Search results for "Electricity"
showing 10 items of 1225 documents
Ion transport and selectivity in nanopores with spatially inhomogeneous fixed charge distributions
2007
Polymeric nanopores with fixed charges show ionic selectivity when immersed in aqueous electrolyte solutions. The understanding of the electrical interaction between these charges and the mobile ions confined in the inside nanopore solution is the key issue in the design of potential applications. The authors have theoretically described the effects that spatially inhomogeneous fixed charge distributions exert on the ionic transport and selectivity properties of the nanopore. A comprehensive set of one-dimensional distributions including the skin, core, cluster, and asymmetric cases are analyzed on the basis of the Nernst-Planck equations. Current-voltage curves, nanopore potentials, and tr…
Field theoretic study of bilayer membrane fusion: I. Hemifusion mechanism
2003
Self-consistent field theory is used to determine structural and energetic properties of metastable intermediates and unstable transition states involved in the standard stalk mechanism of bilayer membrane fusion. A microscopic model of flexible amphiphilic chains dissolved in hydrophilic solvent is employed to describe these self-assembled structures. We find that the barrier to formation of the initial stalk is much smaller than previously estimated by phenomenological theories. Therefore its creation it is not the rate limiting process. The barrier which is relevant is associated with the rather limited radial expansion of the stalk into a hemifusion diaphragm. It is strongly affected by…
Structural characterization of the Borrelia burgdorferi outer surface protein BBA73 implicates dimerization as a functional mechanism.
2013
Borrelia burgdorferi, which is the causative agent of Lyme disease, is transmitted from infected Ixodes ticks to a mammalian host following a tick bite. Upon changing the host organism from an Ixodes tick to a warm-blooded mammal, the spirochete must adapt to very different conditions, which is achieved by altering the expression of several genes in response to a changing environment. Recently, considerable attention has been devoted to several outer surface proteins, including BBA73, that undergo dramatic upregulation during the transmission of B. burgdorferi from infected Ixodes ticks to mammals and that are thought to be important for the establishment and maintenance of the infection. T…
Effect of elliptical deformation on molecular polarizabilities of model carbon nanotubes from atomic increments.
2003
The interacting induced dipole polarization model implemented in our program POLAR is used for the calculation of the dipole-dipole polarizability alpha. The method is tested with single-wall carbon nanotube models as a function of nanotube radius and elliptical deformation. The results for polarizability follow the same trend as reference calculations performed with our version of the program PAPID. For the zigzag tubes, the polarizability is found to follow a remarkably simple law, that is, it varies as the inverse of the radius. A dramatic effect is also found with elliptical deformation. It is found that the polarizability and related properties can be modified continuously and reversib…
Quaternary structure of the European spiny lobster (Palinurus elephas) 1x6-mer hemocyanin from cryoEM and amino acid sequence data.
2002
Abstract Arthropod hemocyanins are large respiratory proteins that are composed of up to 48 subunits (8×6-mer) in the 75 kDa range. A 3D reconstruction of the 1×6-mer hemocyanin from the European spiny lobster Palinurus elephas has been performed from 9970 single particles using cryoelectron microscopy. An 8 A resolution of the hemocyanin 3D reconstruction has been obtained from about 600 final class averages. Visualisation of structural elements such as α-helices has been achieved. An amino acid sequence alignment shows the high sequence identity (>80%) of the hemocyanin subunits from the European spiny lobster P. elephas and the American spiny lobster Panulirus interruptus . Comparison of…
Evidence for substrate binding-induced zwitterion formation in the catalytic Cys-His dyad of the SARS-CoV main protease.
2014
The coronavirus main protease (M(pro)) represents an attractive drug target for antiviral therapy of coronavirus (CoV) infections, including severe acute respiratory syndrome (SARS). The SARS-CoV M(pro) and related CoV proteases have several distinct features, such as an uncharged Cys-His catalytic dyad embedded in a chymotrypsin-like protease fold, that clearly separate these enzymes from archetypical cysteine proteases. To further characterize the catalytic system of CoV main proteases and to obtain information about improved inhibitors, we performed comprehensive simulations of the proton-transfer reactions in the SARS-CoV M(pro) active site that lead to the Cys(-)/His(+) zwitterionic st…
NMR Solution Structure of the Non-RGD Disintegrin Obtustatin
2003
The solution structure of obtustatin, a novel non-RGD disintegrin of 41 residues isolated from Vipera lebetina obtusa venom, and a potent and selective inhibitor of the adhesion of integrin alpha(1)beta(1) to collagen IV, has been determined by two-dimensional nuclear magnetic resonance. Almost the whole set of chemical shifts for 1H, 13C and 15N were assigned at natural abundance from 2D homonuclear and heteronuclear 500 MHz, 600 MHz and 800 MHz spectra at pH 3.0 recorded at 298 K and 303 K. Final structural constraints consisted of 302 non-redundant NOE (95 long-range, 60 medium, 91 sequential and 56 intra-residue), four disulfide bond distances, five chi1 dihedral angles and four hydroge…
The death-domain fold of the ASC PYRIN domain, presenting a basis for PYRIN/PYRIN recognition.
2003
The PYRIN domain is a conserved sequence motif identified in more than 20 human proteins with putative functions in apoptotic and inflammatory signalling pathways. The three-dimensional structure of the PYRIN domain from human ASC was determined by NMR spectroscopy. The structure determination reveals close structural similarity to death domains, death effector domains, and caspase activation and recruitment domains, although the structural alignment with these other members of the death-domain superfamily differs from previously predicted amino acid sequence alignments. Two highly positively and negatively charged surfaces in the PYRIN domain of ASC result in a strong electrostatic dipole …
Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models
2010
Evaluating the free-energy landscape of proteins and the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of simplified coarse-grained (CG) folding models offers an effective way of sampling the landscape but such a treatment, however, may not give the correct description of the effect of the actual protein residues. A general way around this problem that has been put forward in our early work (Fan et al., Theor Chem Acc 1999;103:77-80) uses the CG model as a reference potential for free-energy calculations of diffe…
Atom-based Stochastic and non-Stochastic 3D-Chiral Bilinear Indices and their Applications to Central Chirality Codification
2006
Abstract Non-stochastic and stochastic 2D bilinear indices have been generalized to codify chemical structure information for chiral drugs, making use of a trigonometric 3D-chirality correction factor. In order to evaluate the effectiveness of this novel approach in drug design we have modeled the angiotensin-converting enzyme inhibitory activity of perindoprilate's σ-stereoisomers combinatorial library. Two linear discriminant analysis models, using non-stochastic and stochastic linear indices, were obtained. The models had shown an accuracy of 95.65% for the training set and 100% for the external prediction set. Next the prediction of the σ-receptor antagonists of chiral 3-(3-hydroxypheny…