Rigidity analysis of HIV-1 protease

We present a rigidity analysis on a large number of X-ray crystal structures of the enzyme HIV-1 protease using the 'pebble game' algorithm of the software FIRST. We find that although the rigidity profile remains similar across a comprehensive set of high resolution structures, the profile changes significantly in the presence of an inhibitor. Our study shows that the action of the inhibitors is to restrict the flexibility of the beta-hairpin flaps which allow access to the active site. The results are discussed in the context of full molecular dynamics simulations as well as data from NMR experiments.Comment: 4 pages, 3 figures. Conference proceedings for CMMP conference 2010 which was held at the University of Warwic

Molecular detection of Wolbachia endosymbiont in reptiles and their ectoparasites

Wolbachia, a maternally transmitted Gram-negative endosymbiont of onchocercid nematodes and arthropods, has a role in the biology of their host; thus it has been exploited for the filariasis treatment in humans. To assess the presence and prevalence of this endosymbiont in reptiles and their ectoparasites, blood and tail tissue as well as ticks and mites collected from them were molecularly screened for Wolbachia DNA using two sets of primers targeting partial 16S rRNA and Wolbachia surface protein (wsp) genes. Positive samples were screened for the partial 12S rRNA and cytochrome c oxidase subunit 1 (cox1) genes for filarioids. Of the different species of lizards (Podarcis siculus, Podarcis muralis and Lacerta bilineata) and snakes (Elaphe quatuorlineata and Boa constrictor constrictor) screened from three collection sites, only P. siculus scored positive for Wolbachia 16S rRNA. Among ectoparasites collected from reptiles (Ixodes ricinus ticks and Neotrombicula autumnalis, Ophionyssus sauracum and Ophionyssus natricis mites), I. ricinus (n = 4; 2.8%; 95% CI, 0.9–7) from P. siculus, N. autumnalis (n = 2 each; 2.8%; 95% CI, 0.9–6.5) from P. siculus and P. muralis and O. natricis (n = 1; 14.3%; 95% CI, 0.7–55.4) from Boa constrictor constrictor scored positive for Wolbachia DNA. None of the positive Wolbachia samples scored positive for filarioids. This represents the first report of Wolbachia in reptilian hosts and their ectoparasites, which follows a single identification in the intestinal cells of a filarioid associated with a gecko. This data could contribute to better understand the reptile filarioid-Wolbachia association and to unveil the evolutionary pattern of Wolbachia in its filarial host

Comparative analysis of rigidity across protein families

We present a comparative study in which 'pebble game' rigidity analysis is applied to multiple protein crystal structures, for each of six different protein families. We find that the main-chain rigidity of a protein structure at a given hydrogen bond energy cutoff is quite sensitive to small structural variations, and conclude that the hydrogen bond constraints in rigidity analysis should be chosen so as to form and test specific hypotheses about the rigidity of a particular protein. Our comparative approach highlights two different characteristic patterns ('sudden' or 'gradual') for protein rigidity loss as constraints are removed, in line with recent results on the rigidity transitions of glassy networks

Exact two-spinon dynamical correlation function of the Heisenberg model

We derive the exact contribution of two spinons to the dynamical correlation function of the spin-1/2 Heisenberg model. For this, we use the isotropic limits of the exact form factors that have been recently computed through the quantum affine symmetry of the anisotropic Heisenberg model $XXZ$Comment: 9 pages, Latex, 2 corrections of coefficient

Development of a single crystal sample holder for interfacing ultrahigh vacuum and electrochemical experimentation

Electrocatalyst surfaces prepared under ultrahigh vacuum (UHV) conditions can create model surfaces to better connect theoretical calculations with experimental studies. The development of a single crystal sample holder and inert electrochemical cells prepared with modularity and chemical stability in mind would allow for expensive single crystals to be reused indefinitely in both UHV and electrochemical settings. This sample holder shows reproducible surface preparations for single crystal samples and consistent electrochemical experiments without the introduction of impurities into the surface. The presented setup has been used as a critical piece for the characterization of Cu(111) surfaces under CO2 electrochemical reduction reaction conditions as a test case