ArXived articles by Jørgen Ellegaard Andersen in November 2021

By Jane Jamshidi, jaja@sdu.dk, 12/2/2021

Professor, Centre Director and D-IAS Chair Jørgen Ellegaard Andersen has in November 2021 published three new research results on arXiv with different research collaborators.

The three articles:

 "Topology of protein metastructure andβ-sheet topology" written in collaboration with Hiroyuki Fuji (Osaka Institute of Technology) and  Yuki Koyanagi (SDU).

They introduce a new, simplified model of proteins, which they call protein metastructure. The metastructure of a protein carries information about its secondary structure and β-strand conformations. Furthermore, protein metastructure allows them to associate an object called a fatgraph to a protein, and a fatgraph in turn gives rise to a topological surface. It becomes thus possible to study the topological invariants associated to a protein. They discuss the correspondence between protein metastructures and fatgraphs, and how one can compute topological invariants, such as genus and the number of boundary components, from fatgraphs.

Link to the article on arXiv: https://arxiv.org/abs/2111.14501

"Using Topology to Estimate Structural Similarities of Proteins" written in collaboration with Jens Ledet Jensen & Jakob Toudahl Nielsen (Aarhus University), Yuki Koyanagi (SDU) and Rasmus Villemoes (Prevas A/S).

An effective model for protein structures is important for the study of protein geometry, which, to a large extent, determine the functions of proteins. There are a number of approaches for modelling; one might focus on the conformation of the backbone or H-bonds, and the model may be based on the geometry or the topology of the structure in focus. They focus on the topology of H-bonds in proteins, and explore the link between the topology and the geometry of protein structures.

Link to the article on arXiv: https://arxiv.org/abs/2111.14489

and the third article:

"Prediction of H-Bond Rotations from Protein H-Bond Topology" written in collaboration with Jakob Toudahl Nielsen (Aarhus University), Yuki Koyanagi (SDU) and Rasmus Villemoes (Prevas A/S).

H-bonds are known to play an important role in the folding of proteins into three-dimensional structures, which in turn determine their diverse functions. The conformations around H-bonds are important, in that they can be non-local along the backbone and are therefore not captured by the methods such as Ramachandran plots. We study the relationship between the geometry of H-bonds in proteins, expressed as a spatial rotation between the two bonded peptide units, and their topology, expressed as a subgraph of the protein fatgraph.

Link to the article on arXiv: https://arxiv.org/abs/2111.14459