Biomedical subjects

Ryan M Van Wagoner

Publications and source records attributed to Ryan M Van Wagoner.

3 recordsLinked to original sources

PubMed2006

FeeM, an N-acyl amino acid synthase from an uncultured soil microbe: structure, mechanism, and acyl carrier protein binding.

Attempts to access antibiotics by capturing biosynthetic genes and pathways directly from environmental DNA, which is overwhelmingly derived from uncultured bacteria, have revealed a large and previously unknown family of N-acyl amino acid synthases (NASs). The structure of the NAS FeeM reveals structural similarity to the GCN5-related N-acyl transferases and acylhomoserine lactone synthases. The overall structure has a central beta sheet with alpha helices on both sides. A bound product at a cleft in the beta sheet identifies the active site and the structural basis for catalysis, and sequence conservation in this region indicates a bias for recognition over speed. FeeM interacts with an acyl carrier protein (FeeL), and the structure, mutagenesis, and enzymatic measurements reveal that a small hydrophobic pocket in alpha helix 5 dominates binding of FeeM to FeeL. The structural and mechanistic analyses suggest that the products of FeeM could be bacterial signaling agents.

Acyl Carrier Protein↗

PubMed2003

An improved solution structure for psi-conotoxin PiiiE.

A revised, high-resolution structure of psi-conotoxin Piiie (psi-Piiie), a noncompetitive inhibitor of the nicotinic acetylcholine receptor (nAChR), produced through the use of NMR and molecular modeling calculations is presented. The original structures of psi-Piiie had a relatively high degree of disorder, particularly in the conformation of the disulfide bridges. Our studies utilized (13)C-labeling of selected cysteine residues allowing the resolution of all problems of resonance overlap for the cysteine residues. The improved data were used to produce a new set of structures by a molecular modeling process incorporating relaxation matrix methods for the determination of interproton distance restraints and a combination of distance geometry and simulated annealing for structure generation. The structures produced are very well converged with the RMSD of backbone atom positions of the main body of the peptide improving from 0.73 to 0.13 A. Other indicators of correlation with the experimental data and quality of covalent geometry showed significant improvement in the new structures. The overall conformation of the peptide backbone is similar between the two determinations with the exception of the N-terminus. This difference leads to a significant effect on the predicted distribution of positive charge within psi-Piiie, a property likely to influence interpretation of future mutational studies.

Algorithms↗

PubMed2003

Characterization and three-dimensional structure determination of psi-conotoxin Piiif, a novel noncompetitive antagonist of nicotinic acetylcholine receptors.

A novel inhibitor of nicotinic acetylcholine receptors (nAChRs), psi-conotoxin Piiif, was isolated from the venom of Conus purpurascens and found to have the sequence GOOCCLYGSCROFOGCYNALCCRK-NH2. The sequence is highly homologous to that of psi-conotoxin Piiie, a previously identified noncompetitive inhibitor of Torpedo electroplax nAChR, also isolated from C. purpurascens. Both psi-conotoxins block Torpedo and mouse nicotinic acetylcholine receptors (nAChRs), but psi-Piiif is less potent by a factor of 10(1)-10(2). A high-resolution structure of psi-Piiif was determined by NMR and molecular modeling calculations. Psi-Piiif analogues containing [(13)C]-labeled cysteine at selected positions were synthesized to resolve spectral overlap of Cys side chain proton signals. The structures are well-converged, with backbone atom position RMSDs of 0.21 A for the main body of the peptide between residues 4 and 22 and 0.47 A for all residues. The overall backbone conformation is closely similar to psi-Piiie, the main difference being in the degree of conformational disorder at the two termini. Psi-Piiie and psi-Piiif have similar locations of positive charge density, although psi-Piiif has a lower overall charge. One disulfide bridge of psi-Piiif appears to undergo dynamic conformational fluctuations based on both the model and on experimental observation. Chimeras in which the three intercysteine loops were swapped between psi-Piiie and psi-Piiif were tested for inhibitory activity against Torpedo nAChRs. The third loop, which contains no charged residues in either peptide, is the prime determinant of potency in these psi-conotoxins.

Amino Acid Sequence↗