The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

/pdf/ucsf-chimera-a-visualization-system-for-exploratory-research-59xu54fhxg.pdf

UCSF Chimera--a visualization system for exploratory research and analysis.

Rapid growth in nanotechnology is increasing the likelihood of engineered nanomaterials coming into contact with humans and the environment. Nanoparticles interacting with proteins, membranes, cells, DNA and organelles establish a series of nanoparticle/biological interfaces that depend on colloidal forces as well as dynamic biophysicochemical interactions. These interactions lead to the formation of protein coronas, particle wrapping, intracellular uptake and biocatalytic processes that could have biocompatible or bioadverse outcomes. For their part, the biomolecules may induce phase transformations, free energy releases, restructuring and dissolution at the nanomaterial surface. Probing these various interfaces allows the development of predictive relationships between structure and activity that are determined by nanomaterial properties such as size, shape, surface chemistry, roughness and surface coatings. This knowledge is important from the perspective of safe use of nanomaterials.

Understanding biophysicochemical interactions at the nano–bio interface

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

RELION: implementation of a Bayesian approach to cryo-EM structure determination.

Single-particle electron cryomicroscopy (cryo-EM) is a powerful method for determining the structures of biological macromolecules. With automated microscopes, cryo-EM data can often be obtained in a few days. However, processing cryo-EM image data to reveal heterogeneity in the protein structure and to refine 3D maps to high resolution frequently becomes a severe bottleneck, requiring expert intervention, prior structural knowledge, and weeks of calculations on expensive computer clusters. Here we show that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer. Furthermore, SGD with Bayesian marginalization allows ab initio 3D classification, enabling automated analysis and discovery of unexpected structures without bias from a reference map. These algorithms are combined in a user-friendly computer program named cryoSPARC (http://www.cryosparc.com).

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

The Reoviridae family of dsRNA viruses is characterized by its capacity for endogenous transcription of multipartite genomes within proteinaceous capsids of 1 to 3 layers. These viruses share an inner core particle (ICP) which conforms to icosahedral, T=2*, symmetry, but differ in two major aspects: first, the presence or absence of RNA-capping turrets; second, the number of additional host-specific capsid layers that are often lost upon cell entry. While the role of these additional layers in host infection is generally understood, the absence of asymmetric ICP structures from multilayered reoviruses has obfuscated our understanding on the impact of successive removal of these external layers on the structural organization of the inner capsid and its effect on transcription initiation. Here, we present the 3.4 Å resolution structure of the aquareovirus (ARV) ICP, and atomic models of the capsid shell proteins VP3 and VP6, the transcriptional enzymatic complexes (TECs) VP2 and VP4, and RNA-capping turret protein VP1. These structures reveal significant differences when compared to previously determined, coated ARV structures and the single layered cytoplasmic polyhedrosis virus (CPV). Compared to the ARV virion and infectious subvirion particle (ISVP) structures, the ARV ICP undergoes significant capsid expansion and widening of the TEC’s and turret’s nucleotide processing channels. In contrast to CPV which relies solely on allosteric regulation by binding transcriptional cofactors, these conformational changes suggest the loss of outer capsid layers may regulate transcription initiation in ARV. These results shed new light on the mechanism of transcription initiation amongst turreted, multilayered members of Reoviridae.

/pdf/asymmetric-reconstruction-of-the-aquareovirus-core-at-near-2d28rusx.pdf

Asymmetric reconstruction of the aquareovirus core at near-atomic resolution and mechanism of transcription initiation

Domains of the p50 Central Hub Assembly, Activation, and Inhibition by Tetrahymena Telomerase Holoenzyme

Key to cell entry by non-enveloped viruses is virus-cell interactions at the cell or endosomal membrane. Here, we detail our protocols to capture such interactions between non-enveloped virus bluetongue virus (BTV) and vesicular membrane by cryogenic electron microscopy (cryoEM) and tomography (cryoET). Key steps include virus isolation, liposome preparation, virus-liposome incubation and vitrification, cryoEM and cryoET imaging, data processing for 3D reconstruction, and subtomogram averaging. The protocols can be generally applicable to studies of cell entry by other non-enveloped viruses. For complete details on the use and execution of this protocol, please refer to Xia et al. (2021). 

https://doi.org/10.1016/j.xpro.2022.101825

Using cryoEM and cryoET to visualize membrane penetration of a non-enveloped virus

Seeing Engineered Loops in a Gene Delivery Vehicle by cryoEM

/pdf/author-correction-structure-of-the-trypanosome-paraflagellar-38qwggvlry.pdf

Z. Hong Zhou

Papers

Asymmetric reconstruction of the aquareovirus core at near-atomic resolution and mechanism of transcription initiation

Domains of the p50 Central Hub Assembly, Activation, and Inhibition by Tetrahymena Telomerase Holoenzyme

Using cryoEM and cryoET to visualize membrane penetration of a non-enveloped virus

Seeing Engineered Loops in a Gene Delivery Vehicle by cryoEM

Author Correction: Structure of the trypanosome paraflagellar rod and insights into non-planar motility of eukaryotic cells.