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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.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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MotifAnalyzer-PDZ: A computational program to investigate the evolution of PDZ-binding target specificity.

Jordan Valgardson1,2, Robin Cosbey1, Paul Houser1

  • 1Department of Computer Science, Western Washington University, Bellingham, Washington.

Protein Science : a Publication of the Protein Society
|October 11, 2019
PubMed
Summary

Researchers developed MotifAnalyzer-PDZ to predict protein targets for PDZ domains, crucial for cellular processes. This tool identified novel human PDZ targets and binding interactions in choanoflagellates, advancing our understanding of protein-protein interactions.

Keywords:
PDZ domainsbioinformaticsevolutioninteraction prediction methodspeptide-binding domainsprotein-protein interactionssequence conservation

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Proteomics

Background:

  • Protein recognition of short linear motifs (SLiMs) is vital for cellular functions but challenging due to degenerate binding motifs and transient, low-affinity interactions.
  • PDZ domains are a major family of SLiM-binding domains in the human proteome, interacting with target protein C-termini and playing roles in signaling and trafficking.

Purpose of the Study:

  • To develop a computational tool, MotifAnalyzer-PDZ, for predicting endogenous PDZ domain targets across various proteomes.
  • To identify and biochemically validate novel human PDZ targets using evolutionary sequence conservation.
  • To investigate PDZ domain interactions in non-human organisms, specifically choanoflagellates.

Main Methods:

  • Developed MotifAnalyzer-PDZ, a program to filter and compare motif-satisfying sequences in public proteomes.
  • Predicted and biochemically tested novel human PDZ targets by analyzing sequence conservation.
  • Identified and characterized C-terminal binding sequences for a choanoflagellate PDZ domain (mbSHANK1).
  • Analyzed positional amino acid enrichments in PDZ motif-satisfying sequences across multiple organisms.

Main Results:

  • MotifAnalyzer-PDZ successfully predicted potential PDZ binding targets in humans and other organisms.
  • Novel human PDZ targets were identified and validated through biochemical testing, supported by evolutionary sequence conservation.
  • Three C-terminal sequences in choanoflagellates were found to bind mbSHANK1 with relevant affinities, despite lacking conservation with human SHANK1 targets.
  • These choanoflagellate targets are predicted signaling proteins, homologous to tyrosine kinases.

Conclusions:

  • MotifAnalyzer-PDZ is a versatile tool for investigating potential PDZ domain interactions and can be adapted for other SLiM-binding domains.
  • The study expands the understanding of PDZ domain target recognition across different species.
  • This work provides a foundation for future analyses of SLiM-binding domain interactions in diverse organisms.