Hidden dynamic allostery in a PDZ domain

Chad M Petit; Jun Zhang; Paul J Sapienza; Ernesto J Fuentes; Andrew L Lee

doi:10.1073/pnas.0904492106

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Hidden dynamic allostery in a PDZ domain

Journal article

Open access

Peer reviewed

Hidden dynamic allostery in a PDZ domain

Chad M Petit, Jun Zhang, Paul J Sapienza, Ernesto J Fuentes and Andrew L Lee

Proceedings of the National Academy of Sciences - PNAS, Vol.106(43), pp.18249-18254

10/27/2009

DOI: 10.1073/pnas.0904492106

PMCID: PMC2775317

PMID: 19828436

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Abstract

Structure-function relationships in proteins are predicated on the spatial proximity of noncovalently interacting groups of atoms. Thus, structural elements located away from a protein's active site are typically presumed to serve a stabilizing or scaffolding role for the larger structure. Here we report a functional role for a distal structural element in a PDZ domain, even though it is not required to maintain PDZ structure. The third PDZ domain from PSD-95/SAP90 (PDZ3) has an unusual additional third alpha helix (alpha3) that packs in contiguous fashion against the globular domain. Although alpha3 lies outside the active site and does not make direct contact with C-terminal peptide ligand, removal of alpha3 reduces ligand affinity by 21-fold. Further investigation revealed that the difference in binding free energies between the full-length and truncated constructs is predominantly entropic in nature and that without alpha3, picosecond-nanosecond side-chain dynamics are enhanced throughout the domain, as determined by (2)H methyl NMR relaxation. Thus, the distal modulation of binding function appears to occur via a delocalized conformational entropy mechanism. Without removal of alpha3 and characterization of side-chain dynamics, this dynamic allostery would have gone unnoticed. Moreover, what appeared at first to be an artificial modification of PDZ3 has been corroborated by experimentally verified phosphorylation of alpha3, revealing a tangible biological mechanism for this novel regulatory scheme. This hidden dynamic allostery raises the possibility of as-yet unidentified or untapped allosteric regulation in this PDZ domain and is a very clear example of function arising from dynamics rather than from structure.

Thermodynamics

Ligands

Disks Large Homolog 4 Protein

Peptide Fragments - metabolism

Protein Structure, Secondary

Allosteric Regulation

Models, Molecular

Rats

Intracellular Signaling Peptides and Proteins - metabolism

Peptide Fragments - chemistry

Animals

Membrane Proteins - chemistry

Intracellular Signaling Peptides and Proteins - chemistry

Nuclear Magnetic Resonance, Biomolecular

PDZ Domains

Protein Binding

Membrane Proteins - metabolism

Details

Title: Subtitle: Hidden dynamic allostery in a PDZ domain
Creators: Chad M Petit - Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
Jun Zhang
Paul J Sapienza
Ernesto J Fuentes
Andrew L Lee
Resource Type: Journal article
Publication Details: Proceedings of the National Academy of Sciences - PNAS, Vol.106(43), pp.18249-18254
DOI: 10.1073/pnas.0904492106
PMID: 19828436
PMCID: PMC2775317
NLM abbreviation: Proc Natl Acad Sci U S A
ISSN: 0027-8424
eISSN: 1091-6490
Publisher: National Academy of Sciences; United States
Language: English
Date published: 10/27/2009
Academic Unit: Biochemistry and Molecular Biology
Record Identifier: 9984024515402771

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