Biology subjects

Morris, K. L.

Publications and source records attributed to Morris, K. L..

8 recordsLinked to original sources

bioRxiv2025

Chart Builder: An Interactive Tool for User Driven Data Visualization in the Electron Microscopy Data Bank

The cryogenic sample-electron microscopy (cryoEM) field has generated significant amounts of 3D Electron Microscopy (3DEM) volumetric data and associated metadata, now comprehensively archived in the Electron Microscopy Data Bank (EMDB - www.emdatabank.org) and the Electron Microscopy Public Image Archive (EMPIAR - www.empiar.org). Harnessing the full potential of these resources requires robust, flexible, and publicly accessible tools for data exploration, analysis and retrieval. Here, we present Chart Builder, an interactive web-based platform that enables researchers to create customizable, publication-quality visualizations directly from archival metadata, validation assessments, and cross-reference annotations. Chart Builder integrates the same query-driven and flexible Solr search system as EMDB search, into a user interface with tools to assist users to filter, group, and compare data without programming expertise. It supports multiple chart types (including line, bar, area, scatter (2D and 3D), histogram, bubble, pie, geographic and Venn diagrams) with customizable axes, data series, and statistical operators. Users can apply global filters, define temporal, categorical, or custom query-based axes, and explore multi-dimensional relationships interactively. Chart data-points are linked to their underlying datasets, such that visualisation interaction opens entry-level or archive-level search results for inspection and datasets from charts may be exported in several ways. Findability, accessibility, interoperability and reusability of data are facilitated by these direct access and export mechanisms, including HTML embedding, persistent URL sharing and chart/data download options. By combining interactivity and ease of use with up-to-date access to the EMDB and EMPIAR archive metadata, both computational and experimental communities may explore and visualize current metadata and export to formats for further analysis or as publication-ready figures. Chart Builder promotes community-driven data analysis and empowers users to evaluate trends in the biological 3DEM field. Chart Builder is freely accessible and fully integrated into the EMDB website at https://www.ebi.ac.uk/emdb/statistics/builder/.

biophysics↗

bioRxiv2025

Q-score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps

Atomic coordinate models are important in the interpretation of 3D maps produced with cryoEM and sub-tomogram averaging in cryoET, or more generically, 3D electron microscopy (3DEM). In addition to visual inspection of such maps and models, quantitative metrics convey the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well-fitted models. Here we present new statistical analyses of Q-scores based on its application to [~]10,000 maps and models archived in EMDB and PDB. Further we introduce two new metrics based on Q-score: Q-relative-all and Q-relative-resolution to compare a map and model to all entries in the EMDB and those with similar resolution respectively. We also explore through illustrative examples of proteins, nucleic acids, and small molecules how Q-scores can indicate whether the atomic coordinates are well-fitted to 3DEM maps and whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage, and/or conformational heterogeneity. Lastly, we show examples of how Q-scores can effectively be converted to atomic B-factors. These analyses provide a basis for how Q-scores can be interpreted effectively to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving. SynopsisQ-scores are calculated each atom in models fitted to 3DEM (3D electron microscopy) maps. They measure how well the model fits the map, and also reflect the quality of the map as they correlate to resolution. Here we develop a statistical model for Q-scores applied to many maps and models in the EMDB (Electron Microscopy Database) and PDB (Protein Data Bank) respectively, and show how it can be used to assess the reliability of entire models as well as their subcomponents.

biochemistry↗

bioRxiv2024

EMinsight: a tool to capture cryoEM microscope configuration and experimental outcomes for analysis and deposition.

The widespread adoption of cryoEM technologies for structural biology has pushed the discipline to new frontiers. A significant worldwide effort has refined the Single Particle Analysis (SPA) workflow into a reasonably standardised procedure. Significant investment of development time have been made particularly in sample preparation, microscope data collection efficiency, pipeline analyses and data archiving. The widespread adoption of specific commercial microscopes, software for controlling them and best practises developed at national facilities has also begun to establish a degree of standardisation to data structures coming from the SPA workflow. There is opportunity to capitalise on this moment in the fields maturation, to capture metadata from SPA experiments and correlate this with experimental outcomes, which is presented here in a set of programmes called EMinsight. This tool aims to prototype the framework and types of analyses that could lead to new insights into optimal microscope configurations as well as for defining methods for metadata capture to assist with archiving of cryoEM SPA data. We also envisage this tool to be useful to microscope operators and facilities looking to rapidly generate reports on SPA data collection and screening sessions. SynopsisEMinsight is a Python-based tool for systematically mining metadata from single particle analysis cryoEM experiments. The capture and analysis of metadata facilitates assessment of instrument performance, provides concise reporting of experiment performance and sample quality by analysing preprocessing results, and gathers metadata for deposition. We envisage this approach to benefit the microscope operator, facility managers, database developers and users.

