{"title":"Choosing the right density for a concentrated protein system like gluten in a coarse-grained model","authors":"Łukasz Mioduszewski","doi":"10.1007/s00249-023-01667-8","DOIUrl":null,"url":null,"abstract":"<div><p>Large coarse-grained simulations are often conducted with an implicit solvent, which makes it hard to assess the water content of the sample and the effective concentration of the system. Here the number and the size of cavities and entanglements in the system, together with density profiles, are used to asses the homogeneity and interconnectedness of gluten. This is a continuation of an earlier article, \"Viscoelastic properties of wheat gluten in a molecular dynamics study\" (Mioduszewski and Cieplak 2021b). It turns out there is a wide range of densities (between 1 residue per cubic nanometer and 3 residues/nm<span>\\(^3\\)</span>) where the system is interconnected, but not homogeneous: there are still large empty spaces, surrounded by an entangled protein network. Those findings should be of importance to any coarse-grained simulation of large protein systems.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 6-7","pages":"583 - 591"},"PeriodicalIF":2.2000,"publicationDate":"2023-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"European Biophysics Journal","FirstCategoryId":"2","ListUrlMain":"https://link.springer.com/article/10.1007/s00249-023-01667-8","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOPHYSICS","Score":null,"Total":0}
引用次数: 0
Abstract
Large coarse-grained simulations are often conducted with an implicit solvent, which makes it hard to assess the water content of the sample and the effective concentration of the system. Here the number and the size of cavities and entanglements in the system, together with density profiles, are used to asses the homogeneity and interconnectedness of gluten. This is a continuation of an earlier article, "Viscoelastic properties of wheat gluten in a molecular dynamics study" (Mioduszewski and Cieplak 2021b). It turns out there is a wide range of densities (between 1 residue per cubic nanometer and 3 residues/nm\(^3\)) where the system is interconnected, but not homogeneous: there are still large empty spaces, surrounded by an entangled protein network. Those findings should be of importance to any coarse-grained simulation of large protein systems.
期刊介绍：
The journal publishes papers in the field of biophysics, which is defined as the study of biological phenomena by using physical methods and concepts. Original papers, reviews and Biophysics letters are published. The primary goal of this journal is to advance the understanding of biological structure and function by application of the principles of physical science, and by presenting the work in a biophysical context.
Papers employing a distinctively biophysical approach at all levels of biological organisation will be considered, as will both experimental and theoretical studies. The criteria for acceptance are scientific content, originality and relevance to biological systems of current interest and importance.
Principal areas of interest include:
- Structure and dynamics of biological macromolecules
- Membrane biophysics and ion channels
- Cell biophysics and organisation
- Macromolecular assemblies
- Biophysical methods and instrumentation
- Advanced microscopics
- System dynamics.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
