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Highlights of Coronavirus Structural Studies

Coronavirus Archive

Research Highlights

the best of science obtained using CIISB Core Facilities

EMBO Journal 2022

Cryo-EM structures of CspA27 inside the exit tunnel

  1. Structure and nascent chain contacts in the exit tunnel for CspA27-1.
  2. Structure and nascent chain contacts in the exit tunnel for CspA27-2.
  3. Structure and nascent chain contacts in the exit tunnel for CspA27-3.

Marina V. Rodnina Research Group

Significance

Cellular proteins begin to fold as they emerge from the ribosome. The folding landscape of nascent chains is not only shaped by their amino acid sequence but also by the interactions with the ribosome. Here, we combine biophysical methods with cryo-EM structure determination to show that folding of a β-barrel protein begins with formation of a dynamic α-helix inside the ribosome. As the growing peptide reaches the end of the tunnel, the N-terminal part of the nascent chain refolds to a β-hairpin structure that remains dynamic until its release from the ribosome. Contacts with the ribosome and structure of the peptidyl transferase center depend on nascent chain conformation. These results indicate that proteins may start out as α-helices inside the tunnel and switch into their native folds only as they emerge from the ribosome. Moreover, the correlation of nascent chain conformations with reorientation of key residues of the ribosomal peptidyl-transferase center suggest that protein folding could modulate ribosome activity.

Agirrezabala, X., Samatova, E., Macher, M., Liutkute, M., Maiti, M., Gil-Carton, D., Novacek, J., Valle. M., and Rodnina, M.V.: EMBO J. (2022) e109175, https://doi.org/10.15252/embj.2021109175

 

ACS Nano 2021

Snapshots from simulations representing the release pathways. The rapid pathway category (R1–R3) was divided into (R1) burst genome release, where capsids disintegrate into fragments; (R2) rupture genome release, where capsids split open (most often into two halves); and (R3) bloom genome release, where capsids open wide in one hemisphere without breaking the other. In the rupture and bloom pathways, a majority of the capsid reassembles after the genome release. Occasionally, pentamers of capsid proteins may be detached. The subcategory leaky release (L) started with a slow release and ended with a rapid release. The slow pathway (S1–S3) category was divided into (S1) release through a pore on a twofold axis, (S2) release through a pore on a threefold axis, and (S3) release through multiple pores. Note that slow release was only observed for the noncompact genome. All release examples are shown with the noncompact genome. Color coding: Beads forming the body of the capsid are orange on the outside and purple on the inside of the capsid. The genome is represented by blue beads. Red and green beads represent attractive beads between pentamers.

Robert Vácha Research Group

Significance

Virus-like nanoparticles are protein shells similar to wild-type viruses, and both aim to deliver their content into a cell. Unfortunately, the release mechanism of their cargo/ genome remains elusive. Pores on the symmetry axes were proposed to enable the slow release of the viral genome. In contrast, cryo-EM images showed that capsids of nonenveloped RNA viruses can crack open and rapidly release the genome. We combined in vitro cryo-EM observations of the genome release of three viruses with coarse-grained simulations of generic virus-like nanoparticles to investigate the cargo/genome release pathways. Simulations provided details on both slow and rapid release pathways, including the success rates of individual releases. Moreover, the simulated structures from the rapid release pathway were in agreement with the experiment. Slow release occurred when interactions between capsid subunits were long-ranged, and the cargo/genome was noncompact. In contrast, rapid release was preferred when the interaction range was short and/or the cargo/genome was compact. These findings indicate a design strategy of virus-like nanoparticles for drug delivery.

 

Sukeník, L., Mukhamedova, L., Procházková, M., Škubník, K., Plevka, P., and Vácha, R.:

Cargo Release from Nonenveloped Viruses and Virus-like Nanoparticles: Capsid Rupture or Pore Formation, ABC Nano 2021, 15, 12, 19233–19243, https://doi.org/10.1021/acsnano.1c04814

 

More publications Research Highlights archive

Reader’s Corner

literature to read, science to follow

In this section, a distinct selection of six highly stimulating research publications and reviews published during past 6 months is presented. It is our hope that links to exciting science, which deserves attention of the structural biology community, will help you to locate gems in the steadily expanding jungle of scientific literature. You are welcome to point out to any paper you found interesting by sending a link or citation to readerscorner@ciisb.org. The section is being updated regularly.


 

6 Jan

De novo protein design by deep network hallucination (Nature)

There has been considerable recent progress in protein structure prediction using deep neural networks to predict inter-residue distances from amino acid sequences. Here we investigate whether the information captured by such networks is sufficiently rich to generate new folded proteins with sequences unrelated to those of the naturally occurring proteins used in training the models. We generate random amino acid sequences, and input them into the trRosetta structure prediction network to predict starting residue–residue distance maps, which, as expected, are quite featureless. We then carry out Monte Carlo sampling in amino acid sequence space, optimizing the contrast (Kullback–Leibler divergence) between the inter-residue distance distributions predicted by the network and background distributions averaged over all proteins. Optimization from different random starting points resulted in novel proteins spanning a wide range of sequences and predicted structures. We obtained synthetic genes encoding 129 of the network-‘hallucinated’ sequences, and expressed and purified the proteins in Escherichia coli; 27 of the proteins yielded monodisperse species with circular dichroism spectra consistent with the hallucinated structures. We determined the three-dimensional structures of three of the hallucinated proteins, two by X-ray crystallography and one by NMR, and these closely matched the hallucinated models. Thus, deep networks trained to predict native protein structures from their sequences can be inverted to design new proteins, and such networks and methods should contribute alongside traditional physics-based models to the de novo design of proteins with new functions.

Reader’s Corner Archive

Quote of January

“Imagination is more important than knowledge.”

Albert Einstein

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