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89-473: RNA-dependent RNA polymerase ( RdRp ) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to typical DNA-dependent RNA polymerases , which all organisms use to catalyze the transcription of RNA from a DNA template. RdRp is an essential protein encoded in

178-514: A Markov random field approach has been proposed to infer DNA motifs from DNA-binding domains of proteins. Motif Discovery Algorithms Motif discovery algorithms use diverse strategies to uncover patterns in DNA sequences. Integrating enumerative, probabilistic, and nature-inspired approaches, demonstrate their adaptability, with the use of multiple methods proving effective in enhancing identification accuracy. Enumerative Approach: Initiating

267-487: A catalytic triad , stabilize charge build-up on the transition states using an oxyanion hole , complete hydrolysis using an oriented water substrate. Enzymes are not rigid, static structures; instead they have complex internal dynamic motions – that is, movements of parts of the enzyme's structure such as individual amino acid residues, groups of residues forming a protein loop or unit of secondary structure , or even an entire protein domain . These motions give rise to

356-489: A conformational ensemble of slightly different structures that interconvert with one another at equilibrium . Different states within this ensemble may be associated with different aspects of an enzyme's function. For example, different conformations of the enzyme dihydrofolate reductase are associated with the substrate binding, catalysis, cofactor release, and product release steps of the catalytic cycle, consistent with catalytic resonance theory . Substrate presentation

445-456: A 2013 benchmark. The planted motif search is another motif discovery method that is based on combinatorial approach. Motifs have also been discovered by taking a phylogenetic approach and studying similar genes in different species. For example, by aligning the amino acid sequences specified by the GCM ( glial cells missing ) gene in man, mouse and D. melanogaster , Akiyama and others discovered

534-451: A distinctive secondary structure . " Noncoding " sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix ). Outside of gene exons, there exist regulatory sequence motifs and motifs within the " junk ", such as satellite DNA . Some of these are believed to affect the shape of nucleic acids (see for example RNA self-splicing ), but this

623-477: A first step and then checks that the product is correct in a second step. This two-step process results in average error rates of less than 1 error in 100 million reactions in high-fidelity mammalian polymerases. Similar proofreading mechanisms are also found in RNA polymerase , aminoacyl tRNA synthetases and ribosomes . Conversely, some enzymes display enzyme promiscuity , having broad specificity and acting on

712-473: A fixed-length motif. There are two types of weight matrices. An example of a PFM from the TRANSFAC database for the transcription factor AP-1: The first column specifies the position, the second column contains the number of occurrences of A at that position, the third column contains the number of occurrences of C at that position, the fourth column contains the number of occurrences of G at that position,

801-399: A fold whose organization has been linked to the shape of a right hand with three subdomains termed fingers, palm, and thumb. Only the palm subdomain, composed of a four-stranded antiparallel beta sheet with two alpha helices , is well conserved. In RdRp, the palm subdomain comprises three well-conserved motifs (A, B, and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed;

890-467: A meaning to a sequence of elements of the pattern notation: Thus the pattern [AB] [CDE] F matches the six amino acid sequences corresponding to ACF , ADF , AEF , BCF , BDF , and BEF . Different pattern description notations have other ways of forming pattern elements. One of these notations is the PROSITE notation, described in the following subsection. The PROSITE notation uses

979-493: A pattern which they called the GCM motif in 1996. It spans about 150 amino acid residues, and begins as follows: Here each . signifies a single amino acid or a gap, and each * indicates one member of a closely related family of amino acids. The authors were able to show that the motif has DNA binding activity. A similar approach is commonly used by modern protein domain databases such as Pfam : human curators would select

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1068-428: A pool of sequences known to be related and use computer programs to align them and produce the motif profile (Pfam uses HMMs , which can be used to identify other related proteins. A phylogenic approach can also be used to enhance the de novo MEME algorithm, with PhyloGibbs being an example. In 2017, MotifHyades has been developed as a motif discovery tool that can be directly applied to paired sequences. In 2018,

