pKNOT: the protein KNOT web server

Abstract

Knotted proteins are more commonly observed in recent years due to the enormously growing number of structures in the Protein Data Bank (PDB). Studies show that the knot regions contribute to both ligand binding and enzyme activity in proteins such as the chromophore-binding domain of phytochrome, ketol-acid reductoisomerase or SpoU methyltransferase. However, there are still many misidentified knots published in the literature due to the absence of a convenient web tool available to the general biologists. Here, we present the first web server to detect the knots in proteins as well as provide information on knotted proteins in PDB-the protein KNOT (pKNOT) web server. In pKNOT, users can either input PDB ID or upload protein coordinates in the PDB format. The pKNOT web server will detect the knots in the protein using the Taylor's smoothing algorithm. All the detected knots can be visually inspected using a Java-based 3D graphics viewer. We believe that the pKNOT web server will be useful to both biologists in general and structural biologists in particular.

Figure 1.

An example of the chain smoothing process. The protein is the chromophore-binding domain of bacterial phytochrome (1ZTU). The X-ray structure of 1ZTU (left) is shown in the cartoon representation and two progressively smoothed chains are shown (center and left). The color is ramped by residues from blue at the N-terminus (labeled by N) to red at the C-terminus (labeled by C). The crossover points are numbered sequentially from the N-terminus. The figure-eight knot is characterized by four crossover points, alternately under and over. The structural pictures are produced using Pymol (Delano Scientific, San Carlos, http://pymol.sourceforge.net/).

Figure 2.

The web page of the pKNOT web server. The users can either type in the PDB ID or upload a structural file in the PDB format. When submitting the structural file, the user can choose to either ignore or preserve the breaks in the chain. The default iteration number is set to 500 and the collision threshold, to 0.5 Å.

Figure 3.

Upon query, the pKNOT server will return a table of the CHAIN, LENGTH, KNOT TYPE, CORE, DEPTH and DISPLAY STRUCTURE (upper center). When clicking on the column of KNOT TYPE, the server will return a list of all the proteins of the given knot type in the database of the pKNOT server (lower left). PKNOT also provides a JAVA-based 3D molecular viewer AstexViewer and the users can visualize and manipulate in real time the protein structure and the knot in the protein (lower right).