-binding bacterial proteins such as Protein A, Protein G and Protein A/G are all commonly used to purify, immobilize or detect immunoglobulins.

• The gene for protein L contains five components: a signal sequence of 18 amino acids; a NH2-terminal region (“A”) of 79 residues; five homologous “B” repeats of 72-76 amino acids each; a COOH terminus region of two additional “C” repeats (52 amino acids each); a hydrophilic, proline-rich putative cell wall-spanning region (“W”) after the C repeats; a hydrophobic membrane anchor (“M”).

Protein A 

• Protein A is a 40-60 kDa MSCRAMM surface protein originally found in the cell wall of the bacteria Staphylococcus aureus.

• Protein A binds with moderate affinity to human IgM, IgA and IgE as well as to mouse IgG3 and IgG1.

• In addition to Protein A, other immunoglobulin-binding bacterial proteins such as Protein G, Protein A/G and Protein L are all commonly used to purify, immobilize or detect immunoglobulins.

• Immunoprecipitation studies with protein A conjugated to beads are also commonly used to purify proteins or protein complexes indirectly through antibodies against the protein or protein complex of interest.

• As a pathogen Staphylococcus aureus utilizes Protein A, along with a host of other proteins and surface factors to aid its survival and, thus, virulence.

• Mutants of S. aureus lacking protein A are more efficiently phagocytosed in vitro, and mutants in infection models have diminished virulence.

• One recombinant form of Protein A is called MabSelect.

• Protein A is often immobilized onto a solid support and used as reliable method for purifying total IgG from crude protein mixtures such as serum or ascites fluid, or coupled with one of the above markers to detect the presence of antibodies.

Protein Z 

• Protein Z also known as PROZ is a protein which in humans is encoded by the PROZ gene.

• Protein Z is a member of the coagulation cascade, the group of blood proteins that leads to the formation of blood clots.

• Although it is not enzymatically active, it is structurally related to several serine proteases of the coagulation cascade: factors VII, IX, X and protein C.

• The carboxyglutamate residues (which require vitamin K) bind protein Z to phospholipid surfaces.

• This is done by protein Z-related protease inhibitor (ZPI), but the reaction is accelerated 1000-fold by the presence of protein Z. Oddly, ZPI also degrades factor XI, but this reaction does not require the presence of protein Z. In some studies, deficiency states have been associated with a propensity to thrombosis.

• From a Ramachandran plot, the secondary structure of Protein Z was determined.

• The Ramachandran plot utilizes mathematical equations to determine the possible angles of the amino acids within the primary sequence of Protein Z. The possible angles results in a plot of possible secondary structures.

• The Ramachandran plot for protein Z indicates it will form alpha helices.

• Human Protein Reference Database

Protein S 

• In the circulation, Protein S exists in two forms: a free form and a complex form bound to complement protein C4b.

• The best characterized function of Protein S is its role in the anti coagulation pathway, where it functions as a cofactor to Protein C in the inactivation of Factors Va and VIIIa.

• Protein S can bind to the negatively charged phospholipids and function as a bridging molecule between the apoptotic cell and the phagocyte.

• The bridging property of Protein S enhances the phagocytosis of the apoptotic cell, allowing it to be removed 'cleanly' without any symptoms of tissue damage such as inflammation occurring.

• Mutations in the PROS1 gene can lead to Protein S deficiency which is a rare blood disorder which can lead to an increased risk of thrombosis.

• Protein S has been shown to interact with Factor V. hemostasis

Protein C 

• He named it protein C because it was the third protein ("peak C") that eluted from a DEAE-Sepharose ion-exchange chromotograph.

• Protein C, also known as autoprothrombin IIA and blood coagulation factor XIV, is a zymogenic (inactive) protein, the activated form of which plays an important role in regulating blood clotting, inflammation, cell death and maintaining the permeability of blood vessel walls in humans and other animals.

• Because of EPCR's role, activated protein C is primarily found near endothelial cells (i.e. those that make up the walls of blood vessels), and it is these cells and leukocytes (white blood cells) that APC affects.

• Activated protein C (APC) performs these operations primarily by proteolytically inactivating proteins Factor Va and Factor VIIIa.