1157-444: A primer-dependent mechanism that utilizes a viral protein genome-linked (VPg) primer. The de novo initiation consists in the addition of a NTP to the 3'-OH of the first initiating NTP. During the following elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product. Termination of the nascent RNA chain produced by RdRp is not completely known, however, RdRp termination

1246-464: A quantitative theory of enzyme kinetics, which is referred to as Michaelis–Menten kinetics . The major contribution of Michaelis and Menten was to think of enzyme reactions in two stages. In the first, the substrate binds reversibly to the enzyme, forming the enzyme-substrate complex. This is sometimes called the Michaelis–Menten complex in their honor. The enzyme then catalyzes the chemical step in

1335-439: A range of different physiologically relevant substrates. Many enzymes possess small side activities which arose fortuitously (i.e. neutrally ), which may be the starting point for the evolutionary selection of a new function. To explain the observed specificity of enzymes, in 1894 Emil Fischer proposed that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another. This

1424-550: A sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence analysis , such as BLAST . Such techniques belong to the discipline of bioinformatics . See also consensus sequence . Consider the N -glycosylation site motif mentioned above: This pattern may be written as N{P}[ST]{P} where N = Asn, P = Pro, S = Ser, T = Thr; {X} means any amino acid except X ; and [XY] means either X or Y . The notation [XY] does not give any indication of

1513-451: A single motif: the defining pattern, and various typical patterns. For example, the defining sequence for the IQ motif may be taken to be: where x signifies any amino acid, and the square brackets indicate an alternative (see below for further details about notation). Usually, however, the first letter is I , and both [RK] choices resolve to R . Since the last choice is so wide,

1602-451: A species' normal level; as a result, enzymes from bacteria living in volcanic environments such as hot springs are prized by industrial users for their ability to function at high temperatures, allowing enzyme-catalysed reactions to be operated at a very high rate. Enzymes are usually much larger than their substrates. Sizes range from just 62 amino acid residues, for the monomer of 4-oxalocrotonate tautomerase , to over 2,500 residues in

1691-449: A steady level inside the cell. For example, NADPH is regenerated through the pentose phosphate pathway and S -adenosylmethionine by methionine adenosyltransferase . This continuous regeneration means that small amounts of coenzymes can be used very intensively. For example, the human body turns over its own weight in ATP each day. As with all catalysts, enzymes do not alter the position of

1780-442: A thermodynamically unfavourable one so that the combined energy of the products is lower than the substrates. For example, the hydrolysis of ATP is often used to drive other chemical reactions. Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products. The rate data used in kinetic analyses are commonly obtained from enzyme assays . In 1913 Leonor Michaelis and Maud Leonora Menten proposed

1869-457: Is k cat , also called the turnover number , which is the number of substrate molecules handled by one active site per second. The efficiency of an enzyme can be expressed in terms of k cat / K m . This is also called the specificity constant and incorporates the rate constants for all steps in the reaction up to and including the first irreversible step. Because the specificity constant reflects both affinity and catalytic ability, it

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1958-838: Is orotidine 5'-phosphate decarboxylase , which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that decrease enzyme activity, and activators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH , and many enzymes are (permanently) denatured when exposed to excessive heat, losing their structure and catalytic properties. Some enzymes are used commercially, for example, in

2047-421: Is a process where the enzyme is sequestered away from its substrate. Enzymes can be sequestered to the plasma membrane away from a substrate in the nucleus or cytosol. Or within the membrane, an enzyme can be sequestered into lipid rafts away from its substrate in the disordered region. When the enzyme is released it mixes with its substrate. Alternatively, the enzyme can be sequestered near its substrate to activate

2136-635: Is a useful marker for understanding their evolution. When replicating its (+)ssRNA genome , the poliovirus RdRp is able to carry out recombination . Recombination appears to occur by a copy choice mechanism in which the RdRp switches (+)ssRNA templates during negative strand synthesis. Recombination frequency is determined in part by the fidelity of RdRp replication. RdRp variants with high replication fidelity show reduced recombination, and low fidelity RdRps exhibit increased recombination. Recombination by RdRp strand switching occurs frequently during replication in

