Free energy perturbation study of metal ion-catalyzed proton transfer in water

Aaqvist, Johan

doi:10.1021/j100165a002

Cited by 21 publications

(10 citation statements)

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“…The FEP calculations of reactions (1)- (4) involve creating/annihilating protons, redistributing charge and changing relevant bonded parameters, all given by the OPLS-AA force field. Non-bonded van der Waals parameters for the hydroxide ion, with charges À 1.2 (O) and þ 0.2 (H), were taken from Åqvist's early work 32 that yielded reliable hydration properties in terms of radial distribution function and solvation energy (DG sol % 105 kcal mol À 1 ). Charges for the transient metaphosphate species in reaction (4) were þ 1.1 (P) and À 0.7 (O), with standard OPLS-AA phosphate van der Waals parameters.…”

Section: Methodsmentioning

confidence: 99%

Energetics of activation of GTP hydrolysis on the ribosome

2013

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Several of the steps in protein synthesis on the ribosome utilize hydrolysis of guanosine triphosphate (GTP) as the driving force. This reaction is catalyzed by translation factors that become activated upon binding to the ribosome. The recently determined crystal structure of an elongation factor-Tu ternary complex bound to the ribosome allows the energetics of GTP activation to be explored by computer simulations. A central problem regards the role of the universally conserved histidine, which has been proposed to act as a general base for guanosine triphosphate hydrolysis. Here we report a detailed energetic and structural analysis of different possible protonation states that could be involved in activation of the reaction. We show that the histidine cannot act as a general base, but must be protonated and in its active conformation to promote GTP hydrolysis. We further show that the sarcin-ricin loop of the ribosome spontaneously drives the histidine into the correct conformation for GTP activation.

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Section: Methodsmentioning

confidence: 99%

Energetics of activation of GTP hydrolysis on the ribosome

2013

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“…The procedure outlined below is identical to that used in a recent study'' of the same reaction in water catalysed by different metal ions and further details can be foud in ref. 18 and 7J: The PT reaction between two water molecules can be described as an effective two-state problem corresponding to the VB structures The energies of the two non-adiabatic states are written as i I where AMji) denotes the Morse potential (relative to its minimum value) corresponding to thejth bond in the ith VB structure and the second term and third terms, respectively, denote the bond angle bending contribution and the non-bonded electrostatic and van der Waals' interactions between the reacting groups (subscript r). The factor yii) in the second term is a coupling between bonds that are being broken or formed and those angles that depend on these bonds."…”

Section: Constructing the Evb Potentialmentioning

confidence: 99%

“…All the interaction and EVB parameters for the reacting fragments are listed in Table 1 of ref. 18. The Zn2+ ion was treated with the octahedral 1 + 6-centre model described ear lie^'^ and the parameters and procedure for deriving them is described in ref.…”

Section: Constructing the Evb Potentialmentioning

confidence: 99%

Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase

Warshel

Hwang²,

Åqvist³

1992

Faraday Discuss.

121

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“…In the empirical valence bond approach, a molecule is generally represented by an effective two-state (a covalent state and an ionic state) description in which different nonbonded interactions parameters are used for these two states. [46][47][48][49] In the shell models for ions, the separation between a nucleus and its (spherical) electron cloud is coupled by a harmonic spring and adjusts to the environment. 50 In this article, we show that coupling of the Lennard-Jones interaction parameters to the fluctuating partial charges on the oxygen atoms leads to significant improvements for the fluctuating-charge water models.…”

Section: Introductionmentioning

confidence: 99%

Development of Polarizable Water Force Fields for Phase Equilibrium Calculations

2000

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Recent simulation studies for four dipole-polarizable and for two fluctuating-charge water force fields have demonstrated that none of the force fields studied is capable of yielding a satisfactory description of the vapor-liquid coexistence curve from room temperature to the critical region. The performance of these polarizable force fields can be improved dramatically by introducing an additional coupling between the Lennard-Jones interaction parameters for a pair of oxygen sites and their partial charges (electronic configuration). Two different types of water models are presented which are based on either the three-site simple point charge (SPC) or the four-site transferable intermolecular potential 4 point (TIP4P) water representations. Adiabatic nuclear and electronic sampling Monte Carlo (ANES-MC) simulations in the Gibbs, isobaric-isothermal, and canonical ensembles were performed to calculate vapor-liquid coexistence curves, to determine the temperatures of maximum liquid density, and to evaluate dielectric constants along the coexistence line, respectively. The new SPC-pol-1 force field yields significantly better agreement with the experiment for the saturated vapor and liquid densities, the heats of vaporization, and the liquid-phase dielectric constants than the fixed-charge SPC, SPC/E (simple point charge/extended), TIP4P, and Errington/ Panagiotopoulos (EP) force fields or than any other polarizable force field previously tested. However, the representation of the liquid water structure at ambient conditions is less satisfactory for the SPC-pol force fields. In contrast, the TIP4P-pol force fields produce much better low-temperature liquid structures and, in particular, a density maximum close to T ) 277 K, but their performance for the vapor-liquid equilibria in the near-critical region is less satisfactory. Finally, it is important to note that the SPC-pol-1 force field yields an average molecular dipole moment of 2.5 D for the liquid phase at ambient conditions that is substantially smaller than the value of 2.7 D obtained for its minimum-energy hexamer cluster.

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Free energy perturbation study of metal ion-catalyzed proton transfer in water

Cited by 21 publications

References 1 publication

Energetics of activation of GTP hydrolysis on the ribosome

Energetics of activation of GTP hydrolysis on the ribosome

Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase

Development of Polarizable Water Force Fields for Phase Equilibrium Calculations

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