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Updated: Sep 19, 2025

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library
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Rational Design and Protein Engineering of {SH2 Domain-≫ Flexible Linker-≫ Self-Controlling Peptide} Fusion System

Peng Zhou1, Yunyi Zhang1, Kexin Li1

  • 1Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, Sichuan, China.

Biotechnology and Bioengineering
|June 5, 2025
PubMed
Summary

Engineered self-controlling peptides (SCPs) act as molecular switches. These artificial protein systems, fusing Src SH2 domains with SCPs via flexible linkers, demonstrate reversible control over protein function through phosphorylation.

Keywords:
artificial fusion protein systemcomputational protein designcomputional peptidologymolecular switchphosphorylationprotein engineeringself‐binding peptideself‐controlling peptide

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Area of Science:

  • Biochemistry and Molecular Biology
  • Protein Engineering
  • Synthetic Biology

Background:

  • Self-binding peptides (SBPs) function as molecular switches for protein function.
  • Self-controlling peptides (SCPs) are a subclass of SBPs designed to control protein states.
  • Controlling protein function conversion between biological states is crucial in biological systems.

Purpose of the Study:

  • To design and engineer artificial protein systems with molecular switch functionality using SCPs.
  • To investigate the intramolecular binding dynamics between Src SH2 domains and SCPs.
  • To optimize fusion protein systems for reversible control of protein function.

Main Methods:

  • Rational design and systematic engineering of {SH2-> Flexible Linker (FL)-> SCP} fusion protein systems.
  • Fusion of phosphopeptide binders to the C-terminal tail of human Src SH2 domain via a flexible linker.
  • Structural and energetic analysis of intramolecular SH2-SCP interactions.
  • Optimization of flexible linker length and amino acid composition.

Main Results:

  • Intramolecular SH2-SCP binding mimics intermolecular SH2-phosphopeptide interactions structurally and energetically.
  • Flexible linkers enhance SCP binding affinity to SH2 domains by restricting SCP proximity.
  • A specific {SH2-> poly(G)12-> SCP(SIPM2-K-2)} fusion protein system exhibited robust molecular switch functionality.

Conclusions:

  • Engineered SCPs fused to SH2 domains can function as effective molecular switches.
  • Flexible linkers play a critical role in modulating the binding dynamics and affinity of SCPs.
  • Reversible control of protein function is achievable by externally regulating phosphorylation/dephosphorylation events.