• In 1980, Vehar and Davie discovered that APC also inactivates Factor VIIIa, and soon after, Protein S was recognised as a cofactor by Walker.

• Cofactors in the inactivation of Factor Va and Factor VIIIa include protein S, Factor V, high-density lipoprotein, anionic phospholipids and glycosphingolipids.

• Because of the crucial role that protein C plays as an anticoagulant, those with either deficiencies in protein C, or some kind of resistance to APC, suffer from a significantly increased risk of forming dangerous blood clots (thrombosis).

• In humans, protein C is encoded by the PROC gene, which is found on chromosome 2.

• The gene's symbol approved by the HUGO Gene Nomenclature Committee is "PROC" from "protein C".

• The protein C zymogen is activated when it binds to thrombin, another protein heavily involved in coagulation, and protein C's activation is greatly promoted by the presence of thrombomodulin and endothelial protein C receptors (EPCRs).

• Protein C was first isolated by Johan Stenflo from bovine plasma in 1976, and Stenflo determined it to be a vitamin K-dependent protein.

• Homozygous protein C deficiency and the consequent serious health effects were described in 1984 by several scientists.

• Near the end of that year, Drotrecogin alfa (activated), a recombinant human activated protein C, became the first drug approved by the U.S. Food and Drug Administration (FDA) for treating severe sepsis.

M1 protein 

• The M1 protein is a matrix protein of the influenza virus.

• The M1 protein binds to the viral RNA.

• The M1 protein forms a layer under the patches of host cell membrane that are rich with the viral hemagglutinin, neuraminidase and M2 transmembrane proteins, and facilitates budding of the mature viruses.

• The protein was found to undergo phosphorylation in the host cell.

Apoprotein 

• Apoprotein can refer to: Apoenzyme, the protein part of an enzyme without its characteristic prosthetic group.

• Apolipoprotein, a lipid-binding protein that is a constituent of the plasma lipoprotein.

Ci protein 

• Ci protein, short for Cubitus interruptus, is a zinc finger containing transcription factor involved in the Hedgehog signaling pathway.

• It isn't, however, completely destroyed; part of the protein survives and acts as a repressor in the nucleus, keeping genes responsive to the Hedgehog signal silent.

• The degradation of Ci protein depends on a large multiprotein complex, which contains a serine/threonine kinase of unknown function, an anchoring protein that binds to microtubules (to keep the Ci protein out of the nucleus) and an adaptor protein.

• When the Hedgehog signaling pathway is turned on, the Ci proteolysis is suppressed and the unprocessed CI protein enters the nucleus, where it activates the transcription of its target genes.

• The Patched receptor protein of the Hedgehog signaling pathway, which production acts as a negative feedback, since the resulting increase in Patched protein on the cell surface inhibits the Hedgehog pathway.

• The Wingless protein in Drosophila, which is crucial to the embryogenesis of the fruit fly, and acts through the Wnt signaling pathway.

• MeSH ci+protein,+Drosophila Drosophila cubitus interruptus - The Interactive Fly

cI protein 

• cI protein ("CI", not "CL"), also known as the lambda repressor, is the sole protein expressed in the lysogenic state of Lambda phage.

HMG protein 

• An HMG protein is a proteins involved with chromatin structure.

Protein 4.2 

• Protein 4.2 is a cytoskeleton protein found in red blood cells.

• Erythrocyte membrane protein band 4.2 is a protein that in humans is encoded by the EPB42 gene.

• Erythrocyte membrane protein band 4.2 is an ATP-binding protein which may regulate the association of protein 3 with ankyrin.

• Hereditary elliptocytosis MeSH band+4.2+protein

SKI protein 

• The Ski protein is a nuclear protooncoprotein that is associated with tumors at high cellular concentrations.

• The SKI protein has a 728 amino acid sequence, with multiple domains and is expressed both inside and outside of the nucleus.

• The SKI-Dachshund homology domain (SKI-DHD) contains the helix turn helix domains of the protein and the beta-alpha-beta turn motifs.

• Recent research shows that the SKI protein in cancerous cells acts as a suppressor, inhibiting transforming growth factor β (TFG- β) signaling.