2225-672: Is an example of such a c RdRp enzyme. Bacteriophage homologs of c RdRp, including the similarly single-chain DdRp yonO ( O31945 ), appear to be closer to c RdRps than DdRPs are. Four superfamilies of viruses cover all RNA-containing viruses with no DNA stage: Flaviviruses produce a polyprotein from the ssRNA genome. The polyprotein is cleaved to a number of products, one of which is NS5, an RdRp. It possesses short regions and motifs homologous to other RdRps. RNA replicase found in positive-strand ssRNA viruses are related to each other, forming three large superfamilies. Birnaviral RNA replicase

2314-429: Is available. Many RdRps associate tightly with membranes making them difficult to study. The best-known RdRps are polioviral 3Dpol, vesicular stomatitis virus L, and hepatitis C virus NS5B protein. Many eukaryotes have RdRps that are involved in RNA interference : these amplify microRNAs and small temporal RNAs and produce double-stranded RNA using small interfering RNAs as primers. These RdRps are used in

2403-437: Is described by "EC" followed by a sequence of four numbers which represent the hierarchy of enzymatic activity (from very general to very specific). That is, the first number broadly classifies the enzyme based on its mechanism while the other digits add more and more specificity. The top-level classification is: These sections are subdivided by other features such as the substrate, products, and chemical mechanism . An enzyme

2492-471: Is formed by several motifs containing conserved amino acid residues. Eukaryotic RNA interference requires a cellular RdRp (c RdRp). Unlike the "hand" polymerases, they resemble simplified multi-subunit DdRPs, specifically in the catalytic β/β' subunits, in that they use two sets of double-psi β-barrels in the active site. QDE1 ( Q9Y7G6 ) in Neurospora crassa , which has both barrels in the same chain,

2581-749: Is fully specified by four numerical designations. For example, hexokinase (EC 2.7.1.1) is a transferase (EC 2) that adds a phosphate group (EC 2.7) to a hexose sugar, a molecule containing an alcohol group (EC 2.7.1). Sequence similarity . EC categories do not reflect sequence similarity. For instance, two ligases of the same EC number that catalyze exactly the same reaction can have completely different sequences. Independent of their function, enzymes, like any other proteins, have been classified by their sequence similarity into numerous families. These families have been documented in dozens of different protein and protein family databases such as Pfam . Non-homologous isofunctional enzymes . Unrelated enzymes that have

2670-476: Is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase . Examples are lactase , alcohol dehydrogenase and DNA polymerase . Different enzymes that catalyze the same chemical reaction are called isozymes . The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers (for "Enzyme Commission") . Each enzyme

2759-418: Is often referred to as "the lock and key" model. This early model explains enzyme specificity, but fails to explain the stabilization of the transition state that enzymes achieve. In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continuously reshaped by interactions with the substrate as the substrate interacts with

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2848-462: Is only one of several important kinetic parameters. The amount of substrate needed to achieve a given rate of reaction is also important. This is given by the Michaelis–Menten constant ( K m ), which is the substrate concentration required for an enzyme to reach one-half its maximum reaction rate; generally, each enzyme has a characteristic K M for a given substrate. Another useful constant

2937-451: Is only sometimes the case. For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. They are able to recognize motifs through contact with the double helix's major or minor groove. Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular parts of a cell , or mark them for phosphorylation . Within

3026-404: Is seen. This is shown in the saturation curve on the right. Saturation happens because, as substrate concentration increases, more and more of the free enzyme is converted into the substrate-bound ES complex. At the maximum reaction rate ( V max ) of the enzyme, all the enzyme active sites are bound to substrate, and the amount of ES complex is the same as the total amount of enzyme. V max

3115-476: Is sequence-independent. One major drawback of RNA-dependent RNA polymerase replication is the transcription error rate. RdRps lack fidelity on the order of 10 nucleotides, which is thought to be a direct result of inadequate proofreading. This variation rate is favored in viral genomes as it allows for the pathogen to overcome host defenses trying to avoid infection, allowing for evolutionary growth. Viral/prokaryotic RdRp, along with many single-subunit DdRp, employ

