This work employs highly efficient path-based sampling methods to perform unprecedented free-energy calculations of the base-pairing transition, and finds evidence of triple-hydrogen-bonded neighbors hindering the inside transition.
It is shown that the PMD enhanced sampling approach in combination with force-field MD simulations of conformational transitions that require three or more collective variables (CVs) to describe the processes efficiently localizes the average transition path and simultaneously obtains the free-energy profile along the...
It is found that the conformation of a Trp and a Met near the flavin is crucial to modulate the rate-determining barrier, which differs significantly between the BlrB and AppA proteins.
A quantum chemical investigation of alkynylated purine–pyridazine UBPs is presented, combining Kohn–Sham molecular orbital and energy decomposition analyses to characterize both base-pairing and π–π stacking interactions.
A. Bermejo, J. Bofill, Jordi Poater· Journal of Organic Chemistry· 0 citations
The results reveal that loop-geometry preferences strongly depend on the loop spatial span and, with increasing length, shift from low-span toward large-span geometries, and it is discovered that loop-geometry preferences arise from an interplay between the electrostatic repulsion of phosphate groups and loop overstret...
Michał Jurkowski, Mateusz Kogut, Mikołaj Ławicki et al.· PLoS Computational Biology· 0 citations
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