National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States.
Curr Opin Biotechnol. 2011 Apr;22(2):231-8. doi: 10.1016/j.copbio.2010.11.005. Epub 2010 Dec 17.
Understanding the molecular-level mechanisms that enzymes employ to deconstruct plant cell walls is a fundamental scientific challenge with significant ramifications for renewable fuel production from biomass. In nature, bacteria and fungi use enzyme cocktails that include processive and non-processive cellulases and hemicellulases to convert cellulose and hemicellulose to soluble sugars. Catalyzed by an accelerated biofuels R&D portfolio, there is now a wealth of new structural and experimental insights related to cellulases and the structure of plant cell walls. From this background, computational approaches commonly used in other fields are now poised to offer insights complementary to experiments designed to probe mechanisms of plant cell wall deconstruction. Here we outline the current status of computational approaches for a collection of critical problems in cellulose deconstruction. We discuss path sampling methods to measure rates of elementary steps of enzyme action, coarse-grained modeling for understanding macromolecular, cellulosomal complexes, methods to screen for enzyme improvements, and studies of cellulose at the molecular level. Overall, simulation is a complementary tool to understand carbohydrate-active enzymes and plant cell walls, which will enable industrial processes for the production of advanced, renewable fuels.
理解酶用于解构植物细胞壁的分子水平机制是一项具有重大意义的基础科学挑战，对于从生物质生产可再生燃料具有重要意义。在自然界中，细菌和真菌使用包含可进行性和不可进行性纤维素酶和半纤维素酶的酶混合物将纤维素和半纤维素转化为可溶性糖。在加速生物燃料研发组合的推动下，现在有大量与纤维素酶和植物细胞壁结构相关的新的结构和实验见解。在此背景下，现在通常在其他领域使用的计算方法有望提供与旨在探索植物细胞壁解构机制的实验互补的见解。在这里，我们概述了用于纤维素解构一系列关键问题的计算方法的现状。我们讨论了用于测量酶作用基本步骤速率的路径采样方法、用于理解大分子、细胞酶复合物的粗粒化建模方法、用于筛选酶改进的方法以及分子水平的纤维素研究。总的来说，模拟是理解碳水化合物活性酶和植物细胞壁的补充工具，这将使生产先进可再生燃料的工业过程成为可能。