3204-403: Is the ribosome which is a complex of protein and catalytic RNA components. Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are usually very specific as to what substrates they bind and then the chemical reaction catalysed. Specificity is achieved by binding pockets with complementary shape, charge and hydrophilic / hydrophobic characteristics to

3293-401: Is unique in that it lacks motif C (GDD) in the palm. Mononegaviral RdRp (PDB 5A22) has been automatically classified as similar to (+)−ssRNA RdRps, specifically one from Pestivirus and one from Leviviridae . Bunyaviral RdRp monomer (PDB 5AMQ) resembles the heterotrimeric complex of Orthomyxoviral (Influenza; PDB 4WSB) RdRp. Since it is a protein universal to RNA-containing viruses, RdRp

3382-790: Is useful for comparing different enzymes against each other, or the same enzyme with different substrates. The theoretical maximum for the specificity constant is called the diffusion limit and is about 10 to 10 (M s ). At this point every collision of the enzyme with its substrate will result in catalysis, and the rate of product formation is not limited by the reaction rate but by the diffusion rate. Enzymes with this property are called catalytically perfect or kinetically perfect . Example of such enzymes are triose-phosphate isomerase , carbonic anhydrase , acetylcholinesterase , catalase , fumarase , β-lactamase , and superoxide dismutase . The turnover of such enzymes can reach several million reactions per second. But most enzymes are far from perfect:

3471-614: The DNA polymerases ; here the holoenzyme is the complete complex containing all the subunits needed for activity. Coenzymes are small organic molecules that can be loosely or tightly bound to an enzyme. Coenzymes transport chemical groups from one enzyme to another. Examples include NADH , NADPH and adenosine triphosphate (ATP). Some coenzymes, such as flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), thiamine pyrophosphate (TPP), and tetrahydrofolate (THF), are derived from vitamins . These coenzymes cannot be synthesized by

3560-589: The IUPAC one-letter codes and conforms to the above description with the exception that a concatenation symbol, ' - ', is used between pattern elements, but it is often dropped between letters of the pattern alphabet. PROSITE allows the following pattern elements in addition to those described previously: Some examples: The signature of the C2H2-type zinc finger domain is: A matrix of numbers containing scores for each residue or nucleotide at each position of

3649-440: The aspartic acid residues of these motifs are implied in the binding of Mg and/or Mn. The asparagine residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and, thus, determines whether RNA rather than DNA is synthesized. The domain organization and the 3D structure of the catalytic centre of a wide range of RdRps, even those with a low overall sequence homology, are conserved. The catalytic center

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3738-511: The law of mass action , which is derived from the assumptions of free diffusion and thermodynamically driven random collision. Many biochemical or cellular processes deviate significantly from these conditions, because of macromolecular crowding and constrained molecular movement. More recent, complex extensions of the model attempt to correct for these effects. Enzyme reaction rates can be decreased by various types of enzyme inhibitors. A competitive inhibitor and substrate cannot bind to

3827-414: The (+)ssRNA plant carmoviruses and tombusviruses . Sendai virus (family Paramyxoviridae ) has a linear, single-stranded, negative-sense, nonsegmented RNA genome. The viral RdRp consists of two virus-encoded subunits, a smaller one P and a larger one L. Testing different inactive RdRp mutants with defects throughout the length of the L subunit in pairwise combinations, restoration of viral RNA synthesis

3916-400: The ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are catalytic RNA molecules , also called ribozymes . They are sometimes described as a type of enzyme rather than being like an enzyme, but even in

4005-412: The action of a virus-specific enzyme that could copy RNA from an RNA template. RdRps are highly conserved in viruses and are related to telomerase , though the reason for this was an ongoing question as of 2009. The similarity led to speculation that viral RdRps are ancestral to human telomerase. The most famous example of RdRp is in the polio virus . The viral genome is composed of RNA, which enters

