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.
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...
Designing photochemical properties in proteins is a frontier challenge in biomolecular design, which, when realised, will open new avenues in catalysis and biomolecular electronics. Here we demonstrate an integrated computational design framework, supported by ultrafast spectroscopy, combining protein design, quantum m...
Ethan L. Bungay, Juno Underhill, Mei-Yue Liu et al.· bioRxiv· 0 citations
This chapter highlights how recent advances in time-resolved vibrational spectroscopy and molecular dynamics simulations unravel crowding's effects on water structure and dynamics, and proposes integrative frameworks to connect ultrafast spectroscopic and simulation data with mesoscale biophysical models.
FlexID is an engineered promiscuous ligase that catalyzes the rapid attachment of diverse small-molecule probes to proximal endogenous proteins and operates through a zero-radius, direct-contact mechanism, offering superior spatial precision compared to existing PL tools.
Shi-Zhong A. Dai, Peter E. Cavanagh, Albert Qiang et al.· bioRxiv· 1 citation
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