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Post-translational modifications modulate ligand recognition by the third PDZ domain of the MAGUK protein PSD-95.

Murciano-Calles J, Corbi-Verge C, Candel AM, Luque I, Martinez JC - PLoS ONE (2014)

Bottom Line: The α3 helix is an extra structural element that is not present in other PDZ domains, which links PDZ3 with the following SH3 domain in the PSD-95 protein.This regulatory mechanism was confirmed experimentally via thermodynamic and NMR chemical shift perturbation analyses, discarding intra-domain long-range effects.Taken together, the results presented here reveal the molecular basis of the regulatory role of the α3 extra-element and the effects of post-translational modifications of PDZ3 on its binding affinity, both energetically and dynamically.

View Article: PubMed Central - PubMed

Affiliation: Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, Granada, Spain.

ABSTRACT
The relative promiscuity of hub proteins such as postsynaptic density protein-95 (PSD-95) can be achieved by alternative splicing, allosteric regulation, and post-translational modifications, the latter of which is the most efficient method of accelerating cellular responses to environmental changes in vivo. Here, a mutational approach was used to determine the impact of phosphorylation and succinimidation post-translational modifications on the binding affinity of the postsynaptic density protein-95/discs large/zonula occludens-1 (PDZ3) domain of PSD-95. Molecular dynamics simulations revealed that the binding affinity of this domain is influenced by an interplay between salt-bridges linking the α3 helix, the β2-β3 loop and the positively charged Lys residues in its high-affinity hexapeptide ligand KKETAV. The α3 helix is an extra structural element that is not present in other PDZ domains, which links PDZ3 with the following SH3 domain in the PSD-95 protein. This regulatory mechanism was confirmed experimentally via thermodynamic and NMR chemical shift perturbation analyses, discarding intra-domain long-range effects. Taken together, the results presented here reveal the molecular basis of the regulatory role of the α3 extra-element and the effects of post-translational modifications of PDZ3 on its binding affinity, both energetically and dynamically.

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The ‘supertertiary’ structure of PSD-95 protein.
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pone-0090030-g001: The ‘supertertiary’ structure of PSD-95 protein.

Mentions: Members of the membrane-associated guanylate kinase (MAGUK) family, including postsynaptic density protein-95 (PSD-95; also known as SAP-90 or DLG-4), are known hub proteins. MAGUKs lack enzymatic activity and are structurally organised into several conformationally-independent modular domains that are interconnected by relatively short amino acid sequences; these domains typically comprise three postsynaptic density protein-95/discs large/zonula occludens-1 (PDZ) domains, one SH3 domain and one kinase domain (Figure 1). Structural modelling of the multi-modular organisation of PSD-95 has revealed that the protein develops a level of functional regulation through high conformational plasticity that is achieved mainly by the inter-domain sequences [6]. The term ‘supertertiary structure’ has been proposed to describe the multiplicity of conformations and states of these multi-modular proteins that might coexist and interchange under equilibrium conditions [7], [8].


Post-translational modifications modulate ligand recognition by the third PDZ domain of the MAGUK protein PSD-95.

Murciano-Calles J, Corbi-Verge C, Candel AM, Luque I, Martinez JC - PLoS ONE (2014)

The ‘supertertiary’ structure of PSD-95 protein.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3935999&req=5

pone-0090030-g001: The ‘supertertiary’ structure of PSD-95 protein.
Mentions: Members of the membrane-associated guanylate kinase (MAGUK) family, including postsynaptic density protein-95 (PSD-95; also known as SAP-90 or DLG-4), are known hub proteins. MAGUKs lack enzymatic activity and are structurally organised into several conformationally-independent modular domains that are interconnected by relatively short amino acid sequences; these domains typically comprise three postsynaptic density protein-95/discs large/zonula occludens-1 (PDZ) domains, one SH3 domain and one kinase domain (Figure 1). Structural modelling of the multi-modular organisation of PSD-95 has revealed that the protein develops a level of functional regulation through high conformational plasticity that is achieved mainly by the inter-domain sequences [6]. The term ‘supertertiary structure’ has been proposed to describe the multiplicity of conformations and states of these multi-modular proteins that might coexist and interchange under equilibrium conditions [7], [8].

Bottom Line: The α3 helix is an extra structural element that is not present in other PDZ domains, which links PDZ3 with the following SH3 domain in the PSD-95 protein.This regulatory mechanism was confirmed experimentally via thermodynamic and NMR chemical shift perturbation analyses, discarding intra-domain long-range effects.Taken together, the results presented here reveal the molecular basis of the regulatory role of the α3 extra-element and the effects of post-translational modifications of PDZ3 on its binding affinity, both energetically and dynamically.

View Article: PubMed Central - PubMed

Affiliation: Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, Granada, Spain.

ABSTRACT
The relative promiscuity of hub proteins such as postsynaptic density protein-95 (PSD-95) can be achieved by alternative splicing, allosteric regulation, and post-translational modifications, the latter of which is the most efficient method of accelerating cellular responses to environmental changes in vivo. Here, a mutational approach was used to determine the impact of phosphorylation and succinimidation post-translational modifications on the binding affinity of the postsynaptic density protein-95/discs large/zonula occludens-1 (PDZ3) domain of PSD-95. Molecular dynamics simulations revealed that the binding affinity of this domain is influenced by an interplay between salt-bridges linking the α3 helix, the β2-β3 loop and the positively charged Lys residues in its high-affinity hexapeptide ligand KKETAV. The α3 helix is an extra structural element that is not present in other PDZ domains, which links PDZ3 with the following SH3 domain in the PSD-95 protein. This regulatory mechanism was confirmed experimentally via thermodynamic and NMR chemical shift perturbation analyses, discarding intra-domain long-range effects. Taken together, the results presented here reveal the molecular basis of the regulatory role of the α3 extra-element and the effects of post-translational modifications of PDZ3 on its binding affinity, both energetically and dynamically.

Show MeSH