4094-437: The active site and are involved in catalysis. For example, flavin and heme cofactors are often involved in redox reactions. Enzymes that require a cofactor but do not have one bound are called apoenzymes or apoproteins . An enzyme together with the cofactor(s) required for activity is called a holoenzyme (or haloenzyme). The term holoenzyme can also be applied to enzymes that contain multiple protein subunits, such as

4183-502: The active site. Organic cofactors can be either coenzymes , which are released from the enzyme's active site during the reaction, or prosthetic groups , which are tightly bound to an enzyme. Organic prosthetic groups can be covalently bound (e.g., biotin in enzymes such as pyruvate carboxylase ). An example of an enzyme that contains a cofactor is carbonic anhydrase , which uses a zinc cofactor bound as part of its active site. These tightly bound ions or molecules are usually found in

4272-464: The adaptability of these algorithms in the intricate domain of motif discovery. The E. coli lactose operon repressor LacI ( PDB : 1lcc ​ chain A) and E. coli catabolite gene activator ( PDB : 3gap ​ chain A) both have a helix-turn-helix motif, but their amino acid sequences do not show much similarity, as shown in the table below. In 1997, Matsuda, et al. devised a code they called

4361-407: The animal fatty acid synthase . Only a small portion of their structure (around 2–4 amino acids) is directly involved in catalysis: the catalytic site. This catalytic site is located next to one or more binding sites where residues orient the substrates. The catalytic site and binding site together compose the enzyme's active site . The remaining majority of the enzyme structure serves to maintain

4450-578: The average values of k c a t / K m {\displaystyle k_{\rm {cat}}/K_{\rm {m}}} and k c a t {\displaystyle k_{\rm {cat}}} are about 10 5 s − 1 M − 1 {\displaystyle 10^{5}{\rm {s}}^{-1}{\rm {M}}^{-1}} and 10 s − 1 {\displaystyle 10{\rm {s}}^{-1}} , respectively. Michaelis–Menten kinetics relies on

4539-502: The body de novo and closely related compounds (vitamins) must be acquired from the diet. The chemical groups carried include: Since coenzymes are chemically changed as a consequence of enzyme action, it is useful to consider coenzymes to be a special class of substrates, or second substrates, which are common to many different enzymes. For example, about 1000 enzymes are known to use the coenzyme NADH. Coenzymes are usually continuously regenerated and their concentrations maintained at

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4628-420: The cell through receptor-mediated endocytosis . From there, the RNA acts as a template for complementary RNA synthesis. The complementary strand acts as a template for the production of new viral genomes that are packaged and released from the cell ready to infect more host cells. The advantage of this method of replication is that no DNA stage complicates replication. The disadvantage is that no 'back-up' DNA copy

4717-471: The chemical equilibrium of the reaction. In the presence of an enzyme, the reaction runs in the same direction as it would without the enzyme, just more quickly. For example, carbonic anhydrase catalyzes its reaction in either direction depending on the concentration of its reactants: The rate of a reaction is dependent on the activation energy needed to form the transition state which then decays into products. Enzymes increase reaction rates by lowering

4806-425: The conversion of starch to sugars by plant extracts and saliva were known but the mechanisms by which these occurred had not been identified. French chemist Anselme Payen was the first to discover an enzyme, diastase , in 1833. A few decades later, when studying the fermentation of sugar to alcohol by yeast , Louis Pasteur concluded that this fermentation was caused by a vital force contained within

4895-444: The decades since ribozymes' discovery in 1980–1982, the word enzyme alone often means the protein type specifically (as is used in this article). An enzyme's specificity comes from its unique three-dimensional structure . Like all catalysts, enzymes increase the reaction rate by lowering its activation energy . Some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example

4984-400: The defense mechanisms and can be appropriated by RNA viruses. Their evolutionary history predates the divergence of major eukaryotic groups. RdRp differs from DNA dependent RNA polymerase as it catalyzes RNA synthesis of strands complementary to a given RNA template. The RNA replication process is a four-step mechanism: RNA synthesis can be performed by a primer -independent ( de novo ) or

