Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structure assignment of lucentamycin E and revision of the olefin geometries of the marine-derived lucentamycins.

ABSTRACT: A new lucentamycin analogue, lucentamycin E (5), was isolated from the culture broth of the marine-derived actinomycete Nocardiopsis lucentensis, strain CNR-712. The absolute stereostructure of 5 was assigned by comprehensive analyses of NMR data and by application of the advanced Marfey's method. The planar structure of 5 was analogous to lucentamycins A-D, whereas the olefin geometry of the 3-methyl-4-ethylideneproline moiety was found to be E, opposite of that previously reported. Consequently, a reinvestigation of the olefin geometries of the 3-methyl-4-ethylideneproline residues of lucentamycins A-D showed that the olefin geometries of the substituted proline functionalities must be revised to (2S,3R,E)-3-methyl-4-ethylideneproline.

SUBMITTER: Cha JW

PROVIDER: S-EPMC3689542 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Structure assignment of lucentamycin E and revision of the olefin geometries of the marine-derived lucentamycins.

Cha Jin Wook JW Park Jin-Soo JS Sim Taebo T Nam Sang-Jip SJ Kwon Hak Cheol HC Del Valle Juan R JR Fenical William W

Journal of natural products 20120906 9

A new lucentamycin analogue, lucentamycin E (5), was isolated from the culture broth of the marine-derived actinomycete Nocardiopsis lucentensis, strain CNR-712. The absolute stereostructure of 5 was assigned by comprehensive analyses of NMR data and by application of the advanced Marfey's method. The planar structure of 5 was analogous to lucentamycins A-D, whereas the olefin geometry of the 3-methyl-4-ethylideneproline moiety was found to be E, opposite of that previously reported. Consequentl ...[more]

PMID: 22953793

Similar Datasets

Revision of the Structure of Acremine P from a Marine-Derived Strain of Acremonium persicinum.

Project description:The previously published structure of the fungal metabolite acremine P is revised by re-evaluation of chemical shift values and NOESY data, and by DFT calculations.

| S-EPMC6154672 | biostudies-literature

Entropies Derived from the Packing Geometries within a Single Protein Structure.

Project description:A fast, simple, yet robust method to calculate protein entropy from a single protein structure is presented here. The focus is on the atomic packing details, which are calculated by combining Voronoi diagrams and Delaunay tessellations. Even though the method is simple, the entropies computed exhibit an extremely high correlation with the entropies previously derived by other methods based on quasi-harmonic motions, quantum mechanics, and molecular dynamics simulations. These packing-based entropies account directly for the local freedom and provide entropy for any individual protein structure that could be used to compute free energies directly during simulations for the generation of more reliable trajectories and also for better evaluations of modeled protein structures. Physico-chemical properties of amino acids are compared with these packing entropies to uncover the relationships with the entropies of different residue types. A public packing entropy web server is provided at packing-entropy.bb.iastate.edu, and the application programing interface is available within the PACKMAN (https://github.com/Pranavkhade/PACKMAN) package.

| S-EPMC9219053 | biostudies-literature

Total synthesis and structure revision of the marine metabolite palmerolide A.

Project description: Not available

| S-EPMC2529175 | biostudies-literature

Anti-Mycoplasma Activity of Bacilotetrins C-E, Cyclic Lipodepsipeptides from the Marine-Derived Bacillus subtilis and Structure Revision of Bacilotetrins A and B.

Project description:Mycoplasma hyorhinis most commonly causes polyserositis and arthritis in swine and is a common contaminant during the cell culture in the laboratory. In our continuing research for diverse bioactive compounds from Bacillus subtilis 109GGC020, we discovered uncommon cyclic lipotetrapeptides showing inhibitory activities against M. hyorhinis with similar structures to previously reported bacilotetrins A and B. Bacilotetrins C-E (1-3), new cyclic lipodepsipeptides, were isolated from the EtOAc extract obtained from the fermentation of marine-derived Bacillus subtilis isolated from a marine sponge sample collected from the Gageo reef, Republic of Korea. The structures of 1-3, consisting of three leucine residues, one glutamic acid, and a β-hydroxy fatty acid, were elucidated by detailed analysis of 1D, 2D NMR, and HR-ESIMS data. The absolute configurations of the amino acids and β-hydroxy fatty acid were established by advanced Marfey's method and Mosher's method, respectively. The localization of L- and D-amino acids within the compounds was determined by retention time comparison of each purchased dipeptide standard to the partial hydrolysate products using LC-MS. Compounds 1-3 exhibited anti-mycoplasma activity, with an MIC value of 31 μg/mL, twofold stronger than that of the positive control, BioMycoX®. Detailed analysis and comparison of the spectroscopic data between bacilotetrins A (4) and B (5) and 1-3 led us to revise the structures of 4 and 5.

| S-EPMC8537332 | biostudies-literature

RF-3192C and other polyketides from the marine endophytic <i>Aspergillus niger</i> ASSB4: structure assignment and bioactivity investigation.

