Unreferenced date December 2009 Orphan date February 2009 An HMG protein is a proteins involved with chromatin structure. They endow the chromosome with nuclease sensitivity. They also recruit transcription factor s to bind to Enhancer genetics enhancers . See High mobility group DEFAULTSORT Hmg Protein Category Proteins Protein stub ... more details
Unreferenced date October 2006 Protein turnover is the balance between protein synthesis and Proteolysis protein degradation . More synthesis than breakdown indicates an anabolic state that builds lean tissues, more breakdown than synthesis indicates a catabolic state that burns lean tissues. Protein turnover is believed to decrease with age in all senescence organisms including humans. This results in an increase in the amount of damaged protein within the body. It is unknown if this is a cause or consequence of aging but it seems likely that it is in fact both. The damaged protein results in a slower protein turnover which then results in more damaged protein causing an exponential increase in damage to all protein within the body and to aging. Some bodybuilding supplement s claim to reduce the protein breakdown by reducing or blocking the number of catabolic hormones within the body. This is believed to increase anabolism. However if protein breakdown falls too low then the body would not be able to remove muscle cells that have been damaged during workouts which would in turn prevent the growth of new muscle cells. When older proteins are broken down in the body, they must be replaced. This concept is called protein turnover, and different types of proteins have very different turnover rates. Protein synthesis occurs during the process of Translation biology translation on ribosome s. Protein breakdown occurs generally in two cellular locations br lysosome Lysosomal protease s digest endocytosis endocytosed proteins br cytoplasm Cytoplasmic complexes, called proteasome s, digest older or abnormal proteins that have been tagged with ubiquitin for destruction. DEFAULTSORT Protein Turnover Category Protein biosynthesis Protein stub ... more details
http www.proteopedia.org wiki index.php Rop protein Rop also known as repressor of primer is a small homodimeric four helix bundle protein formed by the antiparallel interaction of two helix turn helix monomers. The protein is expressed in Escherichia coli as a mechanism for regulating the gene copy number s of plasmid s. The Rop protein s structure has been solved to high resolution. ref Banner Due to its small size and known structure, Rop has been used in protein design work to rearrange its helical topology and reengineer its loop regions. ref Kresse In general, the four helix bundle has been extensively used in de novo protein design work as a simple model to understand the relationship between amino acid sequence and structure. References note Banner Banner DW, Kokkinidis M, Tsernoglou D. 1987 . Structure of the ColE1 rop protein at 1.7 A resolution. J Mol Biol 196 3 657 75. note Kresse Kresse HP, Czubayko M, Nyakatura G, Vriend G, Sander C, Bloecker H. 2001 . Four helix bundle topology re engineered monomeric Rop protein variants with different loop arrangements. Protein Eng 14 11 897 901. Category Proteins protein stub de G Protein Rop ... more details
Refimprove date April 2010 Hydrolyzed protein is protein that has been hydrolyze d or broken down into its component amino acid s. While there are many means of achieving this, two of the most common are prolonged boiling in a strong acid acid HVP or strong base or using an enzyme such as the Pancreas pancreatic protease enzyme to stimulate the naturally occurring hydrolytic process. Usages Protein hydrolysis can be used to modify the allergenic properties of infant formula. The size of cow milk proteins in the formula and the milk becomes more suitable for consumption by babies suffering of Milk protein intolerance Expand section date March 2012 Notes & references Reflist See also Acceptable daily intake Acid hydrolyzed vegetable protein E number Food allergy Food intolerance Food labeling regulations disambiguation Glutamic acid Monosodium glutamate Protein allergy DEFAULTSORT Hydrolyzed Protein Category Food additives Category Proteins Category Umami enhancers protein stub es Prote na hidrolizada ja fi Hydrolysoitu valkuainen ... more details
