FisMat2017 - Submission - View

Abstract's title: Linking in domain-swapped protein dimers
Submitting author: Antonio Trovato
Affiliation: University of Padova - Department of Physics and Astronomy "G. Galilei"
Affiliation Address: VIa Marzolo 8, 35131 Padova (PD)
Country: Italy
Oral presentation/Poster (Author's request): Oral presentation
Other authors and affiliations: Marco Baiesi (Padova University, Physics and Astronomy Department), Enzo Orlandini (Padova University, Physics and Astronomy Department), Flavio Seno (Padova University, Physics and Astronomy Department)
Abstract

The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, makes such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter G′, termed Gaussian entanglement, is strongly correlated with the linking number. Based on 110 non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with |G′| > 1. We report that protein configurations with negative mutual entanglement are promoted, and, surprisingly, that intertwining is suppressed in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties.