Showing papers by "Thomas E. Cheatham published in 2004"
TL;DR: A computationally intensive project aimed at carrying out molecular dynamics simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base sequences, which involves a total of approximately 0.6 mus of simulation for systems containing approximately 24,000 atoms.
258 citations
TL;DR: Highlights include the accurate representation of subtle drug-DNA interactions, the detailed study of modified and unusual nucleic acid structures, insight into the influence of dynamics on the structure of DNA, and exploration of the interaction of solvent and ions with nucleic acids.
225 citations
TL;DR: The study provides, within the approximations of the applied all-atom additive force field, a qualitatively complete analysis of the available loop conformational space and the optimal diagonal and lateral loop arrangements appear to be close in energy although a proper inclusion of the loop monovalent cations could stabilize the diagonal architecture.
119 citations
TL;DR: The results for 13 AT pairs and 11 GC pairs in different sequence contexts suggest that buckle and propeller are very flexible (more than roll in TA dinucleotide steps), while stretch is exceptionally stiff.
Abstract: distribution, their correlation matrix is related to the inverse of the stiffness matrix by a simple equation, 〈xixj〉 ) kT(F -1 )ij, where xi is the value of the ith parameter (with the average value subtracted) and F is the stiffness matrix. The effect of the Jacobian arising from the transformation of variables to noncanonical (angular) ones18 was neglected due to small angular fluctuations. The first nanosecond of the simulations and three base pairs at each end were excluded from the analysis. Thus, 13 AT pairs and 11 GC pairs were considered. The “diagonal” force constants (averages and ranges of observed values) are summarized in Table 1. They describe the energy cost associated with the change of only one parameter, while the others retain their equilibrium values. The full list of force constants including coupling terms and energy errors is available as Supporting Information. As can be seen from Table 1, the GC base pair is, on average, stiffer than AT in all parameters except propeller twist and shear for which the values are comparable. The ratios of average force constants for GC and AT pairs with respect to buckle, stretch, and stagger span the range of 1.4-1.7 while the ratio for opening is 3.9. However, the range of observed values (about 10% of the average) blurs this difference, and only stretch and opening remain distinctly stiffer for GC than for AT in all instances. Note that the ratio of the stretch stiffness of the GC and AT base pairs (1.7) is closer to the ratio of the number of their H-bonds (1.5) than to the ratio of their intrinsic (gas phase) interaction energies (2.15 with
42 citations