The M1 protein is a matrix protein of the influenza virus . It forms a coat inside the viral envelope . The M1 protein binds to the viral ribonucleic acid RNA . The binding is not specific to any RNA sequence, and is performed via a peptide sequence rich in base chemistry basic amino acid s. It also has multiple regulatory functions, performed by interaction with the components of the host cell. The mechanisms regulated include a role in the export of the viral ribonucleoprotein s from the host cell nucleus , inhibition of viral transcription genetics transcription , and a role in the virus assembly and budding . The protein was found to undergo phosphorylation in the host cell. The M1 protein forms a layer under the patches of host cell membrane that are rich with the viral hemagglutinin , neuraminidase and M2 protein M2 transmembrane protein s, and facilitates budding of the mature viruses. See also H5N1 genetic structure Sources and notes references Viral proteins DEFAULTSORT M1 Protein Category Membrane biology Category Peripheral membrane proteins Category Influenza Category Viral structural proteins es Prote na M1 ... more details
Orphan date February 2009 Unreferenced date May 2007 In immunology , self protein designates protein s normally produced by a particular organism. A particular organism s immune system should be tolerant to self proteins if not, there is autoimmunity . Category Immunology Immunology stub ... more details
Adenylate Cyclase Associated Protein is an actin binding protein that was originally identified as a binding partner for adenylate cyclase . It binds actin monomers and sequesters them from the polymerization process. The yeast ortholog of CAP is called Srv2. Cytoskeletal Proteins Category Proteins ... more details
Proteinprotein interaction prediction is a field combining bioinformatics and structural biology in an attempt ... proteinprotein interaction s is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical ... of experimental techniques, including yeast two hybrid screening two hybrid systems, protein fragment complementation assays PCA , affinity purification mass spectrometry , protein microarray s, fluorescence ... in other organisms. In addition, a number of bound protein complexes have been structurally solved ... pairs of protein families with similar patterns of presence or absence across large numbers of species ... imply physical interaction. Prediction of co evolved protein pairs based on similar phylogenetic ... protein in the hypothesized interacting pair. If the matrices are sufficiently similar as measured ... ref Ogmen builds a library of known proteinprotein interfaces from the Protein Data Bank PDB , where ... a known structure i.e. present in the Protein Data Bank PDB . Bayesian network modelling Bayesian ... potential protein interaction is a true positive result. These methods are useful because ... circumstantial evidence that a particular pair of proteins might interact. 3D template based protein complex modelling This method ref Aloy ref Chen ref Fukuhara ref Kittichotirat makes use of known protein complex structures to predict as well as structurally model interactions between query protein ... to search for protein complex structures that are homologous to the query sequences. These known ... sequences. This method has the advantage of not only inferring protein interactions but also suggests ... is limited to a relatively small number of known protein complex structures. Supervised learning problem ... the known protein interactions supervise the estimation of a function that can predict whether an interaction .... . Relationship to docking methods The field of proteinprotein interaction prediction is closely related ... more details
Unreferenced auto yes date December 2009 Orphan date February 2009 Merge to Protein sequencing date November 2011 A protein sequencer is a machine that is used to determine the sequence of amino acid s in a protein . They work by tagging and removing one amino acid at a time how? by chemicals? what are these chemicals designed to do , which is analysed and identified. This is done repetitively for the whole polypeptide , until the whole sequence is established. This method has generally been replaced by nucleic acid technology, and it is often easier to identify the sequence of a protein by looking at the DNA that codes for it. Protein methods DEFAULTSORT Protein Sequencer Cell biology stub Category Cell biology ... more details
