Life science has a need for detection methods that are label-free and real-time. In this paper, we have selected staphylococcal protein A （SPA） and swine immunoglobulin G （IgG）, and monitor the bindings between SP...Life science has a need for detection methods that are label-free and real-time. In this paper, we have selected staphylococcal protein A （SPA） and swine immunoglobulin G （IgG）, and monitor the bindings between SPA and swine IgG with different concentrations, as well as the dissociations of SPA-swine IgG complex in different pH values of phosphate buffer by oblique-incidence reflectivity difference （OIRD） in a label-free and real-time fashion. We obtain the ON and OFF reaction dynamic curves corresponding to the bindings and dissociations of SPA and swine IgG. Through our analysis of the experimental results, we have been able to obtain the damping coefficients and the dissociation time of SPA and swine IgG for different pH values of the phosphate buffer. The results prove that the OIRD technique is a competing method for monitoring the dynamic processes of biomolecule interaction and achieving the quantitative information of reaction kinetics.展开更多
Binding and releasing ligands are critical for the biological functions of many proteins,so it is important to determine these highly dynamic processes.Although there are experimental techniques to determine the struc...Binding and releasing ligands are critical for the biological functions of many proteins,so it is important to determine these highly dynamic processes.Although there are experimental techniques to determine the 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,molecular 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 work 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,we observe the process of ligand binding and release while the conventional MD simulations at the same time scale cannot.展开更多
基金Supported by the Key Research Program of Chinese Academy of Sciences
文摘Life science has a need for detection methods that are label-free and real-time. In this paper, we have selected staphylococcal protein A （SPA） and swine immunoglobulin G （IgG）, and monitor the bindings between SPA and swine IgG with different concentrations, as well as the dissociations of SPA-swine IgG complex in different pH values of phosphate buffer by oblique-incidence reflectivity difference （OIRD） in a label-free and real-time fashion. We obtain the ON and OFF reaction dynamic curves corresponding to the bindings and dissociations of SPA and swine IgG. Through our analysis of the experimental results, we have been able to obtain the damping coefficients and the dissociation time of SPA and swine IgG for different pH values of the phosphate buffer. The results prove that the OIRD technique is a competing method for monitoring the dynamic processes of biomolecule interaction and achieving the quantitative information of reaction kinetics.
基金supported by the National Natural Science Foundation of China(No.91953101)the Strategic Priority Research Program of the Chinese Academy of Science(XDB37040202)the Hefei National Science Center Pilot Project Funds,and the New Concept Medical Research Fund of USTC。
文摘Binding and releasing ligands are critical for the biological functions of many proteins,so it is important to determine these highly dynamic processes.Although there are experimental techniques to determine the 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,molecular 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 work 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,we observe the process of ligand binding and release while the conventional MD simulations at the same time scale cannot.
