Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics

Abstract

Hybrid quantum/classical molecular dynamics simulations of the two proton transfer reactions catalyzed by ketosteroid isomerase are presented. The potential energy surfaces for the proton transfer reactions are described with the empirical valence bond method. Nuclear quantum effects of the transferring hydrogen increase the rates by a factor of ~8, and dynamical barrier recrossings decrease the rates by a factor of 3–4. For both proton transfer reactions, the donor-acceptor distance decreases substantially at the transition state. The carboxylate group of the Asp38 side chain, which serves as the proton acceptor and donor in the first and second steps, respectively, rotates significantly between the two proton transfer reactions. The hydrogen bonding interactions within the active site are consistent with the hydrogen bonding of both Asp99 and Tyr14 to the substrate. The simulations suggest that a hydrogen bond between Asp99 and the substrate is present from the beginning of the first proton transfer step, whereas the hydrogen bond between Tyr14 and the substrate is virtually absent in the first part of this step but forms nearly concurrently with the formation of the transition state. Both hydrogen bonds are present throughout the second proton transfer step until partial dissociation of the product. The hydrogen bond between Tyr14 and Tyr55 is present throughout both proton transfer steps. The active site residues are more mobile during the first step than during the second step. The van der Waals interaction energy between the substrate and the enzyme remains virtually constant along the reaction pathway, but the electrostatic interaction energy is significantly stronger for the dienolate intermediate than for the reactant and product. Mobile loop regions distal to the active site exhibit significant structural rearrangements and, in some cases, qualitative changes in the electrostatic potential during the catalytic reaction. These results suggest that relatively small conformational changes of the enzyme active site and substrate strengthen the hydrogen bonds that stabilize the intermediate, thereby facilitating the proton transfer reactions. Moreover, the conformational and electrostatic changes associated with these reactions are not limited to the active site but rather extend throughout the entire enzyme.

Studying Allosteric Regulation in Metal Sensor Proteins Using Computational Methods

“…Well-established protocols were used to simulate the protein and protein-DNA complexes in our studies (Chakravorty & Hammes-Schiffer, 2010;Chakravorty, Kumarasiri, Soudackov, & Hammes-Schiffer, 2008;Chakravorty, Soudackov, & Hammes-Schiffer, 2009). All classical MD simulations were performed using the AMBER 11 suite of programs on a potential energy surface described by the AMBER ff99SB force field with parambsc0 modifications for DNA (Case et al, 2010).…”

Transformation of a series of saturated isomeric steroidal diols by Aspergillus tamarii KITA reveals a precise stereochemical requirement for entrance into the lactonization pathway

“…3␣-Hydroxy-5␣-androstan-17-one (7) 3379 1724 3␣-Hydroxy-5␣-androstan-17-hydrazone (8) 3343 17-Iodo-5␣-androst-16-en-3␣-ol (9) 3343 1628 5␣-Androst-16-en-3␣-ol (10) 3276 1588 5␣-Androstan-3␣,17␣-diol (11) 3344 5␣-Androstan-3␣,16␣-diol (12) 3261…”

“…To date, no single study has determined the metabolic fate of all four isomers of 5␣-androstan-3,17-diol. This is of significance due to the importance of hydrogen bonding in steroid/enzyme interactions [8][9][10][11][12][13][14][15][16] and in determining if specific stereochemistry is handled within different metabolic pathways. We have also modified a previous [17] synthetic strategy to facilitate an expedient route to 3␣-hydroxy containing 17␣-and 17␤-diols that, as with the other analogues [18][19][20][21][22][23] have a broad range of interesting biological activity in their own right [24][25][26][27].…”

Semiclassical evaluation of kinetic isotope effects in 13-atomic system

“…Due to the importance of skeleton motions and possible dynamical effects of environment on hydrogen transfer step in reactions of enzyme catalysis, 58 this multidimensional 13-atomic system may serve as a prototype of hydrogen transfer in enzyme reactions, particularly in approaches where a subset of the atoms ∼50 is treated quantum mechanically and the rest by other methods. 1,10,59,60 The paper is organized as follows. In Sec.…”