All Outputs (15)

Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences (2024)
Journal Article
Maity, H., Nguyen, H. T., Hori, N., & Thirumalai, D. (2024). Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences. Journal of Physical Chemistry Letters, 15(14), 3820–3827. https://doi.org/10.1021/acs.jpclett.3c03553

Repeat RNA sequences self-associate to form condensates. Simulations of a coarse-grained single-interaction site model for (CAG)n (n = 30 and 31) show that the salt-dependent free energy gap, ΔGS, between the ground (perfect hairpin) and the excited... Read More about Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences.

Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences (2024)
Journal Article
Mondal, B., Chakraborty, D., Hori, N., Nguyen, H. T., & Thirumalai, D. (2024). Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences. Journal of Chemical Theory and Computation, 20(7), 2934-2946. https://doi.org/10.1021/acs.jctc.3c01193

Interplay between divalent cations (Mg2+ and Ca2+) and single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), as well as stacking interactions, is important in nucleosome stability and phase separation in nucleic acids. Quantitative techniques... Read More about Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences.

Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time (2023)
Journal Article
Hori, N., & Thirumalai, D. (2023). Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time. Nucleic Acids Research, 51(19), 10737-10751. https://doi.org/10.1093/nar/gkad755

Folding of ribozymes into well-defined tertiary structures usually requires divalent cations. How Mg2+ ions direct the folding kinetics has been a long-standing unsolved problem because experiments cannot detect the positions and dynamics of ions. To... Read More about Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time.

Odd–even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation (2023)
Journal Article
Maity, H., Nguyen, H. T., Hori, N., & Thirumalai, D. (2023). Odd–even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation. Proceedings of the National Academy of Sciences, 120(24), Article e2301409120. https://doi.org/10.1073/pnas.2301409120

Low-complexity nucleotide repeat sequences, which are implicated in several neurological disorders, undergo liquid–liquid phase separation (LLPS) provided the number of repeat units, n, exceeds a critical value. Here, we establish a link between the... Read More about Odd–even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation.

Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics (2022)
Journal Article
Nguyen, H. T., Hori, N., & Thirumalai, D. (2022). Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics. Nature Chemistry, https://doi.org/10.1038/s41557-022-00934-z

Although it is known that RNA undergoes liquid–liquid phase separation, the interplay between the molecular driving forces and the emergent features of the condensates, such as their morphologies and dynamic properties, is not well understood. We int... Read More about Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics.

Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA (2021)
Journal Article
Hori, N., Denesyuk, N. A., & Thirumalai, D. (2021). Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA. Proceedings of the National Academy of Sciences, 118(10), Article e2020837118. https://doi.org/10.1073/pnas.2020837118

Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step... Read More about Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA.

Theory and simulations for RNA folding in mixtures of monovalent and divalent cations (2019)
Journal Article
Nguyen, H. T., Hori, N., & Thirumalai, D. (2019). Theory and simulations for RNA folding in mixtures of monovalent and divalent cations. Proceedings of the National Academy of Sciences, 116(42), 21022-21030. https://doi.org/10.1073/pnas.1911632116

RNA molecules require ions to fold. The problem of how ions of differing sizes and valences drive the folding of RNA molecules is unsolved. Here, we take a major step in its solution by creating a method, based on the theory of polyatomic liquids, to... Read More about Theory and simulations for RNA folding in mixtures of monovalent and divalent cations.

Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent (2019)
Journal Article
Hori, N., Denesyuk, N. A., & Thirumalai, D. (2019). Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent. Biophysical Journal, 116(12), 2400-2410. https://doi.org/10.1016/j.bpj.2019.04.037

The highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions in the absence of ions. For ribozymes, divalent cations are known to be more efficient tha... Read More about Ion Condensation onto Ribozyme Is Site Specific and Fold Dependent.

Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding (2018)
Journal Article
Denesyuk, N. A., Hori, N., & Thirumalai, D. (2018). Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding. Journal of Physical Chemistry B, 122(50), 11860-11867. https://doi.org/10.1021/acs.jpcb.8b08142

How ions affect RNA folding thermodynamics and kinetics is an important but a vexing problem that remains unsolved. Experiments have shown that the free-energy change, δG(c), of RNA upon folding varies with the salt concentration (c) as, δG(c) = k c... Read More about Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding.

Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover (2018)
Journal Article
Hori, N., Denesyuk, N. A., & Thirumalai, D. (2018). Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover. Journal of Physical Chemistry B, 122(49), 11279-11288. https://doi.org/10.1021/acs.jpcb.8b07129

We investigated frictional effects on the folding rates of a human telomerase hairpin (hTR HP) and H-type pseudoknot from the Beet Western Yellow Virus (BWYV PK) using simulations of the Three Interaction Site (TIS) model for RNA. The heat capacity f... Read More about Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover.

Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot (2018)
Journal Article
Roca, J., Hori, N., Baral, S., Velmurugu, Y., Narayanan, R., Narayanan, P., …Ansari, A. (2018). Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot. Proceedings of the National Academy of Sciences, 115(31), E7313-E7322. https://doi.org/10.1073/pnas.1717582115

The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability, and dynamics. Therefore, it is important to... Read More about Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.

Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA (2018)
Journal Article
Chakraborty, D., Hori, N., & Thirumalai, D. (2018). Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA. Journal of Chemical Theory and Computation, 14(7), 3763-3779. https://doi.org/10.1021/acs.jctc.8b00091

We develop a robust coarse-grained model for single- and double-stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking... Read More about Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.

Protein collapse is encoded in the folded state architecture (2017)
Journal Article
Samanta, H. S., Zhuravlev, P. I., Hinczewski, M., Hori, N., Chakrabarti, S., & Thirumalai, D. (2017). Protein collapse is encoded in the folded state architecture. Soft Matter, 13(19), 3622-3638. https://doi.org/10.1039/c7sm00074j

Folded states of single domain globular proteins are compact with high packing density. The radius of gyration, Rg, of both the folded and unfolded states increase as Nν where N is the number of amino acids in the protein. The values of the Flory exp... Read More about Protein collapse is encoded in the folded state architecture.

Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension (2016)
Journal Article
Hori, N., Denesyuk, N. A., & Thirumalai, D. (2016). Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension. Journal of Molecular Biology, 428(14), 2847-2859. https://doi.org/10.1016/j.jmb.2016.06.002

Because of the potential link between − 1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single-molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed ribosomal... Read More about Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension.

How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations (2015)
Journal Article
Tanaka, T., Hori, N., & Takada, S. (2015). How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations. PLoS Computational Biology, 11(7), Article e1004356. https://doi.org/10.1371/journal.pcbi.1004356

Co-translational folding (CTF) facilitates correct folding in vivo, but its precise mechanism remains elusive. For the CTF of a three-domain protein SufI, it was reported that the translational attenuation is obligatory to acquire the functional stat... Read More about How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations.