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100-465: 56030 ENSG00000075568 ENSMUSG00000026116 Q92545 O70472 NM_015348 NM_018497 NM_018872 NP_056163 NP_061360 Transmembrane protein 131 (TMEM131) is a protein that is encoded by the TMEM131 gene in humans. The TMEM131 protein contains three domains of unknown function 3651 (DUF3651) and two transmembrane domains . This protein has been implicated as having
200-520: A carboxyl group, and a variable side chain are bonded . Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO–NH amide moiety into a fixed conformation. The side chains of the standard amino acids, detailed in the list of standard amino acids , have a great variety of chemical structures and properties; it is the combined effect of all of
300-470: A gene may be duplicated before it can mutate freely. However, this can also lead to complete loss of gene function and thus pseudo-genes . More commonly, single amino acid changes have limited consequences although some can change protein function substantially, especially in enzymes . For instance, many enzymes can change their substrate specificity by one or a few mutations. Changes in substrate specificity are facilitated by substrate promiscuity , i.e.
400-430: A semantic web , text mining can find content based on meaning and context (rather than just by a specific word). Additionally, text mining software can be used to build large dossiers of information about specific people and events. For example, large datasets based on data extracted from news reports can be built to facilitate social networks analysis or counter-intelligence . In effect, the text mining software may act in
500-552: A combination of sequence, structure and function, and they can be combined in many different ways. In an early study of 170,000 proteins, about two-thirds were assigned at least one domain, with larger proteins containing more domains (e.g. proteins larger than 600 amino acids having an average of more than 5 domains). Most proteins consist of linear polymers built from series of up to 20 different L -α- amino acids. All proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group,
600-403: A defined conformation . Proteins can interact with many types of molecules, including with other proteins , with lipids , with carbohydrates , and with DNA . It has been estimated that average-sized bacteria contain about 2 million proteins per cell (e.g. E. coli and Staphylococcus aureus ). Smaller bacteria, such as Mycoplasma or spirochetes contain fewer molecules, on
700-851: A detailed review of the vegetable proteins at the Connecticut Agricultural Experiment Station . Then, working with Lafayette Mendel and applying Liebig's law of the minimum , which states that growth is limited by the scarcest resource, to the feeding of laboratory rats, the nutritionally essential amino acids were established. The work was continued and communicated by William Cumming Rose . The difficulty in purifying proteins in large quantities made them very difficult for early protein biochemists to study. Hence, early studies focused on proteins that could be purified in large quantities, including those of blood, egg whites, and various toxins, as well as digestive and metabolic enzymes obtained from slaughterhouses. In
800-478: A little ambiguous and can overlap in meaning. Protein is generally used to refer to the complete biological molecule in a stable conformation , whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable 3D structure. But the boundary between the two is not well defined and usually lies near 20–30 residues. Polypeptide can refer to any single linear chain of amino acids, usually regardless of length, but often implies an absence of
900-410: A particular cell or cell type is known as its proteome . The chief characteristic of proteins that also allows their diverse set of functions is their ability to bind other molecules specifically and tightly. The region of the protein responsible for binding another molecule is known as the binding site and is often a depression or "pocket" on the molecular surface. This binding ability is mediated by
1000-500: A protein carries out its function: for example, enzyme kinetics studies explore the chemical mechanism of an enzyme's catalytic activity and its relative affinity for various possible substrate molecules. By contrast, in vivo experiments can provide information about the physiological role of a protein in the context of a cell or even a whole organism . In silico studies use computational methods to study proteins. Proteins may be purified from other cellular components using
1100-411: A protein is defined by the sequence of a gene, which is encoded in the genetic code . In general, the genetic code specifies 20 standard amino acids; but in certain organisms the genetic code can include selenocysteine and—in certain archaea — pyrrolysine . Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification , which alters
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#17327823410421200-542: A protein that fold into distinct structural units. Domains usually also have specific functions, such as enzymatic activities (e.g. kinase ) or they serve as binding modules (e.g. the SH3 domain binds to proline-rich sequences in other proteins). Short amino acid sequences within proteins often act as recognition sites for other proteins. For instance, SH3 domains typically bind to short PxxP motifs (i.e. 2 prolines [P], separated by two unspecified amino acids [x], although
