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Ubiquitin-binding Domain
Ubiquitin-binding domains (UBDs) are protein domains that recognise and bind non-covalently to ubiquitin through protein-protein interactions. As of 2019, a total of 29 types of UBDs had been identified in the human proteome. Most UBDs bind to ubiquitin only weakly, with binding affinities in the low to mid μM range. Proteins containing UBDs are known as ubiquitin-binding proteins or sometimes as "ubiquitin receptors". Structure Most UBDs are of small size (often less than 50 amino acids) and adopt many different protein folds from multiple fold classes, including all-alpha, all-beta, and alpha/beta folds. Many UBDs can be roughly classified into four broad categories: alpha-helical structures (in some cases as small as a single helix, as in the ubiquitin-interacting motif); zinc fingers; pleckstrin homology (PH) domains; and domains similar to those in ubiquitin-conjugating (also known as E2) enzymes. Other UBDs not fitting these categories can be SH3 domains, PFU domains, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pleckstrin Homology
Pleckstrin homology domain (PH domain) or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton. This domain can bind phosphatidylinositol lipids within biological membranes (such as phosphatidylinositol (3,4,5)-trisphosphate and phosphatidylinositol (4,5)-bisphosphate), and proteins such as the βγ-subunits of heterotrimeric G proteins, and protein kinase C. Through these interactions, PH domains play a role in recruiting proteins to different membranes, thus targeting them to appropriate cellular compartments or enabling them to interact with other components of the signal transduction pathways. Lipid binding specificity Individual PH domains possess specificities for phosphoinositides phosphorylated at different sites within the inositol ring, e.g., some bind phosphatidylinositol (4,5)-bisphosphate but not phosphatidylinositol (3,4,5)-trisphosphate or ph ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Steric Clash
Steric effects arise from the spatial arrangement of atoms. When atoms come close together there is a rise in the energy of the molecule. Steric effects are nonbonding interactions that influence the shape ( conformation) and reactivity of ions and molecules. Steric effects complement electronic effects, which dictate the shape and reactivity of molecules. Steric repulsive forces between overlapping electron clouds result in structured groupings of molecules stabilized by the way that opposites attract and like charges repel. Steric hindrance Steric hindrance is a consequence of steric effects. Steric hindrance is the slowing of chemical reactions due to steric bulk. It is usually manifested in ''intermolecular reactions'', whereas discussion of steric effects often focus on ''intramolecular interactions''. Steric hindrance is often exploited to control selectivity, such as slowing unwanted side-reactions. Steric hindrance between adjacent groups can also affect torsional ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Polarity
In chemistry, polarity is a separation of electric charge leading to a molecule or its chemical groups having an electric dipole moment, with a negatively charged end and a positively charged end. Polar molecules must contain one or more polar bonds due to a difference in electronegativity between the bonded atoms. Molecules containing polar bonds have no molecular polarity if the bond dipoles cancel each other out by symmetry. Polar molecules interact through dipole–dipole intermolecular forces and hydrogen bonds. Polarity underlies a number of physical properties including surface tension, solubility, and melting and boiling points. Polarity of bonds Not all atoms attract electrons with the same force. The amount of "pull" an atom exerts on its electrons is called its electronegativity. Atoms with high electronegativitiessuch as fluorine, oxygen, and nitrogenexert a greater pull on electrons than atoms with lower electronegativities such as alkali metals and alkaline ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Zinc Finger
A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) in order to stabilize the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (''Xenopus laevis'') transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. ''Xenopus laevis'' TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in ''Drosophila''. It often appears as a metal-binding domain in multi-domain proteins. Proteins that contain zinc fingers (zinc finger proteins) are classified into several different structural families. Unlike many other clearly defined supersecondary structures such as Greek keys or β hairpins, there are a number of t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Isoleucine
Isoleucine (symbol Ile or I) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH form under biological conditions), an α-carboxylic acid group (which is in the deprotonated −COO form under biological conditions), and a hydrocarbon side chain with a branch (a central carbon atom bound to three other carbon atoms). It is classified as a non-polar, uncharged (at physiological pH), branched-chain, aliphatic amino acid. It is essential in humans, meaning the body cannot synthesize it, and must be ingested in our diet. Isoleucine is synthesized from pyruvate employing leucine biosynthesis enzymes in other organisms such as bacteria. It is encoded by the codons AUU, AUC, and AUA. Metabolism Biosynthesis As an essential nutrient, it is not synthesized in the body, hence it must be ingested, usually as a component of proteins. In plants and microorganisms, it is synthesized via several steps, startin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophobic
