Studying the Dynamics of a Complex G-Quadruplex System: Insights into the Comparison of MD and NMR Data
Matteo Castelli, Filippo Doria, Mauro Freccero, Giorgio Colombo, Elisabetta Moroni
Abstract
-ions to neutralize the system charge, mimicking the intracellular ionic strength, and using the four-atom water model are found to be the best in reproducing the experimental NMR constraints and data. Our analysis also reveals that in all of the simulated environments residues belonging to the duplex moiety of HIV LTR-III exhibit the highest flexibility.
Topics & Concepts
Molecular dynamicsIonic bondingMicrosecondIonChemical physicsForce field (fiction)Nucleic acidChemistryBiological systemMaterials scienceComputational chemistryComputer sciencePhysicsBiologyAstronomyArtificial intelligenceOrganic chemistryBiochemistryDNA and Nucleic Acid ChemistryAdvanced biosensing and bioanalysis techniquesAdvanced NMR Techniques and Applications