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

    This article has 10 authors:
    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
    This article has been curated by 1 group:
    • 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

    This article has 9 evaluationsAppears in 1 listLatest version Latest activity
  2. Atomic-Level Free Energy Landscape Reveals Cooperative Symport Mechanism of Melibiose Transporter

    This article has 2 authors:
    1. Ruibin Liang
    2. Lan Guan
    This article has been curated by 1 group:
    • 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

    This article has 5 evaluationsAppears in 2 listsLatest version Latest activity
  3. A direct computational assessment of vinculin-actin unbinding kinetics reveals catch bonding behavior

    This article has 5 authors:
    1. Willmor J Peña Ccoa
    2. Fatemah Mukadum
    3. Aubin Ramon
    4. Guillaume Stirnemann
    5. Glen M Hocky

    Reviewed by PREreview

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  4. Interplay of condensate material properties and chromatin heterogeneity governs nuclear condensate ripening

    This article has 7 authors:
    1. Deb Sankar Banerjee
    2. Tafadzwa Chigumira
    3. Rachel M Lackner
    4. Josiah C Kratz
    5. David M Chenoweth
    6. Shiladitya Banerjee
    7. Huaiying Zhang
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      In this potentially valuable study, the authors employed in vivo experiments and theoretical modeling to study the growth dynamics of nuclear condensates. They observed that condensates can exhibit distinct growth modes, as dictated by the competition between condensate surface tension and local elasticity of chromatin. While the theoretical model appears to capture the experimental observations, the level of evidence supporting the proposed growth mechanism is incomplete due to, among other limitations, the multiple fitting parameters and poorly justified Neo-Hookean elasticity.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  5. Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution

    This article has 5 authors:
    1. Kaushik Borthakur
    2. Thomas R. Sisk
    3. Francesco P. Panei
    4. Massimiliano Bonomi
    5. Paul Robustelli

    Reviewed by PREreview

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  6. Enhanced bacterial chemotaxis in confined microchannels: Optimal performance in lane widths matching circular swimming radius

    This article has 4 authors:
    1. Caijuan Yue
    2. Chi Zhang
    3. Rongjing Zhang
    4. Junhua Yuan
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study examines the effects of side-wall confinement on the chemotaxis of swimming bacteria in a shallow microfluidic channel. The authors present solid experimental evidence, combined with geometric analysis and numerical simulations of simplified models, showing that chemotaxis is enhanced when the distance between the side walls is comparable to the intrinsic radius of circular swimming near open surfaces. This study should be of interest to scientists specializing in bacteria-surface interactions.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  7. Ab initio prediction of specific phospholipid complexes and membrane association of HIV-1 MPER antibodies by multi-scale simulations

    This article has 5 authors:
    1. Colleen A Maillie
    2. Kiana Golden
    3. Ian A Wilson
    4. Andrew B Ward
    5. Marco Mravic
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study reports multi-scale molecular dynamics simulations to investigate a class of highly potent antibodies that simultaneously engage with the HIV-1 Envelope trimer and the viral membrane. The work provides insights into how broadly neutralizing antibodies associate with lipids proximal to membrane-associated epitopes to drive neutralization. After extensive revision, the level of evidence is considered solid, although a quantitative assessment of the underlying energetics remain difficult to obtain.

    Reviewed by eLife

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  8. Molecular dynamics simulations illuminate the role of sequence context in the ELF3-PrD-based temperature sensing mechanism in plants

    This article has 5 authors:
    1. Richard J Lindsay
    2. Rafael Giordano Viegas
    3. Vitor BP Leite
    4. Philip A Wigge
    5. Sonya M Hanson
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      In this potentially valuable computational study, the authors conducted atomistic and coarse-grained simulations to probe the temperature-dependent phase behaviors of ELF3, a disordered component of the evening complex in plant. The results aim to highlight the role of polyQ tracts in modulating the temperature sensitivity. The level of evidence is considered incomplete, due to the lack of systematic calibration of the coarse-grained model and limited statistical uncertainty analysis, especially considering the relatively subtle nature of the differences due to temperature change.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  9. Motor clustering enhances kinesin-driven vesicle transport

    This article has 6 authors:
    1. Rui Jiang
    2. Qingzhou Feng
    3. Daguan Nong
    4. You Jung Kang
    5. David Sept
    6. William O. Hancock

    Reviewed by preLights

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  10. Reversing protonation of weakly basic drugs greatly enhances intracellular diffusion and decreases lysosomal sequestration

    This article has 7 authors:
    1. Debabrata Dey
    2. Shir Marciano
    3. Anna Poryval
    4. Ondřej Groborz
    5. Lucie Wohlrabova
    6. Tomás Slanina
    7. Gideon Schreiber
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This is a valuable study on the diffusion rates of drug molecules in human-derived cells, presenting convincing data indicating that their diffusion behavior depends on their charged state. It proposes that blocking drug protonation enhances diffusion and fractional recovery, suggesting improved intracellular availability of weakly basic drugs. The findings are significant for drug design and understanding the biophysical behavior of small molecules in cells.

    Reviewed by eLife

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
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