Paul C. Whitford

TL;DR: Using explicit-solvent simulations of the 70S ribosome, the barrier-crossing attempt frequency was calculated and it is demonstrated that the free-energy barrier of elbow-accommodation is less than 15 k(B)T, in vitro and in vivo.

TL;DR: The data indicate that reversible cross-linking of two cysteine residues in the SH2 domain greatly impacts catalytic function and interdomain communication in Csk and has large effects on residues within the kinase domain, most notably within the active-site cleft.

TL;DR: This study reiterates the roles that cracking and disorder can play in functional molecular motions, in contrast to the downhill mechanical interpretations of the “spring-loaded” model proposed for the HA2 conformational transition.

TL;DR: This study demonstrates how molecular structure can give rise to large-scale collective rearrangements through spontaneous transitions between the A/P–P/E and P/P-E/E ensembles.

TL;DR: Values of Γ2+ computed from molecular dynamics simulations using the model show excellent agreement with both experimental data on the adenine riboswitch and previous explicit-solvent simulations of the SAM-I ribos witch, which confirms the thermodynamic accuracy of the model via the direct relation ofλ2+ to the Mg(2+)-RNA interaction free energy, and provides further support for the predictions from explicit-Solvent calculations.