1300-485: A review is for the product. Such an analysis may need a labeled data set or labeling of the affectivity of words. Resources for affectivity of words and concepts have been made for WordNet and ConceptNet , respectively. Text has been used to detect emotions in the related area of affective computing. Text based approaches to affective computing have been used on multiple corpora such as students evaluations, children stories and news stories. The issue of text mining
1400-510: A role in T cell function and development. TMEM131 also resides in a locus (2q11.1) that is associated with Nievergelt's Syndrome when deleted. TMEM131 has been shown to exhibit hypermethylation in patients with Down Syndrome . The authors of this study proposed that, given TMEM131s supposed function in T cell development and function, this hypermethylation may play a role in the suppressed immune function in patients with Down Syndrome. TMEM131 has also been shown to be up-regulated during
1500-486: A role in biological recognition phenomena involving cells and proteins. Receptors and hormones are highly specific binding proteins. Transmembrane proteins can also serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions. The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse . Membrane proteins contain internal channels that allow such molecules to enter and exit
1600-406: A series of purification steps may be necessary to obtain protein sufficiently pure for laboratory applications. To simplify this process, genetic engineering is often used to add chemical features to proteins that make them easier to purify without affecting their structure or activity. Here, a "tag" consisting of a specific amino acid sequence, often a series of histidine residues (a " His-tag "),
1700-432: A solution known as a crude lysate . The resulting mixture can be purified using ultracentrifugation , which fractionates the various cellular components into fractions containing soluble proteins; membrane lipids and proteins; cellular organelles , and nucleic acids . Precipitation by a method known as salting out can concentrate the proteins from this lysate. Various types of chromatography are then used to isolate
1800-483: A traditional part of social sciences and media studies for a long time. The automation of content analysis has allowed a " big data " revolution to take place in that field, with studies in social media and newspaper content that include millions of news items. Gender bias , readability , content similarity, reader preferences, and even mood have been analyzed based on text mining methods over millions of documents. The analysis of readability, gender bias and topic bias
1900-441: A variety of techniques such as ultracentrifugation , precipitation , electrophoresis , and chromatography ; the advent of genetic engineering has made possible a number of methods to facilitate purification. To perform in vitro analysis, a protein must be purified away from other cellular components. This process usually begins with cell lysis , in which a cell's membrane is disrupted and its internal contents released into
2000-450: A way to improve their results. Within the public sector, much effort has been concentrated on creating software for tracking and monitoring terrorist activities . For study purposes, Weka software is one of the most popular options in the scientific world, acting as an excellent entry point for beginners. For Python programmers, there is an excellent toolkit called NLTK for more general purposes. For more advanced programmers, there's also
2100-475: A wide variety of government, research, and business needs. All these groups may use text mining for records management and searching documents relevant to their daily activities. Legal professionals may use text mining for e-discovery , for example. Governments and military groups use text mining for national security and intelligence purposes. Scientific researchers incorporate text mining approaches into efforts to organize large sets of text data (i.e., addressing
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#17327823410422200-481: Is a knowledge-based search engine for biomedical texts. Text mining techniques also enable us to extract unknown knowledge from unstructured documents in the clinical domain Text mining methods and software is also being researched and developed by major firms, including IBM and Microsoft , to further automate the mining and analysis processes, and by different firms working in the area of search and indexing in general as
2300-420: Is a truism that 80% of business-relevant information originates in unstructured form, primarily text. These techniques and processes discover and present knowledge – facts, business rules , and relationships – that is otherwise locked in textual form, impenetrable to automated processing. Subtasks—components of a larger text-analytics effort—typically include: Text mining technology is now broadly applied to
2400-557: Is also involved in the study of text encryption / decryption . A range of text mining applications in the biomedical literature has been described, including computational approaches to assist with studies in protein docking , protein interactions , and protein-disease associations. In addition, with large patient textual datasets in the clinical field, datasets of demographic information in population studies and adverse event reports, text mining can facilitate clinical studies and precision medicine. Text mining algorithms can facilitate
2500-458: Is attached to one terminus of the protein. As a result, when the lysate is passed over a chromatography column containing nickel , the histidine residues ligate the nickel and attach to the column while the untagged components of the lysate pass unimpeded. A number of different tags have been developed to help researchers purify specific proteins from complex mixtures. Text mining Text mining , text data mining ( TDM ) or text analytics
