Biology subjects

Russo, C. J.

Publications and source records attributed to Russo, C. J..

4 recordsLinked to original sources

bioRxiv2025

Measurement of atomic scattering factors by cryo-electron microscopy

Determination of specimen structure from cryo-electron microscopy (cryo-EM) experiments relies on an accurate model of the electrostatic potential of the specimen. For biological macromolecules, the potential is strongly influenced by the presence of chemical bonds between atoms, a fact unaccounted for by models of electron scattering that are currently standard in the field. We propose a Bayesian approach to the estimation of atomic scattering factors which incorporates the effect of the molecular environment while remaining fast, interpretable and transferable between molecules. Our algorithm infers atomic scattering factors directly from maps of the electrostatic potential determined by cryo-EM single particle analysis, bypassing the need for computationally-intensive theoretical calculations. The algorithm is used to infer empirical scattering factors from high-resolution reconstructions of catalase enzymes. To illustrate its broad applicability, the algorithm is also applied to a training set of publicly-available cryo-EM data. The empirical scattering factors show improved agreement with a test set of cryo-EM reconstructions. The predictions are further validated by comparison with magnetic susceptibility values of organic compounds, as well as by application to the refinement of atomic models. Significance StatementUnderstanding the structure of biomolecules is key to explaining their function. Cryo-electron microscopy is a method for reconstructing the electrostatic potential distribution of a biological macro-molecule, a quantity which contains information about atomic positions and the redistribution of charge due to chemical bonding. These factors should be modelled when inferring the structure of the molecule from its electrostatic potential. We develop an improved model of the potential that takes into account chemical bonding while remaining computationally tractable. The parameters of the model are inferred from a selection of cryo-electron microscopy datasets using Bayesian methods.

biophysics↗

bioRxiv2020

Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP

The RNA polymerase inhibitor, favipiravir, is currently in clinical trials as a treatment for infection with SARS-CoV-2, despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 [A]. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.

molecular biology↗

bioRxiv2020

Structure of the light harvesting 2 complex reveals two carotenoid energy transfer pathways in a photosynthetic bacterium

We report the 2.4 [A] resolution structure of the light harvesting 2 complex (LH2) from Marichromatium (Mch.) purpuratum determined by electron cryo-microscopy. The structure contains a heptameric ring that is unique among all known LH2 structures, explaining the unusual spectroscopic properties of this bacterial antenna complex. Two sets of distinct carotenoids are identified in the structure, and a network of energy transfer pathways from the carotenoids to bacteriochlorophyll a molecules is shown. The geometry imposed by the heptameric ring controls the resonant coupling of the long wavelength energy absorption band. Together, these details reveal key aspects of the assembly and oligomeric form of purple bacterial LH2 complexes that were previously inaccessible by any technique. One Sentence SummaryThe structure of a heptameric LH2 antenna complex reveals new energy transfer pathways and the basis for assembling LH rings.

biochemistry↗

bioRxiv2020

Defocus-dependent Thon-ring fading

The brightness of modern Schottky field-emission guns can produce electron beams that have very high spatial coherence, especially for the weak-illumination conditions that are used for single-particle electron cryo-microscopy in structural biology. Even so, many users have observed defocus-dependent Thon-ring fading that has led them to restrict their data collection strategy to imaging with relatively small defocus values. In this paper, we reproduce the observation of defocus-dependent Thon-ring fading and produce a quantitative analysis and clear explanation of its causes. We demonstrate that a major cause is the delocalization of high-resolution Fourier components outside the field of view of the camera. We also show that it is important to make a correction for linear magnification anisotropy, even if it is quite small, before circular averaging of the Thon rings, as is also true before merging data from particles in many orientations. Under the conditions used in this paper, which are typical of those used in single-particle electron cryomicroscopy, fading of the Thon rings due to source coherence is negligible. The principal conclusion is that much higher values of defocus can be used than is currently thought to be possible. This increased understanding should give electron microscopists the confidence to use higher amounts of defocus to allow, for example, better visibility of their particles and Ewald sphere correction.

biophysics↗