Extension of coarse-grained UNRES force field to treat carbon nanotubes

被引：0
作者：
Adam K. Sieradzan
Magdalena A. Mozolewska
机构：
[1] University of Gdansk,Faculty of Chemistry
[2] Polish Academy of Sciences,Institute of Computer Science
来源：
Journal of Molecular Modeling | 2018年 / 24卷
关键词：
Molecular dynamics; Nanotechnology; Nanotoxicity; Simulations; Single walled carbon nanotube (SWCNT);
D O I：
暂无
中图分类号：
学科分类号：
摘要：
Carbon nanotubes (CNTs) have recently received considerable attention because of their possible applications in various branches of nanotechnology. For their cogent application, knowledge of their interactions with biological macromolecules, especially proteins, is essential and computer simulations are very useful for such studies. Classical all-atom force fields limit simulation time scale and size of the systems significantly. Therefore, in this work, we implemented CNTs into the coarse-grained UNited RESidue (UNRES) force field. A CNT is represented as a rigid infinite-length cylinder which interacts with a protein through the Kihara potential. Energy conservation in microcanonical coarse-grained molecular dynamics simulations and temperature conservation in canonical simulations with UNRES containing the CNT component have been verified. Subsequently, studies of three proteins, bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTs, were performed to examine the influence of CNTs on the structure and dynamics of these proteins. It was found that nanotubes bind to these proteins and influence their structure. Our results show that the UNRES force field can be used for further studies of CNT-protein systems with 3–4 order of magnitude larger timescale than using regular all-atom force fields.
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