2600-422: Is being used in business, particularly, in marketing, such as in customer relationship management . Coussement and Van den Poel (2008) apply it to improve predictive analytics models for customer churn ( customer attrition ). Text mining is also being applied in stock returns prediction. Sentiment analysis may involve analysis of products such as movies, books, or hotel reviews for estimating how favorable
2700-562: Is dictated by the nucleotide sequence of their genes , and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide . A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides . The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in
2800-628: Is found in hard or filamentous structures such as hair , nails , feathers , hooves , and some animal shells . Some globular proteins can also play structural functions, for example, actin and tubulin are globular and soluble as monomers, but polymerize to form long, stiff fibers that make up the cytoskeleton , which allows the cell to maintain its shape and size. Other proteins that serve structural functions are motor proteins such as myosin , kinesin , and dynein , which are capable of generating mechanical forces. These proteins are crucial for cellular motility of single celled organisms and
2900-711: Is high within the DUF3651 and transmembrane regions in the more distant homologs . Orthologs were found in species as distantly related to Humans as the Choanoflagellate Monosiga brevicollis using BLAST and the ALIGN tool through the San Diego Super Computer Biology Workbench. The following table gives information on the homologs of TMEM131. TMEM131 has a single paralog, TMEM131L or KIAA0922 . This gene
3000-469: Is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second. The process of synthesizing a protein from an mRNA template is known as translation . The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme aminoacyl tRNA synthetase "charges"
3100-461: Is inefficient for polypeptides longer than about 300 amino acids, and the synthesized proteins may not readily assume their native tertiary structure . Most chemical synthesis methods proceed from C-terminus to N-terminus, opposite the biological reaction. Most proteins fold into unique 3D structures. The shape into which a protein naturally folds is known as its native conformation . Although many proteins can fold unassisted, simply through
TMEM131 - Misplaced Pages Continue
3200-470: Is located directly adjacent to the ZAP70 gene (98,330,331 - 98,356,323) on the positive DNA strand, as well as numerous pseudogenes at the 2q11.2 locus . A Von Willebrand factor containing gene (VWA3B) is located upstream from TMEM131 on the positive strand (98,703,595 - 98,929,410). TMEM131 is expressed in low to moderate levels throughout most of the body, with slightly increased levels occurring in
3300-560: Is no exception in copyright law of Australia for text or data mining within the Copyright Act 1968 . The Australian Law Reform Commission has noted that it is unlikely that the "research and study" fair dealing exception would extend to cover such a topic either, given it would be beyond the "reasonable portion" requirement. Until recently, websites most often used text-based searches, which only found documents containing specific user-defined words or phrases. Now, through use of
3400-606: Is of importance to publishers who hold large databases of information needing indexing for retrieval. This is especially true in scientific disciplines, in which highly specific information is often contained within the written text. Therefore, initiatives have been taken such as Nature's proposal for an Open Text Mining Interface (OTMI) and the National Institutes of Health 's common Journal Publishing Document Type Definition (DTD) that would provide semantic cues to machines to answer specific queries contained within
3500-404: Is often enormous—as much as 10 -fold increase in rate over the uncatalysed reaction in the case of orotate decarboxylase (78 million years without the enzyme, 18 milliseconds with the enzyme). The molecules bound and acted upon by enzymes are called substrates . Although enzymes can consist of hundreds of amino acids, it is usually only a small fraction of the residues that come in contact with
3600-570: Is roughly synonymous with text mining; indeed, Ronen Feldman modified a 2000 description of "text mining" in 2004 to describe "text analytics". The latter term is now used more frequently in business settings while "text mining" is used in some of the earliest application areas, dating to the 1980s, notably life-sciences research and government intelligence. The term text analytics also describes that application of text analytics to respond to business problems, whether independently or in conjunction with query and analysis of fielded, numerical data. It
3700-535: Is the code for methionine . Because DNA contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon. Genes encoded in DNA are first transcribed into pre- messenger RNA (mRNA) by proteins such as RNA polymerase . Most organisms then process the pre-mRNA (also known as a primary transcript ) using various forms of post-transcriptional modification to form
3800-631: Is the process of deriving high-quality information from text . It involves "the discovery by computer of new, previously unknown information, by automatically extracting information from different written resources." Written resources may include websites , books , emails , reviews , and articles. High-quality information is typically obtained by devising patterns and trends by means such as statistical pattern learning . According to Hotho et al. (2005), there are three perspectives of text mining: information extraction , data mining , and knowledge discovery in databases (KDD). Text mining usually involves
