Hybrid quantum mechanics/molecular mechanics simulations with two-dimensional interpolated corrections: Application to enzymatic processes

Article Abstract:

A 2-D interpolated correction scheme is described and validated by exploring two well-known enzymatic reactions, the S-adenosyl-L-methionine (SAM) dependent methylation of catecholate and the chorismate to prephenate arrangement catalyzed by Bacillus subtilis. The correction energy as a function of the bond-breaking and bond-forming distance was obtained for both the cases and it improves the energetic and geometric descriptions of the reaction.

Quantum theory, Quantum mechanics, Methylation, Chemical properties, S-adenosylmethionine

---

Internal rotation of 1,2-dichloroethane in haloalkane dehalogenase. A test case for analyzing electrostatic effects in enzymes

Article Abstract:

The nature of substrate-enzyme interactions is investigated obtaining the free energy profiles of rotation around the C-C bond in the gas phase, in aqueous solution and in the enzymes environment. Differences between the aqueous solution and enzyme energy profiles are rationalized taking into account the different magnitudes and orientations of the electric field created by the environment in both cases.

Enzymes, Other Basic Organic Chemical Manufacturing, Chemistry, Physical and theoretical, Physical chemistry, Aqueous solution reactions

---

Stabilization of charges and protonation states in the active site of the protein tyrosine phosphatases: a computational study

Article Abstract:

Electrostatic calculations for the pK(sub a) of the ionizable side chains of four different PTPases. The use of a low protein dielectric constant in the calculations is essential to obtaining calculated protonation states that are consistent with catalytic mechanism.

All Other Miscellaneous Chemical Product and Preparation Manufacturing, Catalysts, Chemical preparations, not elsewhere classified, Phosphatases, Tyrosine

Similar abstracts:

• Abstracts: A quantum mechanical/molecular mechanical approach to relaxation dynamics: calculation of the optical properties of solvated bacteriochlorophyll-a
• Abstracts: Hybrid QM/MM potentials of mean force with interpolated corrections. A QM/MM study of the conformational equilibria in the chorismate mutase active site. The role of the enzymatic deformation energy contribution
• Abstracts: Partitioning of small alcohols into dimyristoyl phosphatidylcholine (DMPC) memberanes: volumetric properties. Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy

This website is not affiliated with document authors or copyright owners. This page is provided for informational purposes only. Unintentional errors are possible.