Joint Experimental and Theoretical Investigation of the Interaction Between Antimicrobial Peptides, Gold Nanoparticles and Membranes
Joint Experimental and Theoretical Investigation of the Interaction Between Antimicrobial Peptides, Gold Nanoparticles and Membranes
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抗菌肽、金纳米颗粒和膜之间相互作用的联合实验和理论研究
DOI：
10.1016/j.bpj.2010.12.1359
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发表时间：
2011
期刊：
影响因子：
--
通讯作者：
W. Wenzel
中科院分区：
文献类型：
--
作者：
J. Setzler;Y. Klapper;A. Leifert;T. Strunk;A. Ulrich;U. Simon;R. Benz;W. Wenzel
王倩，安东尼奥斯·萨米奥塔基斯，张曼玉。我们使用计算机模拟来研究合成的crowders对细胞色素c的影响，细胞色素c是一种具有辅因子血红素的小的单结构域蛋白质。通过使用粗粒蛋白质模型和基于结构的（类Go）相互作用，计算了细胞色素在不同大小和形状的拥挤物存在下的折叠能量景观。我们的研究结果表明，给定相同的体积分数的拥挤，折叠的蛋白质的稳定性与拥挤的半径成反比增加。此外，具有各向异性几何形状的拥挤器对折叠的蛋白质施加比各向同性拥挤器更大的稳定作用。这与标度粒子理论的预测是一致的。此外，血红素和细胞色素c蛋白质之间的接触形成的分布被发现是不同的不同类型的拥挤，表明拥挤的几何形状可能是调整血红素蛋白质接触形成的细胞样条件下的关键因素之一。混合人群的前景将被介绍。1146-POS板B56动力学模型的增强采样方法阿布拉罗斯塔，格哈德悍马。我们提出了动力学模型的增强采样方法，如副本交换和模拟回火。有了这些模型，我们得到的抽样方法的统计误差和计算效率的解析表达式。作为一个具体的例子，我们考虑两种状态的蛋白质折叠。一个主要的结果是，使用可比的计算资源，副本交换分子动力学（REMD）和分子动力学（MD）模拟的相对效率是由两个折叠状态之间的转换的数量的比率平均在所有副本在不同的温度下，和转换的数量在单个温度的MD运行。如果与转换时间相比，副本交换频繁，则此公式适用。对于模拟回火（ST）模拟，我们获得了一个关系-
Qian Wang, Antonios Samiotakis, Margaret Cheung. We use computer simulation to investigate the effects of synthetic crowders on cytochrome c, a small single-domain protein with a cofactor heme. The folding energy landscape of cytochrome was computed in the presence of crowders with various sizes and shapes by using a coarse-grained protein model and the structure-based (Go-like) interactions. Our results demonstrated that given the same volume fraction of crowders, the stability of a folded protein inversely increases with the radius of crowders. In addition, a crowder with an anisotropic geometry imposes a greater stabilizing effect on the folded protein than isotropic crowders. This is in agreement with the predictions by the scaled particle theory. In addition, the distribution of contact formation between heme and cytochrome c protein was found to be varied by different types of crowders, demonstrating that the geometry of crowders may be one of the key factors for tuning heme-protein contact formation under cell-like conditions. Prospects of mixed crowders will be presented.1146-Pos Board B56 Kinetic Models of Enhanced Sampling Methods Edina Rosta, Gerhard Hummer. We present kinetic models of enhanced sampling methods such as replica exchange and simulated tempering. With these models we derive analytical expressions for the statistical error and computational efficiency of the sampling methods. As a specific example, we consider two-state protein folding. A main result is that with comparable computational resources used, the relative efficiency of replica exchange molecular dynamics (REMD) and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two folding states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. For simulated tempering (ST) simulations, we obtain a rela-