Size-Independent Quantification of Ligand Binding Site Depth in Receptor Proteins

TL;DR

This paper introduces a web server with two methods, secant plane and tangent sphere, to measure ligand binding site depth in proteins, aiding understanding of protein flexibility and conformational changes.

Contribution

The paper presents a novel web server implementing two size-independent methods for quantifying ligand binding site depth in proteins, validated on real and artificial structures.

Findings

Methods agree well with known data

Both methods effectively measure LBS depth

Applicable to proteins with or without ligand coordinates

Abstract

We have developed a web server that implements two complementary methods to quantify the depth of ligand binding site (LBS) in protein-ligand complexes: the "secant plane" (SP) and "tangent sphere" (TS) methods. The protein molecular centroid (global centroid, GC), and the LBS centroid (local centroid, LC) are first determined. The SP is the plane passing through the LC and normal to the line passing through the LC and the GC. The "exterior side" of the SP is the side opposite GC. The TS is the sphere with center at GC and tangent to the SP at LC. The percentage of protein atoms inside the TS (TS index) and on the exterior side of the SP (SP index), are complementary measures of LBS depth. The SPi is directly proportional to LBS depth while the TSi is inversely proportional. We tested the two methods using a test set of 67 well-characterized protein-ligand structures (Laskowski, et al. 1996), as well as that of an artificial protein in the form of a grid of points in the overall shape of a sphere and in which LBS of any depth can be specified. Results from both the SP and TS methods agree well with reported data (ibid.), and results from the artificial case confirm that both methods are suitable measures of LBS depth. The web server may be used in two modes. In the "ligand mode", user inputs the protein PDB coordinates as well as those of the ligand. The "LBS mode" is the same as the former, except that the ligand coordinates are assumed to be unavailable; hence the user inputs what s/he believes to be the coordinates of the LBS amino acid residues. In both cases, the web server outputs the SP and TS indices. LBS depth is usually directly related to the amount of conformational change a protein undergoes upon ligand binding - ability to quantify it could allows meaningful comparison of protein flexibility and dynamics. The URL of our web server will be announced publicly in due course.