• The SnoN protein was identified as a similar protein and is often discussed in conjugation with the Ski protein in publications.

• SKI protein has been shown to interact with SKIL, NFIX, SNW1, MECP2, HIPK2, Promyelocytic leukemia protein, Mothers against decapentaplegic homolog 3, Mothers against decapentaplegic homolog 1 and Mothers against decapentaplegic homolog 2.

• The protein has a helix-turn-helix motif, a cysteine and histidine rich area which gives rise to the zinc finger motif, a basic amino acid region, and leucine zipper.

• The protein also has hydrophobic regions which come into contact with Smad proteins rich in leucine and phenylalanine amino acid regions.

Protein IB5 

• The protein IB5 is a human parotid salivary protein containing several repeats of a short proline-rich sequence (hence the name of proline rich proteins or PRP for this class of proteins) and known to bind with polyphenols (binding responsible for the astringency mouth feel).

• Protein P16 

• In addition to protein p16, pRB there are many other important tumor suppressors that regulate the cell cycle and one of them is protein p53.

• The p16 protein (p16) is a cyclin-dependent kinase (CDK) inhibitor that decelerates the cell cycle by inactivating the CDKs that phosphorylate retinoblastoma protein (Rb).

• The protein (p16) is a cyclin-dependent kinase (CDK) inhibitor that slows down the progression of the cell cycle by inactivating the Cyclin dependent kinase that phosphorylates the retinoblastoma protein (pRb).

• The progression of cells from G1 phase to S phase is blocked by protein p16, which is a potential tumor suppressor that acts to disrupt the complex cyclin D1 and CDK 4 or 6.

• However, the activities of CDK4/CDK6 are restricted by protein p16 since protein p16 is a potent inhibitor of CDKs.

• Protein p21 is under control of p53 tumor suppressor protein.Some of the biological functions of protein p53 are as a transcriptional factor and also it regulates apoptosis.

• However, when protein p16 is overexpression it leads to cervical cancer because of the functional inactivation of pRb by human papillomavirus E7 protein.

Protein tag 

• Protein tags are peptide sequences genetically grafted onto a recombinant protein.

• These include chitin binding protein (CBP), maltose binding protein (MBP), and glutathione-S-transferase (GST).

• Isopeptag - a covalently binding and genetically encoded tag BCCP Myc-tag Calmodulin-tag FLAG-tag HA-tag His-tag Maltose binding protein-tag Nus-tag Glutathione-S-transferase-tag Green fluorescent protein-tag Thioredoxin-tag S-tag Softag 1 Softag 3 Strep-tag SBP-tag Ty tag Affinity purification Protein array Western blotting

• Chromatography tags are used to alter chromatographic properties of the protein to afford different resolution across a particular separation technique.

Mycoprotein 

• Mycoprotein means protein from fungi.

• To make protein, nitrogen (in the form of ammonia) is added, and vitamins and minerals are needed to support growth.

• The protein is known as a single cell protein(SCP) and was first produced in the early 1980's.

Hemeprotein 

• A hemeprotein (or hemoprotein or haemoprotein), or heme protein, is a metalloprotein containing a heme prosthetic group, either covalently or noncovalently bound to the protein itself.

Hfq protein 

• The Hfq protein (also known as HF-I protein) encoded by the hfq gene was discovered in 1968 as an Escherichia.

• It is now clear that Hfq is an abundant bacterial RNA binding protein which has many important physiological roles.

• The Hfq protein is now known to regulate the translation of two major stress transcription factors (σS (RpoS) and σE (RpoE)) in Enterobacteria.

• All six structures confirm the hexameric ring-shape of a Hfq protein complex.

Paraprotein 

• Paraproteins form a narrow band, or 'spike' in protein electrophoresis as they are all exactly the same protein.

SecY protein 

• The SecY protein is the main transmembrane subunit of the eubacterial protein secretory pathway and a protein-secreting ATPase complex, also known as a translocon.

• The translocase protein subunits are encoded on the bacterial chromosome.

• The translocase pathway comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF).

• The eubacterial secY protein interacts with the signal sequences of secretory proteins as well as with two other components of the protein translocation system: secA and secE.

