A topology framework for macromolecular complexes and condensates

Nano Research, vol. 15, pp. 9809–9817

Abstract

Abstract Macromolecular assemblies such as protein complexes and protein/RNA condensates are involved in most fundamental cellular processes. The arrangement of subunits within these nano-assemblies is critical for their biological function and is determined by the topology of physical contacts within and between the subunits forming the complex. Describing the spatial arrangement of these interactions is of central importance to understand their functional and stability consequences. In this concept article, we propose a circuit topology-based formalism to define the topology of a complex consisting of linear polymeric chains with inter- and intrachain interactions. We apply our method to a system of model polymer chains as well as protein assemblies. We show that circuit topology can categorize different forms of chain assemblies. Our multi-chain circuit topology should aid analysis and predictions of mechanistic and evolutionary principles in the design of macromolecular assemblies.

Authors 5

1. Maziar Heidari Aachen Medical Systems Biophysics and Bioengineering Leiden Academic Centre for Drug Research Faculty of Science, Leiden University

   Leiden University

   Affiliation as printed

   Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, 2333CC, the Netherlands

2. Duane Moes Aachen Medical Systems Biophysics and Bioengineering Leiden Academic Centre for Drug Research Faculty of Science, Leiden University

   Leiden University

   Affiliation as printed

   Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, 2333CC, the Netherlands

3. Otto Schullian Aachen Medical Systems Biophysics and Bioengineering Leiden Academic Centre for Drug Research Faculty of Science, Leiden University

   Leiden University · Freie Universität Berlin

   Affiliation as printed

   Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany

   Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, 2333CC, the Netherlands

4. Barbara Scalvini Aachen Medical Systems Biophysics and Bioengineering Leiden Academic Centre for Drug Research Faculty of Science, Leiden University

   Leiden University

   Affiliation as printed

   Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, 2333CC, the Netherlands

5. Alireza Mashaghi corresponding Aachen Medical Systems Biophysics and Bioengineering Leiden Academic Centre for Drug Research Faculty of Science, Leiden University

   Leiden University · Harvard University

   Affiliation as printed

   Harvard Medical School, Harvard University, 25 Shattuck St, Boston, MA, 02115, USA

   Medical Systems Biophysics and Bioengineering, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden, 2333CC, the Netherlands