ORCID Profile
0000-0002-5212-4369
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Publisher: MDPI AG
Date: 09-10-2019
DOI: 10.3390/MD17100571
Abstract: Since our last review in 2015, the study and use of fucoidan has extended in several research areas. Clinical use of fucoidan for the treatment of renal disease has become available and human safety studies have been undertaken on radiolabeled fucoidan for the purpose of imaging thrombi. Fucoidan has been incorporated into an increasing number of commercially available supplements and topical treatments. In addition, new measuring techniques are now available to assess the biologically relevant uptake of fucoidans and to assist in production. Microbiome modulation and anti-pathogenic effects are increasingly promising applications for fucoidans, due to the need for alternative approaches to antibiotic use in the food chain. This review outlines promising new developments in fucoidan research, including potential future therapeutic use.
Publisher: American Society for Microbiology
Date: 15-06-2006
DOI: 10.1128/JB.01992-05
Abstract: The catalytic core of Escherichia coli DNA polymerase III contains three tightly associated subunits, the α, ε, and θ subunits. The θ subunit is the smallest and least understood subunit. The three-dimensional structure of θ in a complex with the unlabeled N-terminal domain of the ε subunit, ε186, was determined by multidimensional nuclear magnetic resonance spectroscopy. The structure was refined using pseudocontact shifts that resulted from inserting a lanthanide ion (Dy 3+ , Er 3+ , or Ho 3+ ) at the active site of ε186. The structure determination revealed a three-helix bundle fold that is similar to the solution structures of θ in a methanol-water buffer and of the bacteriophage P1 homolog, HOT, in aqueous buffer. Conserved nuclear Overhauser enhancement (NOE) patterns obtained for free and complexed θ show that most of the structure changes little upon complex formation. Discrepancies with respect to a previously published structure of free θ (Keniry et al., Protein Sci. 9: 721-733, 2000) were attributed to errors in the latter structure. The present structure satisfies the pseudocontact shifts better than either the structure of θ in methanol-water buffer or the structure of HOT. satisfies these shifts. The epitope of ε186 on θ was mapped by NOE difference spectroscopy and was found to involve helix 1 and the C-terminal part of helix 3. The pseudocontact shifts indicated that the helices of θ are located about 15 Å or farther from the lanthanide ion in the active site of ε186, in agreement with the extensive biochemical data for the θ-ε system.
Publisher: Wiley
Date: 28-01-2015
Abstract: Successful lead optimization in structure-based drug discovery depends on the correct deduction and interpretation of the underlying structure-activity relationships (SAR) to facilitate efficient decision-making on the next candidates to be synthesized. Consequently, the question arises, how frequently a binding mode (re)-validation is required, to ensure not to be misled by invalid assumptions on the binding geometry. We present an ex le in which minor chemical modifications within one inhibitor series lead to surprisingly different binding modes. X-ray structure determination of eight inhibitors derived from one core scaffold resulted in four different binding modes in the aspartic protease endothiapepsin, a well-established surrogate for e.g. renin and β-secretase. In addition, we suggest an empirical metrics that might serve as an indicator during lead optimization to qualify compounds as candidates for structural revalidation.
Publisher: Springer Science and Business Media LLC
Date: 10-10-2010
DOI: 10.1038/NSMB.1920
Publisher: Walter de Gruyter GmbH
Date: 25-01-2023
Abstract: Tasmania is an island state in south-eastern Australia that has a long and rich history of seaweed use, research, and development. It is a cool-temperate system with 750 macroalgal species currently described. Tasmanian Aboriginal peoples have lived on this land for at least 40,000 years utilising seaweed as food, shelter, water carriers and medicine, as well as for ceremonial reasons. Modern taxonomic investigations began with French naturalist Jacques-Julien Houtou de La Billardière in 1791, and there are 184 type specimens of seaweeds originating from Tasmania. Ecological and physiological studies of seaweed in Tasmania have focussed on the dominant large brown seaweeds (Laminariales and Fucales) and have contributed significantly to the global understanding of these systems, particularly related to community resilience, seaweed-urchin interactions, their habitat-forming role for other species, responses to global change, and restoration of lost habitat. Ocean warming and changing oceanography have caused a 95% decline in surface canopy cover of Macrocystis pyrifera in eastern Tasmania since the 1950s and led to a focus on restoring these lost forests. Tasmanian seaweed communities have a uniquely high proportion (up to ∼90%) of seaweeds that rely solely on CO 2 for photosynthesis, which has implications for responses to ocean acidification. Tasmania has industries that use brown seaweeds for fucoidan extraction and beach-cast harvest for alginates, fertilisers, and feeds for agriculture. New aquaculture initiatives include integrated multi-trophic aquaculture, offshore kelp mariculture and Asparagopsis cultivation for bioactive products to reduce methane emissions in ruminants, as and the development of unexploited species including Caulerpa spp. for food.
