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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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Published on: July 25, 2013

Core-directed protein design. I. An experimental method for selecting stable proteins from combinatorial libraries.

M D Finucane1, M Tuna, J H Lees

  • 1Centre for Biomolecular Design, School of Biological Sciences, University of Sussex, Falmer, Brighton BN1 9QG, U.K.

Biochemistry
|October 8, 1999
PubMed
Summary

This study presents a new experimental method to select stable protein variants by displaying them on phage and using protease treatment to remove unstable ones. This approach aids in designing and stabilizing proteins with specific structures.

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Area of Science:

  • Structural biology
  • Protein engineering
  • Biophysics

Background:

  • Designing proteins with stable hydrophobic cores is crucial for folding and stability.
  • Computational methods test sequences before experimental validation.
  • An experimental approach is needed to complement computational protein design.

Purpose of the Study:

  • To develop and demonstrate an experimental method for selecting stable protein variants.
  • To validate a phage display system for protein stability selection.
  • To aid in the de novo design of proteins with enhanced stability and specificity.

Main Methods:

  • Phage display of hexahistidine-tagged ubiquitin hydrophobic-core mutants.
  • Immobilization on nickel-coated surfaces (Ni-NTA chips and agarose beads).
  • Protease treatment to remove unstable proteins, followed by amplification of stable variants.

Main Results:

  • Successfully selected stable ubiquitin hydrophobic-core mutants using the developed method.
  • Surface plasmon resonance (SPR) allowed direct monitoring and rapid testing of conditions.
  • Ni-NTA agarose beads were effective for preparative selection of the library.

Conclusions:

  • The method effectively selects proteins based on structure and stability, independent of function.
  • This technique can improve stability and structural specificity in de novo protein design.
  • It facilitates the establishment of sequence-structure relationships for protein engineering.