5073-415: The desired motif in large quantities, and extraction of unwanted sequences using clustering. Cleaning then ensures the removal of any confounding elements. Next there is the discovery stage. In this phase sequences are represented using consensus strings or Position-specific Weight Matrices (PWM) . After motif representation, an objective function is chosen and a suitable search algorithm is applied to uncover

5162-433: The energy of the transition state. First, binding forms a low energy enzyme-substrate complex (ES). Second, the enzyme stabilises the transition state such that it requires less energy to achieve compared to the uncatalyzed reaction (ES ). Finally the enzyme-product complex (EP) dissociates to release the products. Enzymes can couple two or more reactions, so that a thermodynamically favorable reaction can be used to "drive"

5251-592: The enzyme urease was a pure protein and crystallized it; he did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley , who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin . These three scientists were awarded the 1946 Nobel Prize in Chemistry. The discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography . This

5340-483: The enzyme at the same time. Often competitive inhibitors strongly resemble the real substrate of the enzyme. For example, the drug methotrexate is a competitive inhibitor of the enzyme dihydrofolate reductase , which catalyzes the reduction of dihydrofolate to tetrahydrofolate. The similarity between the structures of dihydrofolate and this drug are shown in the accompanying figure. This type of inhibition can be overcome with high substrate concentration. In some cases,

5429-422: The enzyme converts the substrates into different molecules known as products . Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and the field of pseudoenzyme analysis recognizes that during evolution, some enzymes have lost

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5518-403: The enzyme. As a result, the substrate does not simply bind to a rigid active site; the amino acid side-chains that make up the active site are molded into the precise positions that enable the enzyme to perform its catalytic function. In some cases, such as glycosidases , the substrate molecule also changes shape slightly as it enters the active site. The active site continues to change until

5607-427: The enzyme. For example, the enzyme can be soluble and upon activation bind to a lipid in the plasma membrane and then act upon molecules in the plasma membrane. Allosteric sites are pockets on the enzyme, distinct from the active site, that bind to molecules in the cellular environment. These molecules then cause a change in the conformation or dynamics of the enzyme that is transduced to the active site and thus affects

5696-480: The existing motif discovery research focuses on DNA motifs. With the advances in high-throughput sequencing, such motif discovery problems are challenged by both the sequence pattern degeneracy issues and the data-intensive computational scalability issues. Process of discovery Motif discovery happens in three major phases. A pre-processing stage where sequences are meticulously prepared in assembly and cleaning steps. Assembly involves selecting sequences that contain

5785-500: The fifth column contains the number of occurrences of T at that position, and the last column contains the IUPAC notation for that position. Note that the sums of occurrences for A, C, G, and T for each row should be equal because the PFM is derived from aggregating several consensus sequences. The sequence motif discovery process has been well-developed since the 1990s. In particular, most of

5874-532: The genomes of most RNA-containing viruses that lack a DNA stage, including SARS-CoV-2 . Some eukaryotes also contain RdRps, which are involved in RNA interference and differ structurally from viral RdRps. Viral RdRps were discovered in the early 1960s from studies on mengovirus and polio virus when it was observed that these viruses were not sensitive to actinomycin D , a drug that inhibits cellular DNA-directed RNA synthesis. This lack of sensitivity suggested

5963-428: The inhibitor can bind to a site other than the binding-site of the usual substrate and exert an allosteric effect to change the shape of the usual binding-site. Sequence motif When a sequence motif appears in the exon of a gene , it may encode the " structural motif " of a protein ; that is a stereotypical element of the overall structure of the protein. Nevertheless, motifs need not be associated with

6052-474: The mixture. He named the enzyme that brought about the fermentation of sucrose " zymase ". In 1907, he received the Nobel Prize in Chemistry for "his discovery of cell-free fermentation". Following Buchner's example, enzymes are usually named according to the reaction they carry out: the suffix -ase is combined with the name of the substrate (e.g., lactase is the enzyme that cleaves lactose ) or to