Publisher: Oxford University Press (OUP)
Date: 28-07-2008
DOI: 10.1093/NAR/GKN489
Publisher: Elsevier BV
Date: 10-2018
Publisher: Elsevier BV
Date: 08-2016
DOI: 10.1016/J.STR.2016.06.010
Abstract: Today the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design. While it is common to search for bound ligands in electron densities calculated directly after an initial refinement cycle, we raise the important question whether this strategy is viable for fragments characterized by low affinities. Here, we describe and provide a collection of high-quality diffraction data obtained from 364 protein crystals treated with erse fragments. Subsequent data analysis showed that ∼25% of all hits would have been missed without further refining the resulting structures. To enable fast and reliable hit identification, we have designed an automated refinement pipeline that will inspire the development of optimized tools facilitating the successful application of fragment-based methods.
Publisher: Elsevier BV
Date: 08-2022
Publisher: MDPI AG
Date: 11-12-2021
DOI: 10.3390/MD19120702
Abstract: Fucoidans are sulfated, complex, fucose-rich polymers found in brown seaweeds. Fucoidans have been shown to have multiple bioactivities, including anti-inflammatory effects, and are known to inhibit inflammatory processes via a number of pathways such as selectin blockade and enzyme inhibition, and have demonstrated inhibition of inflammatory pathologies in vivo. In this current investigation, fucoidan extracts from Undaria pinnatifida, Fucus vesiculosus, Macrocystis pyrifera, Ascophyllum nodosum, and Laminaria japonica were assessed for modulation of pro-inflammatory cytokine production (TNF-α, IL-1β, and IL-6) by human peripheral blood mononuclear cells (PBMCs) and in a human macrophage line (THP-1). Fucoidan extracts exhibited no signs of cytotoxicity in THP-1 cells after incubation of 48 h. Additionally, all fucoidan extracts reduced cytokine production in LPS stimulated PBMCs and human THP-1 cells in a dose-dependent fashion. Notably, the 5–30 kDa subfraction from Macrocystis pyrifera was a highly effective inhibitor at lower concentrations. Fucoidan extracts from all species had significant anti-inflammatory effects, but the lowest molecular weight subfractions had maximal effects at low concentrations. These observations on various fucoidan extracts offer insight into strategies that improve their efficacy against inflammation-related pathology. Further studies should be conducted to elucidate the mechanism of action of these extracts.
Publisher: MDPI AG
Date: 24-12-2020
DOI: 10.3390/MD19010004
Abstract: Compromised lung function is a feature of both infection driven and non-infective pathologies. Viral infections—including the current pandemic strain SARS-CoV-2—that affect lung function can cause both acute and long-term chronic damage. SARS-CoV-2 infection suppresses innate immunity and promotes an inflammatory response. Targeting these aspects of SARS-CoV-2 is important as the pandemic affects greater proportions of the population. In clinical and animal studies, fucoidans have been shown to increase innate immunity and decrease inflammation. In addition, dietary fucoidan has been shown to attenuate pulmonary damage in a model of acute viral infection. Direct inhibition of SARS-CoV-2 in vitro has been described, but is not universal. This short review summarizes the current research on fucoidan with regard to viral lung infections and lung damage.
