PSCDB: a database for protein structural change upon ligand binding

Abstract

Proteins are flexible molecules that undergo structural changes to function. The Protein Data Bank contains multiple entries for identical proteins determined under different conditions, e.g. with and without a ligand molecule, which provides important information for understanding the structural changes related to protein functions. We gathered 839 protein structural pairs of ligand-free and ligand-bound states from monomeric or homo-dimeric proteins, and constructed the Protein Structural Change DataBase (PSCDB). In the database, we focused on whether the motions were coupled with ligand binding. As a result, the protein structural changes were classified into seven classes, i.e. coupled domain motion (59 structural changes), independent domain motion (70), coupled local motion (125), independent local motion (135), burying ligand motion (104), no significant motion (311) and other type motion (35). PSCDB provides lists of each class. On each entry page, users can view detailed information about the motion, accompanied by a morphing animation of the structural changes. PSCDB is available at http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/.

Figure 1.

Components of motion in domain and local motions. (a) Superposition of glucokinase structures (PDBIDs: 1q18, 1sz2) (29) on the largest domains (blue/cyan). The three domains are colored green/yellow, blue/cyan and red/magenta. The structure was divided into two components of motion (green/yellow and blue/cyan, and red/magenta and blue/cyan). (b) Superposition of d-alanine:d-alanine ligase structures (PDBIDs: 2fb9, 2zdq) (30) on the core domains (blue/cyan). Two moving local segments (green/yellow and red/magenta) were identified in the protein motion. The structure was divided into two components of motion (green/yellow and blue/cyan, and red/magenta and blue/cyan).

Figure 2.

Seven classes. The names, abbreviations, and numbers of protein structural changes of the seven classes are shown on the top-page of PSCDB, with the cartoon icons depicting each motion.

Figure 3.

An example of a web page: hypothetical oxidoreductase YIAK (32). The numbers indicate the PSCID and protein name [1], PDB box [2], protein and ligand structures [3], animation button [4], PNG image button [5], function box [6], ligand box [7] and segment box [8].