GLN: a method to reveal unique properties of lasso type topology in proteins.

ABSTRACT: Geometry and topology are the main factors that determine the functional properties of proteins. In this work, we show how to use the Gauss linking integral (GLN) in the form of a matrix diagram-for a pair of a loop and a tail-to study both the geometry and topology of proteins with closed loops e.g. lassos. We show that the GLN method is a significantly faster technique to detect entanglement in lasso proteins in comparison with other methods. Based on the GLN technique, we conduct comprehensive analysis of all proteins deposited in the PDB and compare it to the statistical properties of the polymers. We show how high and low GLN values correlate with the internal exibility of proteins, and how the GLN in the form of a matrix diagram can be used to study folding and unfolding routes. Fina

SUBMITTER: Niemyska W 

PROVIDER: S-EPMC7494857 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature