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Related Concept Videos

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-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 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,...
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...

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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

Dissecting protein-protein interactions using directed evolution.

Daniel A Bonsor1, Eric J Sundberg

  • 1Boston Biomedical Research Institute, 64 Grove Street, Watertown, Massachusetts 02472, United States.

Biochemistry
|February 22, 2011
PubMed
Summary
This summary is machine-generated.

Directed evolution offers a novel combinatorial approach to understand complex protein-protein interactions. This method mimics natural protein evolution to reveal molecular rules governing binding specificity and affinity.

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In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity
09:16

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity

Published on: March 25, 2020

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Protein-protein interactions (PPIs) are fundamental to cellular functions and disease.
  • Current research methods often fail to capture the combinatorial complexity of PPIs.
  • Understanding residue networks is crucial for predicting protein binding specificity and affinity.

Purpose of the Study:

  • To highlight the limitations of traditional methods in studying PPIs.
  • To introduce directed evolution as a powerful tool for dissecting PPIs.
  • To explore how directed evolution can elucidate the molecular basis of protein interactions.

Main Methods:

  • Review of existing literature on protein-protein interaction studies.
  • Discussion of directed evolution as a laboratory technique mimicking natural selection.
  • Analysis of how directed evolution can be applied to engineer proteins with altered binding properties.

Main Results:

  • Traditional single-amino acid studies cannot fully capture the combinatorial nature of PPIs.
  • PPIs involve complex networks of residues that drive affinity and specificity.
  • Directed evolution enables the study of these combinatorial processes on a manageable timescale.

Conclusions:

  • Directed evolution is an emerging and powerful tool for understanding the intricacies of protein-protein interactions.
  • This technique provides insights into the evolutionary processes that govern protein binding.
  • Further application of directed evolution can advance the prediction and engineering of protein interactions.