Publisher: Informa UK Limited
Date: 21-03-2011
DOI: 10.3109/10409238.2011.559451
Abstract: Mass spectrometry is now established as a powerful tool for the study of the stoichiometry, interactions, dynamics, and subunit architecture of large protein assemblies and their subcomplexes. Recent evidence has suggested that the 3D structure of protein complexes can be maintained intact in the gas phase, highlighting the potential of ion mobility to contribute to structural biology. A key challenge is to integrate the compositional and structural information from ion mobility mass spectrometry with molecular modelling approaches to produce 3D models of intact protein complexes. In this review, we focus on the mass spectrometry of protein-nucleic acid assemblies with particular attention to the application of ion mobility, an emerging technique in structural studies. We also discuss the challenges that lie ahead for the full integration of ion mobility mass spectrometry with structural biology.
Publisher: American Chemical Society (ACS)
Date: 12-10-2007
DOI: 10.1021/JA0744753
Abstract: Pseudocontact shifts (PCSs) induced by a site-specifically bound paramagnetic lanthanide ion are shown to provide fast access to sequence-specific resonance assignments of methyl groups in proteins of known three-dimensional structure. Stereospecific assignments of Val and Leu methyls are obtained as well as resonance assignments of all other methyls, including Met epsilonCH3 groups. No prior assignments of the diamagnetic protein are required nor are experiments that transfer magnetization between the methyl groups and the protein backbone. Methyl Cz-exchange experiments were designed to provide convenient access to PCS measurements in situations where a paramagnetic lanthanide is in exchange with a diamagnetic lanthanide. In the absence of exchange, simultaneous 13C-HSQC assignments and PCS measurements are delivered by the newly developed program Possum. The approaches are demonstrated with the complex between the N-terminal domain of the subunit epsilon and the subunit theta of the Escherichia coli DNA polymerase III.
Publisher: MDPI AG
Date: 28-02-2020
DOI: 10.3390/MD18030143
Abstract: Fucoidans are a class of fucose-rich sulfated polysaccharides derived from brown macroalgae that exert a range of biological activities in vitro and in vivo. To generate an unbiased assessment of pathways and processes affected by fucoidan, a placebo-controlled double-blind pilot study was performed in healthy volunteers. Blood s les were taken immediately before and 24 h after ingestion of a single dose of 1 g of Undaria pinnatifida fucoidan (UPF) or placebo. Levels of isolated miRNAs were analyzed using Taqman Open Array Human MicroRNA panels. Out of 754 miRNAs screened, UPF affected a total of 53 miRNAs. Pathway analysis using the TALOS data analysis tool predicted 29 different pathways and processes that were largely grouped into cell surface receptor signaling, cancer-related pathways, the majority of which were previously associated with fucoidans. However, this analysis also identified nine pathways and processes that have not been associated with fucoidans before. Overall, this study illustrates that even a single dose of fucoidans has the potential to affect the expression of genes related to fundamental cellular processes. Moreover, it confirms previous data that fucoidans influence immunity, cancer cells, inflammation, and neurological function.
Publisher: Springer Science and Business Media LLC
Date: 08-05-2011
DOI: 10.1038/NSMB.2069
Publisher: Public Library of Science (PLoS)
Date: 10-08-2010
Publisher: Wiley
Date: 28-09-2012
Publisher: American Chemical Society (ACS)
Date: 25-02-2006
DOI: 10.1021/JA057008Z
Abstract: A novel nuclear magnetic resonance (NMR) strategy based on labeling with lanthanides achieves rapid determinations of accurate three-dimensional (3D) structures of protein-protein complexes. The method employs pseudocontact shifts (PCS) induced by a site-specifically bound lanthanide ion to anchor the coordinate system of the magnetic susceptibility tensor in the molecular frames of the two molecules. Simple superposition of the tensors detected in the two protein molecules brings them together in a 3D model of the protein-protein complex. The method is demonstrated with the 30 kDa complex between two subunits of Escherichia coli polymerase III, comprising the N-terminal domain of the exonuclease subunit epsilon and the subunit theta. The 3D structures of the in idual molecules were docked based on a limited number of PCS observed in 2D 15N-heteronuclear single quantum coherence spectra. Degeneracies in the mutual orientation of the protein structures were resolved by the use of two different lanthanide ions, Dy3+ and Er3+.
