Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures
PDZ domains are abundant interaction hubs found in a number of different proteins and they exhibit characteristic differences in their structure and ligand specificity. Their internal dynamics have been proposed to contribute to their biological activity <i>via</i> changes in conformatio...
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doaj-321301cfffef4edc8a0d3f6e890db7802020-11-25T04:07:13ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-11-01218348834810.3390/ijms21218348Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ StructuresDániel Dudola0Anett Hinsenkamp1Zoltán Gáspári2Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083 Budapest, HungaryFaculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083 Budapest, HungaryFaculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083 Budapest, HungaryPDZ domains are abundant interaction hubs found in a number of different proteins and they exhibit characteristic differences in their structure and ligand specificity. Their internal dynamics have been proposed to contribute to their biological activity <i>via</i> changes in conformational entropy upon ligand binding and allosteric modulation. Here we investigate dynamic structural ensembles of PDZ3 of the postsynaptic protein PSD-95, calculated based on previously published backbone and side-chain S<inline-formula><math display="inline"><semantics><msup><mrow></mrow><mn>2</mn></msup></semantics></math></inline-formula> order parameters. We show that there are distinct but interdependent structural rearrangements in PDZ3 upon ligand binding and the presence of the intramolecular allosteric modulator helix <inline-formula><math display="inline"><semantics><mi>α</mi></semantics></math></inline-formula>3. We have also compared these rearrangements in PDZ1-2 of PSD-95 and the conformational diversity of an extended set of PDZ domains available in the PDB database. We conclude that although the opening-closing rearrangement, occurring upon ligand binding, is likely a general feature for all PDZ domains, the conformer redistribution upon ligand binding along this mode is domain-dependent. Our findings suggest that the structural and functional diversity of PDZ domains is accompanied by a diversity of internal motional modes and their interdependence.https://www.mdpi.com/1422-0067/21/21/8348PDZ domaininternal dynamicsallosteryrestrained molecular dynamics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Dániel Dudola Anett Hinsenkamp Zoltán Gáspári |
spellingShingle |
Dániel Dudola Anett Hinsenkamp Zoltán Gáspári Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures International Journal of Molecular Sciences PDZ domain internal dynamics allostery restrained molecular dynamics |
author_facet |
Dániel Dudola Anett Hinsenkamp Zoltán Gáspári |
author_sort |
Dániel Dudola |
title |
Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures |
title_short |
Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures |
title_full |
Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures |
title_fullStr |
Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures |
title_full_unstemmed |
Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures |
title_sort |
ensemble-based analysis of the dynamic allostery in the psd-95 pdz3 domain in relation to the general variability of pdz structures |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1661-6596 1422-0067 |
publishDate |
2020-11-01 |
description |
PDZ domains are abundant interaction hubs found in a number of different proteins and they exhibit characteristic differences in their structure and ligand specificity. Their internal dynamics have been proposed to contribute to their biological activity <i>via</i> changes in conformational entropy upon ligand binding and allosteric modulation. Here we investigate dynamic structural ensembles of PDZ3 of the postsynaptic protein PSD-95, calculated based on previously published backbone and side-chain S<inline-formula><math display="inline"><semantics><msup><mrow></mrow><mn>2</mn></msup></semantics></math></inline-formula> order parameters. We show that there are distinct but interdependent structural rearrangements in PDZ3 upon ligand binding and the presence of the intramolecular allosteric modulator helix <inline-formula><math display="inline"><semantics><mi>α</mi></semantics></math></inline-formula>3. We have also compared these rearrangements in PDZ1-2 of PSD-95 and the conformational diversity of an extended set of PDZ domains available in the PDB database. We conclude that although the opening-closing rearrangement, occurring upon ligand binding, is likely a general feature for all PDZ domains, the conformer redistribution upon ligand binding along this mode is domain-dependent. Our findings suggest that the structural and functional diversity of PDZ domains is accompanied by a diversity of internal motional modes and their interdependence. |
topic |
PDZ domain internal dynamics allostery restrained molecular dynamics |
url |
https://www.mdpi.com/1422-0067/21/21/8348 |
work_keys_str_mv |
AT danieldudola ensemblebasedanalysisofthedynamicallosteryinthepsd95pdz3domaininrelationtothegeneralvariabilityofpdzstructures AT anetthinsenkamp ensemblebasedanalysisofthedynamicallosteryinthepsd95pdz3domaininrelationtothegeneralvariabilityofpdzstructures AT zoltangaspari ensemblebasedanalysisofthedynamicallosteryinthepsd95pdz3domaininrelationtothegeneralvariabilityofpdzstructures |
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1724429621177352192 |