Gauge symmetries and structure of proteins

Alexander Molochkov,Alexander Begun,Antti Niemi,Y Foka,V Kovalenko,N Brambilla

doi:10.1051/epjconf/201713704004

Abstract

We discuss the gauge field theory approach to protein structure study, which allows a natural way to introduce collective degrees of freedom and nonlinear topological structures. Local symmetry of proteins and its breaking in the medium is considered, what allows to derive Abelian Higgs model of protein backbone, correct folding of which is defined by gauge symmetry breaking due hydrophobic forces. Within this model structure of protein backbone is defined by superposition of one-dimensional topological solitons (kinks), what allows to reproduce the three-dimensional structure of the protein backbone with precision up to 1A and to predict its dynamics.

Highlights

Lattice gauge field theory provides universal framework for analysis of systems with infinite degrees of freedom with corresponding local and global symmetry
According to the generally accepted tests Critical Assessment for Structural Prediction, at the moment this type of practices have the greatest predictive power for the conformation of the protein. The disadvantage of these methods is the lack of sound energy function, which greatly complicates their application for research of dynamic aspects, including the processes of folding, and especially the nature of and reasons for the transition to incorrect protein folding
The corresponding field theory model is based on local symmetry of proteins that will dynamically define tertiary structure of proteins [6]

Summary

Introduction

Lattice gauge field theory provides universal framework for analysis of systems with infinite degrees of freedom with corresponding local and global symmetry. Such a classification scheme as the CATH [4] (http://www.cathdb.info/) and SCOP [5] (http://scop.mrc-lmb.cam.ac.uk/scop/), who develop a taxonomic approach to describe the topology of protein available database PDB, found that despite the differences in their amino acid structures, the number of different shapes is limited Such empirical data provide a conceptual framework for new methods for structure prediction. The disadvantage of these methods is the lack of sound energy function, which greatly complicates their application for research of dynamic aspects, including the processes of folding, and especially the nature of and reasons for the transition to incorrect protein folding All of these approaches are based on data from experimental studies on synchrotron radiation sources. The corresponding field theory model is based on local symmetry of proteins that will dynamically define tertiary structure of proteins [6]

Local symmetry of proteins

Monte-Carlo numerical simulations of the protein structure

Conclusions