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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Protein Networks02:26

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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.
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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces.

H Billur Engin1, Jason F Kreisberg1, Hannah Carter1

  • 1Division of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, United States of America.

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Cancer mutations frequently target protein-protein interactions (PPIs), contributing to tumor heterogeneity. Analyzing mutation patterns reveals novel cancer genes and insights into tumorigenesis, impacting patient outcomes.

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Area of Science:

  • Genomics and Bioinformatics
  • Cancer Biology
  • Structural Biology

Background:

  • Cancer mutations often affect protein functions.
  • Protein-protein interactions (PPIs) are critical in cellular processes.
  • Tumor heterogeneity arises from accumulating genetic alterations.

Purpose of the Study:

  • To investigate if cancer mutations selectively target PPIs.
  • To identify PPIs under positive selection in cancer.
  • To gain mechanistic insights into tumorigenesis by studying mutated PPIs.

Main Methods:

  • Mapped over 1.2 million somatic mutations onto 4,896 protein structures.
  • Analyzed spatial distribution of mutations on protein surfaces and interaction interfaces.
  • Constructed a bipartite network of structurally resolved human PPIs from the Protein Data Bank.

Main Results:

  • 20% of mutations on known cancer gene surfaces perturbed PPIs, significantly enriched for both tumor suppressors and oncogenes.
  • Tumor suppressors, unlike oncogenes, showed significant enrichment of mutations in homo-oligomerization regions.
  • Identified TP53 and beta-2-microglobulin as examples where mutations at interfaces offer insights into perturbed biological circuits and patient survival.
  • Observed an unexpected number of missense mutations in DNA/RNA binding sites.
  • Provided a resource of 3,072 PPI interfaces ranked by mutation rates, highlighting 282 novel candidate cancer genes.

Conclusions:

  • Mutation of specific protein interactions is a key driver of tumor heterogeneity.
  • Understanding these mutated interactions offers insights into tumorigenesis and potential clinical implications.
  • The study provides a valuable resource for identifying novel cancer genes and therapeutic targets.