Top 10 similar words or synonyms for isopeptide

osidic    0.728272

disuphide    0.702050

interprotomer    0.677114

dityrosine    0.676345

scissile    0.672728

adisulfide    0.669352

interflavan    0.664715

isoaspartyl    0.663162

intraprotein    0.655623

autocleavage    0.652034

Top 30 analogous words or synonyms for isopeptide

Article Example
Isopeptide bond The chemistry involved in the formation of these isopeptide bonds also tend to fall into these two categories. In the case of ubiquitin and ubiquitin-like proteins, tend to have a structured pathway of continuously passing along the peptide with a series of reactions, using multiple intermediate enzymes to reach the target protein for the conjugation reaction. The structural enzymes while varying from bacterial and eukaryotic domains, tend to be single enzymes that generally in a single step, fuse the two substrates together for a larger repetitive process of linking and inter-linking the said substrates to form and influence large macromolecular structures.
Isopeptide bond The chemistries of isopeptide bond formation are divided in the same manner as their biological roles. In the case of isopeptides used for conjugating one protein to another for the purpose of signal transduction, the literature is generally dominated by the very well-studied Ubiquitin protein and related proteins. While there are many related proteins to Ubiquitin, such as SUMO, Atg8, Atg12, and so on, they all tend to follow relatively the same protein ligation pathway. Therefore, the best example is to look at Ubiquitin, as while there can be certain differences, Ubiquitin is essentially the model followed in all these cases. The process essentially has three tiers, in the initial step, the activating protein generally denominated as E1 activates the Ubiquitin protein by adenylating it with ATP. Then the adenylated Ubiquitin is essentially activated and can be transferred to a conserved cysteine using a thioester bond which is between the carboxyl group of the c-terminal glycine of the ubiquitin and the sulfur of the E1 cysteine. The activating E1 enzyme then binds with and transfers the Ubiquitin to the next tier, the E2 enzyme which accepts the protein and once again forms a thioester with a conserved bond. The E2 acts to certain degree as an intermediary which then binds to E3 enzyme ligase for the final tier, which leads to the eventual transfer of the ubiquitin or ubiquitin related protein to a lysine site on the targeted protein, or more commonly for ubiquitin, onto ubiquitin itself to form chains of said protein. However, it should be noted that in final tier, there is also a divergence, in that depending on the type of E3 ligase, it may not actually be causing the conjugation. As there are the E3 ligases containing HECT domains, in which they continue this ‘transfer chain’ by accepting once again the ubiquitin via another conserved cysteine and then targeting it and transferring it to the desired target. Yet in case of RING finger domain containing that use coordination bonds with Zinc ions to stabilize their structures, they act more to direct the reaction. By that its meant that once the RING finger E3 ligase binds with the E2 containing the ubiquitin, it simply acts as a targeting device which directs the E2 to directly ligate the target protein at the lysine site. Though this case ubiquitin does represent other proteins related to it well, each protein obviously will have its own nuisances such as SUMO, which tends to be RING finger domain domainated ligases, where the E3 simply acts as the targeting device to direct the ligation by the E2, and not actually performing the reaction itself such as the Ubiquitin E3-HECT ligases. Thus while the internal mechanisms differ such as how proteins participate in the transfer chain, the general chemical aspects such as using thioesters and specific ligases for targeting remain the same.
Isopeptide bond The enzymatic chemistry involved in the formation of isopeptides for structural purposes, is different from the case of ubiquitin and ubiquitin related proteins. In that instead of sequential steps involving multiple enzymes to activate, conjugate and target the substrate. The catalysis is performed by one enzyme and the only precursor step, if there is one, is generally cleavage to activate it from a zymogen. However, the uniformity that exists in the ubiquitin’s case is not so here, as there are numerous different enzymes all performing the reaction of forming the isopeptide bond.
Isopeptide bond An isopeptide bond is an amide bond that is not present on the main chain of a protein. The bond forms between the carboxyl terminus of one protein and the amino group of a lysine residue on another (target) protein.
Isopeptide bond Another case of an isopeptide linking enzyme for structural purposes is the actin cross-linking domain (ACD) of the MARTX toxin protein generated by V. cholerae. While it has been shown that the ACD when performing the catalysis uses magnesium and ATP for the formation of the cross-links the specifics of the mechanism are uncertain. Though an interesting aspect of the cross-link formed in this case, is that it uses a non-terminal Glu to ligate to a non-terminal Lys, which seems to be rare in the process of forming an isopeptide bond. Though the chemistry of ACD is still to be resolved, it shows that isopeptide bond formation is not dependent simply on Asp/Asn for non-terminal isopeptide linkages between proteins.