Visual cavity analysis in molecular simulations

Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel technique, which extracts potential binding sites, represented by cavities, and characterize them by 3D graphs and by amino acids. The binding sites are extracted using an implicit function sampling and graph algorithms. We propose an advanced cavity exploration technique based on the graph parameters and associated amino acids. Additionally, we interactively visualize the graphs in the context of the molecular surface. We apply our method to the analysis of MD simulations of Proteinase 3, where we verify the previously described cavities and suggest a new potential cavity to be studied

Spheres Unions and Intersections and Some of their Applications in Molecular Modeling

Accepted manuscript was chapter 2, pp.17-39, then was published as chapter 4, pp.61-83.International audienceThe geometrical and computational aspects of spheres unions and intersections are described. A practical analytical calculation of their surfaces and volumes is given in the general case: any number of intersecting spheres of any radii. Applications to trilateration and van der Waals surfaces and volumes calculation are considered. The results are compared to those of other algorithms, such as Monte-Carlo methods, regular grid methods, or incomplete analytical algorithms. For molecular modeling, these latter algorithms are shown to give strongly overestimated values when the radii values are in the ranges recommended in the literature, while regular grid methods are shown to give a poor accuracy. Other concepts related to surfaces and volumes of unions of spheres are evoked, such as Connolly's surfaces, accessible surface areas, and solvent excluded volumes

PSMB2 and RPL32 are suitable denominators to normalize gene expression profiles in bronchoalveolar cells-2

Zed to 1); the whiskers on each box represent the SD values. For details see Methods section Gene expression measurements by qRT-PCR. *< 0.05.<p><b>Copyright information:</b></p><p>Taken from "PSMB2 and RPL32 are suitable denominators to normalize gene expression profiles in bronchoalveolar cells"</p><p>http://www.biomedcentral.com/1471-2199/9/69</p><p>BMC Molecular Biology 2008;9():69-69.</p><p>Published online 31 Jul 2008</p><p>PMCID:PMC2529339.</p><p></p

PSMB2 and RPL32 are suitable denominators to normalize gene expression profiles in bronchoalveolar cells-1

Ents with involvement of parenchyma: CXR stages II/III)-Mean(patients without involvement of parenchyma: CXR stage I), Mean(Löfgren's syndrome patients)-Mean(non-Löfgren's syndrome patients), Mean(multi-organ involvement)-Mean(involvement of lung only), Mean(smokers)-Mean(non-smokers), Mean(males)-Mean(females), and Mean(pathological BAL cell count)-Mean(normal BAL cell count) for macrophages, lymphocytes, neutrophils and eosinophils. For more details see the legend to Fig. 2.<p><b>Copyright information:</b></p><p>Taken from "PSMB2 and RPL32 are suitable denominators to normalize gene expression profiles in bronchoalveolar cells"</p><p>http://www.biomedcentral.com/1471-2199/9/69</p><p>BMC Molecular Biology 2008;9():69-69.</p><p>Published online 31 Jul 2008</p><p>PMCID:PMC2529339.</p><p></p

PSMB2 and RPL32 are suitable denominators to normalize gene expression profiles in bronchoalveolar cells-0

Ker box plots; the box represents the 25th–75th percentiles, the median is indicated by a bar across the box, the whiskers on each box represent the minimum and maximum values.<p><b>Copyright information:</b></p><p>Taken from "PSMB2 and RPL32 are suitable denominators to normalize gene expression profiles in bronchoalveolar cells"</p><p>http://www.biomedcentral.com/1471-2199/9/69</p><p>BMC Molecular Biology 2008;9():69-69.</p><p>Published online 31 Jul 2008</p><p>PMCID:PMC2529339.</p><p></p

The inner workings of the hydrazine synthase multiprotein complex

Anaerobic ammonium oxidation (anammox) has a major role in the Earth's nitrogen cycle and is used in energy-efficient wastewater treatment. This bacterial process combines nitrite and ammonium to form dinitrogen (N2) gas, and has been estimated to synthesize up to 50% of the dinitrogen gas emitted into our atmosphere from the oceans. Strikingly, the anammox process relies on the highly unusual, extremely reactive intermediate hydrazine, a compound also used as a rocket fuel because of its high reducing power. So far, the enzymatic mechanism by which hydrazine is synthesized is unknown. Here we report the 2.7 Å resolution crystal structure, as well as biophysical and spectroscopic studies, of a hydrazine synthase multiprotein complex isolated from the anammox organism Kuenenia stuttgartiensis. The structure shows an elongated dimer of heterotrimers, each of which has two unique c-type haem-containing active sites, as well as an interaction point for a redox partner. Furthermore, a system of tunnels connects these active sites. The crystal structure implies a two-step mechanism for hydrazine synthesis: a three-electron reduction of nitric oxide to hydroxylamine at the active site of the γ-subunit and its subsequent condensation with ammonia, yielding hydrazine in the active centre of the α-subunit. Our results provide the first, to our knowledge, detailed structural insight into the mechanism of biological hydrazine synthesis, which is of major significance for our understanding of the conversion of nitrogenous compounds in nature