Chain recognition

Beal, R. E., Toscano-Cantaffa, D., Young, P., Rechsteiner, M., and PiCKART, C. M. The hydrophobic effect contributes to polyubiquitin chain recognition. Biochemistry, 1998, 37, 2925-34. 

The al and a2 chains of type VI collagen are similar in size and contain one N-terminal NC domain and a C-terminal NC domain with two subdomains. Cl and C2. In contrast, the a3 chain is much longer, and the N-terminal NC domain contains 10 subdomains, Nl-NlO, and 5 C-terminal NC subdomains, Cl-C5. The protomer is an ala2a3 heterotrimer. Deletion studies have demonstrated that whereas the C5 subdomain of the a3 chain is required for the extracellular microfibril formation, the Cl subdomain, in all chains, is sufficient for chain recognition and protomer assembly... 

Hadley, E. B. Geltman, S. H. An antiparallel a-helical coiled-coil model system for rapid assessment of side-chain recognition at the hydrophobic interface. J. Am. Chem. Soc. 2006,128,16444-16445. 

These qualitative assays show that one-armed cationic guanidiniocarbonyl pyrrole receptors can indeed effectively bind tetrapeptides even in water. Molecular modeling studies suggest a complex structure as shown for one specific example, the receptor Val-Val-Val-CBS, in Figure 2.3.11. Receptor and substrate form a hydrogen bonded //-sheet which is further stabilized by additional hydrophobic interactions between the apolar groups in the side-chains. Recognition of the tetrapep-tide thus seems to be controlled by a fine balanced interplay between electrostatic and hydrophobic interactions. 

T. Beal et al.. The hydrophobic effect contributes to polyubiquitin chain recognition. Biochemistry 37(1998)2925-2934. 

During the forward folding pathway the newly synthesized chain forms a partially folded single chain intermediate (5435). This folds further to a species with sufficient structure for chain recognition. Three of these intermediates associate into a protrimer in which the chains are associated but not fully folded (36). This species then folds further to the thermostable detergent and protease resistant native trimer. There are no known covalent modifications in the process. A similar process occurs in refolding urea denatured chains in vitro (37). Thermal Unfolding Pathway of Tailspike... 

Endo, Y., Gluck, A. and Wool, l.G. (1991) Ribosomal RNA identity elements for ricin A-chain recognition and catalysis. J Mol Biol, 221, 193-207. 

The functional dynamics of proteins in cells depends on how fast those macromolecules adopt a unique three-dimensional structure and, in addition, how spatial-temporal control of the backbone conformation by external molecules underlies the mechanism of folding and chain recognition in vivo. The numerous con-... 

Finally, we discuss time-resolved results on alkylaniline species.46 One might expect IVR in such species to involve flow of energy from optically active ring modes to the bath of weakly coupled modes associated with the alkyl chain. Recognition of this led Powers et al.10c to their time-integrated studies of IVR as a function of alkyl chain length in the alkylanilines. Our picosecond results are of interest in that they provide points of comparison between time-resolved rate (and coherence) measurements versus inferences from spectral results. 

Substrate specificity The replacement of the jaw region (substrate side-chain recognition) "AA with GG enlarges the pocket. The replacement of coenzyme loop (closes over the substrate) with MV... 

In this transform problem, the product is an ester with two additional carbons on the carbon chain. Recognition of the ester as a carboxylic acid derivative leads to a disconnection at the C-O bond to give a carboxylic acid and the commercially available allyl bromide. The continued retrosynthesis of this carboxylic acid is dictated by the given starting material. The new C-C bond is identified and disconnected. One of the carbons involved is an alpha carbon,... 

Side-chain recognition groups May be the same or different... 

Table 2. Potential glycation sites in the chain recognition region (VR3) in collagen...

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