POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics

Abstract

Analysis of macromolecular/small-molecule binding pockets can provide important insights into molecular recognition and receptor dynamics. Since its release in 2011, the POVME (POcket Volume MEasurer) algorithm has been widely adopted as a simple-to-use tool for measuring and characterizing pocket volumes and shapes. We here present POVME 2.0, which is an order of magnitude faster, has improved accuracy, includes a graphical user interface, and can produce volumetric density maps for improved pocket analysis. To demonstrate the utility of the algorithm, we use it to analyze the binding pocket of RNA editing ligase 1 from the unicellular parasite Trypanosoma brucei, the etiological agent of African sleeping sickness. The POVME analysis characterizes the full dynamics of a potentially druggable transient binding pocket and so may guide future antitrypanosomal drug-discovery efforts. We are hopeful that this new version will be a useful tool for the computational- and medicinal-chemist community.

Figure 1

POVME 2.0 graphical user interface.

Figure 2

A graphical summary of the POVME 2.0 algorithm. A) The user defines an inclusion region. B) The user defines an exclusion region. C) The portion of the inclusion region that is not also in the exclusion region is flooded with equidistant points. D) Any of the points that are close to receptor atoms are deleted. E) Any points outside the convex hull are optionally deleted. F) The user can optionally define a contiguous-points region. G) All points that are not contiguous with that region are similarly deleted.

Figure 3

Volumetric density maps of the REL1 active site. Some regions of the protein have been removed to facilitate visualization. A) The crystallographic pose of the bound ATP molecule. Crystallographic water molecules indicate the location of a secondary binding pocket that is transiently accessible from the ATP-binding pocket. B) The region of the binding pocket identified as “open” at least 95% of the time when the trajectory was aligned by the active-site C_α atoms. C) The same region when the trajectory was aligned by the C_α atoms of the whole protein. D) The region of the binding pocket identified as “open” at least 25% of the time when the active-site-C_α alignment was again used.

Figure 4

POVME 1.0 and 2.0 benchmarks. The graph shows benchmark REL1 pocket volumes as a function of simulation time. POVME 1.0 and 2.0 give nearly the same volume measurements (in black). When the POVME 2.0 convex-hull option is enabled, the volumes are smaller (in gray). The bottom panel, generated using the 1XDN crystal structure, illustrates the difference. When the convex-hull option is enabled, the region of the binding pocket is more accurately captured (solid gray) than when it is deactivated (black wireframe). Some portions of the protein have been removed to facilitate visualization.