PBOND is a web server that predicts the conformation of the peptide bond between any two amino acids. PBOND classifies the peptide bonds into one out of four classes, namely cis imide (cis-Pro), cis amide (cis-nonPro), trans imide (trans-Pro) and trans amide (trans-nonPro). Moreover, for every prediction a reliability index is computed. The underlying structure of the server consists of three s...

Transient UV resonance Raman measurements excited within the amide pi --> pi transitions of a 21 unit alpha-helical peptide has for the first time determined a lower bound for the unfolding rate of the last alpha-helical turn to form a fully random coil peptide. A 3 ns T-jump is generated with 1.9 microm laser pulses, which are absorbed by water. Subsequent 3 ns 204 nm UV pulses excite the amid...

Factor XIII-cross-linked fragment D (double-D) from human fibrin was crystallized in the presence of two different peptide ligands and the X-ray structure determined at 2.3 A. The peptide Gly-Pro-Arg-Pro-amide, which is an analogue of the knob exposed by the thrombin-catalyzed removal of fibrinopeptide A, was found to reside in the gamma-chain holes, and the peptide Gly-His-Arg-Pro-amide, which...

The interplay between the entropically and enthalpically favored products of peptide fragmentation is probed using a combined experimental and theoretical approach. These b2 ion products can take either an oxazolone or diketopiperazine structure. Cleavage after the second amide bond is often a favorable process because the products are small ring structures that are particularly stable. These s...

Humic isoJates from different layers of an organic-matter-rich algal sapropel from Mangrove Lake, Bennuda, were subjected to solid-state 15N nuclear magnetic resonance (NMR) spectroscopy in crder to reveal chemical structural interrelationships tbat allow delineation of diagenetic pathways. Amide-N, most likely from peptide-like material, \Vas found to represent the main organic nitrogen fonu i...

PURPOSE A prior study showed that a tetrapeptide (FGLM-amide) derived from the carboxyl terminus of substance P (SP) and a 12-residue peptide corresponding to the C domain of insulin-like growth factor (IGF)-1 mimic the synergistic effect of the full-length molecules on corneal epithelial wound healing. To develop an effective treatment for persistent corneal epithelial defects, the current stu...

Previous work [Chakrabarti et al. (1992) Biophys. J. 61, 228-234] has shown that basic amino acids and peptides, in which the C-terminal carboxyl groups have been modified to form amides or methyl esters, can be rapidly and efficiently accumulated into large unilamellar vesicle (LUV) systems in response to transmembrane pH gradients (delta pH, inside acidic). In this work, the ability of small ...

The prevalence of obesity-related diabetes is increasing worldwide. Here we report the identification of a pentapeptide, GLP-1(32-36)amide (LVKGRamide), derived from the glucoincretin hormone GLP-1, that increases basal energy expenditure and curtails the development of obesity, insulin resistance, diabetes, and hepatic steatosis in diet-induced obese mice. The pentapeptide inhibited weight gai...

The N-methylacetamide molecule (NMA) is an important model for peptide and protein vibrational spectroscopy as it contains the main amide chromophore. In the past, some observed NMA geometry and spectral features could not be entirely explained at the harmonic level or by a single-conformer model. In particular, the spectra were found to be very dependent on molecular environment. In this work ...

The almiramide N-methylated lipopeptides exhibit promising activity against trypanosomatid parasites. A structure–activity relationship study has been performed to examine the influences of N-methylation and conformation on various strains leishmaniasis protozoan cytotoxicity. synthesis biological analysis twenty-five analogs demonstrated that derivatives with a single methyl group either first...