Publisher: Springer Science and Business Media LLC
Date: 12-12-2010
DOI: 10.1038/NSMB.1971
Abstract: Protein folding is assisted by molecular chaperones. CCT (chaperonin containing TCP-1, or TRiC) is a 1-MDa oligomer that is built by two rings comprising eight different 60-kDa subunits. This chaperonin regulates the folding of important proteins including actin, α-tubulin and β-tubulin. We used an electron density map at 5.5 Å resolution to reconstruct CCT, which showed a substrate in the inner cavities of both rings. Here we present the crystal structure of the open conformation of this nanomachine in complex with tubulin, providing information about the mechanism by which it aids tubulin folding. The structure showed that the substrate interacts with loops in the apical and equatorial domains of CCT. The organization of the ATP-binding pockets suggests that the substrate is stretched inside the cavity. Our data provide the basis for understanding the function of this chaperonin.
Publisher: American Chemical Society (ACS)
Date: 29-12-2006
DOI: 10.1021/JA066995O
Publisher: American Chemical Society (ACS)
Date: 13-09-2006
DOI: 10.1021/JA063584Z
Abstract: Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small ligand molecule bound to its protein target in solution and, simultaneously, its location and orientation with respect to the protein. The method relies on the presence of a lanthanide ion in the protein target and on fast exchange between bound and free ligand. The binding affinity of the ligand and the paramagnetic effects experienced in the bound state are derived from concentration-dependent (1)H and (13)C spectra of the ligand at natural isotopic abundance. Combined with prior knowledge of the crystal or solution structure of the protein and of the magnetic susceptibility tensor of the lanthanide ion, the paramagnetic data define the location and orientation of the bound ligand molecule with respect to the protein from simple 1D NMR spectra. The method was verified with the ternary 30 kDa complex between the lanthanide-labeled N-terminal domain of the epsilon exonuclease subunit from the Escherichia coli DNA polymerase III, the subunit theta, and thymidine. The binding mode of thymidine was found to be very similar to that of thymidine monophosphate present in the crystal structure.
Publisher: MDPI AG
Date: 08-05-2020
DOI: 10.3390/MD18050246
Abstract: Fucoidans are known to be effective inhibitors of inflammation, and of virus binding and cellular entry. Undaria pinnatifida-derived fucoidan (UPF) was assessed in a severe influenza A (H1N1, PR8) infection model in mice. Initially, UPF was gavaged at 3.52 mg daily in a treatment model. Gross lung pathology (consolidation) was significantly reduced as compared to controls. UPF was then presented as a feed supplement at a rate of either nil, 3.52 mg/day or 7.04 mg/day in a prophylactic model, dosed three days before infection. A significant improvement was observed in the clinical signs of ill-health, as well as a reduction in gross lung pathology in animals treated with the higher dose, although there was no significant reduction in lung viral titres.
