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

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.

SUBMITTER: Forste S

PROVIDER: S-EPMC10688499 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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

Förste Stefanie S Vonshak Ohad O Daube Shirley S SS Bar-Ziv Roy H RH Lipowsky Reinhard R Rudorf Sophia S

Microbial cell factories 20231130 1

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 molecul ...[more]

PMID: 38037098

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Dataset Information

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

Publications

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

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