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Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations.

ABSTRACT: The measurement of reaction rate as a function of pH provides essential information about mechanism. These rates are sensitive to the pK(a) values of amino acids directly involved in catalysis that are often shifted by the enzyme active site environment. Experimentally observed pH-rate profiles are usually interpreted using simple kinetic models that allow estimation of "apparent pK(a)" values of presumed general acid and base catalysts. One of the underlying assumptions in these models is that the protonation states are uncorrelated. In this work, we introduce the use of constant pH molecular dynamics simulations in explicit solvent (CpHMD) with replica exchange in the pH-dimension (pH-REMD) as a tool to aid in the interpretation of pH-activity data of enzymes and to test the validity of different kinetic models. We apply the methods to RNase A, a prototype acid-base catalyst, to predict the macroscopic and microscopic pK(a) values, as well as the shape of the pH-rate profile. Results for apo and cCMP-bound RNase A agree well with available experimental data and suggest that deprotonation of the general acid and protonation of the general base are not strongly coupled in transphosphorylation and hydrolysis steps. Stronger coupling, however, is predicted for the Lys41 and His119 protonation states in apo RNase A, leading to the requirement for a microscopic kinetic model. This type of analysis may be important for other catalytic systems where the active forms of the implicated general acid and base are oppositely charged and more highly correlated. These results suggest a new way for CpHMD/pH-REMD simulations to bridge the gap with experiments to provide a molecular-level interpretation of pH-activity data in studies of enzyme mechanisms.

SUBMITTER: Dissanayake T

PROVIDER: S-EPMC4441796 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

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Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations.

Dissanayake Thakshila T Swails Jason M JM Harris Michael E ME Roitberg Adrian E AE York Darrin M DM

Biochemistry 20150206 6

The measurement of reaction rate as a function of pH provides essential information about mechanism. These rates are sensitive to the pK(a) values of amino acids directly involved in catalysis that are often shifted by the enzyme active site environment. Experimentally observed pH-rate profiles are usually interpreted using simple kinetic models that allow estimation of "apparent pK(a)" values of presumed general acid and base catalysts. One of the underlying assumptions in these models is that ...[more]

PMID: 25615525

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Project description:Mercaptoundecanoic acid (MUA) functionalized gold nanoparticles (AuNP-MUA) were synthesized and demonstrated to possess pH-triggered aggregation and re-dispersion, as well as the capability of phase transfer between aqueous and organic phases in response to changes in pH. The pH of aggregation for AuNP-MUA is consistent with the pKa of MUA (pH ~4) in solution, while AuNP-MUA phase transition between aqueous and organic phases occurs at pH ~9. The ion pair formation between the amine group in octadecylamine (ODA), the carboxylate group in MUA, and the hydrophobic alkyl chain of ODA facilitates the phase transfer of AuNP-MUA into an organic medium. The AuNP-MUA were investigated as a reusable catalyst in the catalytic reduction of 4-nitrophenol by borohydride-a model reaction for AuNPs. It was determined that 100% MUA surface coverage completely inhibits the catalytic activity of AuNPs. Decreasing the surface coverage was shown to increase catalytic activity, but this decrease also leads to decreased colloidal stability, recoverability, and reusability in subsequent reactions. At 60% MUA surface coverage, colloidal stability and catalytic activity were achieved, but the surface coverage was insufficient to enable redispersion following pH-induced recovery. A balance between AuNP colloidal stability, recoverability, and catalytic activity with reusability was achieved at 90% MUA surface coverage. The AuNP-MUA catalyst can also be recovered at different pH ranges depending on the recovery method employed. At pH ~4, protonation of the MUA results in reduced surface charge and aggregation. At pH ~9, ODA will form an ion-pair with the MUA and induce phase transfer into an immiscible organic phase. Both the pH-triggered aggregation/re-dispersion and aqueous/organic phase transfer methods were employed for catalyst recovery and reuse in subsequent reactions. The ability to recover and reuse the AuNP-MUA catalyst by two different methods and different pH regimes is significant, based on the fact that nanoparticle-catalyzed reactions may occur under different pH conditions.

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Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations.

Publications

Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations.

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