Biophysics

Escape problem of magnetotactic bacteria - physiological magnetic field strengths help magnetotactic bacteria navigate in simulated sediments

1. Agnese Codutti
2. Mohammad A Charsooghi
3. Konrad Marx
4. Elisa Cerdá-Doñate
5. Omar Munoz
6. Paul Zaslansky
7. Vitali Telezki
8. Tom Robinson
9. Damien Faivre
10. Stefan Klumpp

• Curated by eLife

  eLife Assessment

  This study presents valuable experimental and numerical results on the motility of a magnetotactic bacterium living in sedimentary environments, particularly in environments of varying magnetic field strengths. The evidence supporting the claims of the authors is compelling and the study will be of specific relevance to biophysicists interested in bacterial motility.

Reviewed by eLife

Aquavert – Imaging and Microfluidics for Vertical Swimming of Microorganisms

1. Haley B. Obenshain
2. Isaias Zarate
3. Olivia Hedman-Manzano
4. Jared Goderich
5. Sungho Lee
6. Bryant A. Lopez
7. Emma Varela
8. Ga-Young Kelly Suh
9. Douglas A. Pace
10. Siavash Ahrar

Reviewed by Arcadia Science

Prebiotic Gas Flow Environment Enables Isothermal Nucleic Acid Replication

1. Philipp Schwintek
2. Emre Eren
3. Christof Mast
4. Dieter Braun

• Curated by eLife

  eLife Assessment

  This important work shows how a simple geophysical setting of gas flow over a narrow channel of water can create a physical environment that leads to the isothermal replication of nucleic acids. The work presents compelling evidence for an isothermal polymerase chain reaction in careful experiments involving evaporation and convective flows, complimented with fluid dynamics simulations. This work will be of interest to scientists working on the origin of life and more broadly, on nucleic acids and diagnostic applications.

Reviewed by eLife

Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging

1. Liza Dahal
2. Thomas GW Graham
3. Gina M Dailey
4. Alec Heckert
5. Robert Tjian
6. Xavier Darzacq

• Curated by eLife

  eLife Assessment

  This important study provides data that challenges the standard model that binding of Type 2 Nuclear Receptors to chromatin is limited by the available pool of their common heterodimerization partner Retinoid X Receptor. The evidence supporting the conclusions is compelling, utilizing state-of-the-art single-molecule microscopy. This work will be of broad interest to cell biologists who wish to determine limiting factors in gene regulatory networks.

Reviewed by eLife

Heterogeneity in ligand-bound TRPV1: A comparison of methods in cryo-EM and molecular dynamics simulation

1. Miro A. Astore
2. Robert Blackwell
3. David Silva-Sánchez
4. Pilar Cossio
5. Sonya M. Hanson

Reviewed by PREreview

p53 isoforms have a high aggregation propensity, interact with chaperones and lack binding to p53 interaction partners

1. Anamari Brdar
2. Christian Osterburg
3. Philipp Münick
4. Anne Christin Machel
5. Rajeshwari Rathore
6. Susanne Osterburg
7. Büşra Yüksel
8. Birgit Schäfer
9. Kristina Desch
10. Julian D. Langer
11. Ivan Dikic
12. Volker Dötsch

• Curated by eLife

  eLife Assessment

  This manuscript provides a valuable in-depth biochemical analysis of p53 isoforms, highlighting their aggregation propensity, interaction with chaperones, and potential dominant-negative effects on p53 family members. The study presents solid evidence of isoform-specific properties, which may contribute to protein misfolding and impaired cellular function in cancer. While highly informative, the findings would benefit from further discussion of physiological relevance, given the high isoform expression levels used, and addressing prior evidence of isoform-specific transcriptional activity. Overall, this work significantly advances our understanding of p53 isoform biochemistry and its implications for cancer research.

Reviewed by eLife

Wavenumber-dependent transmission of subthreshold waves on electrical synapses network model of Caenorhabditis elegans

1. Iksoo Chang
2. Taegon Chung
3. Sangyeol Kim

• Curated by eLife

  eLife Assessment

  This study presents numerical results on a framework for understanding the dynamics of subthreshold waves in a network of electrical synapses modeled on the connectome data of the C elegans nematode. The strength of the evidence presented in favor of interference effects being a major component in subthreshold wave dynamics is inadequate and the approach is flawed. Substantial methodological issues are present, including altering the original network structure of the connectome without a clear justification and providing little motivation for the choice of numerical parameters values that were used.

Reviewed by eLife

Twist is the key to the gating of mechanosensitive ion channel NOMPC

1. Jingze Duan
2. Chen Song

• Curated by eLife

  eLife Assessment

  This valuable study uses steered molecular dynamics simulations to interrogate force transmission in the mechanosensitive NOMPC channel, which plays roles including soft-touch perception, auditory function, and locomotion. The finding that the ankyrin spring transmits force through torsional rather than compression forces may help understand the entire TRP channel family. The evidence is, however, considered to be still incomplete. It could be strengthened by testing how the channel responds to different twisting and compressional force magnitudes over longer simulation times to see a full gating motion, or to prove that the partial or initial motion observed relates to physiological gating. Experimental validation of reduced mechano-sensitivity through mutagenesis of proposed ankyrin/TRP domain coupling interactions would be best to enhance the manuscript.

Reviewed by eLife

Discovery of a heparan sulfate binding domain in monkeypox virus H3 as an anti-poxviral drug target combining AI and MD simulations

1. Bin Zheng
2. Meimei Duan
3. Yifen Huang
4. Shangchen Wang
5. Jun Qiu
6. Zhuojian Lu
7. Lichao Liu
8. Guojin Tang
9. Lin Cheng
10. Peng Zheng

• Curated by eLife

  eLife Assessment

  This work presents important findings regarding the interaction of the monkeypox virus (MPXV) attachment H3 protein with the cellular receptor heparan sulfate and the use of this information to develop antivirals potentially effective against all orthopoxviruses. Using a combination of state-of-the art computational and wet experiments the authors present convincing evidence to sustain their claims. These results will interest those working on basic orthopoxviruses biology and antiviral development.

Reviewed by eLife

Atomic-Level Free Energy Landscape Reveals Cooperative Symport Mechanism of Melibiose Transporter

1. Ruibin Liang
2. Lan Guan

• Curated by eLife

  eLife Assessment

  In this potentially important study, the authors employed advanced computational techniques to explore a detailed atomistic description of the mechanism and energetics of substrate translocation in the MelB transporter. The overall approach is solid and reveals the coupling between sodium binding and melibiose transport through a series of conformational transitions, and the results for a mutant are also in qualitative agreement with the experiment, providing further support to the computational analyses. Nevertheless, the level of evidence is considered incomplete since there are concerns regarding the convergence and initial guess of the string calculations, leaving doubts that the computed pathway does not reflect the most energetically favorable mechanism.

Reviewed by eLife