All-atom simulations of biomolecular condensates

IF 6.1 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Current opinion in structural biology Pub Date : 2025-07-03 DOI:10.1016/j.sbi.2025.103101

Miloš T. Ivanović , Robert B. Best

引用次数: 0

Abstract

Biomolecular condensates shape a wide spectrum of physiological and pathological processes, yet the molecular mechanisms underlying their formation and activity are still to be fully understood. Molecular simulations can provide valuable insights into the structure and dynamics of such condensates, and coarse-grained simulations have been widely used to characterize phenomena related to their phase equilibrium. All-atom simulations provide a complementary picture–while too expensive to readily study equilibrium between dense and dilute phases, they offer molecular detail on the dense phase that is missing from coarse-grained models, as well as accurate dynamical information. We provide an overview of this nascent application of atomistic simulations to condensates and the insights they have yielded on their structure and dynamics.

查看原文本刊更多论文

生物分子凝聚物的全原子模拟

生物分子凝聚物形成了广泛的生理和病理过程，但其形成和活动的分子机制仍有待充分了解。分子模拟可以为这类凝析物的结构和动力学提供有价值的见解，粗粒度模拟已被广泛用于表征与其相平衡相关的现象。全原子模拟提供了一幅互补的画面——虽然研究浓相和稀相之间的平衡过于昂贵，但它们提供了粗粒度模型所缺少的致密相的分子细节，以及准确的动力学信息。我们提供了一个概述，这种新生的应用原子模拟冷凝物和见解，他们已经产生了他们的结构和动力学。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Current opinion in structural biology 生物-生化与分子生物学

CiteScore

12.20

自引率

2.90%

发文量

179

审稿时长

6-12 weeks

期刊介绍： Current Opinion in Structural Biology (COSB) aims to stimulate scientifically grounded, interdisciplinary, multi-scale debate and exchange of ideas. It contains polished, concise and timely reviews and opinions, with particular emphasis on those articles published in the past two years. In addition to describing recent trends, the authors are encouraged to give their subjective opinion of the topics discussed. In COSB, we help the reader by providing in a systematic manner: 1. The views of experts on current advances in their field in a clear and readable form. 2. Evaluations of the most interesting papers, annotated by experts, from the great wealth of original publications. [...] The subject of Structural Biology is divided into twelve themed sections, each of which is reviewed once a year. Each issue contains two sections, and the amount of space devoted to each section is related to its importance. -Folding and Binding- Nucleic acids and their protein complexes- Macromolecular Machines- Theory and Simulation- Sequences and Topology- New constructs and expression of proteins- Membranes- Engineering and Design- Carbohydrate-protein interactions and glycosylation- Biophysical and molecular biological methods- Multi-protein assemblies in signalling- Catalysis and Regulation