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LoopGrafter: a web tool for transplanting dynamical loops for protein engineering.

Joan Planas-Iglesias1,2, Filip Opaleny3, Pavol Ulbrich3

  • 1Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.

Nucleic Acids Research
|April 19, 2022
PubMed
Summary

LoopGrafter is a new web server for protein engineering that aids in grafting protein loops. It helps researchers design novel enzymes by improving activity, specificity, and stability through loop transplantation.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Protein engineering aims to enhance enzyme properties like activity, specificity, and stability.
  • Loop regions are crucial for enzyme allosteric control and function, but engineering them is challenging.
  • Existing methods for rational protein design based on loop engineering are limited.

Purpose of the Study:

  • To introduce LoopGrafter, a web server designed to facilitate the process of loop grafting between structurally related proteins.
  • To provide a user-friendly, step-by-step procedure for identifying, analyzing, and transplanting protein loops.
  • To enable the computational design and energetic evaluation of chimeric proteins resulting from loop transplantation.

Main Methods:

  • LoopGrafter analyzes loop geometries, similarities, and dynamics between user-input proteins.
  • The server identifies potential excision and insertion points for loop grafting.
  • It computationally generates all possible chimeric proteins, constructs their 3D models, and performs energetic evaluations.

Main Results:

  • LoopGrafter offers an interactive platform for guided loop grafting.
  • The server calculates and evaluates multiple chimeric protein designs.
  • Users can visualize and download results for detailed structural analysis.

Conclusions:

  • LoopGrafter addresses the scarcity of tools for loop-based rational protein design.
  • The web server simplifies the complex process of protein loop transplantation.
  • It provides a valuable resource for protein engineers seeking to create novel enzymes with improved characteristics.