21 research outputs found
Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus
Fatty acid and retinol-binding proteins (FARs) comprise a family of unusual a-helix rich lipid-binding proteins found exclusively in nematodes. They are secreted into host tissues by parasites of plants, animals and humans. The structure of a FAR protein from the free-living nematode Caenorhabditis elegans is available, but this protein [C. elegans FAR-7 (Ce-FAR-7)] is from a subfamily of FARs that does not appear to be important at the host/parasite interface. We have therefore examined [Necator americanus FAR-1 (Na-FAR-1)] from the blood-feeding intestinal parasite of humans, N. americanus. The 3D structure of Na-FAR-1 in its ligand-free and ligand-bound forms, determined byNMR(nuclear magnetic resonance) spectroscopy and X-ray crystallography respectively, reveals an a-helical fold similar to Ce-FAR-7, but Na-FAR-1 possesses a larger and more complex internal ligandbinding cavity and an additional C-terminal a-helix. Titration of apo-Na-FAR-1 with oleic acid, analysed by NMR chemical shift perturbation, reveals that at least four distinct protein-ligand complexes can be formed. Na-FAR-1 and possibly other FARs may have a wider repertoire for hydrophobic ligand binding, as confirmed in the present study by our finding that a range of neutral and polar lipids co-purify with the bacterially expressed recombinant protein. Finally, we show by immunohistochemistry that Na-FAR-1 is present in adult worms with a tissue distribution indicative of possible roles in nutrient acquisition by the parasite and in reproduction in the male.Instituto de Investigaciones Bioquímicas de La Plat
Comparative genomics of the major parasitic worms
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we report a broad comparative study of 81 genomes of parasitic and non-parasitic worms. We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We reveal extensive lineage-specific differences in core metabolism and protein families historically targeted for drug development. From an in silico screen, we have identified and prioritized new potential drug targets and compounds for testing. This comparative genomics resource provides a much-needed boost for the research community to understand and combat parasitic worms
Identification of rare Lewis oligosaccharide conformers in aqueous solution using enhanced sampling molecular dynamics
Determining
the conformations accessible to carbohydrate ligands in aqueous solution is
important for understanding their biological action. In this work, we evaluate
the conformational free energy surfaces of Lewis oligosaccharides in explicit
aqueous solvent using a multidimensional variant of the swarm-enhanced sampling
molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased
MD simulations, umbrella sampling and accelerated MD approaches. For the sialyl
Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer
landscapes in general agreement with the other biased methods and with triplicate
unbiased 10 ms trajectories;
these simulations find a predominance of closed conformer and a range of low
occupancy open forms. The msesMD simulations also suggest closed-to-open
transitions in the tetrasaccharide are facilitated by changes in ring puckering
of its GlcNAc residue away from the 4C1 form, in line
with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations
predict a minor population of an open form in solution, corresponding to a rare
lectin-bound pose observed crystallographically. Overall, from comparison with
biased MD calculations, we find that triplicate 10 ms unbiased MD simulations may not be enough
to fully sample glycan conformations in aqueous solution. However, the
computational efficiency and intuitive approach of the msesMD method suggest
potential for its application in glycomics as a tool for analysis of
oligosaccharide conformation.</p
Identification of rare Lewis oligosaccharide conformers in aqueous solution using enhanced sampling molecular dynamics
<p>Determining
the conformations accessible to carbohydrate ligands in aqueous solution is
important for understanding their biological action. In this work, we evaluate
the conformational free energy surfaces of Lewis oligosaccharides in explicit
aqueous solvent using a multidimensional variant of the swarm-enhanced sampling
molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased
MD simulations, umbrella sampling and accelerated MD approaches. For the sialyl
Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer
landscapes in general agreement with the other biased methods and with triplicate
unbiased 10 ms trajectories;
these simulations find a predominance of closed conformer and a range of low
occupancy open forms. The msesMD simulations also suggest closed-to-open
transitions in the tetrasaccharide are facilitated by changes in ring puckering
of its GlcNAc residue away from the <sup>4</sup>C<sub>1</sub> form, in line
with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations
predict a minor population of an open form in solution, corresponding to a rare
lectin-bound pose observed crystallographically. Overall, from comparison with
biased MD calculations, we find that triplicate 10 ms unbiased MD simulations may not be enough
to fully sample glycan conformations in aqueous solution. However, the
computational efficiency and intuitive approach of the msesMD method suggest
potential for its application in glycomics as a tool for analysis of
oligosaccharide conformation.</p
Size-Tunable Trehalose-Based Nanocavities: Synthesis, Structure, and Inclusion Properties of Large-Ring Cyclotrehalans
13 páginas, 4 figuras, 1 tabla, esquemas.An efficient strategy toward the synthesis of large-ring cyclodextrin (CD) analogs alternating alpha,alpha'-trehalose disaccharide subunits and pseudoamide segments (cyclotrehalans, CTs), involving a bimolecular macrocyclization reaction as the key step, is reported. NMR and molecular modeling confirmed that the eight and ten alpha-d-glucopyranoside subunits in tetrameric and pentameric CT homologues (CT4 and CT5, respectively) are magnetically equivalent, as in the gamma and epsilonCD counterparts. Yet, the orientation of the monosaccharide constituents is reversed in CTs as compared with CDs, the beta-face being directed to the inside of the nanometric cavity while the alpha-face remains in contact with the bulk solvent. Molecular mechanics and dynamics experiments revealed that the cyclooligosaccharide architecture in CT4 and CT5 is relatively flexible, which is in contrast to that previously observed for the first members of the CT series (CT2 and CT3 oligomers). Thus, although in their fully expanded conformation their cavity size is close to that of gammaCD, the higher mobility of the pseudoamide bridges as compared with classical glycosidic linkages endows these hosts with induced fitting capabilities toward smaller guests.We thank the Spanish Ministerio de Educación y Ciencia (contract numbers CTQ2006-15515-C02-01/BQU, CTQ2007-61180/PPQ, and CTQ2006-08256 and a doctoral fellowship to D.R.-L.) and the Junta de Andalucía.Peer reviewe
Exploring Protein Kinase Conformation Using Swarm-Enhanced Sampling Molecular Dynamics
Protein
plasticity, while often linked to biological function,
also provides opportunities for rational design of selective and potent
inhibitors of their function. The application of computational methods
to the prediction of concealed protein concavities is challenging,
as the motions involved can be significant and occur over long time
scales. Here we introduce the swarm-enhanced sampling molecular dynamics
(sesMD) method as a tool to improve sampling of conformational landscapes.
In this approach, a swarm of replica simulations interact cooperatively
via a set of pairwise potentials incorporating attractive and repulsive
components. We apply the sesMD approach to explore the conformations
of the DFG motif in the protein p38α mitogen-activated protein
kinase. In contrast to multiple MD simulations, sesMD trajectories
sample a range of DFG conformations, some of which map onto existing
crystal structures. Simulated structures intermediate between the
DFG-in and DFG-out conformations are predicted to have druggable pockets
of interest for structure-based ligand design