biophysics↗

bioRxiv2023

PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank

The Protein Data Bank (PDB) archive is the global repository for public-domain 3D biomolecular structural information. The archival nature of the PDB presents certain challenges pertaining to updating or adding associated annotations from trusted external biodata resources. While each Worldwide PDB (wwPDB) partner has made best efforts to provide up-to-date external annotations, accessing and integrating information from disparate wwPDB data centers can be an involved process. To address this issue, the wwPDB has established the PDB Next Generation or NextGen Archive, developed to centralize and streamline access to enriched structural annotations from wwPDB partners and trusted external sources. At present, the archive provides mappings between experimentally determined 3D structures of proteins and UniProt amino acid sequences, together with domain annotations from Pfam, SCOP2, and CATH databases, and intra-molecular connectivity information. Since launch, the PDB NextGen Archive has seen substantial user engagement with over 3.5 million data file downloads, ensuring researchers have access to accurate, up-to-date, and easily accessible structural annotations. Database URLhttp://www.wwpdb.org/ftp/pdb-nextgen-archive-site

bioinformatics↗

bioRxiv2021

Multi-modal adaptor-clathrin contacts drive coated vesicleassembly

Clathrin-coated pits are formed by the recognition of membrane and cargo by the heterotetrameric AP2 complex and the subsequent recruitment of clathrin triskelia. A potential role for AP2 in coated-pit assembly beyond initial clathrin recruitment has not been explored. Clathrin binds the {beta}2 subunit of AP2, and several binding sites on {beta}2 and on the clathrin heavy chain have been identified, but our structural knowledge of these interactions is incomplete and their functional importance during endocytosis is unclear. Here, we analysed the cryo-EM structure of clathrin cages assembled in the presence of {beta}2 hinge and appendage ({beta}2HA) domains. We find that the {beta}2-appendage binds in at least two positions in the cage, demonstrating that multi-modal binding is a fundamental property of clathrin-AP2 interactions. In one position, {beta}2-appendage cross-links two adjacent terminal domains from different triskelia below the vertex. Functional analysis of {beta}2HA-clathrin interactions reveals that endocytosis requires two clathrin interaction sites: a clathrin-box motif on the hinge and the "sandwich site" on the appendage, with the appendage "platform site" having less importance. From these studies and the work of others, we propose that {beta}2-appendage binding to more than one clathrin triskelion is a key feature of the system and likely explains why clathrin assembly is driven by AP2.

biochemistry↗

bioRxiv2021

Conserved Cdk inhibitors show unique structural responses to tyrosine phosphorylation

Balanced proliferation-quiescence decisions are vital during normal development and in tissue homeostasis and their dysregulation underlies tumorigenesis. Entry into proliferative cycles is driven by Cyclin/Cyclin-dependent kinases (Cdks). Conserved Cdk inhibitors (CKIs), p21Cip1/Waf1, p27Kip1 and p57Kip2, bind to Cyclin/Cdks and inhibit Cdk activity. p27 tyrosine phosphorylation, in response to mitogenic signalling, promotes activation of CyclinD/Cdk4 and CyclinA/Cdk2. Tyrosine phosphorylation is conserved in p21 and p57, although the number of sites differs. We use molecular dynamics simulations to compare the structural changes in Cyclin/Cdk/CKI trimers induced by single and multiple tyrosine phosphorylation in CKIs and their impact on CyclinD/Cdk4 and CyclinA/Cdk2 activity. Despite shared structural features, CKI binding induces distinct structural responses in Cyclin/Cdks and the predicted effects of CKI tyrosine phosphorylation on Cdk activity are not conserved across CKIs. Our analyses suggest how CKIs may have evolved to be sensitive to different inputs to give context-dependent control of Cdk activity.

cell biology↗

bioRxiv2019

Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy

Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-length Manduca sexta sGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71{degrees} rotation of the heme-binding {beta} H-NOX and PAS domains. Repositioning of the {beta} H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the {beta} H-NOX domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO.

biochemistry↗

bioRxiv2018

HIV-1 Nefs are cargo-sensitive AP-1 trimerization switches in tetherin and MHC-I downregulation

The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 [A] cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention. The 4.3 [A] structure of a mutant Nef-induced dimer of AP-1 showed how the closed trimer is regulated by the dileucine loop of Nef. HDX-MS and mutational analysis were used to show how cargo dynamics leads to alternative Arf1 trimerization, directing Nef targets to be either retained at the trans-Golgi or sorted to lysosomes. Phosphorylation of the NL4-3 M-Nef was shown to regulate AP-1 trimerization, explaining how O-Nefs lacking this phosphosite counteract tetherin but most M-Nefs do not. These observations show how the higher-order organization of a vesicular coat can be allosterically modulated to direct cargoes to distinct fates.

molecular biology↗