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57-552: The Walker A and Walker B motifs are protein sequence motifs, known to have highly conserved three-dimensional structures . These were first reported in ATP -binding proteins by Walker and co-workers in 1982. Of the two motifs, the A motif is the main "P-loop" responsible for binding phosphate , while the B motif is a much less conserved downstream region. The P-loop is best known for its presence in ATP- and GTP-binding proteins, and

114-507: 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 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

171-671: A P-loop. The A-loop ( aromatic residue interacting with the adenine ring of ATP) refers to conserved aromatic amino acids , essential for ATP-binding, found in about 25 amino acids upstream of the Walker A motif in a subset of P-loop proteins. Walker B motif is a motif in most P-loop proteins situated well downstream of the A-motif. The consensus sequence of this motif was reported to be [RK]-x(3)-G-x(3)-LhhhD, where R, K, G, L and D denote arginine , lysine , glycine , leucine and aspartic acid residues respectively, x represents any of

228-473: 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, the fifth column contains the number of occurrences of T at that position, and

285-633: A bulk material, through either coatings or surface treatments. That is to say, the presence of molecular species (usually organic) or structural features results in high contact angles of water. In recent years, rare earth oxides have been shown to possess intrinsic hydrophobicity. The intrinsic hydrophobicity of rare earth oxides depends on surface orientation and oxygen vacancy levels, and is naturally more robust than coatings or surface treatments, having potential applications in condensers and catalysts that can operate at high temperatures or corrosive environments. Hydrophobic concrete has been produced since

342-510: 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 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

399-540: A gas. where θ can be measured using a contact angle goniometer . Wenzel determined that when the liquid is in intimate contact with a microstructured surface, θ will change to θ W* where r is the ratio of the actual area to the projected area. Wenzel's equation shows that microstructuring a surface amplifies the natural tendency of the surface. A hydrophobic surface (one that has an original contact angle greater than 90°) becomes more hydrophobic when microstructured – its new contact angle becomes greater than

456-399: A high contact angle . Examples of hydrophobic molecules include the alkanes , oils , fats , and greasy substances in general. Hydrophobic materials are used for oil removal from water, the management of oil spills , and chemical separation processes to remove non-polar substances from polar compounds. Hydrophobic is often used interchangeably with lipophilic , "fat-loving". However,

513-413: A higher entropic state which causes non-polar molecules to clump together to reduce the surface area exposed to water and decrease the entropy of the system. Thus, the two immiscible phases (hydrophilic vs. hydrophobic) will change so that their corresponding interfacial area will be minimal. This effect can be visualized in the phenomenon called phase separation. Superhydrophobic surfaces, such as

570-481: 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 a meaning to a sequence of elements of the pattern notation: Thus the pattern [AB] [CDE] F matches

627-479: A short peptide does not form an alpha helix , this suggests that it is the nest, rather than being at the N-terminus of a helix, that is the main phosphate binding feature. Upon nucleotide hydrolysis the loop does not significantly change the protein conformation , but stays bound to the remaining phosphate groups. Walker motif A-binding has been shown to cause structural changes in the bound nucleotide, along

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684-681: A surface having micrometer-sized features or particles ≤ 100 micrometers. The larger particles were observed to protect the smaller particles from mechanical abrasion. In recent research, superhydrophobicity has been reported by allowing alkylketene dimer (AKD) to solidify into a nanostructured fractal surface. Many papers have since presented fabrication methods for producing superhydrophobic surfaces including particle deposition, sol-gel techniques, plasma treatments, vapor deposition, and casting techniques. Current opportunity for research impact lies mainly in fundamental research and practical manufacturing. Debates have recently emerged concerning

741-586: A surface is easily washed away. Patterned superhydrophobic surfaces also have promise for lab-on-a-chip microfluidic devices and can drastically improve surface-based bioanalysis. In pharmaceuticals, hydrophobicity of pharmaceutical blends affects important quality attributes of final products, such as drug dissolution and hardness . Methods have been developed to measure the hydrophobicity of pharmaceutical materials. The development of hydrophobic passive daytime radiative cooling (PDRC) surfaces, whose effectiveness at solar reflectance and thermal emittance

798-410: Is a phenomenon that characterizes surface heterogeneity. When a pipette injects a liquid onto a solid, the liquid will form some contact angle. As the pipette injects more liquid, the droplet will increase in volume, the contact angle will increase, but its three-phase boundary will remain stationary until it suddenly advances outward. The contact angle the droplet had immediately before advancing outward

855-484: Is also found in a variety of proteins with phosphorylated substrates. Major lineages include: Walker A motif , also known as the Walker loop , or P-loop , or phosphate-binding loop , is a motif in proteins that is associated with phosphate binding. The motif has the pattern G-x(4)-GK-[TS], where G, K, T and S denote glycine , lysine , threonine and serine residues respectively, and x denotes any amino acid . It