Publisher: MDPI AG
Date: 04-11-2022
DOI: 10.3390/PHARMACEUTICS14112383
Abstract: Inflammatory bowel disease (IBD) is a complex and multifactorial disorder characterised by relapsing and remitting inflammation of the intestinal tract. Oxidative stress (OS) is the result of an imbalance between production and accumulation of reactive oxygen species (ROS), which has been associated with inflammatory responses and implicated in the exacerbation of IBD. Fucoidan, a sulfated polysaccharide from brown seaweed, is a well-known anti-inflammatory agent and emerging evidence indicates that fucoidan extracts from Macrocystis pyrifera (MPF and DP-MPF) may also modulate oxidative stress. This study investigated the impact of fucoidan extracts, MPF and DP-MPF in a dextran sodium sulphate (DSS)-induced mouse model of acute colitis. 3% DSS was administered in C57BL/6J male mice over a period of 7 days, and MPF and DP-MPF were co-administered orally at a dose of 400 mg/kg body weight. Our results indicated that MPF and DP-MPF significantly prevented body weight loss, improved the disease activity index (DAI), restored colon lengths, reduced the wet colon weight, reduced spleen enlargement, and improved the overall histopathological score. Consistent with the reported anti-inflammatory functions, fucoidan extracts, MPF and DP-MPF significantly reduced the colonic levels of myeloperoxidase (MPO), nitric oxide (NO), malondialdehyde (MDA) and increased the levels of antioxidant enzymes, superoxide dismutase (SOD) and catalase (CAT). In addition, MPF and DP-MPF significantly inhibited levels of pro-inflammatory cytokines in colon-derived tissues. Collectively, our results indicate that MPF and DP-MPF exhibited anti-inflammatory and antioxidant effects representing a promising therapeutic strategy for the cure of IBD.
Publisher: Elsevier BV
Date: 02-2008
DOI: 10.1016/J.PEP.2007.10.005
Abstract: Escherichia coli oligoribonuclease (EcoORN), encoded by the orn gene, is a 3'-5' exonuclease that degrades short single-stranded oligoribonucleotides to rNMPs in the final step of RNA degradation. The orn gene is essential in E. coli, but not in higher organisms, and close homologues are present in other genomes from the beta and gamma sub isions of the Protobacteriaceae, including many pathogenic species. We report here the expression in E. coli of orn and homologues from Mycobacterium smegmatis and human, and large-scale purification of the three enzymes. All three were found to promote the hydrolysis of the 5'-p-nitrophenyl ester of TMP (pNP-TMP) with similar values of Michaelis-Menten parameters (k(cat)=100-650 min(-1), K(M)=0.4-2.0 mM, at pH 8.00 and 25 degrees C, with 1 mM Mn(2+)). Hydrolysis by pNP-TMP by all three enzymes depended on a alent metal ion, with Mn(2+) being preferred over Mg(2+) as cofactor, and was inhibited by Ni(2+). The concentration dependency of Mn(2+) was examined, giving K(Mn) values of 0.2-0.6 mM. The availability of large amounts of the purified enzymes and a simple spectrophotometric assay for ORN activity should facilitate large-scale screening for new inhibitors of bacterial oligoribonucleases.
Publisher: American Chemical Society (ACS)
Date: 13-02-2004
DOI: 10.1021/JA039339M
Abstract: A novel strategy for fast NMR resonance assignment of (15)N HSQC spectra of proteins is presented. It requires the structure coordinates of the protein, a paramagnetic center, and one or more residue-selectively (15)N-labeled s les. Comparison of sensitive undecoupled (15)N HSQC spectra recorded of paramagnetic and diamagnetic s les yields data for every cross-peak on pseudocontact shift, paramagnetic relaxation enhancement, cross-correlation between Curie-spin and dipole-dipole relaxation, and residual dipolar coupling. Comparison of these four different paramagnetic quantities with predictions from the three-dimensional structure simultaneously yields the resonance assignment and the anisotropy of the susceptibility tensor of the paramagnetic center. The method is demonstrated with the 30 kDa complex between the N-terminal domain of the epsilon subunit and the theta subunit of Escherichia coli DNA polymerase III. The program PLATYPUS was developed to perform the assignment, provide a measure of reliability of the assignment, and determine the susceptibility tensor anisotropy.