• SecY is also encoded in the chloroplast genome of some algae where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.

• SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion.

• Cytoplasmic regions 2 and 3, and TM domains 1, 2, 4, 5, 7 and 10 are well conserved: the conserved cytoplasmic regions are believed to interact with cytoplasmic secretion factors, while the TM domains may participate in protein export.

• The chaperone protein SecB is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm.

Whey protein 

• Whey protein is a mixture of globular proteins isolated from whey, the liquid material created as a by-product of cheese production.

• Some preclinical studies in rodents have suggested that whey protein may possess anti-inflammatory or anti-cancer properties; however, human data is lacking.

• The effects of whey protein on human health are of great interest and are currently being investigated as a way of reducing disease risk, as well as a possible supplementary treatment for several diseases.

• Whey protein is commonly marketed and ingested as a dietary supplement, and various health claims have been attributed to it in the alternative medicine community.

• Cow's milk is 20% whey protein and 80% casein protein, whereas human milk is 60% whey and 40% casein.

• The protein fraction in whey (approximately 10% of the total dry solids within whey) comprises four major protein fractions and six minor protein fractions.

• The major protein fractions in whey are beta-lactoglobulin, alpha-lactalbumin, bovine serum albumin and immunoglobulins.

• Whey protein typically comes in three major forms: concentrate, isolate, and hydrolysate.

• Whey is an abundant source of branched-chain amino acids (BCAAs) which are used to fuel working muscles and stimulate protein synthesis.

• When leucine is ingested in high amounts, such as with whey protein supplementation, there is greater stimulation of protein synthesis, which may speed recovery and adaptation to stress (exercise).

• Processing can be by simple drying, or the protein content can be increased by removing lipids and other non-protein materials.

• Concentrates contain a low level of fat and cholesterol but, in general, have higher levels of bioactive compounds, and carbohydrates in the form of lactose — they are 29%–89% protein by weight.

L1 (protein) 

• L1 (protein) has been shown to interact with NUMB.

• L1, also known as L1CAM, is a transmembrane protein; it is a neuronal cell adhesion molecule, member of the L1 protein family, of 200-220 kDa, and involved in axon guidance and cell migration with a strong implication in treatment-resistant cancers.

• The protein encoded by this gene is an axonal glycoprotein belonging to the immunoglobulin superfamily of proteins.

Ku (protein) 

• Ku is a protein that binds to DNA double-strand break ends and is required for the non-homologous end joining (NHEJ) pathway of DNA repair.

• In higher eukaryotes, Ku forms a complex with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form the full DNA-dependent protein kinase, DNA-PK.

SAND protein 

• SAND protein family, first described in Saccharomyces cerevisiae (but also in the animals Fugu rubripes, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens and in the plant Arabidopsis thaliana using comparative genomics), is membrane protein related with vesicle traffic (vacuole fussion in yeasts and lysosome one in mammals and other taxa.

Late protein 

• A late protein is a viral protein that is formed after replication of the virus.

B7 (protein) 

• B7 is a type of peripheral membrane protein found on activated antigen presenting cells (APC) that, when paired with either a CD28 or CD152 (CTLA-4) surface protein on a T cell, can produce a costimulatory signal to enhance or decrease the activity of a MHC-TCR signal between the APC and the T cell, respectively.

• This first interaction involves the CD4 or CD8 proteins which form a complex with the CD3 protein to bind to the MHC molecule of the APC.

• The B7 (B7.1/B7.2) protein is present on the APC and is able to interact with the CD28 receptor on the T cell surface; this is also known as "Signal 2".

• As a result, the T cell is blocked from receiving the B7 protein signal and is not activated.

XK (protein) 

• XK (also known as Kell blood group precursor) is a protein found on human red blood cells and other tissues which is responsible for the Kx antigen which helps determine a person's blood type.

• Mutation of XK protein may lead to McLeod syndrome, a multi-system disorder characterized by hemolytic anemia, myopathy, acanthocytosis, and chorea.

