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Biomedical subjects

Ernesto Nicolás

Publications and source records attributed to Ernesto Nicolás.

3 recordsLinked to original sources

Coupe du roi bisection of proteins. Spontaneous tetramerization of two peptides that span the sequence of the rabbit uteroglobin monomer.

The study of dividing objects into isometric segments has yielded novel approaches to the synthesis of high-symmetry organic compounds. Reported herein is the first application of this concept to a protein, rabbit uteroglobin (UG). Bisection of UG into two identical homochiral segments led to the design of the heterodimeric 70mer peptide alpha(1,2)-S-S-alpha(3,4) that spans the sequence of the native UG monomer. The ability of this compound to form a globular 140mer tetramer consisting of two noncovalently bound heterodimers was assessed by ultracentrifugation at sedimentation equilibrium and by fluorescent spectroscopy. On the other hand, the monomeric peptides alpha(1,2)-SH and alpha(3,4)-SH were shown to selectively form the alpha(1,2)-S-S-alpha(3,4) heterodimer via spontaneous air oxidation in phosphate buffer at neutral pH.

Amino Acid Sequence↗

ENPDA: an evolutionary structure-based de novo peptide design algorithm.

One of the goals of computational chemists is to automate the de novo design of bioactive molecules. Despite significant advances in computational approaches to ligand design and binding energy evaluation, novel procedures for ligand design are required. Evolutionary computation provides a new approach to this design endeavor. We propose an evolutionary tool for de novo peptide design, based on the evaluation of energies for peptide binding to a user-defined protein surface patch. Special emphasis has been placed on the evaluation of the proposed peptides, leading to two different evaluation heuristics. The software developed was successfully tested on the design of ligands for the proteins prolyl oligopeptidase, p53, and DNA gyrase.

Algorithms↗

Solid-phase synthesis of the cyclic lipononadepsipeptide [N-Mst(Ser1), d-Ser4, L-Thr6, L-Asp8, L-Thr9]syringotoxin.

An optimized solid-phase strategy for the preparation of the cyclic lipononadepsipeptide [N-Mst(L-Ser1), D-Ser4, L-Thr6, L-Asp8, L-Thr9]syringotoxin is reported. The strategy is based on the use of a mild orthogonal protection scheme and the incorporation of the nonproteinogenic amino acid (Z)-Dhb into the peptide chain as the dipeptide Fmoc-Thr(tBu)-(Z)-Dhb-OH. The didehydrodipeptide was synthesized by a water-soluble carbodiimide-induced beta-elimination of a protected dipeptide containing a residue of Thr with its free hydroxy side chain unprotected.

Anti-Infective Agents↗