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  A circuit topology approach to categorizing changes in biomolecular structure

Schullian, O., Woodard, J., Tirandaz, A., & Mashaghi, A. (2020). A circuit topology approach to categorizing changes in biomolecular structure. Frontiers in Physics, 8: 5. doi:10.3389/fphy.2020.00005.

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Schullian, Otto1, Autor           
Woodard, Jaie, Autor
Tirandaz, Arash, Autor
Mashaghi, Alireza, Autor
Affiliations:
1Markus Miettinen, Theorie & Bio-Systeme, Max Planck Institute of Colloids and Interfaces, Max Planck Society, ou_3070372              

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 Zusammenfassung: The biological world is composed of folded linear molecules of bewildering topological complexity and diversity. The topology of folded biomolecules such as proteins and ribonucleic acids is often subject to change during biological processes. Despite intense research, we lack a solid mathematical framework that summarizes these operations in a principled manner. Circuit topology, which formalizes the arrangements of intramolecular contacts, serves as a general mathematical framework to analyze the topological characteristics of folded linear molecules. In this work, we translate familiar molecular operations in biology, such as duplication, permutation, and elimination of contacts, into the language of circuit topology. We show that for such operations there are corresponding matrix representations as well as basic rules that serve as a foundation for understanding these operations within the context of a coherent algebraic framework. We present several biological examples and provide a simple computational framework for creating and analyzing the circuit diagrams of proteins and nucleic acids. We expect our study and future developments in this direction to facilitate a deeper understanding of natural molecular processes and to provide guidance to engineers for generating complex polymeric materials.

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Sprache(n): eng - English
 Datum: 2020-01-302020
 Publikationsstatus: Erschienen
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 Identifikatoren: DOI: 10.3389/fphy.2020.00005
BibTex Citekey: 10.3389/fphy.2020.00005
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Titel: Frontiers in Physics
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: Lausanne : Frontiers Media
Seiten: - Band / Heft: 8 Artikelnummer: 5 Start- / Endseite: - Identifikator: ISSN: 2296-424X