More Like this

1. Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps

   https://doi.org/10.3389/fmolb.2021.644133  

   Gilbert, Benjamin R.; Thornburg, Zane R.; Lam, Vinson; Rashid, Fatema-Zahra M.; Glass, John I.; Villa, Elizabeth; Dame, Remus T.; Luthey-Schulten, Zaida (July 2021, Frontiers in Molecular Biosciences)

   null (Ed.)

   JCVI-syn3A is a genetically minimal bacterial cell, consisting of 493 genes and only a single 543 kbp circular chromosome. Syn3A’s genome and physical size are approximately one-tenth those of the model bacterial organism Escherichia coli ’s, and the corresponding reduction in complexity and scale provides a unique opportunity for whole-cell modeling. Previous work established genome-scale gene essentiality and proteomics data along with its essential metabolic network and a kinetic model of genetic information processing. In addition to that information, whole-cell, spatially-resolved kinetic models require cellular architecture, including spatial distributions of ribosomes and the circular chromosome’s configuration. We reconstruct cellular architectures of Syn3A cells at the single-cell level directly from cryo-electron tomograms, including the ribosome distributions. We present a method of generating self-avoiding circular chromosome configurations in a lattice model with a resolution of 11.8 bp per monomer on a 4 nm cubic lattice. Realizations of the chromosome configurations are constrained by the ribosomes and geometry reconstructed from the tomograms and include DNA loops suggested by experimental chromosome conformation capture (3C) maps. Using ensembles of simulated chromosome configurations we predict chromosome contact maps for Syn3A cells at resolutions of 250 bp and greater and compare them to the experimental maps. Additionally, the spatial distributions of ribosomes and the DNA-crowding resulting from the individual chromosome configurations can be used to identify macromolecular structures formed from ribosomes and DNA, such as polysomes and expressomes. 

   more » « less
2. The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins

   https://doi.org/10.1038/s41589-024-01638-w  

   Agarwal, Vinayak; McShan, Andrew C (June 2024, Nature Chemical Biology)

   Artificial intelligence-driven advances in protein structure prediction in recent years have raised the question: has the protein structure-prediction problem been solved? Here, with a focus on nonglobular proteins, we highlight the many strengths and potential weaknesses of DeepMind’s AlphaFold2 in the context of its biological and therapeutic applications. We summarize the subtleties associated with evaluation of AlphaFold2 model quality and reliability using the predicted local distance difference test (pLDDT) and predicted aligned error (PAE) values. We highlight various classes of proteins that AlphaFold2 can be applied to and the caveats involved. Concrete examples of how AlphaFold2 models can be integrated with experimental data in the form of small-angle X-ray scattering (SAXS), solution NMR, cryo-electron microscopy (cryo-EM) and X-ray diffraction are discussed. Finally, we highlight the need to move beyond structure prediction of rigid, static structural snapshots toward conformational ensembles and alternate biologically relevant states. The overarching theme is that careful consideration is due when using AlphaFold2-generated models to generate testable hypotheses and structural models, rather than treating predicted models as de facto ground truth structures. 

   more » « less
3. High-throughput structures of protein–ligand complexes at room temperature using serial femtosecond crystallography

   https://doi.org/10.1107/S2052252519011655  

   Moreno-Chicano, Tadeo; Ebrahim, Ali; Axford, Danny; Appleby, Martin V.; Beale, John H.; Chaplin, Amanda K.; Duyvesteyn, Helen M.; Ghiladi, Reza A.; Owada, Shigeki; Sherrell, Darren A.; et al (November 2019, IUCrJ)

   High-throughput X-ray crystal structures of protein–ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein–ligand complexes using SFX. 

   more » « less
4. Solar flare catalog based on SDO/AIA EUV images: Composition and correlation with GOES/XRS X-ray flare magnitudes

   https://doi.org/10.3389/fspas.2022.1031211  

   van der Sande, Kiera; Flyer, Natasha; Berger, Thomas E.; Gagnon, Riana (November 2022, Frontiers in Astronomy and Space Sciences)

   Supervised Machine Learning (ML) models for solar flare prediction rely on accurate labels for a given input data set, commonly obtained from the GOES/XRS X-ray flare catalog. With increasing interest in utilizing ultraviolet (UV) and extreme ultraviolet (EUV) image data as input to these models, we seek to understand if flaring activity can be defined and quantified using EUV data alone. This would allow us to move away from the GOES single pixel measurement definition of flares and use the same data we use for flare prediction for label creation. In this work, we present a Solar Dynamics Observatory (SDO) Atmospheric Imaging Assembly (AIA)-based flare catalog covering flare of GOES X-ray magnitudes C, M and X from 2010 to 2017. We use active region (AR) cutouts of full disk AIA images to match the corresponding SDO/Helioseismic and Magnetic Imager (HMI) SHARPS (Space weather HMI Active Region Patches) that have been extensively used in ML flare prediction studies, thus allowing for labeling of AR number as well as flare magnitude and timing. Flare start, peak, and end times are defined using a peak-finding algorithm on AIA time series data obtained by summing the intensity across the AIA cutouts. An extremely randomized trees (ERT) regression model is used to map SDO/AIA flare magnitudes to GOES X-ray magnitude, achieving a low-variance regression. We find an accurate overlap on 85% of M/X flares between our resulting AIA catalog and the GOES flare catalog. However, we also discover a number of large flares unrecorded or mislabeled in the GOES catalog. 

   more » « less
5. Spatial Persistence of High Strain Events During Brittle Failure

   https://doi.org/10.1029/2024GL110668  

   McBeck, Jessica; Cordonnier, Benoît; Zhu, Wenlu; Renard, François (October 2024, Geophysical Research Letters)

   Abstract The onset of brittle failure in rocks includes dilatancy and strain localization. To better understand this nucleation process, we analyze the evolution of the local three‐dimensional strain tensor using X‐ray tomograms acquired during triaxial compression experiments on granite and sandstone. The onset of the localization of the compaction, dilation, and shear strain occurs when ∼65% of the rock volume experiences dilation. Tracking the locations of the high strains throughout loading suggests that the deformation that occurs early in loading influences the location of the system‐sized fracture network that produces macroscopic failure. This influence is larger in the sandstone experiments than the granite experiments, likely due to the microstructure of the sandstone. These results have important implications for detecting precursors to catastrophic failure. 

   more » « less