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Structural stability, acidity, and halide selectivity of the fluoride riboswitch recognition site

Using static and dynamics DFT methods we show that the Mg2+/F-/phosphate/water cluster at the center of the fluoride riboswitch is stable by its own and, once assembled, does not rely on any additional factor from the overall RNA fold. Further, we predict that the pKa of the water molecule bridging two Mg cations is around 8.4. We also demonstrate that the halide selectivity of the fluoride riboswitch is determined by the stronger Mg-F bond, which is capable of keeping together the cluster. Replacing F- with Cl- results in a cluster that is unstable under dynamic conditions. Similar conclusions on the structure and energetics of the cluster in the binding pocket of fluoride-inhibited pyrophosphatase suggest that the peculiarity of fluoride is in its ability to establish much stronger metal-halide bonds

A.P. thanks the Spanish MINECO for a Ramón y Cajal contract (RYC-2009-05226) and European Commission for a Career Integration Grant (CIG09-GA-2011-293900).

American Chemical Society (ACS)

Manager: Ministerio de Economía y Competitividad (Espanya)
Author: Chawla, Mohit
Credendino, Raffaele
Poater Teixidor, Albert
Oliva, Romina
Cavallo, Luigi
Abstract: Using static and dynamics DFT methods we show that the Mg2+/F-/phosphate/water cluster at the center of the fluoride riboswitch is stable by its own and, once assembled, does not rely on any additional factor from the overall RNA fold. Further, we predict that the pKa of the water molecule bridging two Mg cations is around 8.4. We also demonstrate that the halide selectivity of the fluoride riboswitch is determined by the stronger Mg-F bond, which is capable of keeping together the cluster. Replacing F- with Cl- results in a cluster that is unstable under dynamic conditions. Similar conclusions on the structure and energetics of the cluster in the binding pocket of fluoride-inhibited pyrophosphatase suggest that the peculiarity of fluoride is in its ability to establish much stronger metal-halide bonds
A.P. thanks the Spanish MINECO for a Ramón y Cajal contract (RYC-2009-05226) and European Commission for a Career Integration Grant (CIG09-GA-2011-293900).
Format: application/pdf
Document access: http://hdl.handle.net/10256/13301
Language: eng
Publisher: American Chemical Society (ACS)
Collection: info:eu-repo/semantics/altIdentifier/doi/10.1021/ja510549b
info:eu-repo/semantics/altIdentifier/issn/0002-7863
info:eu-repo/semantics/altIdentifier/eissn/1520-5126
info:eu-repo/grantAgreement/MICINN//RYC-2009-05226/ES/RYC-2009-05226/
info:eu-repo/grantAgreement/EC/FP7/293900/EU/Ab initio Statics and Molecular Dynamics Simulation of Olefin Metathesis Catalysts for pharmacological purposes/COMPUTEDRUG
Rights: Tots els drets reservats
Subject: Funcional de densitat, Teoria del
Density functionals
Title: Structural stability, acidity, and halide selectivity of the fluoride riboswitch recognition site
Type: info:eu-repo/semantics/article
Repository: DUGiDocs

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