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  3. Segdesign: A Modular Framework For Controllable Protein Segment Engineering.
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  3. Segdesign: A Modular Framework For Controllable Protein Segment Engineering.

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SegDesign: A modular framework for controllable protein segment engineering.

Chenjie Feng1,2,3,4, Junbo Yin1,3,4, Chao Zha1,3,4

  • 1Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.

Protein Science : a Publication of the Protein Society
|March 25, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

SegDesign enables precise local protein structure engineering by remodeling specific regions without altering the overall protein fold. This framework facilitates controlled protein modification for mechanistic studies and optimization.

Keywords:
local structural remodelingprotein backbone remodelingprotein design frameworkprotein engineering workflowsprotein segment engineeringsecondary‐structure control

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Protein Engineering

Background:

  • Controllable local protein structure engineering is crucial for mechanistic studies and protein optimization.
  • Existing methods often focus on global scaffold design, limiting precise, region-specific modifications while maintaining protein integrity.

Purpose of the Study:

  • Introduce SegDesign, a modular framework for segment-level protein engineering.
  • Enable user-defined manipulation of secondary structures in targeted protein regions.
  • Facilitate the generation of traceable and experimentally testable protein variants.

Main Methods:

  • SegDesign integrates backbone reconstruction, sequence redesign, and multi-stage structural evaluation.
  • The framework allows for user-defined secondary-structure manipulation of selected regions.
  • AlphaFold3 modeling was used to validate structural changes.

    • Main Results:

    • SegDesign successfully converted a flexible loop in Gallus gallus terminal deoxynucleotidyl transferase (GgTdT) into a stable α-helix or β-strand.
    • Global protein fold was preserved during local structure modification.
    • The approach demonstrated generality across six additional enzyme applications.

    Conclusions:

    • SegDesign provides an accessible paradigm for controllable local protein structure engineering.
    • The framework supports both mechanistic investigations and applied protein engineering settings.
    • SegDesign enables precise modification of protein structures for diverse applications.