A transport protein variously referred to as a transmembrane pump , transporter protein , escort protein , fatty acid transport protein , cation transport protein , or anion transport protein is a protein which serves the function of moving other materials within an organism . Transport proteins are vital to the growth and life of all living things. There are several different kinds of transport proteins. Carrier protein s are proteins involved in the movement of ions , small molecules , or macromolecules , such as another protein, across a biological membrane. ref Sadava, David, et al. Life, the Science of Biology, 9th Edition. Macmillan Publishers, 2009. ISBN 1429219629. pg 119. ref Carrier proteins are integral membrane proteins that is they exist within and span the membrane across which they transport substances. The proteins may assist in the movement of substances by facilitated diffusion or active transport . These mechanisms of movement are known as carrier mediated transport . ref Thompson, Liz A. Passing the North Carolina End of Course Test for Biology. American Book Company, Inc. 2007. ISBN 1598071394. pg. 97. ref Each carrier protein is designed to recognize only one substance or one group of very similar substances. Research has correlated defects in specific carrier proteins with specific diseases. ref Sadava, David, Et al. Life, the Science of Biology, 9th Edition. Macmillan Publishers, 2009. ISBN 1429219629. pg 119. ref A membrane transport protein or simply transporter is a membrane protein ref MeshName Membrane transport proteins ref which acts as such a carrier. A vesicular transport protein is a membrane protein transmembrane or membrane associated protein . It regulates or facilitates the movement by vesicle biology vesicles of the contents of the cell. ref MeshName Vesicular Transport Proteins ref References reflist Category Transport proteins de Transportprotein ru uk ... more details
unreferenced date April 2011 Protein bars are food bars that contain a high proportion of protein. Dietary purpose Protein bars are targeted to people who are searching for a source of protein that doesn t need preparation. There are different kinds of food bars to fill different purposes. Unlike energy bar s, which focus on providing food energy , or meal replacement bars , which intend to replace the variety of nutrients in a meal, protein bars usually lack food energy and vitamins minerals. Protein bars are mainly used by sports people athletes for muscle building. There are protein bars that are taken simply because of the protein only, others have a combination with carbohydrates for recovering muscle tissue after sports. Various diets based on proteins exist. In France special regulation is present for hyperprot in bars. In more and more markets protein is known for satiety levels. Protein bar niche In addition to other nutrients, the human body needs protein to build muscles. In the fitness and medical fields it is generally accepted that protein after exercise helps build the muscles used. Whey is one of the most often used proteins for protein bars for sports reasons. Issues Many popular protein bars such as Powerbar are known for their high levels of sugar. Sugar from natural sources such as fruit are thought to be healthier after workouts than other sugars, and many health experts argue that sugar from fruit improves athletic performance. References http www.active.com nutrition Articles Get enough protein after your next workout.htm http www.fredericpatenaude.com fruit article.html Category Dietary supplements Category Bodybuilding supplements Category Snack foods Category Breakfast foods ... more details
by the structures of the isomerase domain s of some of its members. A protein family is a group of evolution arily related protein s, and is often nearly synonymous with gene family . The term protein family should not be confused with Family biology family as it is used in taxonomy. Proteins ... protein structure three dimensional structures , functions, and significant sequence similarity ... tool for identifying the members of protein families. Currently, over 60,000 protein families have been defined, ref V.Kunin, I. Cases, A.J. Enrigh, V. de Lorenzo, C.A. Ouzounis, Myriads of protein families ... ambiguity in the definition of protein family leads different researchers to wildly varying numbers. Terminology and usage As with many biological terms, the use of protein family is somewhat context ..., Dayhoff introduced the concept of a protein superfamily. ref Dayhoff, M.O., Computer analysis of protein sequences, Fed. Proc. 33, 2314 2316, 1974. ref ref Dayhoff, M.O., McLaughlin, P.J., Barker, W.C., and Hunt, L.T., Evolution of sequences within protein superfamilies,Naturwissenschaften 62, 154 161, 1975. ref ref Dayhoff, M.O., The origin and evolution of protein superfamilies, Fed. Proc. 35, 2132 2138, 1976. ref Other terms such as protein class , protein group , and protein sub family ... these terms are being used in a particular context. Protein domains and motifs The concept of protein family was conceived at a time when very few protein structures or sequences were known at that time ... units or Protein domain domains . Due to evolutionary shuffling , different domains in a protein have evolved independently. This has led, in recent years, to a focus on families of protein domains ... at the end of this article . Regions of each protein have differing functional constraints features critical to the structure and function of the protein . For example, the active site of an enzyme ..., a proteinprotein binding interface may consist of a large surface with constraints on the hydrophobicity ... more details
. Protein S deficiency is the underlying cause of a small proportion of cases of disseminated ... Protein S Deficiency And Thrombophilia at proteinsdeficiency.com http www.med.uiuc.edu hematology PtProtS.htm Protein S Deficiency University of Illinois Articles cite journal author ten Kate ... PROS1 c.1113T GG frameshift mutation in a family with mixed type I type III protein S deficiency journal ... more details
distinguish G proteinProtein 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 ref name Sjobring 1991 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 DNA recombinant forms of Protein G. Other antibody binding proteins 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. Each of these immunoglobulin binding proteins has a different antibody binding profile in terms of the portion of the antibody that is recognized and the species and type of antibodies it will bind. Folding of Protein G, B1 Domain An Ab initio quantum chemistry methods 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 hydrophobe hydrophobic core Amino acid residues followed by small adjustments. ref name Kmiecik 1994 The folding events are as follows a Beta hairpin hairpin is formed, stabilized by residues W43, Y45, and F52. Residue contacts between residue F30, in an Alpha helix helix ... in a globular protein . The protein G B1 domain is aka. GB1 often used as part of a fusion protein ... L, Kastern W, et al title Streptococcal protein G. Gene structure and protein binding properties journal ... cite journal author Kmiecik S, Kolinski A title Folding pathway of the b1 domain of protein G explored ... Yuan Cheng, Dinshaw J Patel, An efficient system for small protein expression and refolding, Biochemical ... Category Proteins de Protein G es Prote na G Streptococcus ru G ... more details
Other uses Precursor disambiguation Infobox protein family Symbol Name Propeptides image width caption Pfam Pfam clan InterPro SMART PROSITE MEROPS SCOP TCDB OPM family 292 OPM protein 1wn8 CAZy CDD A protein precursor , also called a pro protein or pro peptide , is an inactive protein or peptide that can be turned into an active form by posttranslational modification . The name of the precursor for a protein is often prefixed by pro . Examples include proinsulin and proopiomelanocortin . Protein precursors are often used by an organism when the subsequent protein is potentially harmful, but needs to be available on short notice and or in large quantities. Enzyme precursors are called zymogen s or proenzyme s. Examples are enzymes of the digestive tract in humans. Some protein precursors are secreted from the cell. Many of these are synthesized with an N terminal signal peptide that targets them for secretion. Like other proteins that contain a signal peptide, their name is prefixed by pre . They are thus called pre pro proteins or pre pro peptides . ref name cell cite book author Alberts, Bruce title Molecular biology of the cell publisher Garland Science location New York year 2002 isbn 0 8153 3218 1 oclc doi page 760 ref The signal peptide is cleaved off in the endoplasmic reticulum . ref name cell An example is preproinsulin . References reflist Category Proteins protein stub de Pr kursor Proteine fr Pr curseur prot ique it Precursore nl Prote ne precursor ... more details
Orphan date April 2012 Protein sparing is the process by which the body derives energy from sources other than protein. Such sources can include adipose fatty tissues , dietary fats and carbohydrates . Protein sparing conserves muscle tissue. The balance between digestible protein DP and digestible energy DE in the diet is a key factor. Decreasing dietary DP DE ratio results in an increase of protein conservation. The amino acids are not catabolized for energy, and are conserved in the body in a greater ratio. The amount of protein used in the body is influenced by the percentage that is digestible by the body, and the total quantity of protein fed to the body. Bodybuilding and other strength training promotes the utilization and conservation of protein s amino acids in the body. Using alternate energy sources lessens the amount of amino acids that will be metabolized for energy. An increase of protein in the diet does not lead to greater protein efficiency, more protein will be lost, but a greater amount of protein will be conserved in the body through sheer volume, staying a step ahead of the metabolization of amino acids for energy. This supposedly happens roughly two days after a water fast , according to fasting proponents. External links Arguments for http drbenkim.com fasting.html 5 Water fasting for health recovery Ben Kim chiropractor http www.ajcn.org cgi content abstract 41 3 540 Evidence for protein sparing in protein supplemented low calorie diets American Journal of Clinical Nutrition Arguments against request additions Scientific analysis http www.uoguelph.ca fishnutrition Publications Bureau 2004 VIISINA.pdf Factors affecting metabolic waste products in fish University of Guelph Category Proteins ... more details