912-399: Is based on this principle. Inspired by it , many functional superhydrophobic surfaces have been prepared. An example of a bionic or biomimetic superhydrophobic material in nanotechnology is nanopin film . One study presents a vanadium pentoxide surface that switches reversibly between superhydrophobicity and superhydrophilicity under the influence of UV radiation. According to

969-434: Is mostly an entropic effect originating from the disruption of the highly dynamic hydrogen bonds between molecules of liquid water by the nonpolar solute, causing the water to form a clathrate -like structure around the non-polar molecules. This structure formed is more highly ordered than free water molecules due to the water molecules arranging themselves to interact as much as possible with themselves, and thus results in

1026-513: Is present in many ATP or GTP utilizing proteins; it is the β phosphate of the nucleotide that is bound. The lysine (K) residue in the Walker A motif, together with the main chain NH atoms, are crucial for nucleotide -binding. It is a glycine -rich loop preceded by a beta strand and followed by an alpha helix ; these features are typically part of an α/β domain with four strands sandwiched between two helices on each side. The phosphate groups of

1083-403: Is termed contact angle hysteresis and can be used to characterize surface heterogeneity, roughness, and mobility. Surfaces that are not homogeneous will have domains that impede motion of the contact line. The slide angle is another dynamic measure of hydrophobicity and is measured by depositing a droplet on a surface and tilting the surface until the droplet begins to slide. In general, liquids in

1140-452: Is termed the advancing contact angle. The receding contact angle is now measured by pumping the liquid back out of the droplet. The droplet will decrease in volume, the contact angle will decrease, but its three-phase boundary will remain stationary until it suddenly recedes inward. The contact angle the droplet had immediately before receding inward is termed the receding contact angle. The difference between advancing and receding contact angles

1197-476: 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 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

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1254-484: Is the chemical property of a molecule that is seemingly repelled from a mass of water (called a hydrophobe ). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, thus, prefer other neutral molecules and nonpolar solvents . Because water molecules are polar, hydrophobes do not dissolve well among them. Hydrophobic molecules in water often cluster together, forming micelles . Water on hydrophobic surfaces will exhibit

1311-493: 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 a fixed-length motif. There are two types of weight matrices. An example of

1368-585: 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, 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

1425-516: The nucleotide are also coordinated to a divalent cation such as a magnesium , calcium , or manganese (II) ion. Apart from the conserved lysine, a feature of the P-loop used in phosphate binding is a compound LRLR nest comprising the four residues xxGK, as above, whose main chain atoms form a phosphate-sized concavity with the NH groups pointing inwards. The synthetic hexapeptide SGAGKT has been shown to bind inorganic phosphate strongly; since such

1482-418: The "three-dimensional chain code" for representing the protein structure as a string of letters. This encoding scheme reveals the similarity between the proteins much more clearly than the amino acid sequence (example from article): The code encodes the torsion angles between alpha-carbons of the protein backbone . "W" always corresponds to an alpha helix. Hydrophobic In chemistry , hydrophobicity

1539-470: The 20 standard amino acids and h denotes a hydrophobic amino acid. This motif was changed to be hhhhDE, where E denotes a glutamate residue. The aspartate and glutamate also form a part of the DEAD/DEAH motifs found in helicases . The aspartate residue co-ordinates magnesium ions, and the glutamate is essential for ATP hydrolysis . There is considerable variability in the sequence of this motif, with

1596-552: The Cassie–Baxter state exhibit lower slide angles and contact angle hysteresis than those in the Wenzel state. Dettre and Johnson discovered in 1964 that the superhydrophobic lotus effect phenomenon was related to rough hydrophobic surfaces, and they developed a theoretical model based on experiments with glass beads coated with paraffin or TFE telomer. The self-cleaning property of superhydrophobic micro- nanostructured surfaces

1653-399: The Cassie–Baxter state is more mobile than in the Wenzel state. We can predict whether the Wenzel or Cassie–Baxter state should exist by calculating the new contact angle with both equations. By a minimization of free energy argument, the relation that predicted the smaller new contact angle is the state most likely to exist. Stated in mathematical terms, for the Cassie–Baxter state to exist,

1710-464: 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

1767-416: The applicability of the Wenzel and Cassie–Baxter models. In an experiment designed to challenge the surface energy perspective of the Wenzel and Cassie–Baxter model and promote a contact line perspective, water drops were placed on a smooth hydrophobic spot in a rough hydrophobic field, a rough hydrophobic spot in a smooth hydrophobic field, and a hydrophilic spot in a hydrophobic field. Experiments showed that

Walker motifs - Misplaced Pages Continue

1824-447: 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, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but

1881-424: 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 the probability of X or Y occurring in

1938-406: 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 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

1995-402: The electrons reduce V to V . The oxygen vacancies are met by water, and it is this water absorbency by the vanadium surface that makes it hydrophilic. By extended storage in the dark, water is replaced by oxygen and hydrophilicity is once again lost. A significant majority of hydrophobic surfaces have their hydrophobic properties imparted by structural or chemical modification of a surface of

