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Recently, Baugh et al. discovered that a distal point mutation (F130L) in streptavidin causes no distinct variation to the structure of the binding pocket but a 1000-fold reduction in biotin binding affinity. In this work, we carry out molecular dynamics simulations and apply an end-state free energy method to calculate the binding free energies of biotin(More)
An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y.(More)
The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein-specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin(More)
Energy control is the most important problem for wireless sensor networks, and the primary performance objectives are energy conservation and the design of an efficient energy strategy for prolonging the whole networks' lifetime. As the applications of wireless sensor networks increase, the network protocols become more and more complex. But all the(More)
The Fenna-Matthews-Olson (FMO) light-harvesting complex is now one of the primary model systems for the study of excitation energy transfer (EET). However, the mechanism of the EET in this system is still controversial. In this work, molecular dynamics simulations and the electrostatic-embedding quantum-mechanics/molecular-mechanics single-point(More)
A newly developed AMBER compatible force ¯eld with coupled backbone torsion potential terms (AMBER03 2D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the-helix in the ¯nal(More)
The alcohol-based cosolvent 2,2,2-trifluoroethanol (TFE) has been used widely in protein science and engineering. Many experimental and computational studies of its impact on protein structure have been carried out, but consensus on the mechanism has not been reached. In the past decade, several molecular mechanical models have been proposed to model the(More)
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