Binding flexibility

Desmet et al. (291) used a truncated (deadend elimination) search procedure to bind flexible peptides to the MHC I receptor. The translation/rotational space covered 6636 relative orientations and each nonglycine/proline residue of the peptide had 47 main-chain con-formers. Side chains had threefold rotations about their chi angles and 28 side chains of the receptor were allowed to rotate. Seventy-four low energy structures were obtained with an average rmsd of 1 A. The lowest energy structure had an rmsd of 0.56 A. Peptides up to 20 residues were docked with this procedure. 

The receptor site is clearly asymmetric. Chirality is Important, both by simple inspection of cases and supported by discrete sub-structural contributions. The R-configuration for both cyclic and acyclic analogs is favored at uptake sites. If we assume the amino and carboxyl groups to bind specifically, then the cavity between these sites is most likely a flexible, narrow gap. Congeners are permitted to bind (flexibility), but all substituents from the 2- to... 

Table 7.1 shows a number of excellent binders developed to date. Binders properties include - besides the actual binding - flexibility when used for electrodes, insolubility in the electrolyte, compactness, chemical and electrochemical stability, and easy application to electrode paints. The binder should be able to satisfy all of these properties simultaneously. This is a difficult task, and only two binders that comply with all these requisites have been found polyvinylidene fluoride (PVDF) and styrene-butadiene copolymer (SBR). 

At this stage it was demonstrated that reduced lariat ethers could bind cations more strongly than the neutral, parent compounds. These structures, when reduced, exhibit cation binding affinities much closer to those of cryptands than do the neutral lariat ethers and behave as if they are more rigid, cryptand-like structures as well. In contrast to the cryptands, they can be switched back to their low-binding, flexible structures on demand using electrochemical or chemical oxidation. 

The simulations of the avidin-biotin complex (Izrailev et ah, 1997) showed that a major difficulty involved in studies of the binding and flexibility of... 

Flexible 3D alignment of a set of ligands binding to the same target and/or CoMFA analysis allowing the perception of a pharmacophore for this target. 

A, C W Murray, D E Clark, D R Westhead and M D Eldridge 1998. Flexible Docking using Tabu rch and an Empirical Estimate of Binding Affinity. Proteins Structure, Function and Genetics 167-382. 

IV, ] Ruppert and A N Jain 1996. Hammerhead Fast, Fully Automated Docking of Flexible ands to Protein Binding Sites. Chemistry and Biology 3 449-462. 

Built-Up Mica. When the primary property needed for a particular appHcation is insulation, budt-up mica made by binding layered mica spHttings together serves as a substitute for the more expensive sheet mica. The principal uses for built-up mica are segment plate, molding plate, flexible plate, heater plate, and tape (7). 

The oxygen affinity of the derivative was shown to be about half that of unmodified hemoglobin under similar conditions, but a degree of cooperativity was preserved. Kquilihrium and kinetic ligand-binding studies on this derivative have been interpreted (62) to show a perturbed R state. It is beheved that although the reaction is between the two P-chains, aP-dimers function independentiy, probably through a flexible connection. 

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