hA molecular switch in amyloid assembly: Met35 and amyloid beta-protein oligomerization

Aberrant protein oligomerization is an important pathogenetic process in vivo. In Alzheimer's disease (AD), the amyloid beta-protein (Abeta) forms neurotoxic oligomers. The predominant in vivo Abeta alloforms, Abeta40 and Abeta42, have distinct oligomerization pathways. Abeta42 monomers oligomerize into pentamer/hexamer units (paranuclei) which self-associate to form larger oligomers. Abeta40 does not form these paranuclei, a fact which may explain the particularly strong linkage of Abeta42 with AD. Here, we sought to determine the structural elements controlling paranucleus formation as a first step toward the development of strategies for treating AD. Because oxidation of Met(35) is associated with altered Abeta assembly, we examined the role of Met(35) in controlling Abeta oligomerization. Oxidation of Met(35) in Abeta42 blocked paranucleus formation and produced oligomers indistinguishable in size and morphology from those produced by Abeta40. Systematic structural alterations of the C(gamma)(35)-substituent group revealed that its electronic nature, rather than its size (van der Waals volume), was the factor controlling oligomerization pathway choice. Preventing assembly of toxic Abeta42 paranuclei through selective oxidation of Met(35) thus represents a potential therapeutic approach for AD

Molecular Dynamics Studies of the Nucleoprotein of Influenza A Virus: Role of the Protein Flexibility in RNA Binding

The influenza viruses contain a segmented, negative stranded RNA genome. Each RNA segment is covered by multiple copies of the nucleoprotein (NP). X-ray structures have shown that NP contains well-structured domains juxtaposed with regions of missing electron densities corresponding to loops. In this study, we tested if these flexible loops gated or promoted RNA binding and RNA-induced oligomerization of NP. We first performed molecular dynamics simulations of wt NP monomer and trimer in comparison with the R361A protein mutated in the RNA binding groove, using the H1N1 NP as the initial structure. Calculation of the root-mean-square fluctuations highlighted the presence of two flexible loops in NP trimer: loop 1 (73–90), loop 2 (200–214). In NP, loops 1 and 2 formed a 10–15 Å-wide pinch giving access to the RNA binding groove. Loop 1 was stabilized by interactions with K113 of the adjacent β-sheet 1 (91–112) that interacted with the RNA grove (linker 360–373) via multiple hydrophobic contacts. In R361A, a salt bridge formed between E80 of loop 1 and R208 of loop 2 driven by hydrophobic contacts between L79 and W207, due to a decreased flexibility of loop 2 and loop 1 unfolding. Thus, RNA could not access its binding groove in R361A; accordingly, R361A had a much lower affinity for RNA than NP. Disruption of the E80-R208 interaction in the triple mutant R361A-E80A-E81A increased its RNA binding affinity and restored its oligomerization back to wt levels in contrast with impaired levels of R361A. Our data suggest that the flexibility of loops 1 and 2 is required for RNA sampling and binding which likely involve conformational change(s) of the nucleoprotein

The impact of aerodynamics on fuel consumption in railway applications

The main consequence of on air flow surrounding a moving train resides in the aerodynamic drag and a certain pressure distribution on the frontal and lateral surfaces of the vehicle. The actual value of the aerodynamic drag (if pre-determined) may lead to a more accurate design of the whole locomotive power transmission. The aerodynamic drag may be estimated by using two specific experiments: the traction method and the free launch method. While the first one uses highly complex equipment, the second is easier to use due to the relative low number of devices required. The present work’s main goal is to illustrate the importance of aerodynamic design of the railway vehicles, as their performances are influenced by the aerodynamic drag. In order to illustrate the influence of the aerodynamic shape of o locomotive body, we have chosen the latest diesel model available on the local market, the Class 621 EGM locomotives, currently in service at the national passenger railway operator, CFR Călători SA

Experimental determinations of the aerodynamic drag for vehicles subjected to the ground effect

A moving vehicle creates a flow of the surrounding air, continuous and compressible fluid. When the movement is at a constant speed, the air flow is not time dependent and the flow distribution lines are constant. In fact, however, a vehicle moves in an environment where the air itself is in a continuous motion. In addition, there are many side obstacles, such as passing objects, stationary vehicles, artwork, etc. All these factors affect the air flow along the vehicle. The shape and speed of the current lines are affected as compared with time. Based on these considerations, the aerodynamics of any ground vehicle is a non-stationary process. The study of non-stationary phenomena may be related to a steady state study using finite difference method, in which time is divided into finite intervals Δt, small enough so that during a specific period a phenomenon may be considered as stationary. If speeds involved are in subsonic regime, solving the equations of motion is simplified. We may consider therefore that the vehicle is moving at speed V1 in the air mass at rest, or both, the vehicle is at rest in a stream of air at speed V1 (this is the particular case of the wind tunnels). For speeds of up to Mach 0.5, the effect of compressibility of air does not influence at all or has very little influence on a flow. In this case, the air density may be considered constant. Also, the effect of viscosity can be neglected in most of the space occupied by the fluid. In order to illustrate the influence of the aerodynamic drag on a ground-effect vehicle we performed a test in the subsonic wind tunnel of the INCAS