Unreferenced date December 2009 Protein catabolism is the breakdown of protein s into amino acid s and simple derivative compounds, for transport into the cell through the plasma membrane and ultimately for the polymerisation into new proteins via the use of ribonucleic acids RNA and ribosome s. Protein catabolism, which is the breakdown of macromolecules , is essentially a digestion process. Protein catabolism is most commonly carried out by non specific endo and exo proteases . However specific proteases are used for cleaving of proteins for regulatory and protein trafficking purposes. One example is the subclass of proteolytic enzymes called oligopeptidase . The amino acids produced by catabolism may be directly recycled, used to make new amino acids, or undergo amino acid catabolism to be converted to other compounds via the Krebs cycle . See also amino acid synthesis . See also Anabolism Metabolism Protein metabolism DEFAULTSORT Protein Catabolism Category Metabolism Metabolism stub ca Catabolisme de les prote nes es Catabolismo de prote nas sr Proteinski katabolizam ... more details
Image Hexon.svg thumb Diagram of how a virus capsid can be constructed using multiple copies of just two protein molecules A viral protein is a protein generated by a virus . ref MeshName Viral Proteins ref Many are structural, forming the viral envelope and capsid . ref MeshName Viral Structural Proteins ref However, there are also viral nonstructural protein s and viral regulatory and accessory protein s. More than 490 have been identified. ref name pmid18974184 cite journal author Chatr aryamontri A, Ceol A, Peluso D, et al. title VirusMINT a viral protein interaction database journal Nucleic Acids Res. volume 37 issue Database issue pages D669 73 year 2009 month January pmid 18974184 doi 10.1093 nar gkn739 url http nar.oxfordjournals.org cgi pmidlookup?view long&pmid 18974184 pmc 2686573 ref Aggregated, these proteins can form inclusion bodies . References Reflist Virus topics Viral proteins DEFAULTSORT Viral Protein Category Viral proteins virus stub ar es Prote na viral ... more details
Refimprove date March 2009 In molecular biology protein structure describes the various levels of organization of protein molecules. Proteins are an important class of biological macromolecules present ... are nanoparticle s definition 1 100 nm . Each protein polymer also known as a polypeptide consists ... under 40 residues the term peptide is frequently used instead of protein. To be able to perform their biological ... field of structural biology , which employs techniques such as X ray crystallography , protein NMR NMR spectroscopy , and dual polarisation interferometry to determine the structure of proteins. Protein ... author Brocchieri L, Karlin S title Protein length in eukaryotic and prokaryotic proteomes date ... Acids Research pmc 1150220 ref Very large aggregates can be formed from protein subunit s for example, many thousand actin molecules assemble into a microfilament . A protein may undergo reversible structural changes in performing its biological function. The alternative structures of the same protein ... are called conformational change s. Levels of protein structure File Main protein structure levels en.svg thumb left 250px Protein structure , from primary to quaternary structure. There are four distinct levels of protein structure. Primary structure Main Protein primary structure The primary structure ... together by Covalent bond covalent or peptide bond s, which are made during the process of protein biosynthesis ... where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotide s in DNA is Transcription .... The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of a protein can be determined by methods such as Edman degradation or Mass spectrometry Protein identification tandem mass spectrometry . Often however, it is read directly ... is lost so, protein is made up of amino acid residues Post translational modifications such as disulfide ... more details