3900-631: Is very similar to TMEM131, but it does not include the second two of the three DUF3651 regions. Protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues . Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions , DNA replication , responding to stimuli , providing structure to cells and organisms , and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which
4000-509: Is viewed as being legal. As text mining is transformative, meaning that it does not supplant the original work, it is viewed as being lawful under fair use. For example, as part of the Google Book settlement the presiding judge on the case ruled that Google's digitization project of in-copyright books was lawful, in part because of the transformative uses that the digitization project displayed—one such use being text and data mining. There
4100-617: The Gensim library, which focuses on word embedding-based text representations. Text mining is being used by large media companies, such as the Tribune Company , to clarify information and to provide readers with greater search experiences, which in turn increases site "stickiness" and revenue. Additionally, on the back end, editors are benefiting by being able to share, associate and package news across properties, significantly increasing opportunities to monetize content. Text analytics
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4200-492: The amino acid leucine for which he found a (nearly correct) molecular weight of 131 Da . Early nutritional scientists such as the German Carl von Voit believed that protein was the most important nutrient for maintaining the structure of the body, because it was generally believed that "flesh makes flesh." Around 1862, Karl Heinrich Ritthausen isolated the amino acid glutamic acid . Thomas Burr Osborne compiled
4300-574: The lymph nodes , uterus and T cells. Expression data in developing fruit fly embryos is available from the BDGP in situ homepage. The primary function of the TMEM131 protein is not well understood. The human form has 1883 amino acid residues, with an isoelectric point of 8.74 and a molecular mass of 205,100 daltons . It has been shown to contain two transmembrane domains at residues 1,091-1,111 and 1,118-1,138. Three DUF3651 regions are located on
4400-644: The muscle sarcomere , with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids. Short proteins can also be synthesized chemically by a family of methods known as peptide synthesis , which rely on organic synthesis techniques such as chemical ligation to produce peptides in high yield. Chemical synthesis allows for the introduction of non-natural amino acids into polypeptide chains, such as attachment of fluorescent probes to amino acid side chains. These methods are useful in laboratory biochemistry and cell biology , though generally not for commercial applications. Chemical synthesis
4500-645: The sperm of many multicellular organisms which reproduce sexually . They also generate the forces exerted by contracting muscles and play essential roles in intracellular transport. A key question in molecular biology is how proteins evolve, i.e. how can mutations (or rather changes in amino acid sequence) lead to new structures and functions? Most amino acids in a protein can be changed without disrupting activity or function, as can be seen from numerous homologous proteins across species (as collected in specialized databases for protein families , e.g. PFAM ). In order to prevent dramatic consequences of mutations,
4600-497: The 1700s by Antoine Fourcroy and others, who often collectively called them " albumins ", or "albuminous materials" ( Eiweisskörper , in German). Gluten , for example, was first separated from wheat in published research around 1747, and later determined to exist in many plants. In 1789, Antoine Fourcroy recognized three distinct varieties of animal proteins: albumin , fibrin , and gelatin . Vegetable (plant) proteins studied in
4700-572: The 1950s, the Armour Hot Dog Company purified 1 kg of pure bovine pancreatic ribonuclease A and made it freely available to scientists; this gesture helped ribonuclease A become a major target for biochemical study for the following decades. The understanding of proteins as polypeptides , or chains of amino acids, came through the work of Franz Hofmeister and Hermann Emil Fischer in 1902. The central role of proteins as enzymes in living organisms that catalyzed reactions
4800-498: The 20,000 or so proteins encoded by the human genome, only 6,000 are detected in lymphoblastoid cells. Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid, for example AUG ( adenine – uracil – guanine )
4900-519: The EC number system provides a functional classification scheme. Similarly, the gene ontology classifies both genes and proteins by their biological and biochemical function, but also by their intracellular location. Sequence similarity is used to classify proteins both in terms of evolutionary and functional similarity. This may use either whole proteins or protein domains , especially in multi-domain proteins . Protein domains allow protein classification by
5000-601: The N-terminal side of the two adjacent transmembrane domains. These are located at residues 173-245, 502-582, and 639-708. The intercellular location of the protein has not been experimentally determined, but it is thought to reside in either the plasma membrane or endoplasmic reticulum , with each domain on both the N-terminal and C-terminal sides of the transmembrane regions being cytosolic. It contains numerous phosphorylation sites which have been shown both experimentally and with bioinformatic tools. Bioinformatic analysis of
