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马丁尼 3 号碳水化合物粗粒度力场。

Martini 3 Coarse-Grained Force Field for Carbohydrates.

机构信息

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands.

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.

出版信息

J Chem Theory Comput. 2022 Dec 13;18(12):7555-7569. doi: 10.1021/acs.jctc.2c00757. Epub 2022 Nov 7.

Abstract

The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the present work, we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme which decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals were developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the polyglucoses dextran (water-soluble) and cellulose (water insoluble but soluble in ionic liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids. We show they are able to reproduce membrane properties and induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach.

摘要

马蒂尼 3 力场是马蒂尼粗粒化模型的全面重新参数化,用于生物分子模拟。由于改进了相互作用平衡,它可以更准确地描述凝聚相系统。在本工作中,我们开发了一种在马蒂尼 3 框架内准确参数化碳水化合物分子的一致策略。特别是,我们开发了一种规范映射方案,将任意大的碳水化合物分解为有限数量的片段。这些片段的珠型通过匹配单糖和二糖的物理化学性质来分配。此外,还制定了分配键、角度和二面角的指南。这些指南比马蒂尼 2 力场更能准确描述碳水化合物构象。我们表明,使用这种方法获得的模型能够准确地再现碳水化合物水溶液的渗透压。此外,我们提供的证据表明,该模型能够正确地区分多聚糖葡聚糖(水溶性)和纤维素(水不溶性但可溶于离子液体)的溶解度。最后,我们证明了新的构建块可以应用于糖脂。我们表明它们能够再现膜性质并诱导外周膜蛋白的结合。这些测试案例证明了我们方法的有效性和可转移性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1387/9753587/67a929cc4c02/ct2c00757_0001.jpg

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