Biomedical subjects

David L Jakeman

Publications and source records attributed to David L Jakeman.

11 recordsLinked to original sources

PubMed2006

Structure-activity analysis of quorum-sensing signaling peptides from Streptococcus mutans.

Streptococcus mutans secretes and utilizes a 21-amino-acid signaling peptide pheromone to initiate quorum sensing for genetic competence, biofilm formation, stress responses, and bacteriocin production. In this study, we designed and synthesized a series of truncated peptides and peptides with amino acid substitutions to investigate their structure-activity relationships based on the three-dimensional structures of S. mutans wild-type signaling peptide UA159sp and C-terminally truncated peptide TPC3 from mutant JH1005 defective in genetic competence. By analyzing these peptides, we demonstrated that the signaling peptide of S. mutans has at least two functional domains. The C-terminal structural motif consisting of a sequence of polar hydrophobic charged residues is crucial for activation of the signal transduction pathway, while the core alpha-helical structure extending from residue 5 to the end of the peptide is required for receptor binding. Peptides in which three or more residues were deleted from the C terminus did not induce genetic competence but competitively inhibited quorum sensing activated by UA159sp. Disruption of the amphipathic alpha-helix by replacing the Phe-7, Phe-11, or Phe-15 residue with a hydrophilic residue resulted in a significant reduction in or complete loss of the activity of the peptide. In contrast to the C-terminally truncated peptides, these peptides with amino acid substitutions did not compete with UA159sp to activate quorum sensing, suggesting that disruption of the hydrophobic face of the alpha-helical structure results in a peptide that is not able to bind to the receptor. This study is the first study to recognize the importance of the signaling peptide C-terminal residues in streptococcal quorum sensing.

Amino Acid Sequence↗

PubMed2006

Substrate flexibility of a 2,6-dideoxyglycosyltransferase.

We report the first 2,6-dideoxysugar-O-glycosyltransferase with substrate flexibility at the 2 position, confirm the function of a putative NDP-hexose 2,3-dehydratase in the jadomycin B biosynthetic gene cluster and deduce the substrate flexibility of downstream enzymes in l-digitoxose assembly, enabling reprogramming of biosynthetic gene clusters to modify sugar substituents.

Glycosyltransferases↗

PubMed2006

Fungal zymosan induces leukotriene production by human mast cells through a dectin-1-dependent mechanism.

BACKGROUND: Fungi are capable of causing or exacerbating inflammatory disease in the airways. We have previously demonstrated that zymosan and peptidoglycan induce the production of cysteinyl leukotrienes from human mast cells. However, the mechanisms of pathogen-induced leukotriene production by immune effector cells are very poorly understood. The coreceptor dectin-1, through a Syk tyrosine kinase-dependent pathway, can mediate some responses to fungal challenge, but its expression by mast cells and its involvement in lipid mediator responses have not been assessed. OBJECTIVE: In the current study, the potential role of dectin-1 in zymosan-induced leukotriene production from human mast cells was examined. METHODS: Human mast cells were examined for dectin-1 mRNA and protein expression. Human mast cells were incubated with either zymosan or peptidoglycan in the presence or absence of specific inhibitors for dectin-1 or Syk tyrosine kinase and mediator production examined. RESULTS: Human mast cells were found to express a functional isoform of dectin-1. Both peptidoglycan and zymosan induced significant amounts of leukotriene (LT)-B4 and LTC4. The dectin-1 inhibitors laminarin and glucan phosphate reduced the LTC4 response to zymosan by more than 60% but did not alter peptidoglycan responses. Inhibitors of Syk tyrosine kinase activity significantly decreased LTC4 production in response to both peptidoglycan and zymosan. CONCLUSION: These data demonstrate mast cell expression of the coreceptor dectin-1 and a role for this molecule in the generation of cysteinyl leukotrienes. CLINICAL IMPLICATIONS: These findings suggest new approaches to the selective inhibition of lipid mediator production in response to fungal infection or exposure.

Blotting, Western↗

PubMed2006

Culture conditions improving the production of jadomycin B.

The jadomycins are a unique family of benzoxazolophenanthridine antibiotics produced by Streptomyces venezuelae ISP5230 following heat or ethanol shock or phage infection. We have modified the culture conditions by altering the carbon source, buffer, inoculum size, and timing of ethanol shock, thereby reducing growing times and improving jadomycin B production. Our optimized conditions use glucose as the carbon source, MOPS as buffer, low concentrations of phosphate, a defined inoculum concentration and an immediate ethanol shock to induce jadomycin B production; results that contrast previous studies. The altered media will facilitate the isolation of related jadomycin B congeners.

