Lee Wei Yang
National Tsing Hua University School of Life Science, Taiwan
Title: GNM 2.0- A database housing protein dynamics data of >11,000 PDB structures revealing dynamics prerequisites for protein functions and interactions
Biography
Biography: Lee Wei Yang
Abstract
Proteins function through advantageously utilizing a repertoire of possible modes of intrinsic motions. Understanding such motions, of which the importance has been acknowledged in year 2013’s Nobel Prize in Chemistry, is essential to accurately predict two body interactions, channel gating mechanisms and enzyme catalysis. Here, we present the only dynamics database that houses dynamics data (vibrational normal modes) of protein structures in a size commensurate with Protein Data Bank (PDB). The interface that presents such data is state of the art of its kind. Given the wealth of the data, we are able to find dynamics traits for enzyme active sites. Such traits are later used to predict the locations of enzyme active sites for protein structures of a resolution as low as 20 Å. We further data-mined the database and develop the concept of intrinsic dynamics domains (IDDs), including a domain plane (D-plane) and a domain axis (D-axis). It is found that a protein interacts with another at the interface where D-plane cuts through and forming a near-vertical angle between two intersecting D-axes from the two proteins over a set of 68 protein–protein complexes. The findings are then used to define quantitative criteria to filter out docking decoys unlikely to be native whereby the chance to find near-native hits is doubled. Our results also show that in 95% of the DNA-protein complexes, the DNA is cut through by protein’s D-plane. The dynamics database, GNM 2.0, is made available at http://dyn.life.nthu.edu.tw/gnmdb and IDD website is provided at http://dyn.life.nthu.edu.tw/IDD/IDD.php.
