Sieradzan Adam K, Mozolewska Magdalena A
Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308, Gdansk, Poland.
Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, 01-248, Warsaw, Poland.
J Mol Model. 2018 Apr 26;24(5):121. doi: 10.1007/s00894-018-3656-1.
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. Graphical abstract Bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTsᅟ.
碳纳米管（CNTs）因其在纳米技术各个领域的潜在应用，近来受到了广泛关注。为了实现其切实可行的应用，了解它们与生物大分子，尤其是蛋白质的相互作用至关重要，而计算机模拟对于此类研究非常有用。经典的全原子力场显著限制了模拟的时间尺度和系统规模。因此，在本工作中，我们将碳纳米管纳入了粗粒度的统一残基（UNRES）力场。碳纳米管被表示为一个刚性的无限长圆柱体，它通过木原势与蛋白质相互作用。在包含碳纳米管成分的UNRES微正则粗粒度分子动力学模拟中的能量守恒以及正则模拟中的温度守恒已得到验证。随后，对三种蛋白质，即牛血清白蛋白（BSA）、大豆过氧化物酶（SBP）和α-胰凝乳蛋白酶（CT），在有和没有碳纳米管的情况下进行了研究，以考察碳纳米管对这些蛋白质结构和动力学的影响。结果发现，纳米管与这些蛋白质结合并影响其结构。我们的结果表明，与使用常规全原子力场相比，UNRES力场可用于对碳纳米管 - 蛋白质系统进行时间尺度大3 - 4个数量级的进一步研究。图形摘要 有和没有碳纳米管的牛血清白蛋白（BSA）、大豆过氧化物酶（SBP）和α-胰凝乳蛋白酶（CT）。
