Unknown

Dataset Information

0

Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom.


ABSTRACT: Protein filaments are dynamic entities that respond to external stimuli by slightly or substantially modifying the internal binding geometries between successive protomers. This results in overall changes in the filament architecture, which are difficult to model due to the helical character of the system. Here, we describe how distortions in RecA nucleofilaments and their consequences on the filament-DNA and bound DNA-DNA interactions at different stages of the homologous recombination process can be modeled using the PTools/Heligeom software and subsequent molecular dynamics simulation with NAMD. Modeling methods dealing with helical macromolecular objects typically rely on symmetric assemblies and take advantage of known symmetry descriptors. Other methods dealing with single objects, such as MMTK or VMD, do not integrate the specificities of regular assemblies. By basing the model building on binding geometries at the protomer-protomer level, PTools/Heligeom frees the building process from a priori knowledge of the system topology and enables irregular architectures and symmetry disruption to be accounted for. Graphical abstract: Model of ATP hydrolysis-induced distortions in the recombinant nucleoprotein, obtained by combining RecA-DNA and two RecA-RecA binding geometries.

SUBMITTER: Boyer B 

PROVIDER: S-EPMC8329462 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

altmetric image

Publications

Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom.

Boyer Benjamin B   Laurent Benoist B   Robert Charles H CH   Prévost Chantal C  

Bio-protocol 20210720 14


Protein filaments are dynamic entities that respond to external stimuli by slightly or substantially modifying the internal binding geometries between successive protomers. This results in overall changes in the filament architecture, which are difficult to model due to the helical character of the system. Here, we describe how distortions in RecA nucleofilaments and their consequences on the filament-DNA and bound DNA-DNA interactions at different stages of the homologous recombination process  ...[more]

Similar Datasets

| S-EPMC4345291 | biostudies-literature
| S-EPMC7111435 | biostudies-literature
| S-EPMC7398641 | biostudies-literature
| S-EPMC2755486 | biostudies-literature
| S-EPMC10785670 | biostudies-literature
| S-EPMC3437854 | biostudies-other
| S-EPMC11875018 | biostudies-literature
| S-EPMC6717291 | biostudies-literature
| S-EPMC9049742 | biostudies-literature
| S-EPMC11316705 | biostudies-literature