Publisher: MDPI AG
Date: 22-12-2021
DOI: 10.3390/MD20010012
Abstract: Fucoidan compounds may increase immune activity and are known to have cancer inhibitory effects in vitro and in vivo. In this study, we aimed to investigate the effect of fucoidan compounds on ex vivo human peripheral blood mononuclear cells (PBMCs), and to determine their cancer cell killing activity both solely, and in combination with an immune-checkpoint inhibitor drug, Nivolumab. Proliferation of PBMCs and interferon gamma (IFNγ) release were assessed in the presence of fucoidan compounds extracted from Fucus vesiculosus, Undaria pinnatifida and Macrocystis pyrifera. Total cell numbers and cell killing activity were assessed using a hormone resistant prostate cancer cell line, PC3. All fucoidan compounds activated PBMCs, and increased the effects of Nivolumab. All fucoidan compounds had significant direct cytostatic effects on PC3 cells, reducing cancer cell numbers, and PBMCs exhibited cell killing activity as measured by apoptosis. However, there was no fucoidan mediated increase in the cell killing activity. In conclusion, fucoidan compounds promoted proliferation and activity of PBMCs and added to the effects of Nivolumab. Fucoidan compounds all had a direct cytostatic effect on PC3 cells, as shown through their proliferation reduction, while their killing was not increased.
Publisher: Royal Society of Chemistry (RSC)
Date: 2021
DOI: 10.1039/D0CC06299E
Abstract: A tetracationic imidazolium-based catenane is reported which is selective for bromide over other halides in aqueous media.
Publisher: MDPI AG
Date: 14-01-2019
DOI: 10.3390/MD17010054
Abstract: Fucoidan, the sulfated fucose-rich polysaccharide derived from brown macroalgae, was reported to display some anti-cancer effects in in vitro and in vivo models that included apoptosis and cell cycle arrest. The proposed mechanisms of action involve enhanced immune surveillance and direct pro-apoptotic effects via the activation of cell signaling pathways that remain largely uncharacterized. This study aimed to identify cellular pathways influenced by fucoidan using an unbiased genetic approach to generate additional insights into the anti-cancer effects of fucoidan. Drug–gene interactions of Undaria pinnatifida fucoidan were assessed by a systematic screen of the entire set of 4,733 halpoid Saccharomyces cerevsiae gene deletion strains. Some of the findings were confirmed using cell cycle analysis and DNA damage detection in non-immortalized human dermal fibroblasts and colon cancer cells. The yeast deletion library screen and subsequent pathway and interactome analysis identified global effects of fucoidan on a wide range of eukaryotic cellular processes, including RNA metabolism, protein synthesis, sorting, targeting and transport, carbohydrate metabolism, mitochondrial maintenance, cell cycle regulation, and DNA damage repair-related pathways. Fucoidan also reduced clonogenic survival, induced DNA damage and G1-arrest in colon cancer cells, while these effects were not observed in non-immortalized human fibroblasts. Our results demonstrate global effects of fucoidan in erse cellular processes in eukaryotic cells and further our understanding about the inhibitory effect of Undaria pinnatifida fucoidan on the growth of human cancer cells.
Publisher: Elsevier BV
Date: 11-2013
DOI: 10.1016/J.JMB.2013.04.006
Abstract: DNA polymerase III, a decameric 420-kDa assembly, simultaneously replicates both strands of the chromosome in Escherichia coli. A subassembly of this holoenzyme, the seven-subunit cl loader complex, is responsible for loading the sliding cl (β2) onto DNA. Here, we use structural information derived from ion mobility mass spectrometry (IM-MS) to build three-dimensional models of one form of the full cl loader complex, γ3δδ'ψχ (254 kDa). By probing the interaction between the cl loader and a single-stranded DNA (ssDNA) binding protein (SSB4) and by identifying two distinct conformational states, with and without ssDNA, we assemble models of ψχ-SSB4 (108 kDa) and the cl loader-SSB4 (340 kDa) consistent with IM data. A significant increase in measured collision cross-section (~10%) of the cl loader-SSB4 complex upon DNA binding suggests large conformational rearrangements. This DNA bound conformation represents the active state and, along with the presence of ψχ, stabilises the cl loader-SSB4 complex. Overall, this study of a large heteromeric complex analysed by IM-MS, coupled with integrative modelling, highlights the potential of such an approach to reveal structural features of previously unknown complexes of high biological importance.
