Single‐Particle Reconstruction of Biological Molecules—Story in a Sample (Nobel Lecture)

Frank, Joachim

doi:10.1002/anie.201802770

Cited by 39 publications

(25 citation statements)

References 99 publications

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“…While developments in cryogenic electron microscopy [60][61][62][63] have revolutionized structural biology [64], NMR spectroscopy remains the most powerful tools to study protein dynamics, especially IDRs and IDPs, with residue-specific resolution [65]. RNA-binding proteins are a large family of proteins with high sequence variability in their IDRs.…”

Section: Discussionmentioning

confidence: 99%

Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins

Chen¹,

Huang²

2020

IJMS

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RNA-binding proteins (RBPs) have intrinsically disordered regions (IDRs) whose biophysical properties have yet to be explored to the same extent as those of the folded RNA interacting domains. These IDRs are essential to the formation of biomolecular condensates, such as stress and RNA granules, but dysregulated assembly can be pathological. Because of their structural heterogeneity, IDRs are best studied by NMR spectroscopy. In this study, we used NMR spectroscopy to investigate the structural propensity and self-association of the IDR of the RBP Musashi-1. We identified two transient α-helical regions (residues ~208–218 and ~270–284 in the IDR, the latter with a polyalanine tract). Strong NMR line broadening in these regions and circular dichroism and micrography data suggest that the two α-helical elements and the hydrophobic residues in between may contribute to the formation of oligomers found in stress granules and implicated in Alzheimer’s disease. Bioinformatics analysis suggests that polyalanine stretches in the IDRs of RBPs may have evolved to promote RBP assembly.

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Section: Discussionmentioning

confidence: 99%

Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins

Chen¹,

Huang²

2020

IJMS

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“…Through application of advanced imaging techniques, single-particle cryogenic electron microscopy (cryo-EM) [2][3][4] allows macromolecules in an in vitro suspension to be experimentally visualized en masse after rapid freezing in vitreous ice at a rate that is assumed to be faster than the overall reconfiguration time of the system. 5 As a result, the ensemble of frozen molecules closely approximates the equilibrium distribution of states immediately prior to being frozen.…”

Section: Introductionmentioning

confidence: 99%

Simulation of cryo-EM ensembles from atomic models of molecules exhibiting continuous conformations

Seitz

Acosta-Reyes

Schwander

et al. 2019

Preprint

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Molecular machines visit a continuum of conformational states as they go through work cycles required for their metabolic functions. Single-molecule cryo-EM of suitable in vitro systems affords the ability to collect a large ensemble of projections depicting the continuum of structures and assign occupancies, or free energies, to the observed states.Through the use of machine learning and dimension reduction algorithms it is possible to determine a low-dimensional free energy landscape from such data, allowing the basis for molecular function to be elucidated. In the absence of ground truth data, testing and validation of such methods is quite difficult, however. In this work, we propose a workflow for generating simulated cryo-EM data from an atomic model subjected to conformational changes. As an example, an ensemble of structures and their multiple projections was created from heat shock protein Hsp90 with two defined conformational degrees of freedom. All scripts for reproducing this workflow are available online. 1

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“…This article highlights only Joachim Frank's main contributions to the ribosome field, and is not a comprehensive review of the literature. His work on the theoretical aspects of the single-particle 3D-EM methods, which started in the late 1960s with his PhD work, is best summarized in his Nobel lecture (Frank, 2018).…”

Section: Introductionmentioning

confidence: 99%

Joachim Frank's Binding with the Ribosome

Agrawal

2019

Structure

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With recent technological advancements, single-particle cryogenic electron microscopy (cryo-EM) is now the technique of choice to study structure and function of biological macromolecules at near-atomic resolution. Many single-particle EM reconstruction methods necessary for these advances were pioneered by Joachim Frank, and were optimized using the ribosome as a benchmark specimen. In doing so, he made several landmark contributions to the understanding of the structure and function of ribosomes. These include the first 3D visualization of ribosome-bound transfer RNAs, the first experimentally derived structures of the primary complexes formed during the bacterial translation elongation cycle, and the critical ribosomal conformational transitions required for translation. Over the years, his laboratory studied many important functional complexes of the ribosome from both eubacterial and eukaryotic systems, including ribosomes from pathogenic organisms. This article presents a brief account of the contributions made by Joachim Frank to the ribosome field.

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Single‐Particle Reconstruction of Biological Molecules—Story in a Sample (Nobel Lecture)

Cited by 39 publications

References 99 publications

Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins

Musashi-1: An Example of How Polyalanine Tracts Contribute to Self-Association in the Intrinsically Disordered Regions of RNA-Binding Proteins

Simulation of cryo-EM ensembles from atomic models of molecules exhibiting continuous conformations

Joachim Frank's Binding with the Ribosome

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