Can graph theory discriminate between aptamer-protein configurations?

Abstract

Graph theory has been extensively applied in the study of proteins, although few applications still exist on biomolecules like aptamer-protein complexes, whose structure is in silico obtained. Aptamers represent a challenging field of research, especially for their involvement in therapy, diagnosis and early detection of illness; furthermore, the in vivo procedures to synthetize them are quite expensive and more time-consuming than those in silico. This paper is focused on the question if and how general network parameters are able to anticipate some features of those biomolecules. The rationale resides in the fact that, studying a large set of aptamer-angiopoietin complexes, two different types of conformers are manifest. Both types could be present in a real sample with their relative amount reflecting, in a typical population shift scenario, the affinity of the whole sample.