KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids

Julie Bernauer 1, 2 Rasmus Fonseca 3, 2, 1 Henry Van den Bedem 4
1 AMIB - Algorithms and Models for Integrative Biology
CNRS - Centre National de la Recherche Scientifique : UMR8623, X - École polytechnique, Inria Saclay - Ile de France, UP11 - Université Paris-Sud - Paris 11, LRI - Laboratoire de Recherche en Informatique, LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
Abstract : Noncoding ribonucleic acids (RNA) play a critical role in a wide variety of cellular processes, ranging from regulating gene expression to post-translational modification and protein synthesis. Their activity is modulated by highly dynamic exchanges between three-dimensional conformational substates, which are difficult to characterize experimentally and computationally. Here, we present an innovative, entirely kinematic computational procedure to efficiently explore the native ensemble of RNA molecules. Our procedure projects degrees of freedom onto a subspace of conformation space defined by distance constraints in the tertiary structure. The dimensionality reduction enables efficient exploration of conformational space. We show that the conformational distributions obtained with our method broadly sample the conformational landscape observed in NMR experiments. Compared to normal mode analysis-based exploration, our procedure diffuses faster through the experimental ensemble while also accessing conformational substates to greater precision. Our results suggest that conformational sampling with a highly reduced but fully atomistic representation of noncoding RNA expresses key features of their dynamic nature.
Type de document :
Communication dans un congrès
RECOMB 2015, Apr 2015, Warsaw, Poland. 9029 2015, Research in Computational Molecular Biology. 〈www.recomb2015.pl〉. 〈10.1007/978-3-319-16706-0_11〉
Liste complète des métadonnées

https://hal.inria.fr/hal-01257755
Contributeur : Mireille Regnier <>
Soumis le : lundi 18 janvier 2016 - 11:16:24
Dernière modification le : jeudi 10 mai 2018 - 02:06:41

Identifiants

Citation

Julie Bernauer, Rasmus Fonseca, Henry Van den Bedem. KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids. RECOMB 2015, Apr 2015, Warsaw, Poland. 9029 2015, Research in Computational Molecular Biology. 〈www.recomb2015.pl〉. 〈10.1007/978-3-319-16706-0_11〉. 〈hal-01257755〉

Partager

Métriques

Consultations de la notice

222