MAP_CHANNELS: a computation tool to aid in the visualization and characterization of solvent channels in macromolecular crystals

Abstract

A computation tool is described that facilitates visualization and characterization of solvent channels or pores within macromolecular crystals. A scalar field mapping the shortest distance to protein surfaces is calculated on a grid covering the unit cell and is written as a map file. The map provides a multiscale representation of the solvent channels, which when viewed in standard macromolecular crystallographic software packages gives an intuitive sense of the solvent channel architecture. The map is analysed to yield descriptors of the topology and the morphology of the solvent channels, including bottleneck radii, tortuosity, width variation and anisotropy.

The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order

“…This structure was then used as a starting model for molecular-replacement solutions of the other tetragonal thermolysin structures. Pore diameters were calculated with MAP_CHANNELS (Juers & Ruffin, 2014). The resulting structure (PDB entry 6b6q) was then used as the starting point for molecular replacement of the other orthorhombic trypsin structures.…”

“…Protein volumes were calculated with MSROLL using a probe radius of 1.5 Å (Connolly, 1983). Pore diameters were calculated with MAP_CHANNELS (Juers & Ruffin, 2014). General manipulations, overlays and calculation of crystal contacts were performed with EdPDB (Zhang & Matthews, 1995).…”

“…The RT solvent content, sol , is based on a V M calculation (Matthews, 1968). The maximum pore radius (Å ) was calculated with MAP_CHANNELS (Juers & Ruffin, 2014) using the coordinates from RT xylose soaks determined here (triclinic lysozyme, orthorhombic trypsin, hexagonal thermolysin and tetragonal thermolysin) and, for the other proteins, structures in the Protein Data Bank with similar cell dimensions to the RT crystals used here (trigonal trypsin, PDB entry 1ghz; tetragonal lysozyme, PDB entry 5kxo; thaumatin, PDB entry 5kw3; insulin, PDB entry 1b2g; Katz et al, 2001;Russi et al, 2017;Diao, 2003). The boundary solvent contraction and bulk fraction, Á T sol,bdy and f bulk , are from fits of (1) and (2) to data in Fig.…”

Lysozyme crystals dyed with bromophenol blue: where has the dye gone?

“…Solvent channels in the lysozyme crystals were calculated with and without dye using MAP_CHANNELS (Juers & Ruffin, 2014) in Coot (Emsley & Cowtan, 2004;Emsley et al, 2010). The Mogul plugin in Coot was used to check ligand restraint outliers (Smart et al, 2018).…”

Protein crystal based materials for nanoscale applications in medicine and biotechnology

“…In Kisljuk, Kachalova, and Lanina (), they have developed CHANNEL, a software package designed to identify channels within protein crystals by building up a spatial graph of intersecting spheres of defined radii to elucidate interconnected cavities within the unit cell. More recently, Juers and Ruffin () have developed MAP_CHANNELS, a computational tool designed to aid in the visualization of solvent channels in macromolecular crystals and to quantitatively characterize those channels with metrics relevant for the study of guest molecule transport.…”