Showing papers in "Journal of Structural Biology in 2007"

TL;DR: EMAN2 has been under development for the last two years, with a completely refactored image processing library, and a wide range of features to make it much more flexible and extensible than EMAN1.

TL;DR: Methods for interactive visualization and analysis of density maps available in the UCSF Chimera molecular modeling package enable segmentation, fitting, coarse modeling, measuring and coloring ofdensity maps for elucidating structures of large molecular assemblies such as virus particles, ribosomes, microtubules, and chromosomes.

TL;DR: The refinement of three-dimensional reconstructions and correction for the contrast transfer function of the microscope are important steps in the determination of macromolecular structures by single particle electron microscopy.

TL;DR: Bsoft is a software package written for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image processing that allows shell scripting of processes and allows subtasks to be distributed across multiple computers for concurrent processing.

TL;DR: SPARX as mentioned in this paper is a new image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination, which includes a graphical user interface that provides a complete graphical programming environment with an extensive library of Python scripts that perform specific TEM-related computational tasks, and a core library of fundamental C++ image processing functions.

TL;DR: A correlative fluorescence light microscopy-electron microscopy approach, which guides the search for the structures of interest and allows electron microscopy to zoom in on them, and the total dose spent on locating regions of interest is negligible.

TL;DR: The utility of CG-MD simulations for studies of membrane/protein interactions is demonstrated, including to the bacterial sugar transporter LacY and a number of membrane peptides and proteins used to characterize their interactions with lipid bilayers.

TL;DR: A real-time alignment and reconstruction scheme for electron microscopic tomography (EMT) has been developed and integrated within the UCSF tomography data collection software and has proven to be quite adequate to assess sample quality, or to screen for the best data set for full-resolution reconstruction.

TL;DR: A similar ThT binding mode in amyloid fibrils, where cavities of an appropriate size running parallel to the fibril axis have previously been proposed in several amyloids fibrIL models are proposed.

TL;DR: A method to analyze and reconstruct electron microscopic images of macromolecular helical polymers, the iterative helical real space reconstruction (IHRSR) algorithm, which can show that when there is disorder or heterogeneity, when the specimens diffract weakly, or when Bessel functions overlap, it can do far better with this method than can be done using traditional Fourier-Bessel approaches.

TL;DR: It is proposed that ThT binds in cavities running parallel to the fibril axis, e.g., between the protofilaments forming the fbrils, which have been proposed previously in insulin fibrils and several other amyloid fibrIL models.

TL;DR: Although the central pore of AQP1 is found to be gas permeable, the pure POPE bilayer provides a much larger cross-sectional area, thus exhibiting a much lower free energy barrier for CO2 and O2 permeation, which may only be physiologically relevant in membranes of low gas permeability.

TL;DR: The crystal structures of HSA-myristate in a complex of aspirin and of salicylic acid, respectively are determined and provide the structural evidence of esterase activity of H SA, and demonstrate the conformational plasticity of Hsa on drug binding.

TL;DR: A new software system 2dx is presented, which is designed as a user-friendly, platform-independent software package for electron crystallography, which assists in the management of an image-processing project, guides the user through the processing of 2D crystal images, and provides transparence for processing tasks and results.

TL;DR: The particle selection system applies a hierarchical screening procedure to identify molecular particles in EM micrographs and has been successfully applied to macromolecular structural analyses.

TL;DR: AutO3DEM as mentioned in this paper is an automation system designed to accelerate the computationally intensive process of three-dimensional structure determination from images of vitrified icosahedral virus particles, which can be run in parallel mode on multi-processor systems.

TL;DR: Simulation results for the ribosome are reported, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date, and it is demonstrated that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers.

TL;DR: Crystal structures are used to investigate and review channels and pathways for the transfer of substrates and products to, and from, the redox active catalytic sites of photosystem II (PSII), and unique features in the electron transfer pathway of PSII are discussed.

TL;DR: The skeleton of a siliceous skeletal system of the Western Pacific hexactinellid sponge comprises an elaborate cylindrical lattice-like structure with at least six hierarchical levels spanning the length scale from nanometers to centimeters.

TL;DR: An overview of the current state of the programs and some applications to cryo-electron tomography is given, i.e. to write standalone programs for simple tasks that are combined through shell scripting to provide more complex functionality, and to communicate with other software via common image formats.

TL;DR: The synergistic effects in cell envelope assemblies, the hypothetical role of S-layers for cell shape formation, and the existence of a common function are discussed in view of new insights.

TL;DR: The results show that the orientation of odorants within a homology modelling-derived binding pocket of olfactory receptor orthologs is defined by evolutionary conserved amino acid positions.

TL;DR: In-cell NMR approaches in Xenopus laevis oocytes are reviewed and potential future applications in other eukaryotic cell types are evaluated.

TL;DR: Irregular structural motifs have been revealed with the growing number of structures determined and the helix-peptide-helix motif is correlated with the ion translocation function.

TL;DR: Synchrotron radiation phase-contrast X-ray tomographic microscopy was applied to observation and identification of the features of spruce anatomy at the cellular lengthscale and it is suggested that the position of sub-voxel-sized features can be determined indirectly using watershed segmentation.

TL;DR: The program RIVEM (Radial Interpretation of Viral Electron density Maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram that permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface.

TL;DR: A one-bead coarse-grained model that enables dynamical simulations of proteins on the time scale of tens of microseconds is presented and is found to be reliable for application to substrate docking simulations, which are currently in progress.

TL;DR: Low-density HDL assembly is found to proceed in two broad steps, aggregation of proteins and lipids driven by the hydrophobic effect which occurs on a approximately 1 micros time scale, followed by the optimization of the protein structure driven by increasingly specific protein-protein interactions.

TL;DR: High-energy X-ray scattering and in situ loading revealed macroscopic, mineral, and collagen Young's moduli in the separate material phases of bone: collagen and carbonated hydroxyapatite.

TL;DR: A computational method is described that allows the measurement of the signal-to-noise ratio and resolution of a three-dimensional structure obtained by single particle electron microscopy and reconstruction and is available to the microscopy community.