An Approach to comparing protein structures and origami models - Part 2. Multi-domain proteins

Abstract

Protein structure is an important field of research, with particular significance in its potential applications in biomedicine and nanotechnology. In a recent study, we presented a general approach for comparing protein structures and origami models and demonstrated it with single-domain proteins. For example, the analysis of the α-helical barrel of the outer membrane protein A (OmpA) suggests that there are similar patterns between its structure and the Kresling origami model, providing insight into structure-activity relationships. Here we demonstrate that our approach can be expanded beyond single-domain proteins to also include multi-domain proteins, and to study dynamic processes of biomolecules. Two examples are given: (1) The eukaryotic chaperonin (TRiC) protein is compared with a newly generated origami model, and with an origami model that is constructed from two copies of the Flasher origami model, and (2) the CorA Magnesium transport system is compared with a newly generated origami model and with an origami model that combines the Kresling and Flasher origami models. Based on the analysis of the analog origami models, it is indicated that it is possible to identify building blocks for constructing assembled origami models that are analogous to protein structures. In addition, it is identified that the expansion/collapse mechanisms of the TRiC and CorA are auxetic. Namely, these proteins require a single motion for synchronized folding along two or three axes.