In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as 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 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, the two terms are not synonymous. While hydrophobic substances are usually lipophilic, there are exceptions, suc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
VHS Protein Domain
In molecular biology, the VHS protein domain is approximately 140 residues long. Its name is an acronym derived from its occurrence in VPS-27, Hrs and STAM. It is a domain commonly found in the N-terminus of many proteins. Function VHS domains are thought to be very important in vesicular trafficking, in particular, aiding membrane targeting and cargo recognition role. Structure Resolution of the crystal structure of the VHS domain of ''Drosophila'' Hrs and human TOM1 revealed that it consists of eight helices arranged in a double-layer superhelix. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members. Classification Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups: * STAM/EAST/ STAM2(Hbp) which all share the domain composition VHS- SH3- ITAM and carry one or two ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Motif Interacting With Ubiquitin
Motif may refer to: General concepts * Motif (chess composition), an element of a move in the consideration of its purpose * Motif (folkloristics), a recurring element that creates recognizable patterns in folklore and folk-art traditions * Motif (music), a salient recurring fragment or succession of notes * Motif (narrative), any recurring element in a story that has symbolic significance or the reason behind actions * Motif (textile arts), a recurring element or fragment that, when joined together, creates a larger work * Motif (visual arts), a repeated theme or pattern Biochemistry * Sequence motif, a sequence pattern of nucleotides in a DNA sequence or amino acids in a protein * Short linear motif, a stretch of protein sequence that mediates protein–protein interaction * Structural motif, a pattern in a protein structure formed by the spatial arrangement of amino acids Other uses * ''Motif'' (2019 film), 2019 Malaysian Malay-language crime drama film * ''Motif'' (al ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CUE Domain
Cue or CUE may refer to: Event markers * Sensory cue, in perception (experimental psychology) *Cue (theatrical), the trigger for an action to be carried out at a specific time, in theatre or film *Cue (show control), the electronic rendering of the specific action(s) to be carried out at a specific time by a show control system * Voice cue, in dance, words or sounds that help match rhythmic patterns of steps with the music *Cue mark, in motion picture film to signal projectionists of reel changes *Cue, a vocal message given by a group fitness instructor to inform participants of upcoming sequences, such as a change in stretching direction Music and audio * Cue (band), a Swedish musical group *Cue tone, a message consisting of audio tones, used to prompt an action. *Cue (audio), to determine the desired initial playback point in a piece of recorded music *Cue sheet (computing), a metadata file that describes how the tracks of an audio track are laid out *Source cue, music that eman ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UBA Protein Domain
Ubiquitin-associated (UBA) domains are protein domains that non-covalently interact with ubiquitin through protein-protein interactions. Ubiquitin is a small protein that is covalently linked to other proteins as part of intracellular signaling pathways, often as a signal for protein degradation. UBA domains are among the most common ubiquitin-binding domains. Function Proteins containing UBA domains are involved in a variety of additional cell processes, such as nucleotide excision repair (NER), spindle pole body duplication, and cell growth. Protein degradation via the ubiquitin proteasome system (UPS) allows the cell to selectively negatively regulate intracellular proteins. Protein degradation helps to maintain protein quality control, signalling, and cell cycle progression. UBA has been proposed to limit ubiquitin chain elongation and to target polyubiquitinated proteins to the 26S proteasome for degradation. They have been identified in modular proteins involved in p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PFU Domain
PFU may refer to: *PFU Limited, a Japanese information technology company *Plaque-forming unit, a measure used in virology *Peoples' Friendship University of Russia The Peoples' Friendship University of Russia (russian: Российский университет дружбы народов), also known as RUDN University and, until 1992, Patrice Lumumba University in honor of the hero Patrice Lumumba, is a ..., an educational and research institution located in Moscownonaligned countries * ''Pfu'' DNA polymerase, an enzyme {{Disambiguation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
