Woods R J
Complex Carbohydrate Research Center, Department of Biochemistry, University of Georgia, Athens 30602, USA.
Glycoconj J. 1998 Mar;15(3):209-16. doi: 10.1023/a:1006984709892.
Computational methods have had a long history of application to carbohydrate systems and their development in this regard is discussed. The conformational analysis of carbohydrates differs in several ways from that of other biomolecules. Many glycans appear to exhibit numerous conformations coexisting in solution at room temperature and a conformational analysis of a carbohydrate must address both spatial and temporal properties. When solution nuclear magnetic resonance data are used for comparison, the simulation must give rise to ensemble-averaged properties. In contrast, when comparing to experimental data obtained from crystal structures a simulation of a crystal lattice, rather than of an isolated molecule, is appropriate. Molecular dynamics simulations are well suited for such condensed phase modeling. Interactions between carbohydrates and other biological macromolecules are also amenable to computational approaches. Having obtained a three-dimensional structure of the receptor protein, it is possible to model with accuracy the conformation of the carbohydrate in the complex. An example of the application of free energy perturbation simulations to the prediction of carbohydrate-protein binding energies is presented.
计算方法在碳水化合物体系中的应用已有很长历史，本文将讨论其在这方面的发展情况。碳水化合物的构象分析在几个方面与其他生物分子不同。许多聚糖在室温下的溶液中似乎呈现出多种共存的构象，对碳水化合物的构象分析必须兼顾空间和时间特性。当使用溶液核磁共振数据进行比较时，模拟必须得出系综平均性质。相比之下，当与从晶体结构获得的实验数据进行比较时，对晶格而非孤立分子进行模拟才合适。分子动力学模拟非常适合这种凝聚相建模。碳水化合物与其他生物大分子之间的相互作用也适合采用计算方法。在获得受体蛋白的三维结构后，就有可能精确模拟复合物中碳水化合物的构象。本文给出了一个应用自由能微扰模拟预测碳水化合物 - 蛋白质结合能的例子。
