Transition-state structural refinement with GRACE and CHARMM: Flexible QM/MM modelling for lactate dehydrogenase

Turner, Alexander J.; Moliner, Vicent; Williams, Ian H.

doi:10.1039/a808364i

Cited by 122 publications

(143 citation statements)

References 24 publications

Supporting

Mentioning

131

Contrasting

Unclassified

Order By: Relevance

“…[48][49][50] In equation 1, HL stands for the high level chosen to obtain the corrected estimation of the activation free energy. In our case M06-2X/6-31+G(d,p) 34,35 has been used.…”

Section: Free Energy Calculationsmentioning

confidence: 99%

See 1 more Smart Citation

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

et al. 2015

View full text Add to dashboard Cite

The promiscuous activity of the enzyme o-Succinylbenzoate Synthase (OSBS) from the actinobacteria Amycolatopsis is investigated by means of QM/MM methods, using both Density Functional Theory and Semiempirical Hamiltonians. This enzyme catalyzes not only the dehydration of 2-succinyl-6R-hydroxy-2,4-cyclohexadiene-1R-carboxylate but also catalyzes racemization of different acylaminoacids, being N-succinyl-Rphenylglycine the best substrate. We investigated the molecular mechanisms for both reactions exploring the Potential Energy Surface. Then, Molecular Dynamics simulations were performed to obtain the free energy profiles and the averaged interaction energies of enzymatic residues with the reacting system. Our results confirm the plausibility of the reaction mechanisms proposed in the literature, with a good agreement between theoretical and experimentally-derived activation free energies. Our simulations unravel the role played by the different residues in each of the two possible reactions. The presence of flexible loops in the active site and the selection of structural modifications in the substrate seem to be key elements to promote the promiscuity of this enzyme.

show abstract

“…[48][49][50] In equation 1, HL stands for the high level chosen to obtain the corrected estimation of the activation free energy. In our case M06-2X/6-31+G(d,p) 34,35 has been used.…”

Section: Free Energy Calculationsmentioning

confidence: 99%

“…HL calculations are carried out under the effect of the field created by the MM environment, where the electrostatic coupling between the QM and MM subsystems is calculated using point charges on the QM atoms. [48][49][50] …”

Section: Free Energy Calculationsmentioning

confidence: 99%

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Then, by a series of energy maximizations along a reactive mode and minimizations in all space directions conjugate to that a saddle point is iteratively constructed ("conjugate peak refinement"). A comparable approach for saddle-point optimization in complex systems has been introduced by Williams et al 92,93 In a first step, all atoms within a radius of 10 Å were allowed to move and the CPR-refinement performed. In the next step, the exterior of this zone was minimized with the atoms refined before being restrained to their position.…”

Section: Stationary Pointsmentioning

confidence: 99%

A QM–MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems

2003

View full text Add to dashboard Cite

The implementation of a hybrid QM-MM approach combining ab initio and density functional methods of TURBOMOLE with the molecular mechanics program package CHARMM is described. An interface has been created to allow data exchange between the two applications. With this method the efficient multiprocessor capabilities of TURBOMOLE can be utilized with CHARMM running as a single processor application. Therefore, features of nonparallel running code in CHARMM like the TRAVEL module for locating saddle points or VIBRAN for the calculation of second derivatives can be exploited by running the CPU intensive QM calculations in parallel. To test the methodology, several small systems are studied with both Hartree-Fock and density functional methods and varying QM-MM boundaries. Also, the computationally efficient RI-J method has been examined for use in QM-MM applications. A B(12) cofactor containing cobalt has been studied, to examine systems with a large QM region and transition metals. All tested methods perform satisfactory in comparison with pure quantum calculations. Additionally, algorithms for the characterization of saddle points have been tested for their potential use in QM-MM problems. The TRAVEL module of CHARMM has been applied to the Menshutkin reaction in the condensed phase, and a saddle point was located. This saddle point was verified by calculation of a steepest descent path connecting educt, transition state, and product, and by calculation of vibrational modes.

show abstract

“…Different computational groups' proposals differ in the order in which the proton and hydride ions are transferred. Some found a mechanism in which the hydride transfer preceded proton transfer in a stepwise manner (Yadav et al 1991;Ranganathan & Gready 1997), while others predicted a concerted but asynchronous reaction in which the proton transfer was largely completed in the transition state (TS) of the reaction (Wilkie & Williams 1992;Moliner et al 1997;Turner et al 1999;Ferrer et al 2005a). A very flexible treatment of the environment (Moliner & Williams 2000) generated a potential energy surface (PES) showing the coexistence of both mechanistic pathways.…”

Section: Introductionmentioning

confidence: 99%

Theoretical site-directed mutagenesis: Asp168Ala mutant of lactate dehydrogenase

Ferrer

Tuñón

Moliner

et al. 2008

J. R. Soc. Interface.

View full text Add to dashboard Cite

Molecular simulations based on the use of hybrid quantum mechanics/molecular mechanics methods are able to provide detailed information about the complex enzymatic reactions and the consequences of specific mutations on the activity of the enzyme. In this work, the reduction of pyruvate to lactate catalysed by wild-type and Asp168Ala mutant lactate dehydrogenase (LDH) has been studied by means of simulations using a very flexible molecular model consisting of the full tetramer of the enzyme, together with the cofactor NADH, the substrate and solvent water molecules. Our results indicate that the Asp168Ala mutation provokes a shift in the pK a value of Glu199 that becomes unprotonated at neutral pH in the mutant enzyme. This change compensates the loss of the negative charge of Asp168, rendering a still active enzyme. Thus, our methodology gives a calculated barrier height for the Asp168Ala mutant 3 kcal mol K1 higher than that for wild-type LDH, which is in very good agreement with the experiment. The computed potential energy surfaces reveal the reaction pathways and transition structures for the wild-type and mutant enzymes. Hydride transfer is less advanced and the proton transfer is more advanced in the Asp168Ala mutant than in the wild type. This approach provides a very powerful tool for the analysis of the roles of key active-site residues.

show abstract

Transition-state structural refinement with GRACE and CHARMM: Flexible QM/MM modelling for lactate dehydrogenase

Cited by 122 publications

References 24 publications

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

A QM–MM interface between CHARMM and TURBOMOLE: Implementation and application to systems in bulk phase and biologically active systems

Theoretical site-directed mutagenesis: Asp168Ala mutant of lactate dehydrogenase

Contact Info

Product

Resources

About