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Conformation gating as a mechanism for enzyme specificity.
The gate is effective in reducing the binding rate for a ligand 0.4 A bulkier by three orders of magnitude, which suggests a mechanism for achieving enzyme specificity without sacrificing efficiency.
Molecular Dynamics of Acetylcholinesterase Dimer Complexed with Tacrine
The dynamic properties of acetylcholinesterase dimer from Torpedo californica liganded with tacrine (AChE−THA) in solution using molecular dynamics suggest that transport of solvent molecules participating in catalysis can occur across the porous wall, contributing to the efficiency of the enzyme.
Critical soil bulk density and strength for pea seedling root growth as related to other soil factors
Automated ligand placement and refinement with a combined force field and shape potential.
- S. Wlodek, A. Skillman, A. Nicholls
- Physics, ChemistryActa crystallographica. Section D, Biological…
- 1 July 2006
An automated computational procedure for fitting a ligand into its electron density with the use of the MMFF94 force field and a Gaussian shape description has been developed and the final results are structures realistically strained to fit the crystallographic data.
Acetylcholinesterase: role of the enzyme's charge distribution in steering charged ligands toward the active site.
Evolution appears to have built a redundant electrostatic steering capability into this important enzyme through the overall distribution of its thousands of partially charged atoms, which helps to rationalize, many surprising experimental results obtained recently for human acetylcholinesterase.
Simulation of charge-mutant acetylcholinesterases.
It is concluded that the mutation experiments do not disprove that electrostatic steering substantially affects the catalytic rate of acetylcholinesterase, and the electrostatic field of the enzyme is found to increase the rate constants by about an order of magnitude in both the wild type and the mutants.
ON THE MECHANISM OF ACETYLCHOLINESTERASE ACTION : THE ELECTROSTATICALLY INDUCED ACCELERATION OF THE CATALYTIC ACYLATION STEP
Brownian dynamics simulations of the encounter kinetics between the active site of the wild-type and Glu199 mutant of Torpedo californica acetylcholinesterase (TcAChE) with a charged substrate were...
Ligand Entropy in Gas-Phase, Upon Solvation and Protein Complexation. Fast Estimation with Quasi-Newton Hessian.
The Hessian matrix of second derivatives built by a quasi-Newton optimizer during geometry optimization of a molecule with a classical molecular potential in these three environments can be used to predict vibrational entropies.
Binding of tacrine and 6-chlorotacrine by acetylcholinesterase.
The results suggest that electron density redistribution upon tacrine chlorination is mainly responsible for the increased attraction potential between pronated inhibitor molecule and adjacent aromatic groups of Phe-330 and Trp-84.
The SAMP1 solvation challenge: further lessons regarding the pitfalls of parametrization.
The results are consistent with earlier reports, namely, that more physical charges perform better and that radii parametrization can both improve and also dramatically worsen results, with the latter suggesting a failure to capture all of the basic physics of solvation.