scholarly journals CryoEM structure of the antibacterial target PBP1b at 3.3 Å resolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nathanael A. Caveney ◽  
Sean D. Workman ◽  
Rui Yan ◽  
Claire E. Atkinson ◽  
Zhiheng Yu ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Acid Anhydride ◽  
Atomic Resolution ◽  
Inherent Difficulty ◽  
Penicillin Binding Proteins ◽  
Antibiotic Development ◽  
Class A ◽  
Membrane Mimetic ◽  
Antibacterial Target ◽  
Resolution Structure

AbstractThe pathway for the biosynthesis of the bacterial cell wall is one of the most prolific antibiotic targets, exemplified by the widespread use of β-lactam antibiotics. Despite this, our structural understanding of class A penicillin binding proteins, which perform the last two steps in this pathway, is incomplete due to the inherent difficulty in their crystallization and the complexity of their substrates. Here, we determine the near atomic resolution structure of the 83 kDa class A PBP from Escherichia coli, PBP1b, using cryogenic electron microscopy and a styrene maleic acid anhydride membrane mimetic. PBP1b, in its apo form, is seen to exhibit a distinct conformation in comparison to Moenomycin-bound crystal structures. The work herein paves the way for the use of cryoEM in structure-guided antibiotic development for this notoriously difficult to crystalize class of proteins and their complex substrates.

scholarly journals A resolution record for cryoEM

2021 ◽  
Vol 10 ◽  
Author(s):  
Jonathan Ashmore ◽  
Bridget Carragher ◽  
Peter B Rosenthal ◽  
William Weis
Keyword(s):  
Electron Microscopy ◽  
Image Analysis ◽  
Structure Determination ◽  
Test Specimen ◽  
Structural Information ◽  
Atomic Resolution ◽  
Fast Growing ◽  
Cryo Electron Microscopy ◽  
New Instrument ◽  
Resolution Structure

Cryo electron microscopy (cryoEM) is a fast-growing technique for structure determination. Two recent papers report the first atomic resolution structure of a protein obtained by averaging images of frozen-hydrated biomolecules. They both describe maps of symmetric apoferritin assemblies, a common test specimen, in unprecedented detail. New instrument improvements, different in the two studies, have contributed better images, and image analysis can extract structural information sufficient to resolve individual atomic positions. While true atomic resolution maps will not be routine for most proteins, the studies suggest structures determined by cryoEM will continue to improve, increasing their impact on biology and medicine.

scholarly journals Squalamine and Aminosterol Mimics Inhibit the Peptidoglycan Glycosyltransferase Activity of PBP1b

Antibiotics ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 373
Author(s):  
Adrien Boes ◽  
Jean Michel Brunel ◽  
Adeline Derouaux ◽  
Frédéric Kerff ◽  
Ahmed Bouhss ◽  
...  
Keyword(s):  
Fluorescence Anisotropy ◽  
Bacterial Cell ◽  
Chain Elongation ◽  
Penicillin Binding Proteins ◽  
Class A ◽  
Lipid Ii ◽  
Bacterial Cell Death ◽  
Glycan Chain ◽  
Competitive Inhibitors ◽  
Antibacterial Target

Peptidoglycan (PG) is an essential polymer of the bacterial cell wall and a major antibacterial target. Its synthesis requires glycosyltransferase (GTase) and transpeptidase enzymes that, respectively, catalyze glycan chain elongation and their cross-linking to form the protective sacculus of the bacterial cell. The GTase domain of bifunctional penicillin-binding proteins (PBPs) of class A, such as Escherichia coli PBP1b, belong to the GTase 51 family. These enzymes play an essential role in PG synthesis, and their specific inhibition by moenomycin was shown to lead to bacterial cell death. In this work, we report that the aminosterol squalamine and mimic compounds present an unexpected mode of action consisting in the inhibition of the GTase activity of the model enzyme PBP1b. In addition, selected compounds were able to specifically displace the lipid II from the active site in a fluorescence anisotropy assay, suggesting that they act as competitive inhibitors.

scholarly journals Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age

2019 ◽  
Vol 75 (1) ◽  
pp. 3-11 ◽  
Author(s):  
Alok K. Mitra
Keyword(s):  
Electron Microscopy ◽  
Structural Biology ◽  
Atomic Resolution ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Single Particles ◽  
Cryo Electron Microscopy ◽  
Electron Microscopes ◽  
Resolution Single ◽  
Resolution Structure

Structural biology is going through a revolution as a result of transformational advances in the field of cryo-electron microscopy (cryo-EM) driven by the development of direct electron detectors and ultrastable electron microscopes. High-resolution cryo-EM images of isolated biomolecules (single particles) suspended in a thin layer of vitrified buffer are subjected to powerful image-processing algorithms, enabling near-atomic resolution structures to be determined in unprecedented numbers. Prior to these advances, electron crystallography of two-dimensional crystals and helical assemblies of proteins had established the feasibility of atomic resolution structure determination using cryo-EM. Atomic resolution single-particle analysis, without the need for crystals, now promises to resolve problems in structural biology that were intractable just a few years ago.

scholarly journals Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction

Viruses ◽  
2017 ◽  
Vol 9 (11) ◽  
pp. 321 ◽  
Author(s):  
Nikéa Pittman ◽  
Adam Misseldine ◽  
Lorena Geilen ◽  
Sujata Halder ◽  
J. Smith ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Image Reconstruction ◽  
Atomic Resolution ◽  
3D Image ◽  
3D Image Reconstruction ◽  
Resolution Structure

scholarly journals Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

2021 ◽  
Vol 18 (2) ◽  
pp. 156-164 ◽  
Author(s):  
Catherine L. Lawson ◽  
Andriy Kryshtafovych ◽  
Paul D. Adams ◽  
Pavel V. Afonine ◽  
Matthew L. Baker ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Structure Data ◽  
Model Evaluation ◽  
Data Bank ◽  
High Accuracy ◽  
Atomic Resolution ◽  
Software Developers ◽  
Data Archives ◽  
Modeling Software

AbstractThis paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

Atomic-resolution Studies of Ca3Co4O9 using in-situ Scanning Transmission Electron Microscopy

2008 ◽  
Vol 14 (S2) ◽  
pp. 436-437 ◽  
Author(s):  
G Yang ◽  
Y Zhao ◽  
K Sader ◽  
A Bleloch ◽  
RF Klie
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
New Mexico ◽  
Scanning Transmission Electron Microscopy ◽  
Atomic Resolution ◽  
Scanning Transmission Electron ◽  
Transmission Electron ◽  
Scanning Transmission

Extended abstract of a paper presented at Microscopy and Microanalysis 2008 in Albuquerque, New Mexico, USA, August 3 – August 7, 2008

Sign in / Sign up

Export Citation Format

Share Document