Hadden Jodi A, French Alfred D, Woods Robert J
Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602.
Biopolymers. 2013 Oct;99(10):746-56. doi: 10.1002/bip.22279.
Molecular dynamics (MD) simulations of cellulose microfibrils are pertinent to the paper, textile, and biofuels industries for their unique capacity to characterize dynamic behavior and atomic-level interactions with solvent molecules and cellulase enzymes. While high-resolution crystallographic data have established a solid basis for computational analysis of cellulose, previous work has demonstrated a tendency for modeled microfibrils to diverge from the linear experimental structure and adopt a twisted conformation. Here, we investigate the dependence of this twisting behavior on computational approximations and establish the theoretical basis for its occurrence. We examine the role of solvent, the effect of nonbonded force field parameters [partial charges and van der Waals (vdW) contributions], and the use of explicitly modeled oxygen lone pairs in both the solute and solvent. Findings suggest that microfibril twisting is favored by vdW interactions, and counteracted by both intrachain hydrogen bonds and solvent effects at the microfibril surface.
纤维素微纤丝的分子动力学（MD）模拟对于造纸、纺织和生物燃料行业具有重要意义，因为它具有独特的能力来表征动态行为以及与溶剂分子和纤维素酶的原子级相互作用。虽然高分辨率晶体学数据为纤维素的计算分析奠定了坚实基础，但先前的研究表明，建模的微纤丝有偏离线性实验结构并采用扭曲构象的趋势。在此，我们研究这种扭曲行为对计算近似的依赖性，并为其发生建立理论基础。我们研究了溶剂的作用、非键合力场参数[部分电荷和范德华（vdW）贡献]的影响，以及溶质和溶剂中明确建模的氧孤对的使用。研究结果表明，范德华相互作用有利于微纤丝扭曲，而链内氢键和微纤丝表面的溶剂效应则会抵消这种扭曲。
