Visual Support for the Loop Grafting Workflow on Proteins

TL;DR

This work presents LoopGrafter, a visualization system that supports protein loop grafting by organizing the workflow into six phases and pairing interactive 2D abstractions with a 3D view. The approach emphasizes phase-specific visuals (secondary structures, loop geometry, flexibility, cross-correlation, loop pairing, and grafting) to help experts identify candidate loops and evaluate grafting viability. Evaluations on real-case scenarios and multiple case studies show the visual toolkit improves understanding, reduces trial-and-error, and accelerates decision making, while expert feedback highlights both benefits and areas for improved 3D handling and novice accessibility. The work contributes a design study methodology, a cohesive multi-view interface, and an open-source implementation that can be extended to broader protein engineering tasks.

Abstract

In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the experts design the transfer of the desired function from one protein to another. This process is denoted as loop grafting. We designed a set of interactive visualizations that provide experts with visual support through all the loop grafting pipeline steps. The workflow is divided into several phases, reflecting the steps of the pipeline. Each phase is supported by a specific set of abstracted 2D visual representations of proteins and their loops that are interactively linked with the 3D View of proteins. By sequentially passing through the individual phases, the user shapes the list of loops that are potential candidates for loop grafting. Finally, the actual in-silico insertion of the loop candidates from one protein to the other is performed, and the results are visually presented to the user. In this way, the fully computational rational design of proteins and their loops results in newly designed protein structures that can be further assembled and tested through in-vitro experiments. We showcase the contribution of our visual support design on a real case scenario changing the enantiomer selectivity of the engineered enzyme. Moreover, we provide the readers with the experts' feedback.

Figures (8)

• Figure 1: On the left, a loop consisting of two $\alpha$-helices and a coil. On the right, a loop consisting of two $\beta$-strands and a coil.
• Figure 2: Proposed visualization layout. (A) The overview that serves as the navigation through the loop grafting pipeline. (B) 3D View showing a superimposition of the two proteins, with loop 1ISP_A_147 highlighted (red). (C) Scaffold Loop List showing identified candidate (top) and the unprocessed (bottom) loops. The list is enriched with contextual information based on the current state of the pipeline (now showing selected replacements for candidate loops). (D) Each grafting pipeline phase is represented by a single collapsible tab that contains specific visual representations and interactions. For example, the Loop Pairing phase (E) consists of 1D representations of proteins and their loops. Underneath, custom visualizations allow users to compare individual loops and pick desired replacements.
• Figure 3: The Secondary Structures tab with Scaffold (PDB ID 1isp, red) and Insert (PDB ID 1g66, blue) proteins. The secondary structures are encoded with glyphs (helices and arrows). The first -sheet from the Scaffold protein and a coil region right after it are brushed (light red) to change the secondary structure assignment. The tooltip shows details about the endpoint of the brushed region.
• Figure 4: Visual support of the Loop Exploration phase. (A) Overview of the proteins and their loops, (B) selected pairs of loops from the Scaffold and Insert proteins in detail, and (C) depiction of geometric properties of these loops and their comparison.
• Figure 5: The original design (later discarded), depicting geometrical properties as grayscale bars directly above the bracket-shaped glyphs representing loops.