Ligand Binding and Release Investigated by Contact-guided Iterative Multiple Independent Molecular Dynamics Simulations
- Received Date: 2020-10-12
- Accepted Date: 2020-11-04
- Rev Recd Date: 2020-10-30
- Available Online: 2020-11-27
Abstract: Binding and release of ligands are critical for biological functions of many proteins, and thus it is important to determine these highly dynamic processes. Although there are experimental techniques to determine structure of a protein-ligand complex, it only provides a static picture of the system. With the rapid increase of computing power and improved algorithms, molecule dynamics (MD) simulations have diverse of superiority in probing the binding and release process. However, it remains a great challenge to overcome the time and length scales when the system becomes large. This article presents an enhanced sampling tool for ligand binding and release, which is based on iterative multiple independent MD simulations guided by contacts formed between the ligand and the protein. From the simulation results on adenylate kinase (AdK), we observe the process of ligand binding and release while the conventional MD simulations at the same time scale cannot.
|Citation:||Xinfan Hua, Du Xinzheng, Zhiyong Zhang. Ligand Binding and Release Investigated by Contact-guided Iterative Multiple Independent Molecular Dynamics Simulations[J]. Chinese Journal of Chemical Physics .|