Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: The case of histone lysine methyltransferase SET7/9

Article Abstract:

Ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are performed with the umbrella sampling method to determine free energy profiles for histone lysine methylation catalyzed by SET7/9. The results have shown that a combination of the electrostatic preorganization in enzyme and the hydrogen bond network reorganization in solution is necessary for the enormous catalytic power of the histone lysine methyl-transferase SET7/9.

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Two-metal-ion mechanism for hammerhead-ribozyme catalysis

Article Abstract:

A two-metal-ion model for hammerhead-ribozyme catalysis, based on density functional quantum mechanical calculations is described and analyzed. It catalyzes a transesterification reaction that converts a 5',3' diester to a 2',3' cyclic phosphate diester through an S(sub N)2 mechanism.

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The thermodynamics and kinetics of protein folding: a lattice model analysis of multiple pathways with intermediates

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Research is presented investigating the kinetics and thermodynamics on a simple lattice cube by folding a representative sequence of a 125-residue protein model subject to Monte Carlo dynamics.

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