Protein splicing is an intramolecular reaction of a particular protein in which an internal protein segment called an intein is removed from a precursor protein with a ligation of C terminal and N terminal external proteins called extein s on both sides. The splicing junction of the precursor protein is mainly a cysteine or a serine , which are amino acid s containing a nucleophilic side chain . The protein splicing reactions which are known now do not require exogenous cofactors or energy sources such as adenosine triphosphate ATP or guanosine triphosphate GTP . Normally, splicing is associated only with Splicing genetics pre mRNA splicing . Types of inteins The type of the splicing proteins is categorized into four classes maxi intein, mini intein, trans splicing intein, and alanine intein. The maxi inteins are N and C terminal splicing domains containing an endonuclease domain. The mini inteins are typical N and C terminal splicing domains however, the endonuclease domain is not present. The trans splicing inteins are split inteins which are divided into N termini and C termini. Alanine inteins have the splicing junction of an alanine instead of a cysteine or a serine, in both of which the protein splicing occurs. History Protein splicing was reported by two groups Anraku and Stevens in 1990. They both discovered a Saccharomyces cerevisiae VMA1 in a precursor of a vacuolar H sup sup ATPase . The amino acid sequence of the N and C termini corresponded to 70 of that of a vacuolar H sup sup ATPase from other organisms, while the amino acid sequence of the central position corresponded to 30 of that of the yeast HO nuclease External links http starokadomskyy.narod.ru work intein eng.html Short review http starokadomskyy.narod.ru Protein splicing eng.pdf Starokadomskyy PL. Protein Splicing, 2007 http www.neb.com neb inteins.html Protein splicing mechanism and intein structure MeshName Protein Splicing Category Proteins Category Protein biosynthesis de Proteinsplei en fa ... more details
Unreferenced date December 2009 File 1axc tricolor.png thumb right Assembled human Proliferating Cell Nuclear Antigen PCNA PDB PDBe 1AXC , a sliding DNA clamp protein that is part of the DNA replication complex and serves as a processivity factor for DNA polymerase. The three individual polypeptide chains that make up the trimer are shown. In biochemistry , a trimer is a macromolecular Complex chemistry complex formed by three, usually covalent bond non covalently bound , macromolecule s like protein s or nucleic acid s. A homo trimer would be formed by three identical molecule s. A hetero trimer would be formed by three different macromolecules. Collagen is an example of homo trimeric protein. See also Protein quaternary structure DEFAULTSORT Protein Trimer Category Proteins Biochem stub sr Proteinski trimer ... more details
Protein deacetylase any enzyme that removes acetyl groups from lysine amino acid s in protein s. The main ones are histone deacetylase s HDACs and sirtuin s SIRT1,2,3,5 . Because histone proteins were the first known substrate for protein deacetylases the later all tend to be called HDAC s of one class or another. Human protein deacetylase enzymes have been categorized into Class I HDAC1,2,3,8 Class II HDAC4,5,6,7,9,10 , Class III SIRT1,2,3,5,6 , Class IV HDAC11 and its related enzymes . Class III are the Nicotinamide adenine dinucleotide NAD dependent protein deacetylases. References reflist Category Enzymes ... more details
Orphan date April 2012 unreferenced date November 2011 A helminth protein , or helminthic antigen , is a protein derived from a parasitic worm that causes an immune reaction. The most commonly seen antigens of this sort are derived from the schistosomes . Helminth proteins may be used to develop antibodies in animals and humans to protect against parasitic infections. Category Proteins med stub protein stub ... more details
Vav is a family of proteins involved in cell signalling . They act as guanine nucleotide exchange factors GEFs for small G protein s of the Rho family . GEF activity is mediated via module of tandem RhoGEF domain DH PH domain PH domains. Vav proteins also appear to exhibit GEF independent functions. There are three members of this family VAV1 Vav1 VAV2 Vav2 VAV3 Vav3 protein stub Category Protein families de Vav Proteine ... more details
Protein crops are crop s that provide substantial protein , a large class of naturally occurring complex combinations of amino acid s. Such crops, including various oilseed s and grain s, are important in meeting the nutrient requirements of farm animal s. EU Common Agricultural Policy designates certain protein crops as eligible for support, such as pea s, field bean s, and sweet lupin s. References CRS article Report for Congress Agriculture A Glossary of Terms, Programs, and Laws, 2005 Edition url http ncseonline.org nle crsreports 05jun 97 905.pdf author Jasper Womach Category Crops ... more details
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