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

Research output: Contribution to journalArticleResearchpeer review

Authors

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

External Research Organisations

  • Max Planck Institute of Colloids and Interfaces
  • Weizmann Institute of Science

Details

Original languageEnglish
Article number244
JournalMicrobial cell factories
Volume22
Issue number1
Publication statusPublished - 30 Nov 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 subject areas

Cite this

Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips. / Förste, Stefanie; Vonshak, Ohad; Daube, Shirley S. et al.
In: Microbial cell factories, Vol. 22, No. 1, 244, 30.11.2023.

Research output: Contribution to journalArticleResearchpeer 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 Nov 30;22(1):244. 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 ; Vol. 22, No. 1.
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