6141-626: The motif discovery journey, the enumerative approach witnesses algorithms meticulously generating and evaluating potential motifs. Pioneering this domain are Simple Word Enumeration techniques, such as YMF and DREME, which systematically go through the sequence in search of short motifs. Complementing these, Clustering-Based Methods such as CisFinder employ nucleotide substitution matrices for motif clustering, effectively mitigating redundancy. Concurrently, Tree-Based Methods like Weeder and FMotif exploit tree structures, and Graph Theoretic-Based Methods (e.g., WINNOWER) employ graph representations, demonstrating

6230-531: The motifs. Finally the post-processing stage involves evaluating the discovered motifs. There are software programs which, given multiple input sequences, attempt to identify one or more candidate motifs. One example is the Multiple EM for Motif Elicitation (MEME) algorithm, which generates statistical information for each candidate. There are more than 100 publications detailing motif discovery algorithms; Weirauch et al . evaluated many related algorithms in

6319-455: The pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif . Several notations for describing motifs are in use but most of them are variants of standard notations for regular expressions and use these conventions: The fundamental idea behind all these notations is the matching principle, which assigns

6408-528: The precise orientation and dynamics of the active site. In some enzymes, no amino acids are directly involved in catalysis; instead, the enzyme contains sites to bind and orient catalytic cofactors . Enzyme structures may also contain allosteric sites where the binding of a small molecule causes a conformational change that increases or decreases activity. A small number of RNA -based biological catalysts called ribozymes exist, which again can act alone or in complex with proteins. The most common of these

6497-473: The predictions. This probabilistic framework adeptly captures the inherent uncertainty associated with motif discovery. Advanced Approach: Evolving further, advanced motif discovery embraces sophisticated techniques, with Bayesian modeling taking center stage. LOGOS and BaMM, exemplifying this cohort, intricately weave Bayesian approaches and Markov models into their fabric for motif identification. The incorporation of Bayesian clustering methods enhances

6586-847: The presence of dsRNA, and is less widely distributed than other RNAi components as it lost in some animals, though still found in C. elegans , P. tetraurelia , and plants . This presence of dsRNA triggers the activation of RdRp and RNAi processes by priming the initiation of RNA transcription through the introduction of siRNAs. In C. elegans , siRNAs are integrated into the RNA-induced silencing complex, RISC , which works alongside mRNAs targeted for interference to recruit more RdRps to synthesize more secondary siRNAs and repress gene expression. Enzyme Enzymes ( / ˈ ɛ n z aɪ m z / ) are proteins that act as biological catalysts by accelerating chemical reactions . The molecules upon which enzymes may act are called substrates , and

6675-866: The probabilistic foundation, providing a holistic framework for pattern recognition in DNA sequences. Nature-Inspired and Heuristic Algorithms: A distinct category unfolds, wherein algorithms draw inspiration from the biological realm. Genetic Algorithms (GA) , epitomized by FMGA and MDGA, navigate motif search through genetic operators and specialized strategies. Harnessing swarm intelligence principles, Particle Swarm Optimization (PSO) , Artificial Bee Colony (ABC) algorithms, and Cuckoo Search (CS) algorithms, featured in GAEM, GARP, and MACS, venture into pheromone-based exploration. These algorithms, mirroring nature's adaptability and cooperative dynamics, serve as avant-garde strategies for motif identification. The synthesis of heuristic techniques in hybrid approaches underscores

6764-418: The probability of X or Y occurring in the pattern. Observed probabilities can be graphically represented using sequence logos . Sometimes patterns are defined in terms of a probabilistic model such as a hidden Markov model . The notation [XYZ] means X or Y or Z , but does not indicate the likelihood of any particular match. For this reason, two or more patterns are often associated with

6853-406: The reaction and releases the product. This work was further developed by G. E. Briggs and J. B. S. Haldane , who derived kinetic equations that are still widely used today. Enzyme rates depend on solution conditions and substrate concentration . To find the maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation

