ProPores2: Web Service and Stand-Alone Tool for Identifying, Manipulating, and Visualizing Pores in Protein Structures

Abstract

Surface pockets, cavities, and tunnels in the 3D structures of proteins play integral functional roles such as enabling enzymatic catalysis, ligand binding, or transport of ions or small molecules across biomembranes. ProPores2 facilitates understanding and analysis of these processes by identifying pores and lining residues, determining their axes, and opening closed connections via side-chain rotation. The fast stand-alone tool introduces a novel mode for pore identification, improved axis determination, and additional features such as parallel batch processing and a graphical user interface. The new web service features an integrated and customizable protein viewer with an option to analyze and view more than one structure at once. This feature facilitates side-by-side comparisons of pores in different conformations of the same protein or of identified pores before and after opening gates within the same protein. ProPores2 is freely and publicly available at https://service.bioinformatik.uni-saarland.de/propores.

A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer

“…These fully closed structures were submitted to the ProPores2 webserver ( Hollander et al, 2021 ) to identify and parameterise cavities within the protein. The closing of the pedal bin converts the outer cavity from the transmembrane domain into a larger enclosed cavity at the interface of the AT3 and SNGH domains ( Figure 7A ) This pore has a volume of ~4780 Å 3 and includes both the SGNH catalytic triad comprising residues Asp618, His621, and Ser430 ( Figure 7B ) and at the membrane surface the proposed catalytic residues of the AT3 domain, namely His25 and Tyr194.…”

A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer

“…These fully closed structures were submitted to the ProPores2 webserver (93) to identify and parameterise cavities within the protein. The closing of the pedal bin converts the outer cavity from the transmembrane domain into a larger enclosed cavity at the interface of the AT3 and SNGH domains ( Figure 7A ) This pore has a volume of ∼4,780 Å 3 and includes both the SGNH catalytic triad comprising residues Asp618, His621 and Ser430, and at the membrane surface the proposed catalytic residues of the AT3 domain, namely, His25 and Tyr194.…”