MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio‐Temporo‐Chemical Properties Across and Along Protein Voids

Abstract

Figure 1: Proposed methods for a set of tunnels in protein structures computed within an ensemble of molecular dynamics. (a) One timestep of DhaA haloalkane dehalogenase with 39 tunnels leading to one active site; (b) heat map of one selected tunnel (STH) showing the evolution of the tunnel width over time (the left side represents the active site, the right side represents the tunnel gorge, and the vertical axis represents the time); (c) detailed exploration of the tunnel bottleneck contour (collar) over time; (d) 3D tunnel cut right at the bottleneck shown together with the surrounding amino acids. AbstractStudying the characteristics of proteins and their inner void space, including their geometry, physico-chemical properties and dynamics are instrumental for evaluating the reactivity of the protein with other small molecules. The analysis of long simulations of molecular dynamics produces a large number of voids which have to be further explored and evaluated. In this paper we propose three new methods: two of them convey important properties along the long axis of a selected void during molecular dynamics and one provides a comprehensive picture across the void. The first two proposed methods use a specific heat map to present two types of information: an overview of all detected tunnels in the dynamics and their bottleneck width and stability over time, and an overview of a specific tunnel in the dynamics showing the bottleneck position and changes of the tunnel length over time. These methods help to select a small subset of tunnels, which are explored individually and in detail. For this stage we propose the third method, which shows in one static image the temporal evolvement of the shape of the most critical tunnel part, i.e., its bottleneck. This view is enriched with abstract depictions of different physicochemical properties of the amino acids surrounding the bottleneck. The usefulness of our newly proposed methods is demonstrated on a case study and the feedback from the domain experts is included. The biochemists confirmed that our novel methods help to convey the information about the appearance and properties of tunnels in a very intuitive and comprehensible manner.

Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization

“…These techniques include the work of Lindow et al [LBBH13] where the authors study the migration of a selected inner cavity within protein over time and aggregate the occupied void space to form so called dynamic cavities. Byška et al [BJG*15] present an abstracted representation of the evolution of the bottleneck of a selected protein tunnel over time. The concept was extended to study the whole tunnel along its centerline [BMG*16].…”

Scale-Space Splatting: Reforming Spacetime for Cross-Scale Exploration of Integral Measures in Molecular Dynamics

“…This is a geometric approach to the extraction of the spatial configuration of a protein-ligand interaction. MoleCollar and Tunnel Heat Map [9] are works by Byška et al where they reform the properties of a protein tunnel into the tunnel's centre line and the tunnel's cross section. In AnimoAminoMiner [10], the authors focus on amino acids lining the tunnel and their temporal development.…”

Visualization of Biomolecular Structures: State of the Art Revisited

“…Byška et al . [BJG*15] used an aggregated bottleneck contour (collar) to focus on a given channel constriction. Bidmon et al .…”