71 citations · 183 across the 7 of their papers we have counts for
7 papers
Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time
Naoto Hori, D. Thirumalai
Folding of ribozymes into well-defined tertiary structures usually requires divalent cations. How Mg ions direct the folding kinetics has been a long-standing unsolved probl…
Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent
Naoto Hori, Natalia A. Denesyuk, D. Thirumalai
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 i…
Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover
Naoto Hori, Natalia A. Denesyuk, D. Thirumalai
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…
Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA
Debayan Chakraborty, Naoto Hori, Dave Thirumalai
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…
Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot
Jorjethe Roca, Naoto Hori, Yogambigai Velmurugu +4
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 th…
Protein Collapse is Encoded in the Folded State Architecture
Himadri S. Samanta, Pavel I. Zhuravlev, Michael Hinczewski +3
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon additio…
Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension
Naoto Hori, Natalia A. Denesyuk, D. Thirumalai
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 bee…