Biomedical subjects

W John Cooper

Publications and source records attributed to W John Cooper.

4 recordsLinked to original sources

PubMed2006

Pressure perturbation calorimetry of helical peptides.

Pressure perturbation calorimetry quantifies the temperature dependence of a solute's thermal expansion coefficient, providing information about solute-solvent interactions. We tested the idea that pressure perturbation calorimetry can provide information about solvent-accessible surface area by studying peptides with different secondary structures. The peptides comprised two host-guest series: one predominately an alpha-helix, the other predominately a polyproline II helix. In aqueous buffer, we find a correlation between the amount of secondary structure as assessed by circular dichroism spectropolarimetry and the pressure perturbation calorimetry data. We conclude that pressure perturbation calorimetry can provide information about the exposure of polar and nonpolar surface area. Data acquired in a buffered urea solution, however, are not as easily interpreted.

Calorimetry↗

PubMed2005

Molecular recognition with designed peptides and proteins.

The design of proteins and peptides as molecular receptors is a rapidly growing area of research. Two primary approaches have been utilized, involving the minimization of known protein binding motifs or the de novo design of binding pockets within well-folded protein structures. These approaches are complementary and help define the minimum requirements necessary for biomolecular recognition. Recent advances in this area include the design of cavities within helix bundles for the binding of anesthetics, the design of beta-hairpins for the recognition of nucleotides and oligonucleotides, the redesign of protein binding sites for unique ligands, and the design of mini-proteins via protein grafting for the recognition of proteins and DNA. These advances provide exciting new opportunities to develop novel biosensors, de novo designed catalysts, exogenously triggered synthetic signal transduction cascades, and novel approaches to therapeutic treatments.

Models, Molecular↗

PubMed2005

Turn residues in beta-hairpin peptides as points for covalent modification.

Beta-turns are important sites for protein-protein and protein-peptide interactions, but little research has explored synthetic modifications of turn residue side-chains in a beta-hairpin peptide. To this end, beta-hairpin peptides were synthesized containing the type I' turn sequence Val-Asn-Gly-Lys with modifications at Asn and Lys. We found that these variations impose a small penalty, demonstrating that beta-turns are capable of displaying a range of functionality, which may be exploited for biomolecular recognition and medicinal applications. [structure: see text]

Amino Acid Sequence↗

PubMed2005

Minimalist protein design: a beta-hairpin peptide that binds ssDNA.

A 28-residue beta-hairpin dimer (WKWK)2 with two Trp and two Lys residues on one face of each beta-sheet was shown to form a complex with single-stranded oligonucleotides at low micromolar concentrations. Each beta-hairpin of the dimer contains a cross-strand Trp-Trp pair in a diagonal orientation which has previously been shown to create a cleft for the intercalation of aromatic guests such as adenine (J. Am. Chem. Soc. 2003, 125, 9580). The beta-hairpin dimer binds 5-residue ssDNA sequences 5'-AAAAA-3', 5'-TTTTT-3', and 5'-CCCCC-3' in water with dissociation constants in the range of 12-30 muM. A weak energetic preference for binding to sequence 5'-AAAAA-3' was observed, which is believed to result from stronger stacking interactions between Trp and the adenine base. The interaction of 5'-AAAAA-3' with the Lys and Trp residues of the peptide was evident by NMR, and a 1:1 association was demonstrated. The recognition of an 11-residue ssDNA sequence occurred with a dissociation constant of 3 muM under near-physiological ionic strength and pH, demonstrating that the beta-hairpin dimer binds ssDNA as strongly as many naturally occurring proteins. The salt dependence of the interaction of the 11-residue oligonucleotide with the peptide dimer indicates that Trp-nucleobase stacking interactions contribute about -4 kcal/mol to recognition, which is much greater than the contribution of nonionic interactions in unstructured peptides containing Trp. Moreover, recognition of the ssDNA demonstrated reduced salt dependence relative to the corresponding duplex, resulting in selectivity for ssDNA under high salt conditions. Peptide (WKWK)2 is a relevant mimic of OB-fold (oligonucleotide/oligosaccharide-binding) proteins which bind ssDNA on the surface of a beta-sheet.

DNA, Single-Stranded↗