title: Circuit topology of proteins and nucleic acids.
abstract: Folded biomolecules display a bewildering structural complexity and diversity. They have therefore been analyzed in terms of generic topological features. For instance, folded proteins may be knotted, have beta-strands arranged into a Greek-key motif, or display high contact order. In this perspective, we present a method to formally describe the topology of all folded linear chains and hence provide a general classification and analysis framework for a range of biomolecules. Moreover, by identifying the fundamental rules that intrachain contacts must obey, the method establishes the topological constraints of folded linear chains. We also briefly illustrate how this circuit topology notion can be applied to study the equivalence of folded chains, the engineering of artificial RNA structures and DNA origami, the topological structure of genomes, and the role of topology in protein folding.
authors.affiliation: FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands. Electronic address: mashaghi@amolf.nl.
authors.forename: Alireza
authors.initials: A
authors.lastname: Mashaghi
authors.affiliation: FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands.
authors.forename: Roeland J
authors.initials: RJ
authors.lastname: van Wijk
authors.affiliation: FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands.
authors.forename: Sander J
authors.initials: SJ
authors.lastname: Tans
mesh_terms: D002875:Chromosomes / Q000737:chemistry; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D059370:RNA Folding