15,827 research outputs found
Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex.
The nuclear pore complex mediates nucleocytoplasmic transport in all eukaryotes and is among the largest cellular assemblies of proteins, collectively known as nucleoporins. Nucleoporins are organized into distinct subcomplexes. We optimized the isolation of a putative membrane-coating subcomplex of the nuclear pore complex, the heptameric Nup84 complex, and analyzed its structure by EM. Our data confirmed the previously reported 'Y' shape. We discerned additional structural details, including specific hinge regions at which the particle shows great flexibility. We determined the three-dimensional structures of two conformers, mapped the localization of two nucleoporins within the subcomplex and docked known crystal structures into the EM maps. The free ends of the Y-shaped particle are formed by beta-propellers; the connecting segments consist of alpha-solenoids. Notably, the same organizational principle is found in the clathrin triskelion, which may share a common evolutionary origin with the heptameric complex
Shapes of Semiflexible Polymer Rings
The shape of semiflexible polymer rings is studied over their whole range of
flexibility. Investigating the joint distribution of asphericity and nature of
asphericity as well as their respective averages we find two distinct shape
regimes depending on the flexibility of the polymer. For small perimeter to
persistence length the fluctuating rings exhibit only planar, elliptical
configurations. At higher flexibilities three dimensional, crumpled structures
arise. Analytic calculations for tight polymer rings confirm an elliptical
shape in the stiff regime.Comment: 4 pages, 3 figures, Version as published in Phys. Rev. Let
Flexibility of the N-Terminal mVDAC1 Segment Controls the Channel’s Gating Behavior
Since the solution of the molecular structures of members of the voltage dependent anion channels (VDACs), the N-terminal α-helix has been the main focus of attention, since its strategic location, in combination with its putative conformational flexibility, could define or control the channel’s gating characteristics. Through engineering of two double-cysteine mVDAC1 variants we achieved fixing of the N-terminal segment at the bottom and midpoint of the pore. Whilst cross-linking at the midpoint resulted in the channel remaining constitutively open, cross-linking at the base resulted in an “asymmetric” gating behavior, with closure only at one electric field´s orientation depending on the channel’s orientation in the lipid bilayer. Additionally, and while the native channel adopts several well-defined closed states (S1 and S2), the cross-linked variants showed upon closure a clear preference for the S2 state. With native-channel characteristics restored following reduction of the cysteines, it is evident that the conformational flexibility of the N-terminal segment plays indeed a major part in the control of the channel’s gating behavior
An investigation into the Gustafsson limit for small planar antennas using optimisation
The fundamental limit for small antennas provides a guide to the
effectiveness of designs. Gustafsson et al, Yaghjian et al, and
Mohammadpour-Aghdam et al independently deduced a variation of the
Chu-Harrington limit for planar antennas in different forms. Using a
multi-parameter optimisation technique based on the ant colony algorithm,
planar, meander dipole antenna designs were selected on the basis of lowest
resonant frequency and maximum radiation efficiency. The optimal antenna
designs across the spectrum from 570 to 1750 MHz occupying an area of were compared with these limits calculated using the
polarizability tensor. The results were compared with Sievenpiper's comparison
of published planar antenna properties. The optimised antennas have greater
than 90% polarizability compared to the containing conductive box in the range
, so verifying the optimisation algorithm. The generalized
absorption efficiency of the small meander line antennas is less than 50%, and
results are the same for both PEC and copper designs.Comment: 6 pages, 10 figures, in press article. IEEE Transactions on Antennas
and Propagation (2014
Analysis of Three-Dimensional Protein Images
A fundamental goal of research in molecular biology is to understand protein
structure. Protein crystallography is currently the most successful method for
determining the three-dimensional (3D) conformation of a protein, yet it
remains labor intensive and relies on an expert's ability to derive and
evaluate a protein scene model. In this paper, the problem of protein structure
determination is formulated as an exercise in scene analysis. A computational
methodology is presented in which a 3D image of a protein is segmented into a
graph of critical points. Bayesian and certainty factor approaches are
described and used to analyze critical point graphs and identify meaningful
substructures, such as alpha-helices and beta-sheets. Results of applying the
methodologies to protein images at low and medium resolution are reported. The
research is related to approaches to representation, segmentation and
classification in vision, as well as to top-down approaches to protein
structure prediction.Comment: See http://www.jair.org/ for any accompanying file
SlicerAstro: a 3-D interactive visual analytics tool for HI data
SKA precursors are capable of detecting hundreds of galaxies in HI in a
single 12 hours pointing. In deeper surveys one will probe more easily faint HI
structures, typically located in the vicinity of galaxies, such as tails,
filaments, and extraplanar gas. The importance of interactive visualization has
proven to be fundamental for the exploration of such data as it helps users to
receive immediate feedback when manipulating the data. We have developed
SlicerAstro, a 3-D interactive viewer with new analysis capabilities, based on
traditional 2-D input/output hardware. These capabilities enhance the data
inspection, allowing faster analysis of complex sources than with traditional
tools. SlicerAstro is an open-source extension of 3DSlicer, a multi-platform
open source software package for visualization and medical image processing.
We demonstrate the capabilities of the current stable binary release of
SlicerAstro, which offers the following features: i) handling of FITS files and
astronomical coordinate systems; ii) coupled 2-D/3-D visualization; iii)
interactive filtering; iv) interactive 3-D masking; v) and interactive 3-D
modeling. In addition, SlicerAstro has been designed with a strong, stable and
modular C++ core, and its classes are also accessible via Python scripting,
allowing great flexibility for user-customized visualization and analysis
tasks.Comment: 18 pages, 11 figures, Accepted by Astronomy and Computing.
SlicerAstro link: https://github.com/Punzo/SlicerAstro/wiki#get-slicerastr
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