• GeneReviews/NCBI/NIH/UW entry on McLeod Neuroacanthocytosis Syndrome XK at BGMUT Blood Group Antigen Gene Mutation Database at NCBI, NIH MeSH XK+protein,+human

• XK is located on the X chromosome and absence of the XK protein is an X-linked disease.

• XK is a membrane transport protein of unknown action.

RACK protein 

• RACK is an acronym for Receptor for Activated C-Kinase and is responsible for the binding of active forms of the protein kinase C (PKC) family of enzymes.

• See also RICK protein, Receptor for Inactive C-Kinase.

Flavoprotein 

• Hugo Theorell and coworkers showed that a bright-yellow-coloured yeast protein, identified previously as essential for cellular respiration, could be separated into apoprotein and a bright-yellow pigment.

• This led to the discovery that the protein studied required not riboflavin but flavin mononucleotide to be catalytically active Similar experiments with D-amino acid oxidase led to the identification of flavin adenine dinucleotide (FAD) as a second form of flavin utilised by enzymes.

• It compares the protein structures to elucidate phylogenetic relationships.

TC10 protein 

• TC10 is a small (~21 kDa) signaling G protein (more specifically a GTPase), and is a member of the Rho family of GTPases.

HuD (protein) 

• HuD (protein) has been shown to interact with NXF1.

• HuD otherwise known as ELAV-like protein 4 is a protein that in humans is encoded by the ELAVL4 gene.

• The HuD/ELAVL4 protein is an RNA-binding protein.

Nucleoprotein 

• A nucleoprotein is any protein which is structurally associated with nucleic acid (either DNA or RNA).

• Telomerase, a RNP (RNA/protein complex), and Protamines are also nucleoproteins.

Hop (protein) 

• Hop (the abbreviation stands for Hsp70/Hsp90 Organizing Protein, occasionally written HOP) is the Hsp70-Hsp90 organizing protein.

• It functions as a co-chaperone which reversibly links together the protein chaperones Hsp70 and Hsp90.

• Hop (protein) has been shown to interact with PRNP and Heat shock protein 90kDa alpha (cytosolic), member A1.

• Apart from its role in the Hsp70/Hsp90 "chaperone machine" it seems to participate in other protein complexes too (for example in the signal transduction complex EcR/USP and in the Hepatitis B virus reverse transcriptase complex, which enables the viral replication).

• The family of these proteins is referred to as STI1 (stress inducible protein) and can be divided into yeast, plant, and animal STI1 (Hop).

• The TPR motif is a very common structural feature used by many proteins and provides the ability of directing protein-protein interactions.

Proteins@home 

• Proteins@Home is a large-scale non-profit protein structure prediction project utilizing distributed computing to perform a lot of computations in a small amount of time.

• From their website: The amino acid sequence of a protein determines its three-dimensional structure, or 'fold'.

• Enumerating the allowed sequences for a given fold is known as the 'inverse protein folding problem'.

• A number of other distributed computing projects are also contributing to the protein folding idea.

• This large-scale mapping of protein sequence space will have applications for predicting protein structure and function, for understanding protein evolution, and for designing new proteins.

Arc (protein) 

• Arc, for activity-regulated cytoskeleton-associated protein (also known as Arg3.1), is a plasticity protein first characterized in 1995.

• Arc is a member of the immediate-early gene (IEG) family, a rapidly activated class of genes functionally defined by their ability to be transcribed in the presence of protein synthesis inhibitors.

• The Arc gene, located on chromosome 15 in the mouse[1], chromosome 7 in the rat[2], and chromosome 8 in the human[3], is conserved across vertebrate species and has low sequence homology to spectrin, a cytoskeletal protein involved in forming the actin cellular cortex.

• Arc is widely considered to be an important protein in neurobiology because of its activity regulation, localization, and utility as a marker for plastic changes in the brain.

• The Arc transcript is the first known IEG that is entirely dependent upon activation of the mitogen-activated protein kinase or MAP kinase (MAPK) cascade, a pathway important for regulation of cell growth and survival.

• The common factor for these signaling molecules involves activation of cyclic-AMP and its downstream target protein kinase A (PKA).

• As such, direct pharmacological activation of cAMP by forskolin or 8-Br-cAMP robustly increases Arc levels while H89, a PKA antagonist, blocks these effects as does further downstream blockade of mitogen-activated protein kinase kinase [sic] (MEK).