Publisher: Elsevier BV
Date: 03-2010
Publisher: Wiley
Date: 02-2021
DOI: 10.14814/PHY2.14730
Publisher: American Chemical Society (ACS)
Date: 28-10-2016
DOI: 10.1021/ACS.JMEDCHEM.6B01195
Abstract: Crystallography is frequently used as follow-up method to validate hits identified by biophysical screening cascades. The capacity of crystallography to directly screen fragment libraries is often underestimated, due to its supposed low-throughput and need for high-quality crystals. We applied crystallographic fragment screening to map the protein-binding site of the aspartic protease endothiapepsin by in idual soaking experiments. Here, we report on 41 fragments binding to the catalytic dyad and adjacent specificity pockets. The analysis identifies already known warheads but also reveals hydrazide, pyrazole, or carboxylic acid fragments as novel functional groups binding to the dyad. A remarkable swapping of the S1 and S1' pocket between structurally related fragments is explained by either steric demand, required displacement of a well-bound water molecule, or changes of trigonal-planar to tetrahedral geometry of an oxygen functional group in a side chain. Some warheads simultaneously occupying both S1 and S1' are promising starting points for fragment-growing strategies.
Publisher: Springer Science and Business Media LLC
Date: 06-2006
DOI: 10.1007/S10858-006-9002-4
Abstract: Anisotropic magnetic susceptibility tensors chi of paramagnetic metal ions are manifested in pseudocontact shifts, residual dipolar couplings, and other paramagnetic observables that present valuable long-range information for structure determinations of protein-ligand complexes. A program was developed for automatic determination of the chi-tensor anisotropy parameters and amide resonance assignments in proteins labeled with paramagnetic metal ions. The program requires knowledge of the three-dimensional structure of the protein, the backbone resonance assignments of the diamagnetic protein, and a pair of 2D 15N-HSQC or 3D HNCO spectra recorded with and without paramagnetic metal ion. It allows the determination of reliable chi-tensor anisotropy parameters from 2D spectra of uniformly 15N-labeled proteins of fairly high molecular weight. Ex les are shown for the 185-residue N-terminal domain of the subunit epsilon from E. coli DNA polymerase III in complex with the subunit theta and La3+ in its diamagnetic and Dy3+, Tb3+, and Er3+ in its paramagnetic form.
Publisher: Elsevier BV
Date: 02-2009
Publisher: MDPI AG
Date: 25-03-2021
DOI: 10.3390/DERMATOPATHOLOGY8020012
Abstract: Atopic dermatitis is a multifactorial pathology that includes perturbations of gene expression and increased adhesion of Staphylococcus aureus. Fucoidans are seaweed-derived sulfated fucose-rich polysaccharides that are known to be anti-inflammatory and may inhibit adhesion of pathogens. Fucoidan was assessed for effects on gene expression of an in vitro 3D model of atopic dermatitis. It was also assessed for inhibitory effects on the adhesion of bacteria onto 3D reconstructed skin. Fucoidan significantly altered gene expression in the atopic dermatitis model, and there was a trend to reduce periostin levels. Fucoidan significantly inhibited the adhesion of Staphylococcus aureus and Cutibacterium acnes but did not affect the adhesion of Staphylococcus epidermidis. Fucoidan may be a useful topical agent to assist in the management of atopic dermatitis.
Publisher: American Chemical Society (ACS)
Date: 12-11-2005
DOI: 10.1021/JA0564259
Abstract: Paramagnetic metal ions can induce molecular alignment with respect to the magnetic field. This alignment generates residual anisotropic chemical shifts (RACS) due to nonisotropic averaging over the molecular orientations. Using a 30 kDa protein-protein complex, the RACS effects are shown to be significant for heteronuclear spins with large chemical shift anisotropies, lanthanide ions with large anisotropic magnetic susceptibility tensors, and measurements at high magnetic field. Therefore, RACS must be taken into account when pseudocontact shifts are measured by comparison of chemical shifts observed between complexes with paramagnetic and diamagnetic lanthanide ions. The results are of particular importance when different pseudocontact shifts measured for the 1HN, 15N, and 13C' spins of a peptide group are used to restrain its orientation with respect to the electronic magnetic susceptibility tensor in structure calculations.
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Ahyoung Park.