Anti-Bacterial Agents↗

PubMed2006

Ring-opening dynamics of jadomycin A and B and dalomycin T.

[structure: see text] A novel oxazolone ring-opening and interconversion process between the two jadomycin diastereomeric forms has been characterized by NMR spectroscopy. An analogue, dalomycin T, has been isolated for the first time and does not undergo interconversion.

Isoquinolines↗

PubMed2005

An improved method for the synthesis of nucleoside triphosphate analogues.

[reaction: see text] Nucleoside monophosphates, when activated by trifluoroacetic anhydride and N-methylimidazole, efficiently couple with a variety of electron-deficient diphosphonates in a reproducible and efficient manner (<2 h, >72% isolated yield). Unlike traditional methods for the preparation of nucleoside 5'-beta,gamma-methylenetriphosphate analogues, there is no requirement for predrying, or conversion to specific salt forms, of commercially available nucleoside monophosphate starting materials.

Acetic Anhydrides↗

PubMed2005

Novel and expanded jadomycins incorporating non-proteogenic amino acids.

Jadomycin B is a secondary metabolite produced, in response to stress, by Streptomyces venezuelae ISP5230 grown in nutrient-deprived media. We present definitive electrospray ionization mass spectrometry data identifying a series of novel jadomycins with non-proteogenic amino acids incorporated into the oxazolone ring of the secondary metabolite, and strengthening evidence for the existence of an aldimine intermediate in the biosynthetic pathway. We also demonstrate that the size of the oxazolone ring can be expanded by incorporating beta-amino acids.

Amino Acids↗

PubMed2005

Structural characterization of the antimicrobial peptide pleurocidin from winter flounder.

Pleurocidin is an antimicrobial peptide that was isolated from the mucus membranes of winter flounder (Pseudopleuronectes americanus) and contributes to the initial stages of defense against bacterial infection. From NMR structural studies with the uniformly (15)N-labeled peptide, a structure of pleurocidin was determined to be in a random coil conformation in aqueous solution whereas it assumes an alpha-helical structure in TFE and in dodecylphosphocholine (DPC) micelles. From (15)N relaxation studies, the helix is a rigid structure in the membrane-mimicking environment. Strong NOESY cross-peaks from the pleurocidin to the aliphatic chain on DPC confirm that pleurocidin is contained within the DPC micelle and not associated with the surface of the micelle. From diffusion studies it was determined that each micelle contains at least two pleurocidin molecules.

Amino Acid Sequence↗

PubMed2005

Novel jadomycins: incorporation of non-natural and natural amino acids.

Electrospray ionization mass spectrometry of extracts from Streptomyces venezuelae ISP5230 cultures grown on chemically synthesized non-natural L-amino acids, D-amino acids or any of the 20 natural amino acids demonstrated incorporation of the amino acid into a jadomycin B analogue.

Amino Acids↗

PubMed2002

Orientation of 1,3-bisphosphoglycerate analogs bound to phosphoglycerate kinase.

We have previously reported dissociation constants for a range of bisphosphonate analogs of 1,3-bisphospho-D-glyceric acid binding to yeast phosphoglycerate kinase. Data for the unsymmetrical analogs were difficult to interpret because it was not clear in which of the two possible orientations these ligands bound. Here we report a novel NMR method for quantifying orientation preference based on relaxation effects induced by titration with CrADP, which is applied to these ligands. It is shown that all ligands can bind in both orientations but that the driving force for the orientational preference is to put the alpha,alpha-difluoromethanephosphonate group in the "basic patch" (nontransferable phosphate) position. The relevance to the design of phosphoglycerate kinase inhibitors is discussed.

Diphosphonates↗

PubMed2002

Solid-phase oligosaccharide and glycopeptide synthesis using glycosynthases.

Enzymatic approaches for the preparation of oligosaccharides are interesting alternatives to traditional chemical synthesis, the main advantage being the regio- and stereoselectivity offered without the need for protecting groups. The use of solid-phase techniques offers easy workup procedures and the prospect of automatability. Here, we report the first application of glycosynthases to solid-phase oligosaccharide synthesis by use of the 51 kDa serine and glycine mutants of Agrobacterium sp. beta-glucosidase, Abg E358S and E358G. Acceptors were linked to PEGA resin through a backbone amide linker (BAL), and using these mutated enzymes, a galactose moiety was transferred from a donor sugar, alpha-D-galactosyl fluoride, with high efficiency (>90%) together with excellent recovery of material. Furthermore, it was demonstrated that a resin-bound model glycopeptide was also an acceptor for the glycosynthase.

Acetylation↗