2052-420: The following inequality must be true. A recent alternative criterion for the Cassie–Baxter state asserts that the Cassie–Baxter state exists when the following 2 criteria are met:1) Contact line forces overcome body forces of unsupported droplet weight and 2) The microstructures are tall enough to prevent the liquid that bridges microstructures from touching the base of the microstructures. A new criterion for

2109-492: The functionally important aspartate on the tip of the second β-strand. 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 a distinctive secondary structure . " Noncoding " sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from

2166-584: 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 the existing motif discovery research focuses on DNA motifs. With the advances in high-throughput sequencing, such motif discovery problems are challenged by both

2223-425: The leaves of the lotus plant, are those that are extremely difficult to wet. The contact angles of a water droplet exceeds 150°. This is referred to as the lotus effect , and is primarily a chemical property related to interfacial tension , rather than a chemical property. In 1805, Thomas Young defined the contact angle θ by analyzing the forces acting on a fluid droplet resting on a solid surface surrounded by

2280-576: The line of the induced fit model of enzyme binding. PTPs ( protein tyrosine phosphatases ) that catalyse the hydrolysis of an inorganic phosphate from a phosphotyrosine residue (the reverse of a tyrosine kinase reaction) contain a motif which folds into a P-loop-like structure with an arginine in the place of the conserved lysine. The conserved sequence of this motif is C-x(5)-R-[ST], where C and R denote cysteine and arginine residues respectively. Pyridoxal phosphate (PLP) utilizing enzymes such as cysteine synthase have also been said to resemble

2337-458: The mid-20th century. Active recent research on superhydrophobic materials might eventually lead to more industrial applications. A simple routine of coating cotton fabric with silica or titania particles by sol-gel technique has been reported, which protects the fabric from UV light and makes it superhydrophobic. An efficient routine has been reported for making polyethylene superhydrophobic and thus self-cleaning. 99% of dirt on such

Walker motifs - Misplaced Pages Continue

2394-409: The only invariant features being a negatively charged residue following a stretch of bulky, hydrophobic amino acids. There is a hypothesis that the Walker A phosphate binding motif can be evolutionarily related to Rossman 's fold phosphate binding motif because of the shared principles in the location of the binding loop between the first β-strand and α-helix in the αβα sandwich fold and positioning of

2451-408: The original. However, a hydrophilic surface (one that has an original contact angle less than 90°) becomes more hydrophilic when microstructured – its new contact angle becomes less than the original. Cassie and Baxter found that if the liquid is suspended on the tops of microstructures, θ will change to θ CB* : where φ is the area fraction of the solid that touches the liquid. Liquid in

2508-454: 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 a single motif: the defining pattern, and various typical patterns. For example,

2565-473: 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

2622-866: 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

2679-520: 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 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

2736-516: 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

2793-433: 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 the desired motif in large quantities, and extraction of unwanted sequences using clustering. Cleaning then ensures

2850-537: 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 the IUPAC one-letter codes and conforms to the above description with the exception that a concatenation symbol, ' - ',

2907-421: The study, any surface can be modified to this effect by application of a suspension of rose-like V 2 O 5 particles, for instance with an inkjet printer . Once again hydrophobicity is induced by interlaminar air pockets (separated by 2.1 nm distances). The UV effect is also explained. UV light creates electron-hole pairs , with the holes reacting with lattice oxygen, creating surface oxygen vacancies, while

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2964-437: The surface chemistry and geometry at the contact line affected the contact angle and contact angle hysteresis , but the surface area inside the contact line had no effect. An argument that increased jaggedness in the contact line enhances droplet mobility has also been proposed. Many hydrophobic materials found in nature rely on Cassie's law and are biphasic on the submicrometer level with one component air. The lotus effect

3021-509: The switch between Wenzel and Cassie-Baxter states has been developed recently based on surface roughness and surface energy . The criterion focuses on the air-trapping capability under liquid droplets on rough surfaces, which could tell whether Wenzel's model or Cassie-Baxter's model should be used for certain combination of surface roughness and energy. Contact angle is a measure of static hydrophobicity, and contact angle hysteresis and slide angle are dynamic measures. Contact angle hysteresis

3078-494: The two terms are not synonymous. While hydrophobic substances are usually lipophilic, there are exceptions, such as the silicones and fluorocarbons . The term hydrophobe comes from the Ancient Greek ὑδρόφοβος ( hydróphobos ), "having a fear of water", constructed from Ancient Greek ὕδωρ (húdōr)  'water' and Ancient Greek φόβος (phóbos)  'fear'. The hydrophobic interaction

3135-513: 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 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

3192-750: The use of multiple methods proving effective in enhancing identification accuracy. Enumerative Approach: Initiating 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

3249-457: Was reported in 1977. Perfluoroalkyl, perfluoropolyether, and RF plasma -formed superhydrophobic materials were developed, used for electrowetting and commercialized for bio-medical applications between 1986 and 1995. Other technology and applications have emerged since the mid-1990s. A durable superhydrophobic hierarchical composition, applied in one or two steps, was disclosed in 2002 comprising nano-sized particles ≤ 100 nanometers overlaying

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