scholarly journals Mechanisms of Differential Allosteric Modulation in Homologous Proteins: Insights from the Analysis of Internal Dynamics and Energetics of PDZ Domains

2014 ◽  
Vol 10 (12) ◽  
pp. 5677-5689 ◽  
Author(s):  
Giulia Morra ◽  
Alessandro Genoni ◽  
Giorgio Colombo
Keyword(s):  
Allosteric Modulation ◽  
Pdz Domains ◽  
Homologous Proteins ◽  
Internal Dynamics

scholarly journals Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures

2020 ◽  
Vol 21 (21) ◽  
pp. 8348
Author(s):  
Dániel Dudola ◽  
Anett Hinsenkamp ◽  
Zoltán Gáspári
Keyword(s):  
Ligand Binding ◽  
General Feature ◽  
Allosteric Modulation ◽  
Side Chain ◽  
Ligand Specificity ◽  
Structural Rearrangements ◽  
Pdz Domains ◽  
Postsynaptic Protein ◽  
Conformational Diversity ◽  
Structural Ensembles

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 via 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 S2 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 α3. 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.

The Genesis and Internal Dynamics of El Salvador's People's Revolutionary Army, 1970–1976

2014 ◽  
Vol 38 (01) ◽  
pp. 102-129
Author(s):  
ALBERTO MARTÍN ÁLVAREZ ◽  
EUDALD CORTINA ORERO
Keyword(s):  
Latin America ◽  
El Salvador ◽  
Early Years ◽  
Left Wing ◽  
Internal Dynamics ◽  
Internal Coherence ◽  
The 1960S

AbstractUsing interviews with former militants and previously unpublished documents, this article traces the genesis and internal dynamics of the Ejército Revolucionario del Pueblo (People's Revolutionary Army, ERP) in El Salvador during the early years of its existence (1970–6). This period was marked by the inability of the ERP to maintain internal coherence or any consensus on revolutionary strategy, which led to a series of splits and internal fights over control of the organisation. The evidence marshalled in this case study sheds new light on the origins of the armed Salvadorean Left and thus contributes to a wider understanding of the processes of formation and internal dynamics of armed left-wing groups that emerged from the 1960s onwards in Latin America.

Direct Actions in the Czech Environmental Movement

2020 ◽  
Vol 53 (3) ◽  
pp. 137-156
Author(s):  
Arnošt Novák
Keyword(s):  
Czech Republic ◽  
Collective Action ◽  
Direct Action ◽  
Environmental Movement ◽  
Environmental Movements ◽  
Internal Dynamics ◽  
Historical Experience ◽  
Ideal Types ◽  
Environmental Milieu ◽  
Liberal Concept

Direct actions constitute an important repertoire of action for environmental movements in Western countries. This article differentiates two ideal types of this repertoire of action: the anarchist concept, which understands direct action in terms of values and as a preferred way of doing things; and the liberal concept, which uses direct action in an instrumental way. Based on my empirical research in post-socialist Czech Republic, the article focuses on debates over environmentalism and, to be more precise, on uses of direct actions by environmental organizations. It explains why the liberal concept was very limited and why direct action as a preferred way of doing things has not become a part of the repertoire of collective action. The article argues that the movement was politically moderate due to a combination of reasons: the very specific historical experience of the Czech environmental movement, which inclines it to use dialogue rather than confrontations with power; the fear of political hostility and marginalization by the state; and the internal dynamics of the environmental milieu.

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