Biophysics

Unveiling mutation effects on the structural dynamics of the main protease from SARS-CoV-2 with hybrid simulation methods

1. P. Gasparini
2. E.A. Philot
3. S.Q. Pantaleão
4. N.E.S.M. Torres-Bonfim
5. A. Kliousoff
6. R.C.N. Quiroz
7. D. Perahia
8. R.P. Simões
9. A.J. Magro
10. A.L. Scott

Reviewed by ScreenIT

Effect of malaria parasite shape on its alignment at erythrocyte membrane

1. Anil K Dasanna
2. Sebastian Hillringhaus
3. Gerhard Gompper
4. Dmitry A Fedosov

• Curated by eLife

  Evaluation Summary:

  This manuscript studies the alignment of malaria parasites (merozoites) at the surface of red blood cells (RBCs), a key element of their reproduction cycle during the blood stage of the disease. Building on a computational model the authors developed previously, which incorporates the stochastic nature of RBC deformations and adhesive bonds between the merozoite and RBC, it is demonstrated that parasite shape plays a key role in its alignment dynamics. In particular, the authors shed new light on the egg-like shape typically observed in Plasmodium merozoites, which has important implications for how effectively the parasite can survive and multiply.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Reviewed by eLife

SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged due to glycan interaction

1. Yihan Huang
2. Bradley S. Harris
3. Shiaki A. Minami
4. Seongwon Jung
5. Priya S. Shah
6. Somen Nandi
7. Karen A. McDonald
8. Roland Faller

Reviewed by ScreenIT

Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication

1. Moises Ernesto Romero
2. Chunhong Long
3. Daniel La Rocco
4. Anusha Mysore Keerthi
5. Dajun Xu
6. Jin Yu

Reviewed by ScreenIT

SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern

1. Alice Triveri
2. Stefano A. Serapian
3. Filippo Marchetti
4. Filippo Doria
5. Silvia Pavoni
6. Fabrizio Cinquini
7. Elisabetta Moroni
8. Andrea Rasola
9. Francesco Frigerio
10. Giorgio Colombo

Reviewed by ScreenIT

Interaction between SARS-CoV-2 spike glycoprotein and human skin models: a molecular dynamics study

1. Marc Domingo
2. Jordi Faraudo

Reviewed by ScreenIT

The mechanism of MICU-dependent gating of the mitochondrial Ca2+uniporter

1. Vivek Garg
2. Junji Suzuki
3. Ishan Paranjpe
4. Tiffany Unsulangi
5. Liron Boyman
6. Lorin S Milescu
7. W Jonathan Lederer
8. Yuriy Kirichok

• Curated by eLife

  Evaluation Summary:

  This paper examines the roles and mechanisms of how subunits of the mitochondrial calcium uniporter complex (MCUcx) regulate calcium uptake by mitochondria, a process that serves to match the rate of ATP generation to cellular metabolic needs. Based on direct electrophysiological recordings of MCUcx, the authors find that the MICU1 subunit potentiates channel activity in a calcium-dependent manner but does not block the channel at low calcium levels, challenging current models of MCU regulation. This work will be of significant interest to biophysicists and cell biologists interested in mitochondrial biology, bioenergetics, and ion channel and calcium signaling mechanisms.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes

1. Shawn M. Costello
2. Sophie R. Shoemaker
3. Helen T. Hobbs
4. Annalee W. Nguyen
5. Ching-Lin Hsieh
6. Jennifer A. Maynard
7. Jason S. McLellan
8. John E. Pak
9. Susan Marqusee

Reviewed by ScreenIT

First-principles model of optimal translation factors stoichiometry

1. Jean-Benoît Lalanne
2. Gene-Wei Li

• Curated by eLife

  Evaluation Summary:

  This paper presents a theoretical analysis of the abundance of components of the translation machinery (ribosomes, initiation, elongation and release factors, tRNA synthetases) in bacteria. These proteins make up a large fraction of the total proteome and their abundance is closely linked to cell growth. That the stoichiometry of the different components is adjusted such as to maximize the growth rate has been postulated a long time ago, but was so far only studied in detail for ribosomes and EF-Tu, the most abundant elongation factor. Here, the authors extend these earlier works to an unprecedented level of detail and provide a complete analysis based on this idea and derive the optimal stoichiometry for all these factor, which they find to be in good agreement with the observed abundance in different bacteria. This provides new evidence supporting the idea of proteome optimization for maximal growth.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Atomistic Simulations and In Silico Mutational Profiling of Protein Stability and Binding in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms

1. Gennady M. Verkhivker
2. Steve Agajanian
3. Deniz Yasar Oztas
4. Grace Gupta

Reviewed by ScreenIT