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arXiv 2023年

作者： Park, Hyun Yu, Boyuan Park, Juhae Sun, Ge Tajkhorshid, Emad de Pablo, Juan J. Schneider, Ludwig Theoretical and Computational Biophysics Group NIH Resource Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign UrbanaIL61801 United States Center for Biophysics and Quantitative Biology University of Illinois at Urbana-Champaign UrbanaIL61801 United States Data Science and Learning Division Argonne National Laboratory LemontIL60439 United States Pritzker School of Molecular Engineering University of Chicago 5640 Ellis Ave ChicagoIL60637 United States Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Biochemistry University of Illinois at Urbana-Champaign UrbanaIL61801 United States

A machine learning approach is presented to accelerate the computation of block polymer morphology evolution for large domains over long timescales. The strategy exploits the separation of characteristic times between coarse-grained particle evolution on the monomer scale and slow morphological evolution over mesoscopic scales. In contrast to empirical continuum models, the proposed approach learns stochastically driven defect annihilation processes directly from particle-based simulations. A UNet architecture that respects different boundary conditions is adopted, thereby allowing periodic and fixed substrate boundary conditions of arbitrary shape. Physical concepts are also introduced via the loss function and symmetries are incorporated via data augmentation. The model is validated using three different use cases. Explainable artificial intelligence methods are applied to visualize the morphology evolution over time. This approach enables the generation of large system sizes and long trajectories to investigate defect densities and their evolution under different types of confinement. As an application, we demonstrate the importance of accessing late-stage morphologies for understanding particle diffusion inside a single block. This work has implications for directed self-assembly and materials design in micro-electronics, battery materials, and membranes. Copyright © 2023, The Authors. All rights reserved.

关键词： Block copolymers

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Isoleucine gate blocks K+ conduction in C-type inactivation

arXiv

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arXiv 2024年

作者： Treptow, Werner Liu, Yichen Bassetto, Carlos A.Z. Pinto, Bernardo I. Alves, João Chipot, Christophe Bezanilla, Francisco Roux, Benoît Universidade de Brasília DF CEP 70904-970 Brazil Department of Biochemistry and Molecular Biology The University of Chicago ChicagoIL60637 United States Department of Neurobiology The University of Chicago ChicagoIL60637 United States Laboratoire International Associe Centre National de la Recherche Scientifique University of Illinois at Urbana−Champaign Université de Lorraine Université de Lorraine Unité Mixte de Recherche No. 7019 B.P. 70239 Vandœuvre-lès-Nancy cedex 54506 France NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology Department of Physics University of Illinois at Urbana−Champaign UrbanaIL61801 United States Centro Interdisciplinario de Neurociencia de Valparaíso Facultad de Ciencias Universidad de Valparaíso Valparaíso Chile

Many voltage-gated potassium (Kv) channels display a time-dependent phenomenon called C-type inactivation, whereby prolonged activation by voltage leads to the inhibition of ionic conduction, a process that involves a conformational change at the selectivity filter toward a non-conductive state. Recently, a high-resolution structure of a strongly inactivating triple-mutant channel kv1.2-kv2.1-3m revealed a novel conformation of the selectivity filter that is dilated at its outer end, distinct from the well-characterized conductive state. While the experimental structure was interpreted as the elusive non-conductive state, molecular dynamics simulations and electrophysiology measurements demonstrate that the dilated filter of kv1.2-kv2.1-3m, however, is conductive and, as such, cannot completely account for the inactivation of the channel observed in functional experiments. An additional conformational change implicating isoleucine residues at position 398 along the pore lining segment S6 is required to effectively block ion conduction. It is shown that the I398 residues from the four subunits act as a state-dependent hydrophobic gate located immediately beneath the selectivity filter. As a critical piece of the C-type inactivation machinery, this structural feature is the potential target of a broad class of QA blockers and negatively charged activators thus opening new research directions towards the development of drugs that specifically modulate gating-states of Kv channels. © 2024, CC BY.

关键词： Electrophysiology

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A Kinetic Description of Cytosolic K + Binding to the Human Sertotonin Transporter Under Turnover Conditions

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Biophysical Journal 2020年第3期118卷 443a-443a页

作者： Zhiyu Zhao Emad Tajkhorshid Department of Biochemistry Center for Biophysics and Quantitative Biology University of Illinois Urbana IL USA NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute University of Illinois Urbana IL USA

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