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

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 sy...

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Bibliographic Details
Published in:Microbial cell factories 2023-11, Vol.22 (1), p.1-244, Article 244
Main Authors: Förste, Stefanie, Vonshak, Ohad, Daube, Shirley S., Bar-Ziv, Roy H., Lipowsky, Reinhard, Rudorf, Sophia
Format: Article
Language:English
Subjects:
Binding
Biochips
Biology
Biotechnology
Computer applications
Density
Diffusion
Diffusion rate
Efficiency
Fabrication
Knowledge bases (artificial intelligence)
Mathematical models
Nanotechnology
Protein biosynthesis
Protein synthesis
Proteins
Self-assembly
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Summary: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.
ISSN:1475-2859
1475-2859
DOI:10.1186/s12934-023-02237-5