5100-709: The ability of many enzymes to bind and process multiple substrates . When mutations occur, the specificity of an enzyme can increase (or decrease) and thus its enzymatic activity. Thus, bacteria (or other organisms) can adapt to different food sources, including unnatural substrates such as plastic. Methods commonly used to study protein structure and function include immunohistochemistry , site-directed mutagenesis , X-ray crystallography , nuclear magnetic resonance and mass spectrometry . The activities and structures of proteins may be examined in vitro , in vivo , and in silico . In vitro studies of purified proteins in controlled environments are useful for learning how
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#17327823410425200-405: The addition of a single methyl group to a binding partner can sometimes suffice to nearly eliminate binding; for example, the aminoacyl tRNA synthetase specific to the amino acid valine discriminates against the very similar side chain of the amino acid isoleucine . Proteins can bind to other proteins as well as to small-molecule substrates. When proteins bind specifically to other copies of
5300-607: The alpha carbons are roughly coplanar . The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone. The end with a free amino group is known as the N-terminus or amino terminus, whereas the end of the protein with a free carboxyl group is known as the C-terminus or carboxy terminus (the sequence of the protein is written from N-terminus to C-terminus, from left to right). The words protein , polypeptide, and peptide are
5400-531: The amino acid side chains in a protein that ultimately determines its three-dimensional structure and its chemical reactivity. The amino acids in a polypeptide chain are linked by peptide bonds . Once linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone. The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that
5500-404: The application of natural language processing (NLP), different types of algorithms and analytical methods. An important phase of this process is the interpretation of the gathered information. A typical application is to scan a set of documents written in a natural language and either model the document set for predictive classification purposes or populate a database or search index with
5600-574: The binding of a substrate molecule to an enzyme's active site , or the physical region of the protein that participates in chemical catalysis. In solution, proteins also undergo variation in structure through thermal vibration and the collision with other molecules. Proteins can be informally divided into three main classes, which correlate with typical tertiary structures: globular proteins , fibrous proteins , and membrane proteins . Almost all globular proteins are soluble and many are enzymes. Fibrous proteins are often structural, such as collagen ,
5700-570: The body of a multicellular organism. These proteins must have a high binding affinity when their ligand is present in high concentrations, but must also release the ligand when it is present at low concentrations in the target tissues. The canonical example of a ligand-binding protein is haemoglobin , which transports oxygen from the lungs to other organs and tissues in all vertebrates and has close homologs in every biological kingdom . Lectins are sugar-binding proteins which are highly specific for their sugar moieties. Lectins typically play
5800-558: The cell is as enzymes , which catalyse chemical reactions. Enzymes are usually highly specific and accelerate only one or a few chemical reactions. Enzymes carry out most of the reactions involved in metabolism , as well as manipulating DNA in processes such as DNA replication , DNA repair , and transcription . Some enzymes act on other proteins to add or remove chemical groups in a process known as posttranslational modification. About 4,000 reactions are known to be catalysed by enzymes. The rate acceleration conferred by enzymatic catalysis
5900-436: The cell surface and an effector domain within the cell, which may have enzymatic activity or may undergo a conformational change detected by other proteins within the cell. Antibodies are protein components of an adaptive immune system whose main function is to bind antigens , or foreign substances in the body, and target them for destruction. Antibodies can be secreted into the extracellular environment or anchored in
6000-752: The cell's machinery through the process of protein turnover . A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids , proteins are essential parts of organisms and participate in virtually every process within cells . Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism . Proteins also have structural or mechanical functions, such as actin and myosin in muscle and
6100-450: The cell. Many ion channel proteins are specialized to select for only a particular ion; for example, potassium and sodium channels often discriminate for only one of the two ions. Structural proteins confer stiffness and rigidity to otherwise-fluid biological components. Most structural proteins are fibrous proteins ; for example, collagen and elastin are critical components of connective tissue such as cartilage , and keratin
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#17327823410426200-621: The chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states. Biochemists often refer to four distinct aspects of a protein's structure: Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures while they perform their functions. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as " conformations ", and transitions between them are called conformational changes. Such changes are often induced by
