Change in allosteric network affects binding affinities of PDZ domains: Analysis through perturbation response scanning

Z. Nevin Gerek, Sefika Ozkan

Research output: Contribution to journalArticle

80 Citations (Scopus)

Abstract

The allosteric mechanism plays a key role in cellular functions of several PDZ domain proteins (PDZs) and is directly linked to pharmaceutical applications; however, it is a challenge to elaborate the nature and extent of these allosteric interactions. One solution to this problem is to explore the dynamics of PDZs, which may provide insights about how intramolecular communication occurs within a single domain. Here, we develop an advancement of perturbation response scanning (PRS) that couples elastic network models with linear response theory (LRT) to predict key residues in allosteric transitions of the two most studied PDZs (PSD-95 PDZ3 domain and hPTP1E PDZ2 domain). With PRS, we first identify the residues that give the highest mean square fluctuation response upon perturbing the binding sites. Strikingly, we observe that the residues with the highest mean square fluctuation response agree with experimentally determined residues involved in allosteric transitions. Second, we construct the allosteric pathways by linking the residues giving the same directional response upon perturbation of the binding sites. The predicted intramolecular communication pathways reveal that PSD-95 and hPTP1E have different pathways through the dynamic coupling of different residue pairs. Moreover, our analysis provides a molecular understanding of experimentally observed hidden allostery of PSD-95. We show that removing the distal third alpha helix from the binding site alters the allosteric pathway and decreases the binding affinity. Overall, these results indicate that (i) dynamics plays a key role in allosteric regulations of PDZs, (ii) the local changes in the residue interactions can lead to significant changes in the dynamics of allosteric regulations, and (iii) this might be the mechanism that each PDZ uses to tailor their binding specificities regulation.

Original languageEnglish (US)
Article numbere1002154
JournalPLoS Computational Biology
Volume7
Issue number10
DOIs
StatePublished - Oct 2011

Fingerprint

PDZ Domains
Domain Analysis
Allosteric Regulation
Affine transformation
Scanning
Binding sites
Binding Sites
perturbation
Perturbation
binding sites
Pathway
communication
Linear Models
Communication
Mean Square
drug
Drug products
protein
Fluctuations
Proteins

ASJC Scopus subject areas

  • Cellular and Molecular Neuroscience
  • Ecology
  • Molecular Biology
  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Computational Theory and Mathematics

Cite this

Change in allosteric network affects binding affinities of PDZ domains : Analysis through perturbation response scanning. / Gerek, Z. Nevin; Ozkan, Sefika.

In: PLoS Computational Biology, Vol. 7, No. 10, e1002154, 10.2011.

Research output: Contribution to journalArticle

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