• Arc mRNA is localized to activated synaptic sites in an NMDA receptor-dependent manner, where the newly translated protein is believed to play a critical role in learning and memory-related molecular processes.

• While Arc mRNA is subject to degradation by NMD, the translated protein contains a PEST sequence at amino acids 351-392, indicating proteasome-dependent degradation.

• Changes in Arc mRNA and/or protein are correlated with a number of behavioral paradigms including cued fear conditioning, contextual fear conditioning, spatial memory, operant conditioning, and inhibitory avoidance.

• Once transported, the translated protein is 396 residues in length, with an N-terminus located at amino acids 1-25, a C-terminus at 155-396 (note that the spectrin homology located at 228-380 within the C-terminal), and a putative coiled coil domain at amino acids 26-154.

• Additionally, the protein has binding sites for endophilin 3 and dynamin 2 at amino acids 89-100 and 195-214, respectively.

• Synaptically localized Arc protein interacts with dynamin and endophilin, proteins involved in clathrin-mediated endocytosis, and facilitates the removal of AMPA receptors from the plasma membrane.

FIS (protein) 

• FIS is a nucleoid-associated protein in E. coli.

• It is a DNA binding protein.

Talin protein 

• TALIN is a high-molecular-weight cytoskeletal protein concentrated at regions of cell-substratum contact and, in lymphocytes, at cell-cell contacts.

• Discovered in 1983 by Keith Burridge and colleagues, talin is a ubiquitous cytosolic protein that is found in high concentrations in focal adhesions.

• Talin also binds with high affinity to vinculin, another cytoskeletal protein concentrated at points of cell adhesion.

• A structure-function analysis reported recently provides a cogent structural model (see top right) to explain talin-dependent integrin activation in three steps: TLN1; TLN2; Actin-binding protein Merlin (protein) an acronym for "Moesin-Ezrin-Radixin-Like Protein" Talin-1 UniProtKB/Swiss-Prot entry Q9Y490 Talin substrate for calpain - PMAP The Proteolysis Map animation.

IHH (Protein) 

• Indian hedgehog homolog (Drosophila), also known as IHH, is a protein which in humans is encoded by the IHH gene.

• The Indian Hedgehog protein is one of three proteins in the mammalian hedgehog family, the others being desert hedgehog (DHH) and Sonic hedgehog (SHH).

Nef (protein) 

• Nef (Negative Regulatory Factor) is a protein expressed by primate lentiviruses.

• "HIV protein hides infected cells from immune system".

Eos (protein) 

• Eos (also called EosFP) is a photoactivatable fluorescent protein (PAFP).

• Wild-type Eos is a tetrameric protein.

• Because Eos is available in monomeric forms, it can also be used to observe the kinetics and trafficking of single molecules as a fusion protein.

GAK (protein) 

• Cyclin G-associated kinase is homologous in function to the protein auxilin which when in association with Hsc70 uncoats clathrin in neuronal cells.

• In all eukaryotes, the cell cycle is governed by cyclin-dependent protein kinases (CDKs), whose activities are regulated by cyclins and CDK inhibitors in a diverse array of mechanisms that involve the control of phosphorylation and dephosphorylation of Ser, Thr or Tyr residues.

Lipoprotein-X 

• The protein component is dominated by albumin, located in the core, and by apolipoprotein C, located on the surface of the particle.

• It is characterized by its high content of phospholipids (66% by weight) and unesterified cholesterol (22%), and its low content of protein (6%), cholesterol esters (3%), and triglycerides (3%).

• II. Isolation and partial characterization of the protein moieties of low density lipoproteins".

GalP (protein) 

• GalP is an integral membrane protein present in Escherichia coli (1, 2).

• Transmembrane protein List of proteins Horne, P., and Henderson, P. J. (1983) The association of proton movement with galactose transport into subcellular membrane vesicles of Escherichia coli.

• Cairns, M. T., McDonald, T. P., Horne, P., Henderson, P. J., and Baldwin, S. A. (1991) Cytochalasin B as a probe of protein structure and substrate recognition by the galactose/H+ transporter of Escherichia coli.

