Govardhan Reddy

Conformational Switching between ON and OFF States Proceeds through Multiple Pathways in the SAM-III Translational Riboswitch

The paper uses molecular dynamics simulations to study conformational switching in a SAM-III riboswitch, showing Mg2+ stabilizes the ON-state and multiple pathways contribute to the transition between ON and OFF states.

Mg2+-Dependent Multistep Folding and Stabilization of the GAAA Tetraloop-Receptor Interaction in a Group I Intron

The paper uses simulations to study how Mg2+ ions influence the folding and stabilization of the GAAA tetraloop-receptor interaction in a group I intron.

Dimerization Mechanism of HIV-1 RNA Hairpins to Extended Duplex Structures

This study identifies the dimerization mechanism of HIV-1 RNA hairpins to extended duplex structures using simulations, revealing intermediates and ion-dependent pathways.

Transition Metal Binding Drives Folding of a Metalloregulatory Riboswitch by Modulating Conformational Flexibility at Helical Junctions

This study shows how Co2+ binding drives folding of the NiCo riboswitch by stabilizing non-canonical base pairs and modulating conformational flexibility at helical junctions.

Conformational Pathways of Translational T-box Riboswitch Governing tRNA Recognition for Gene Regulation

This study uses computer simulations to reveal the conformational pathways of a T-box riboswitch in recognizing tRNA, showing three thermodynamic states and their dependence on Mg2+ concentration, with implications for antibiotic development.

Hierarchically ordered multi-timescale structural dynamics of the intrinsically disordered p53 transactivation domain

The paper characterizes the multi-timescale structural dynamics of the p53 transactivation domain using NMR and simulations, revealing a hierarchical energy landscape.

Metal Ion Sensing by Tetraloop-Like RNA Fragment: Role of Compact Intermediates with Non-Native Metal Ion-RNA Inner Shell Contacts

This study investigates how Mg2+ and Ca2+ ions influence the folding of a tetraloop RNA motif through direct and indirect binding modes, revealing non-native metal-RNA contacts and their impact on folding stability.