1,524 research outputs found
Donor-strand exchange in chaperone-assisted pilus assembly revealed in atomic detail by molecular dynamics
Adhesive multi-subunit fibres are assembled on the surface of many pathogenic bacteria via the chaperone-usher pathway. In the periplasm, a chaperone donates a β-strand to a pilus subunit to complement its incomplete immunoglobulin-like fold. At the outer membrane, this is replaced with
a β-strand formed from the N-terminal extension (Nte) of an incoming pilus subunit by a donorstrand exchange (DSE) mechanism. This reaction has previously been shown to proceed via a concerted mechanism, in which the Nte interacts with the chaperone:subunit complex before the
chaperone has been displaced, forming a ternary intermediate. Thereafter, the pilus and chaperone
β-strands have been postulated to undergo a strand swap by a ‘zip-in-zip-out’ mechanism, whereby the chaperone strand zips out, residue by residue, as the Nte simultaneously zips in. Here, molecular dynamics simulations have been used to probe the DSE mechanism during formation of
the Salmonella enterica Saf pilus at an atomic level, allowing the direct investigation of the zip-inzip-
out hypothesis. The simulations provide an explanation of how the incoming Nte is able to dock and initiate DSE due to inherent dynamic fluctuations within the chaperone:subunit complex. The chaperone donor-strand is shown to unbind from the pilus subunit residue by residue, in direct
support of the zip-in-zip-out hypothesis. In addition, an interaction of a residue towards the Nterminus
of the Nte with a specific binding pocket (P*) on the adjacent pilus subunit is shown to stabilise the DSE product against unbinding, which also proceeds by a zippering mechanism. Together, the study provides an in-depth picture of DSE, including the first insights into the
molecular events occurring during the zip-in-zip-out mechanism
Quantum Circuits for the Unitary Permutation Problem
We consider the Unitary Permutation problem which consists, given unitary
gates and a permutation of , in
applying the unitary gates in the order specified by , i.e. in
performing . This problem has been
introduced and investigated by Colnaghi et al. where two models of computations
are considered. This first is the (standard) model of query complexity: the
complexity measure is the number of calls to any of the unitary gates in
a quantum circuit which solves the problem. The second model provides quantum
switches and treats unitary transformations as inputs of second order. In that
case the complexity measure is the number of quantum switches. In their paper,
Colnaghi et al. have shown that the problem can be solved within calls in
the query model and quantum switches in the new model. We
refine these results by proving that quantum switches
are necessary and sufficient to solve this problem, whereas calls
are sufficient to solve this problem in the standard quantum circuit model. We
prove, with an additional assumption on the family of gates used in the
circuits, that queries are required, for any
. The upper and lower bounds for the standard quantum circuit
model are established by pointing out connections with the permutation as
substring problem introduced by Karp.Comment: 8 pages, 5 figure
Structure of a bacterial type IV secretion core complex at subnanometre resolution
Type IV secretion (T4S) systems are able to transport DNAs and/or proteins through the membranes of bacteria. They form large multiprotein complexes consisting of 12 proteins termed VirB1-11 and VirD4. VirB7, 9 and 10 assemble into a 1.07 MegaDalton membrane-spanning core complex (CC), around which all other components assemble. This complex is made of two parts, the O-layer inserted in the outer membrane and the I-layer inserted in the inner membrane. While the structure of the O-layer has been solved by X-ray crystallography, there is no detailed structural information on the I-layer. Using high-resolution cryo-electron microscopy and molecular modelling combined with biochemical approaches, we determined the I-layer structure and located its various components in the electron density. Our results provide new structural insights on the CC, from which the essential features of T4S system mechanisms can be derived
Contribution du traitement des images-satellite à la cartographie des pâturages sahéliens
Certains pâturages sahéliens se sont considérablement dégradés au cours des années de sécheresse 1972-1973. Face à cette situation, il est devenu indispensable de procéder à d'importants travaux d'inventaires actualisés des ressources fourragères. Ces inventaires concernent des superficies de plus en plus vastes et s'orientent vers l'étude de l'évolution des parcours. Les images-satellites offrent une solution à quelques-uns des problèmes nouveaux posés par l'étude de régions immenses à des périodes successives. Mais l'interprétation des images-satellite exige une approche globale au travers d'unités synthétiques: les Unités Paysages Pastorales. Traitées par informatique à 1/100 000, les images-satellite permettent d'importants travaux de reconnaissance. Employées conjointement avec des observations de terrain et des photographies aériennes, elles rendent possible la cartographie actualisée des ressources pastorale
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