6300-441: The chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes. With the exception of certain types of RNA , most other biological molecules are relatively inert elements upon which proteins act. Proteins make up half the dry weight of an Escherichia coli cell, whereas other macromolecules such as DNA and RNA make up only 3% and 20%, respectively. The set of proteins expressed in
6400-490: The construction of enormously complex signaling networks. As interactions between proteins are reversible, and depend heavily on the availability of different groups of partner proteins to form aggregates that are capable to carry out discrete sets of function, study of the interactions between specific proteins is a key to understand important aspects of cellular function, and ultimately the properties that distinguish particular cell types. The best-known role of proteins in
6500-408: The derivative unit kilodalton (kDa). The average size of a protein increases from Archaea to Bacteria to Eukaryote (283, 311, 438 residues and 31, 34, 49 kDa respectively) due to a bigger number of protein domains constituting proteins in higher organisms. For instance, yeast proteins are on average 466 amino acids long and 53 kDa in mass. The largest known proteins are the titins , a component of
6600-473: The development and differentiation of T cells, and has been shown to have relatively high levels of expression in T cells relative to other tissue types. TMEM131 is located on the negative DNA strand (see Sense ) of chromosome 2 from 98,372,799 - 98,612,354. The gene product is a 6,657 base pair mRNA with 41 predicted exons in the human gene. Ensembl predicts ten alternative splice forms, four of which are protein coding. Promoter prediction and analysis
6700-451: The erroneous conclusion that they might be composed of a single type of (very large) molecule. The term "protein" to describe these molecules was proposed by Mulder's associate Berzelius; protein is derived from the Greek word πρώτειος ( proteios ), meaning "primary", "in the lead", or "standing in front", + -in . Mulder went on to identify the products of protein degradation such as
6800-468: The information extracted. The document is the basic element when starting with text mining. Here, we define a document as a unit of textual data, which normally exists in many types of collections. Text analytics describes a set of linguistic , statistical , and machine learning techniques that model and structure the information content of textual sources for business intelligence , exploratory data analysis , research , or investigation. The term
6900-406: The key actors, the key communities or parties, and general properties such as robustness or structural stability of the overall network, or centrality of certain nodes. This automates the approach introduced by quantitative narrative analysis, whereby subject-verb-object triplets are identified with pairs of actors linked by an action, or pairs formed by actor-object. Content analysis has been
7000-534: The late 1700s and early 1800s included gluten , plant albumin , gliadin , and legumin . Proteins were first described by the Dutch chemist Gerardus Johannes Mulder and named by the Swedish chemist Jöns Jacob Berzelius in 1838. Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula , C 400 H 620 N 100 O 120 P 1 S 1 . He came to
7100-478: The major component of connective tissue, or keratin , the protein component of hair and nails. Membrane proteins often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane . A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydration , are called dehydrons . Many proteins are composed of several protein domains , i.e. segments of
7200-443: The mature mRNA, which is then used as a template for protein synthesis by the ribosome . In prokaryotes the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the nucleoid . In contrast, eukaryotes make mRNA in the cell nucleus and then translocate it across the nuclear membrane into the cytoplasm , where protein synthesis then takes place. The rate of protein synthesis
7300-405: The membranes of specialized B cells known as plasma cells . Whereas enzymes are limited in their binding affinity for their substrates by the necessity of conducting their reaction, antibodies have no such constraints. An antibody's binding affinity to its target is extraordinarily high. Many ligand transport proteins bind particular small biomolecules and transport them to other locations in
7400-523: The mining of in-copyright works (such as by web mining ) without the permission of the copyright owner is illegal. In the UK in 2014, on the recommendation of the Hargreaves review , the government amended copyright law to allow text mining as a limitation and exception . It was the second country in the world to do so, following Japan , which introduced a mining-specific exception in 2009. However, owing to
7500-496: The nobel prize in 1972, solidified the thermodynamic hypothesis of protein folding, according to which the folded form of a protein represents its free energy minimum. With the development of X-ray crystallography , it became possible to determine protein structures as well as their sequences. The first protein structures to be solved were hemoglobin by Max Perutz and myoglobin by John Kendrew , in 1958. The use of computers and increasing computing power also supported
7600-500: The order of 50,000 to 1 million. By contrast, eukaryotic cells are larger and thus contain much more protein. For instance, yeast cells have been estimated to contain about 50 million proteins and human cells on the order of 1 to 3 billion. The concentration of individual protein copies ranges from a few molecules per cell up to 20 million. Not all genes coding proteins are expressed in most cells and their number depends on, for example, cell type and external stimuli. For instance, of
