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Related Concept Videos

Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

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Multi-pass Transmembrane Proteins and β-barrels01:09

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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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Protein Organization01:24

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

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Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

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Published on: July 25, 2013

Protein design through systematic catalytic loop exchange in the (beta/alpha)8 fold.

Adrián Ochoa-Leyva1, Xavier Soberón, Filiberto Sánchez

  • 1Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca, Morelos 62271, México.

Journal of Molecular Biology
|February 24, 2009
PubMed
Summary

This study introduces a novel protein engineering method using loop exchange in (beta/alpha)(8) proteins to increase diversity beyond point mutations. This approach successfully generated folded variants, enabling exploration of new protein functions.

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Area of Science:

  • Protein Engineering
  • Directed Evolution
  • Enzyme Catalysis

Background:

  • Directed evolution is limited by methods introducing variability, primarily random point mutations.
  • Existing methods restrict the scope of functional modifications achievable through protein engineering.
  • A need exists for strategies that combine rational design with combinatorial diversity for enhanced protein engineering.

Purpose of the Study:

  • To develop a novel protein engineering strategy by exchanging natural loops within a (beta/alpha)(8) fold.
  • To increase diversity in functionally important regions while maintaining protein stability.
  • To explore the tolerance of protein scaffolds to loop exchange and assess the impact on folding and stability.

Main Methods:

  • Employed loop exchange within the (beta/alpha)(8) fold using phosphoribosylanthranilate isomerase as a scaffold.
  • Fused variant libraries to chloramphenicol acetyl transferase (CAT) gene as an in vivo folding reporter.
  • Utilized saturation mutagenesis at specific positions to facilitate structural fit of exchanged loops.

Main Results:

  • 30% to 90% of generated mutants across different libraries exhibited proper folding.
  • Exchanged loops of varied sizes and sequences were accepted at different positions within the scaffold.
  • Variability introduced at hinge regions significantly influenced the generation of folded proteins.

Conclusions:

  • The study presents a generalizable method for exchanging loops within the (beta/alpha)(8) fold.
  • This approach offers a novel starting point for screening novel enzyme activities.
  • The method allows for modest diversions from original protein activities, expanding engineering possibilities.