Project description:Chemical investigation of the methanolic extract of endophytic Aspergillus niger SB4, isolated from the marine alga Laurencia obtuse, afforded the pentacyclic polyketide, RF-3192C (1), the dimeric coumarin orlandin (2), fonsecin B (3), TMC-256A1 (4), cyclo-(Leu-Ala) (5), and cerebroside A (6).The chemical structure of RF-3192C (1) is assigned herein for the first time using 1D/2D NMR and HRESI-MS. Additionally, the revision of the NMR assignments of orlandin (2) was reported herein as well. Investigation of the antimicrobial activities of isolated compounds revealed the high activity of RF-3192C (1) against Pseudomonas aeruginosa and Bacillus subtilis, and moderate activity against yeast. Moreover, an in vitro cytotoxic activity against liver (HEPG2), cervical (HELA), lung (A549), prostate (PC3), and breast (MCF7) cancer cell lines of the isolated compounds was evaluated. The isolation and taxonomical characterization of the producing fungus was reported as well.

| S-EPMC10993419 | biostudies-literature

Assignment of Absolute Configurations of Two Promising Anti-Helicobacter pylori Agents from the Marine Sponge-Derived Fungus Aspergillus niger L14.

Project description:A chemical investigation into endozoic fungus Aspergillus niger L14 derived from the marine sponge of Reniera japonica collected off Xinghai Bay (China) resulted in the isolation of two dimeric naphtho-γ-pyrones, fonsecinone A (1) and isoaurasperone A (2). Through a combination of ECD spectra and X-ray diffraction analysis, the chiral axes of compounds 1 and 2 were unambiguously determined as Rα-configurations. Bioassay results indicated that these substances exhibited remarkably inhibitory effects on human pathogens Helicobacter pylori G27 and 159 with MIC values of ≤4 μg/mL, which are similar to those of the positive control, ampicillin sodium. To the best of our knowledge, this is the first report on absolute configuration of 1 and crystallographic data of 2, as well as their potent anti-H. pylori activities.

| S-EPMC8399357 | biostudies-literature

Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.

Project description:BackgroundA number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. However the termini of the segments are often ill-defined and it is difficult to decide unambiguously which residues at the edge of the segments have to be included. In addition, there is a "twilight zone" where secondary structure segments depart significantly from the idealized models of Pauling and Corey. For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure.MethodsTo address these problems, we have developed a method for secondary structure assignment, called KAKSI. Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures).ResultsA detailed comparison of KAKSI assignments with those of STRIDE and PSEA reveals that KAKSI assigns slightly longer helices and strands than STRIDE in case of one-to-one correspondence between the segments. However, KAKSI tends also to favor the assignment of several short helices when STRIDE and PSEA assign longer, kinked, helices. Helices assigned by KAKSI have geometrical characteristics close to those described in the PDB. They are more linear than helices assigned by other methods. The same tendency to split long segments is observed for strands, although less systematically. We present a number of cases of secondary structure assignments that illustrate this behavior.ConclusionOur method provides valuable assignments which favor the regularity of secondary structure segments.

| S-EPMC1249586 | biostudies-literature

Revision of the Li13Si4 structure.

Project description:Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li-Si system is the phase Li13Si4 (trideca-lithium tetra-silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10-13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si-Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si-Si dumbbells at z = 0.5.

| S-EPMC3884973 | biostudies-literature

Structure Revision of the Lomaiviticins.

Project description:The lomaiviticins are dimeric genotoxic metabolites that contain unusual diazocyclopentadiene functional groups and 2-4 deoxyglycoside residues. Because only 6 of 19 carbon atoms in the monomeric aglycon unit are proton-attached, their structure determination by NMR spectroscopic analysis is difficult. Prior structure elucidation efforts established that the two halves of the lomaiviticins are joined by a single carbon-carbon bond appended to an oxidized cyclohexenone ring. This ring was believed to comprise a 4,5-dihydroxycyclohex-2-ene-1-one. The bridging bond was positioned at C6. This structure proposal has not been tested because no lomaiviticin has been prepared by total chemical synthesis or successfully analyzed by X-ray crystallography. Here, we disclose microED studies which establish that (-)-lomaiviticin C contains a 4,6-dihydroxy-cyclohex-2-ene-1-one residue, that the bridging carbon-carbon bond is located at C5, and that the orientation of the cyclohexenone ring and configuration of the secondary glycoside are reversed, relative to their original assignment. High-field (800 MHz) NMR analysis supports the revised assignment and suggests earlier efforts were misled by a combination of a near-zero 3JH4,H5 coupling constant and a 4JC,H coupling interpreted as a 3JC,H coupling. DFT calculations of the expected 13C chemical shifts and C-H coupling constants provide further robust support for the structure revision. Because the interconversion of lomaiviticins A, B, and C has been demonstrated, these findings apply to each isolate. These studies clarify the structures of this family of metabolites and underscore the power of microED analysis in natural product structure determination.

| S-EPMC8935351 | biostudies-literature

MS-Derived Isotopic Fine Structure Reveals Forazoline A as a Thioketone-Containing Marine-Derived Natural Product.

Project description:Forazoline A is a structurally complex PKS-NRPS hybrid produced by marine-derived Actinomadura sp. During the course of studies highlighting the application of IFS analysis as a powerful tool for natural products analysis, we were alerted to an earlier misinterpretation with respect to forazoline A structure elucidation. In particular, IFS reveals that forazoline A contains a thioketone moiety rarely seen in secondary metabolites and, thus, constitutes an even more intriguing structure than originally thought.

| S-EPMC7494057 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data