7700-440: The physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors . Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes . Once formed, proteins only exist for a certain period and are then degraded and recycled by
7800-530: The possibility for scholars to analyze millions of documents in multiple languages with very limited manual intervention. Key enabling technologies have been parsing, machine translation , topic categorization , and machine learning. The automatic parsing of textual corpora has enabled the extraction of actors and their relational networks on a vast scale, turning textual data into network data. The resulting networks, which can contain thousands of nodes, are then analyzed by using tools from network theory to identify
7900-585: The problem of unstructured data ), to determine ideas communicated through text (e.g., sentiment analysis in social media ) and to support scientific discovery in fields such as the life sciences and bioinformatics . In business, applications are used to support competitive intelligence and automated ad placement , among numerous other activities. Many text mining software packages are marketed for security applications , especially monitoring and analysis of online plain text sources such as Internet news , blogs , etc. for national security purposes. It
8000-424: The process of cell signaling and signal transduction . Some proteins, such as insulin , are extracellular proteins that transmit a signal from the cell in which they were synthesized to other cells in distant tissues . Others are membrane proteins that act as receptors whose main function is to bind a signaling molecule and induce a biochemical response in the cell. Many receptors have a binding site exposed on
8100-1047: The process of structuring the input text (usually parsing , along with the addition of some derived linguistic features and the removal of others, and subsequent insertion into a database ), deriving patterns within the structured data , and finally evaluation and interpretation of the output. 'High quality' in text mining usually refers to some combination of relevance , novelty , and interest. Typical text mining tasks include text categorization , text clustering , concept/entity extraction, production of granular taxonomies, sentiment analysis , document summarization , and entity relation modeling ( i.e. , learning relations between named entities ). Text analysis involves information retrieval , lexical analysis to study word frequency distributions, pattern recognition , tagging / annotation , information extraction , data mining techniques including link and association analysis, visualization , and predictive analytics . The overarching goal is, essentially, to turn text into data for analysis, via
8200-534: The protein or proteins of interest based on properties such as molecular weight, net charge and binding affinity. The level of purification can be monitored using various types of gel electrophoresis if the desired protein's molecular weight and isoelectric point are known, by spectroscopy if the protein has distinguishable spectroscopic features, or by enzyme assays if the protein has enzymatic activity. Additionally, proteins can be isolated according to their charge using electrofocusing . For natural proteins,
8300-566: The protein using the NetPhos tool predicted 145 potential phosphorylation sites throughout the entire length of the protein. Protein interaction analysis for TMEM131 has been carried out using computational tools. No interactions were identified through the MINT database. A STRING search revealed ten possible protein interactions through text mining , although none of these should be considered actual protein-protein interactions. Closer analysis of
8400-427: The proteins in the cytoskeleton , which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses , cell adhesion , and the cell cycle . In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized . Digestion breaks the proteins down for metabolic use. Proteins have been studied and recognized since
8500-485: The restriction of the Information Society Directive (2001), the UK exception only allows content mining for non-commercial purposes. UK copyright law does not allow this provision to be overridden by contractual terms and conditions. The European Commission facilitated stakeholder discussion on text and data mining in 2013, under the title of Licenses for Europe. The fact that the focus on
8600-410: The results shows very little potential for these predictions to be real. The IntAct tool was also used, and this revealed a potential interaction had been found with Superoxide dismutase 2 ( SOD2 ), which had been identified in a yeast Two-hybrid screening study. TMEM131 is conserved throughout all of its orthologs . The entire protein is highly conserved in primate orthologs, while conservation
8700-582: The same molecule, they can oligomerize to form fibrils; this process occurs often in structural proteins that consist of globular monomers that self-associate to form rigid fibers. Protein–protein interactions also regulate enzymatic activity, control progression through the cell cycle , and allow the assembly of large protein complexes that carry out many closely related reactions with a common biological function. Proteins can also bind to, or even be integrated into, cell membranes. The ability of binding partners to induce conformational changes in proteins allows
