MOTIVATION Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for pairwise sequence alignment, but it ignores information that could conceivably increase the power of remote homolog detection. We examine the validity of this assum...

A muramyl peptide that induces excess slow-wave sleep in rats, rabbits, and cats has recently been isolated from human urine. We now report that synthetic acetylmuramyl-L-alanyl-D-isoglutamine ("muramyl dipeptide") and its lysyl derivative (acetylmuramyl-L-alanyl-D-isoglutaminyllysine) can mimic the somnogenic effects of the natural peptide. Both compounds are also pyrogenic and may cause other...

Different from the conventional irreversible covalent conjugations, a simple and efficient dynamic Schiff base covalent assembly is developed to construct the stable and smart dipeptide-protein hydrogels under mild conditions. Diphenylalanine-hemoglobin hydrogel is chosen to investigate the gelation formation process and mechanism. It is found that such assembled dipeptide-protein hydrogels are...

The first reported hybrid artificial neural network-genetic algorithm (ANN-GA) approach for the optimization of on-capillary dipeptide derivatization is presented. More specifically, genetic optimization proved valuable in the determination of effective network structure with three defined parameter inputs: (i) phthalic anhydride injection volume, (ii) time of injection, and (iii) voltage, for ...

An account of x-ray crystallographic studies of monoclinic porcine pepsin crystals is presented. The chain fold specific for aspartyl proteases is described in detail. As the results of 2-A refinement have shown, the actual structure is that of ethanol-inhibited pepsin. The structure, although close to those of fungal aspartyl proteases, has some specific features: one of them is an insertion n...

Nanotubes formed by the aqueous assembly of a proline-lysine dipeptide (1) were used to create the hydrophobic microenvironments required to catalyze the aldol reaction in water. The self-assembly process occurred most efficiently in the presence of the substrates, producing an array of homogeneous nanotubes under the reaction conditions. The nanotubes formed by dipeptide 1 served as an efficie...

Mild, efficient and racemization-free synthesis of N-protected α, β-unsaturated γ-amino esters with unprecedented high E- stereoselectivity is described. This method is found to be compatible with Boc-, Fmoc- and other side chain protecting groups. The crystal conformations of the vinylogous γ-amino esters in monomers and in homo- and mixed dipeptides are studied. Further, the vinylogous homo-d...