Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips

Publikation: Beitrag in FachzeitschriftArtikelForschungPeer-Review

Autoren

  • Stefanie Förste
  • Ohad Vonshak
  • Shirley S. Daube
  • Roy H. Bar-Ziv
  • Reinhard Lipowsky
  • Sophia Rudorf

Externe Organisationen

  • Max-Planck-Institut für Kolloid- und Grenzflächenforschung
  • Weizmann Institute of Science
Forschungs-netzwerk anzeigen

Details

OriginalspracheEnglisch
Aufsatznummer244
FachzeitschriftMicrobial cell factories
Jahrgang22
Ausgabenummer1
Frühes Online-Datum30 Nov. 2023
PublikationsstatusVeröffentlicht - Dez. 2023

Abstract

Protein complex assembly facilitates the combination of individual protein subunits into functional entities, and thus plays a crucial role in biology and biotechnology. Recently, we developed quasi-twodimensional, silicon-based compartmental biochips that are designed to study and administer the synthesis and assembly of protein complexes. At these biochips, individual protein subunits are synthesized from locally confined high-density DNA brushes and are captured on the chip surface by molecular traps. Here, we investigate single-gene versions of our quasi-twodimensional synthesis systems and introduce the trap-binding efficiency to characterize their performance. We show by mathematical and computational modeling how a finite trap density determines the dynamics of protein-trap binding and identify three distinct regimes of the trap-binding efficiency. We systematically study how protein-trap binding is governed by the system’s three key parameters, which are the synthesis rate, the diffusion constant and the trap-binding affinity of the expressed protein. In addition, we describe how spatially differential patterns of traps modulate the protein-trap binding dynamics. In this way, we extend the theoretical knowledge base for synthesis, diffusion, and binding in compartmental systems, which helps to achieve better control of directed molecular self-assembly required for the fabrication of nanomachines for synthetic biology applications or nanotechnological purposes.

ASJC Scopus Sachgebiete

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Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips. / Förste, Stefanie; Vonshak, Ohad; Daube, Shirley S. et al.
in: Microbial cell factories, Jahrgang 22, Nr. 1, 244, 12.2023.

Publikation: Beitrag in FachzeitschriftArtikelForschungPeer-Review

Förste S, Vonshak O, Daube SS, Bar-Ziv RH, Lipowsky R, Rudorf S. Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips. Microbial cell factories. 2023 Dez;22(1):244. Epub 2023 Nov 30. doi: 10.1186/s12934-023-02237-5
Förste, Stefanie ; Vonshak, Ohad ; Daube, Shirley S. et al. / Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips. in: Microbial cell factories. 2023 ; Jahrgang 22, Nr. 1.
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AU - Lipowsky, Reinhard

AU - Rudorf, Sophia

N1 - Open Access funding enabled and organized by Projekt DEAL. Positions of all authors, consumables, and equipment were funded by the respective institutions (see author affiliations).

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