8800-581: The sample, allowing scientists to obtain more information and analyze larger structures. Computational protein structure prediction of small protein structural domains has also helped researchers to approach atomic-level resolution of protein structures. As of April 2024 , the Protein Data Bank contains 181,018 X-ray, 19,809 EM and 12,697 NMR protein structures. Proteins are primarily classified by sequence and structure, although other classifications are commonly used. Especially for enzymes
8900-430: The sequencing of complex proteins. In 1999, Roger Kornberg succeeded in sequencing the highly complex structure of RNA polymerase using high intensity X-rays from synchrotrons . Since then, cryo-electron microscopy (cryo-EM) of large macromolecular assemblies has been developed. Cryo-EM uses protein samples that are frozen rather than crystals, and beams of electrons rather than X-rays. It causes less damage to
9000-540: The solution to this legal issue was licenses, and not limitations and exceptions to copyright law, led representatives of universities, researchers, libraries, civil society groups and open access publishers to leave the stakeholder dialogue in May 2013. US copyright law , and in particular its fair use provisions, means that text mining in America, as well as other fair use countries such as Israel, Taiwan and South Korea,
9100-423: The stratification and indexing of specific clinical events in large patient textual datasets of symptoms, side effects, and comorbidities from electronic health records, event reports, and reports from specific diagnostic tests. One online text mining application in the biomedical literature is PubGene , a publicly accessible search engine that combines biomedical text mining with network visualization. GoPubMed
9200-405: The substrate, and an even smaller fraction—three to four residues on average—that are directly involved in catalysis. The region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site . Dirigent proteins are members of a class of proteins that dictate the stereochemistry of a compound synthesized by other enzymes. Many proteins are involved in
9300-716: The surrounding amino acids may determine the exact binding specificity). Many such motifs has been collected in the Eukaryotic Linear Motif (ELM) database. Topology of a protein describes the entanglement of the backbone and the arrangement of contacts within the folded chain. Two theoretical frameworks of knot theory and Circuit topology have been applied to characterise protein topology. Being able to describe protein topology opens up new pathways for protein engineering and pharmaceutical development, and adds to our understanding of protein misfolding diseases such as neuromuscular disorders and cancer. Proteins are
9400-400: The tRNA molecules with the correct amino acids. The growing polypeptide is often termed the nascent chain . Proteins are always biosynthesized from N-terminus to C-terminus . The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass , which is normally reported in units of daltons (synonymous with atomic mass units ), or
9500-472: The tertiary structure of the protein, which defines the binding site pocket, and by the chemical properties of the surrounding amino acids' side chains. Protein binding can be extraordinarily tight and specific; for example, the ribonuclease inhibitor protein binds to human angiogenin with a sub-femtomolar dissociation constant (<10 M) but does not bind at all to its amphibian homolog onconase (> 1 M). Extremely minor chemical changes such as
9600-440: The text without removing publisher barriers to public access. Academic institutions have also become involved in the text mining initiative: Computational methods have been developed to assist with information retrieval from scientific literature. Published approaches include methods for searching, determining novelty, and clarifying homonyms among technical reports. The automatic analysis of vast textual corpora has created
9700-472: Was insulin , by Frederick Sanger , in 1949. Sanger correctly determined the amino acid sequence of insulin, thus conclusively demonstrating that proteins consisted of linear polymers of amino acids rather than branched chains, colloids , or cyclols . He won the Nobel Prize for this achievement in 1958. Christian Anfinsen 's studies of the oxidative folding process of ribonuclease A, for which he won
9800-466: Was carried out using El Dorado through the Genomatix software page. The predicted promoter region spans 1002 base pairs from 98,611,892 through 98,612,893 on the minus strand of chromosome 2. The program predicted two potential transcriptional start locations. The first spans 216 base pairs from 98,612,501 through 98,612,716. The second spans 182 base pairs from 98,612,262 through 98,612,443. TMEM131
9900-455: Was demonstrated in Flaounas et al. showing how different topics have different gender biases and levels of readability; the possibility to detect mood patterns in a vast population by analyzing Twitter content was demonstrated as well. Text mining computer programs are available from many commercial and open source companies and sources. Under European copyright and database laws ,
10000-581: Was not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was in fact a protein. Linus Pauling is credited with the successful prediction of regular protein secondary structures based on hydrogen bonding , an idea first put forth by William Astbury in 1933. Later work by Walter Kauzmann on denaturation , based partly on previous studies by Kaj Linderstrøm-Lang , contributed an understanding of protein folding and structure mediated by hydrophobic interactions . The first protein to have its amino acid chain sequenced
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