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Related Concept Videos

Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
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In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Exploring the Structure-Function Loop Adaptability of a (β/α)(8)-Barrel Enzyme through Loop Swapping and Hinge

Adrián Ochoa-Leyva1, Francisco Barona-Gómez, Gloria Saab-Rincón

  • 1Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, C.P. 62210, México.

Journal of Molecular Biology
|June 4, 2011
PubMed
Summary

Protein engineering can be advanced by adapting loop swapping, a method that mimics natural evolution to create novel enzymes. This strategy explores diverse protein sequences beyond point mutations, enhancing functional adaptation.

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Last Updated: Jun 1, 2026

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Published on: January 16, 2016

Area of Science:

  • Protein Engineering
  • Enzyme Evolution
  • Molecular Biology

Background:

  • Protein evolution frequently involves sequence changes in loop regions, crucial for natural adaptation.
  • Designing novel enzymes in the lab by imitating natural loop evolution remains a significant challenge.

Purpose of the Study:

  • To develop and validate a loop-swapping strategy for enzyme engineering.
  • To explore sequence requirements for functional adaptation of swapped loops in (β/α)(8)-barrel enzymes.
  • To establish a method for measuring functional adaptation in vivo.

Main Methods:

  • Developed an overlap PCR strategy to introduce sequence diversity at hinge residues, mimicking antibody loop variability.
  • Generated protein libraries by swapping functional loop units within an enzyme scaffold.
  • Evaluated library folding competence and functional proficiency, quantifying as a Structure-Function Loop Adaptability value.

Main Results:

  • The strategy successfully explored functional sequence space, revealing sequence requirements for loop adaptation.
  • Functional variants retaining original activity were generated at higher frequencies compared to traditional methods.
  • Enzyme kinetics and circular dichroism provided molecular insights into variant function and structure.

Conclusions:

  • Loop swapping, combined with hinge residue diversification, offers a novel protein engineering strategy for divergent sequence exploration.
  • This approach facilitates the design of novel enzymes and provides insights into natural enzyme evolution mechanisms.
  • The Structure-Function Loop Adaptability value offers a quantitative measure for assessing protein engineering outcomes.