Picobirnaviruses encode a protein with repeats of the ExxRxNxxxE motif

International audiencePicobirnaviruses possess a bisegmented double-stranded RNA genome. While the segment 2 encodes the RNA-dependent RNA polymerase, the segment 1 displays two open reading frames (ORFs). ORF2 was recently shown to code the capsid precursor and ORF1 product has not been characterized. In this study, we show that the three ORF1 sequences available in databases and representing three phylogenetically distant picobirnaviruses (two from human and one from rabbit hosts) encode proteins of various sizes (106–224 residues and without proline and cysteine) harbouring a particular sequence motif (ExxRxNxxxE) repeated four to ten times, dependingonthe virus species. Several algorithms predicted the three proteins to be mainly unfolded in the domains containing the repeats. The glycine-rich 25–40 amino acid long C-terminal domains containing hydrophobic residues with a periodicity of 3–4 residues are predicted structurally different of the upstream domains containing the motif repetitions. The ExxRxNxxxE sequence was not previously identified as a short linear motif in eukaryotic and prokaryotic proteins. Its function remains elusive

What Computational Methods can Teach us about the Alzheimer-Protective Nature of A2V- and A2T-Mutant Amyloid-Beta Oligomers

International audienceno abstrac

Selective probing of a NADPH site controlled light-induced enzymatic catalysis

International audienceAchieving molecular recognition of NADPH binding sites is a compelling strategy to control many redox biological processes. The NADPH sites recognize the ubiquitous NADPH cofactor via highly conserved binding interactions, despite differences in the regulation of the hydride transfer in redox active proteins. We recently developed a photoactive NADPH substitute, called nanotrigger NT synchronizing the initiation of enzymatic catalysis of the endothelial NO-synthase (eNOS) with a laser pulse. Spatial and temporal control of enzymatic activity by such a designed light-driven activator would benefit from achieving molecular selectivity, i.e. activation of a single NADPH-mediated enzyme. In this work, we probe the ability of NT to discriminate between two NADPH sites with light. The selected NADPH sites belong to dihydrofolate reductase dihydrofolate reductase enzyme (DHFR) and endothelial NO-synthase (eNOS). Ultrafast kinetics showed that NT could not activate DHFR catalysis with a laser pulse in contrast with the observed trigger of eNOS catalysis leading to NO formation. Homology modelling, molecular dynamics simulations showed that NT discriminated between the two NADPH sites by different donor to acceptor distances and by local steric effects hindering light activation of DHFR catalysis. The data suggested that the narrow NADPH site required a tight fit of the nanotrigger at a suitable distance/angle to the electron acceptor for a specific activation of the catalysis. The ability of the nanotrigger to activate eNOS combined with a low reactivity in unfavourable NADPH sites makes NT a highly promising tool for targeting eNOS in endothelial cells with a laser pulse. Cop 2009 John Wiley and Sons, Ltd

Molecular structure of the NQTrp inhibitor with the Alzheimer A1-28 monomer

International audienceno abstrac

A molecular switch in amyloid assembly: Met35 and amyloid beta-protein oligomerization.

Aberrant protein oligomerization is an important pathogenetic process in vivo. In Alzheimer's disease (AD), the amyloid beta-protein (Abeta) forms neurotoxic oligomers. The predominant in vivo Abeta alloforms, Abeta40 and Abeta42, have distinct oligomerization pathways. Abeta42 monomers oligomerize into pentamer/hexamer units (paranuclei) which self-associate to form larger oligomers. Abeta40 does not form these paranuclei, a fact which may explain the particularly strong linkage of Abeta42 with AD. Here, we sought to determine the structural elements controlling paranucleus formation as a first step toward the development of strategies for treating AD. Because oxidation of Met(35) is associated with altered Abeta assembly, we examined the role of Met(35) in controlling Abeta oligomerization. Oxidation of Met(35) in Abeta42 blocked paranucleus formation and produced oligomers indistinguishable in size and morphology from those produced by Abeta40. Systematic structural alterations of the C(gamma)(35)-substituent group revealed that its electronic nature, rather than its size (van der Waals volume), was the factor controlling oligomerization pathway choice. Preventing assembly of toxic Abeta42 paranuclei through selective oxidation of Met(35) thus represents a potential therapeutic approach for AD