Results 141 to 150 of about 3,678,372 (337)

Modeling conformational ensembles of slow functional motions in Pin1-WW.

PLoS Computational Biology, 2010
Protein-protein interactions are often mediated by flexible loops that experience conformational dynamics on the microsecond to millisecond time scales. NMR relaxation studies can map these dynamics.
Faruck Morcos, Santanu Chatterjee, Christopher L McClendon, Paul R Brenner, Roberto López-Rendón, John Zintsmaster, Maria Ercsey-Ravasz, Christopher R Sweet, Matthew P Jacobson, Jeffrey W Peng, Jesús A Izaguirre   +10 more
doaj   +1 more source

Dammarenediol II enhances etoposide‐induced apoptosis by targeting O‐GlcNAc transferase and Akt/GSK3β/mTOR signaling in liver cancer

Molecular Oncology, EarlyView.
Etoposide induces DNA damage, activating p53‐dependent apoptosis via caspase‐3/7, which cleaves PARP1. Dammarenediol II enhances this apoptotic pathway by suppressing O‐GlcNAc transferase activity, further decreasing O‐GlcNAcylation. The reduction in O‐GlcNAc levels boosts p53‐driven apoptosis and influences the Akt/GSK3β/mTOR signaling pathway ...
Jaehoon Lee, Byung‐Cheol Han, Gi‐Bang Koo, Jihye Park, Mijin Kwon, Young Bin Park, Jae‐Mun Choi, Seung‐Ho Lee, Sangho Roh   +8 more
wiley   +1 more source

REinforcement learning based Adaptive samPling: REAPing Rewards by Exploring Protein Conformational Landscapes

, 2018
One of the key limitations of Molecular Dynamics simulations is the computational intractability of sampling protein conformational landscapes associated with either large system size or long timescales.
Cheng, Kevin J., Shamsi, Zahra, Shukla, Diwakar   +2 more
core   +2 more sources

Rethinking plastic waste: innovations in enzymatic breakdown of oil‐based polyesters and bioplastics

FEBS Open Bio, EarlyView.
Plastic pollution remains a critical environmental challenge, and current mechanical and chemical recycling methods are insufficient to achieve a fully circular economy. This review highlights recent breakthroughs in the enzymatic depolymerization of both oil‐derived polyesters and bioplastics, including high‐throughput protein engineering, de novo ...
Elena Rosini, Nicolò Antonelli, Gianluca Molla   +2 more
wiley   +1 more source

Conformational dynamics of the ABC transporter McjD seen by single‐molecule FRET

EMBO Journal, 2018
ABC transporters utilize ATP for export processes to provide cellular resistance against toxins, antibiotics, and harmful metabolites in eukaryotes and prokaryotes.
Florence Husada, K. Bountra, Konstantinos Tassis, Marijn de Boer, M. Romano, S. Rebuffat, K. Beis, T. Cordes   +7 more
semanticscholar   +1 more source

Homologous expression and purification of human HAX‐1 for structural studies

FEBS Open Bio, EarlyView.
This research protocol provides detailed instructions for cloning, expressing, and purifying large quantities of the intrinsically disordered human HAX‐1 protein, N‐terminally fused to a cleavable superfolder GFP, from mammalian cells. HAX‐1 is predicted to undergo posttranslational modifications and to interact with membranes, various cellular ...
Mariana Grieben
wiley   +1 more source

The photoswitchable cannabinoid azo‐HU308 enables optical control of Ca2+ dynamics in INS‐1 β‐cells via off‐target effects on TRPC channels

FEBS Open Bio, EarlyView.
Light activation of the photoswitchable cannabinoid ligand azo‐HU308 triggers Ca2+ influx in pancreatic β‐cells through TRPC channels, independent of CB2 cannabinoid receptors. This reveals a non‐GPCR pathway for cannabinoid modulation of β‐cell Ca2+ dynamics and establishes azo‐HU308 as an optical tool to study cannabinoid signaling through TRP ...
Alexander E. G. Viray, James A. Frank
wiley   +1 more source

Enhanced sampling of multidimensional free-energy landscapes using adaptive biasing forces

, 2010
We propose an adaptive biasing algorithm aimed at enhancing the sampling of multimodal measures by Langevin dynamics. The underlying idea consists in generalizing the standard adaptive biasing force method commonly used in conjunction with molecular ...
Chipot, Chris, Lelièvre, Tony
core   +3 more sources

Analysis of Treacher Collins syndrome 4‐associated mutations in Schizosaccharomyces pombe

FEBS Open Bio, EarlyView.
Fission yeast models carrying Treacher Collins syndrome type 4‐associated mutations reveal that impaired processivity of RNA polymerase I leads to defective rRNA transcription. This study highlights the essential role of a conserved arginine residue in Pol I elongation and provides mechanistic insight into the pathogenesis of ribosomopathies.
Kei Kawakami, Hiroaki Kato
wiley   +1 more source

Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning

Molecules
The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the ...
Jianzhong Chen, Jian Wang, Wanchun Yang, Lu Zhao, Juan Zhao, Guodong Hu   +5 more
doaj   +1 more source