• Macpherson, A. J., Jones-Mortimer, M. C., Horne, P., and Henderson, P. J. (1983) Identification of the GalP galactose transport protein of Escherichia coli.

• Demchenko, A. P. (1986) Fluorescence analysis of protein dynamics.

Protein domain 

• A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain.

• Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins.

• The most important factor governing the folding of a protein into 3D structure is the distribution of polar and non-polar side chains.

• The organisation of large proteins by structural domains represents an advantage for protein folding, with each domain being able to individually fold, accelerating the folding process and reducing a potentially large combination of residue interactions.

• The Levinthal paradox states that if an averaged sized protein would sample all possible conformations before finding the one with the lowest energy, the whole process would take billions of years.

• Domain motions can be inferred by comparing different structures of a protein, or they can be directly observed using spectra measured by neutron spin echo spectroscopy.

Protein ligand 

• In biochemistry, a protein ligand is an atom, a molecule or an ion which can bind to a specific site (the binding site) on a protein.

• Main methods to study protein-ligand interactions are principal hydrodynamic and calorimetric techniques, and principal spectroscopic and structural methods such as Fourier transform spectroscopy Raman spectroscopy Fluorescence spectroscopy Circular dichroism Nuclear magnetic resonance Mass spectrometry Atomic force microscope Paramagnetic probes Dual Polarisation Interferometry Other techniques include: fluorescence intensity, bimolecular fluorescence complementation, FRET (fluorescent resonance energy transfer) / FRET quenching surface plasmon resonance, Bio-Layer Interferometry, Coimmunopreciptation indirect ELIS, equilibrium dialysis, gel electrophoresis, far western blot, fluorescence polarization anisotropy, electron paramagnetic resonance, Microscale Thermophoresis The dramatically increased computing power of supercomputers and personal computers has made it possible to study protein-ligand interactions also by means of computational chemistry.

Protein design 

• Protein design is the design of new protein molecules, either from scratch or by making calculated variations on a known structure.

• Protein design involves identifying novel sequences within this subset, in particular those with a physiologically active native state.

• Therefore protein design is the search for sequences which have the chosen structure as a free energy minimum.

• A free, open-source software package for protein design and prediction of mutation effects on protein folding stabilities and binding affinities.

• Ancestral reconstruction Molecular design software PEGylation Protein engineering Protein structure prediction software Software for molecular modeling Meganucleases Dahiyat, Bassil I. & Mayo, Stephen L. (1997), "De Novo Protein Design: Fully Automated Sequence Selection", Science 278 (5335): 82–87, doi:10.1126/science.278.5335.82, PMID 9311930  Sander, Chris; Vriend, Gerrit; Bazan, Fernando; et al., Amnon; Nakamura, Haruki; Ribas, Luis; Finkelstein, Alexei V.; Lockhart, Andrew et al. (1992), "Protein Design on computers.

• Protein design requires an understanding of the molecular interactions that stabilize proteins in specific folded configurations; experience has shown, however, that it does not require an understanding of the dynamical process by which proteins fold.

• In Mad Cow Disease, there exists a healthy protein with a fatal weakness: there is another conformation this protein can "comfortably" take; the abnormally folded shape has very little free energy and is therefore very stable.

• For reasons that are not yet fully understood, this mis-folded prion protein has the ability to catalyze other proteins of its type to also adopt the mis-folded prion shape, which results in a disease-generating cascade of previously functional proteins quickly becoming misfolded.

• The iterative nature of this process allows IPRO to make additive mutations to the protein sequence that collectively improve the specificity towards the desired substrates and/or cofactors.

Protein trimer 

• Collagen is an example of homo-trimeric protein.

Protein THEMIS 

• Protein THEMIS is a protein that in humans is encoded by the THEMIS gene.

• This protein plays a regulatory role in both positive and negative T cell selection during late thymocyte development.

• Themis is also the name of a Titan in Greek mythology who weighed the fates of humans, an apt choice since protein is important in deciding the fate of the T cell during development.

• The protein functions through T-cell antigen receptor signaling, and is necessary for proper lineage commitment and maturation of T-cells.