1. Simulation-based survey of TMEM16 family reveals that robust lipid scrambling requires an open groove

    This article has 4 authors:
    1. Christina A Stephens
    2. Niek van Hilten
    3. Lisa Zheng
    4. Michael Grabe
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study provides information on the TMEM16 family of membrane proteins, which play roles in lipid scrambling and ion transport. By simulating 27 structures representing five distinct family members, the authors captured hundreds of lipid scrambling events, offering insights into the mechanisms of lipid translocation and the specific protein regions involved in these processes. However, while the data on groove dilation is compelling, the evidence for outside-the-groove scramblase activity without experimental validation is inadequate and is based on a limited set of observed events.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 2 listsLatest version Latest activity
  2. Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange

    This article has 3 authors:
    1. Ameya Harmalkar
    2. Sergey Lyskov
    3. Jeffrey J Gray
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      The authors report how a previously published method, ReplicaDock, can be used to improve predictions from AlphaFold-multimer (AFm) for protein docking studies. The level of improvement is modest for cases where AFm is successful; for cases where AFm is not as successful, the improvement is more significant, although the accuracy of prediction is also notably lower. The evidence for the ReplicaDock approach being more predictive than AFm is particularly convincing for the antibody-antigen test case. Overall, the study makes a valuable contribution by combining data- and physics-driven approaches.

    Reviewed by eLife

    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  3. Flexibility in PAM Recognition Expands DNA Targeting in xCas9

    This article has 5 authors:
    1. Kazi A Hossain
    2. Lukasz Nierzwicki
    3. Modesto Orozco
    4. Jacek Czub
    5. Giulia Palermo
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This manuscript describes a fundamental investigation of the functioning of Cas9 and in particular on how variant xCas9 expands DNA targeting ability by an increase-flexibility mechanism. The authors provide compelling evidence to support their mechanistic models and the relevance of flexibility and entropy in recognition. This work can be of interest to a broad community of structural biophysicists, computational biologists, chemists, and biochemists.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  4. PROTAC-induced Protein Structural Dynamics in Targeted Protein Degradation

    This article has 3 authors:
    1. Kingsley Y Wu
    2. Ta I Hung
    3. Chia-en A Chang
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study provides important computational insights into the dynamics of PROTAC-induced degradation complexes, offering a convincing demonstration that differences in degradation efficacy can be linked to linker properties. The analyses address reproducibility considerations comprehensively, reinforcing the study's conclusions. Overall, these findings are significant for advancing cancer treatments and will be of broad interest to both biochemists and biophysicists.

    Reviewed by eLife

    This article has 10 evaluationsAppears in 1 listLatest version Latest activity
  5. Tension-induced suppression of allosteric conformational changes explains coordinated stepping of kinesin-1

    This article has 10 authors:
    1. Tsukasa Makino
    2. Ryo Kanada
    3. Teppei Mori
    4. Ken-ichi Miyazono
    5. Yuta Komori
    6. Haruaki Yanagisawa
    7. Shoji Takada
    8. Masaru Tanokura
    9. Masahide Kikkawa
    10. Michio Tomishige

    Reviewed by Review Commons

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  6. Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments

    This article has 9 authors:
    1. Jessica Flowers
    2. Nathaniel Echols
    3. Galen Correy
    4. Priya Jaishankar
    5. Takaya Togo
    6. Adam R Renslo
    7. Henry van den Bedem
    8. James S Fraser
    9. Stephanie A Wankowicz
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This work presents a valuable extension of qFit-ligand, a computational method for modeling conformational heterogeneity of ligands in X-ray crystallography and cryo-EM density maps. The evidence presented for improved capabilities through careful validation against the previous version, notably in expanding ligand sampling within the conformational space, is solid yet still incomplete. The enhanced methodology demonstrates practical utility for challenging applications, including macrocyclic compound modeling and crystallographic drug fragment screening.

    Reviewed by eLife

    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  7. Mechanical stresses govern myoblast fusion and myotube growth

    This article has 9 authors:
    1. Yoann Le Toquin
    2. Sushil Dubey
    3. Aleksandra Ardaševa
    4. Lakshmi Balasubramaniam
    5. Emilie Delaune
    6. Valérie Morin
    7. Amin Doostmohammadi
    8. Christophe Marcelle
    9. Benoît Ladoux

    Reviewed by preLights

    This article has 1 evaluationAppears in 1 listLatest version Latest activity
  8. Kinetic regulation of kinesin’s two motor domains coordinates its stepping along microtubules

    This article has 5 authors:
    1. Yamato Niitani
    2. Kohei Matsuzaki
    3. Erik Jonsson
    4. Ronald D. Vale
    5. Michio Tomishige

    Reviewed by Review Commons

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  9. Cell-cycle and Age-Related Modulations of Mouse Chromosome Stiffness

    This article has 5 authors:
    1. Ning Liu
    2. Wenan Qiang
    3. Philip Jordan
    4. John F Marko
    5. Huanyu Qiao
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable paper describes the stiffness of meiotic chromosomes in both oocytes and spermatocytes. The authors identify differences in stiffness between meiosis I and II chromosomes, as well as an age-dependent increase in stiffness in meiosis I (and meiosis II) chromosomes, results that are highly significant for the field of chromosome biology. The report is, however, mostly descriptive and the mechanisms underlying age-dependent changes in chromosome stiffness remain unclear. The evidence suggesting that changes in stiffness are independent of cohesin, which is known to deteriorate with age, is still incomplete.

    Reviewed by eLife

    This article has 8 evaluationsAppears in 1 listLatest version Latest activity
  10. ATP-release pannexin channels are gated by lysophospholipids

    This article has 12 authors:
    1. Erik Henze
    2. Russell N. Burkhardt
    3. Bennett W. Fox
    4. Tyler J. Schwertfeger
    5. Eric Gelsleichter
    6. Kevin Michalski
    7. Lydia Kramer
    8. Margret Lenfest
    9. Jordyn M. Boesch
    10. Hening Lin
    11. Frank C. Schroeder
    12. Toshimitsu Kawate

    Reviewed by Biophysics Colab

    This article has 2 evaluationsAppears in 2 listsLatest version Latest activity
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