6942-733: The reaction rate of the enzyme. In this way, allosteric interactions can either inhibit or activate enzymes. Allosteric interactions with metabolites upstream or downstream in an enzyme's metabolic pathway cause feedback regulation, altering the activity of the enzyme according to the flux through the rest of the pathway. Some enzymes do not need additional components to show full activity. Others require non-protein molecules called cofactors to be bound for activity. Cofactors can be either inorganic (e.g., metal ions and iron–sulfur clusters ) or organic compounds (e.g., flavin and heme ). These cofactors serve many purposes; for instance, metal ions can help in stabilizing nucleophilic species within

7031-516: The richness of enumeration strategies. Probabilistic Approach: Diverging into the probabilistic realm, this approach capitalizes on probability models to discern motifs within sequences. MEME, a deterministic exemplar, employs Expectation-Maximization for optimizing Position Weight Matrices (PWMs) and unraveling conserved regions in unaligned DNA sequences. Contrasting this, stochastic methodologies like Gibbs Sampling initiate motif discovery with random motif position assignments, iteratively refining

7120-410: The same enzymatic activity have been called non-homologous isofunctional enzymes . Horizontal gene transfer may spread these genes to unrelated species, especially bacteria where they can replace endogenous genes of the same function, leading to hon-homologous gene displacement. Enzymes are generally globular proteins , acting alone or in larger complexes . The sequence of the amino acids specifies

7209-412: The structure which in turn determines the catalytic activity of the enzyme. Although structure determines function, a novel enzymatic activity cannot yet be predicted from structure alone. Enzyme structures unfold ( denature ) when heated or exposed to chemical denaturants and this disruption to the structure typically causes a loss of activity. Enzyme denaturation is normally linked to temperatures above

7298-519: The substrate is completely bound, at which point the final shape and charge distribution is determined. Induced fit may enhance the fidelity of molecular recognition in the presence of competition and noise via the conformational proofreading mechanism. Enzymes can accelerate reactions in several ways, all of which lower the activation energy (ΔG , Gibbs free energy ) Enzymes may use several of these mechanisms simultaneously. For example, proteases such as trypsin perform covalent catalysis using

7387-405: The substrates. Enzymes can therefore distinguish between very similar substrate molecules to be chemoselective , regioselective and stereospecific . Some of the enzymes showing the highest specificity and accuracy are involved in the copying and expression of the genome . Some of these enzymes have " proof-reading " mechanisms. Here, an enzyme such as DNA polymerase catalyzes a reaction in

7476-399: The synthesis of antibiotics . Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, and enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew. By the late 17th and early 18th centuries, the digestion of meat by stomach secretions and

7565-438: The type of reaction (e.g., DNA polymerase forms DNA polymers). The biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others (such as Nobel laureate Richard Willstätter ) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926, James B. Sumner showed that

7654-486: The yeast cells called "ferments", which were thought to function only within living organisms. He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells." In 1877, German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme , which comes from Ancient Greek ἔνζυμον (énzymon)  ' leavened , in yeast', to describe this process. The word enzyme

7743-581: Was first done for lysozyme , an enzyme found in tears, saliva and egg whites that digests the coating of some bacteria; the structure was solved by a group led by David Chilton Phillips and published in 1965. This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail. Enzymes can be classified by two main criteria: either amino acid sequence similarity (and thus evolutionary relationship) or enzymatic activity. Enzyme activity . An enzyme's name

7832-427: Was observed in some combinations. This positive L–L interaction is referred to as intragenic complementation and indicates that the L protein is an oligomer in the viral RNA polymerase complex. The use of RdRp plays a major role in RNA interference in eukaryotes, a process used to silence gene expression via small interfering RNAs ( siRNAs ) binding to mRNA rendering them inactive. Eukaryotic RdRp becomes active in

7921-457: Was used later to refer to nonliving substances such as pepsin , and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897. In a series of experiments at the University of Berlin , he found that sugar was fermented by yeast extracts even when there were no living yeast cells in

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