Hu Guang
Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China.
Methods Mol Biol. 2021;2253:21-35. doi: 10.1007/978-1-0716-1154-8_3.
Allostery is a fundamental regulatory mechanism in the majority of biological processes of molecular machines. Allostery is well-known as a dynamic-driven process, and thus, the molecular mechanism of allosteric signal transmission needs to be established. Elastic network models (ENMs) provide efficient methods for investigating the intrinsic dynamics and allosteric communication pathways in proteins. In this chapter, two ENM methods including Gaussian network model (GNM) coupled with Markovian stochastic model, as well as the anisotropic network model (ANM), were introduced to identify allosteric effects in hemoglobins. Techniques on model parameters, scripting and calculation, analysis, and visualization are shown step by step.
变构是大多数分子机器生物过程中的一种基本调节机制。变构作为一种由动力学驱动的过程而广为人知，因此，需要建立变构信号传递的分子机制。弹性网络模型（ENM）为研究蛋白质的内在动力学和变构通讯途径提供了有效的方法。在本章中，介绍了两种ENM方法，包括结合马尔可夫随机模型的高斯网络模型（GNM）以及各向异性网络模型（ANM），以识别血红蛋白中的变构效应。逐步展示了模型参数、脚本编写与计算、分析以及可视化等技术。
