Solvent Entropy Contributions to Catalytic Activity in Designed and Optimized Kemp Eliminases.

We analyze the role of solvation for enzymatic catalysis in two distinct, artificially designed Kemp Eliminases, KE07 and KE70, and mutated variants that were optimized by laboratory directed evolution. Using a spatially resolved analysis of hydration patterns, intermolecular vibrations, and local solvent entropies, we identify distinct classes of hydration water and follow their changes upon substrate binding and transition state formation for the designed KE07 and KE70 enzymes and their evolved variants. We observe that differences in hydration of the enzymatic systems are concentrated in the active site and undergo significant changes during substrate recruitment. For KE07, directed evolution reduces variations in the hydration of the polar catalytic center upon substrate binding, preserving strong protein-water interactions, while the evolved enzyme variant of KE70 features a more hydrophobic reaction center for which the expulsion of low-entropy water molecules upon substrate binding is substantially enhanced. While our analysis indicates a system-dependent role of solvation for the substrate binding process, we identify more subtle changes in solvation for the transition state formation, which are less affected by directed evolution.

[1]  Christopher B. Stanley,et al.  Description of Hydration Water in Protein (Green Fluorescent Protein) Solution. , 2017, Journal of the American Chemical Society.

[2]  S. Corezzi,et al.  Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water. , 2016, Soft matter.

[3]  E. Williams,et al.  Role of water in stabilizing ferricyanide trianion and ion-induced effects to the hydrogen-bonding water network at long distance. , 2015, Journal of the American Chemical Society.

[4]  B. Halle,et al.  Protein hydration dynamics in aqueous solution. , 1996, Faraday discussions.

[5]  Eric A. Althoff,et al.  Kemp elimination catalysts by computational enzyme design , 2008, Nature.

[6]  Pengyu Y. Ren,et al.  Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. , 2011, Journal of chemical theory and computation.

[7]  Franci Merzel,et al.  Is the first hydration shell of lysozyme of higher density than bulk water? , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[8]  E. Duboué-Dijon,et al.  Characterization of the Local Structure in Liquid Water by Various Order Parameters , 2015, The journal of physical chemistry. B.

[9]  Yousung Jung,et al.  On the absolute thermodynamics of water from computer simulations: a comparison of first-principles molecular dynamics, reactive and empirical force fields. , 2012, The Journal of chemical physics.

[10]  A. Warshel,et al.  Electrostatic basis for enzyme catalysis. , 2006, Chemical reviews.

[11]  Arieh Warshel,et al.  Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis. , 2011, Biochemistry.

[12]  Teresa Head-Gordon,et al.  The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70. , 2016, Physical chemistry chemical physics : PCCP.

[13]  W. Thiel,et al.  Distinct Protein Hydration Water Species Defined by Spatially Resolved Spectra of Intermolecular Vibrations , 2017, The journal of physical chemistry. B.

[14]  Diwakar Shukla,et al.  OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. , 2013, Journal of chemical theory and computation.

[15]  Hans Frauenfelder,et al.  Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions , 2004 .

[16]  Martin Gruebele,et al.  An extended dynamical hydration shell around proteins , 2007, Proceedings of the National Academy of Sciences.

[17]  Samir Kumar Pal,et al.  Biological water at the protein surface: Dynamical solvation probed directly with femtosecond resolution , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Pengyu Y. Ren,et al.  Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation , 2003 .

[19]  W. Goddard,et al.  Two-phase thermodynamic model for efficient and accurate absolute entropy of water from molecular dynamics simulations. , 2010, The journal of physical chemistry. B.

[20]  H. Frauenfelder,et al.  Protein folding is slaved to solvent motions , 2006, Proceedings of the National Academy of Sciences.

[21]  Greg L. Hura,et al.  Hydration dynamics near a model protein surface. , 2004, Biophysical journal.

[22]  K. E. Starling,et al.  Thermodynamic Properties of a Rigid‐Sphere Fluid , 1970 .

[23]  A. Sokolov,et al.  Dynamics in protein powders on the nanosecond-picosecond time scale are dominated by localized motions. , 2013, The journal of physical chemistry. B.

[24]  Teresa Head-Gordon,et al.  The Importance of the Scaffold for de Novo Enzymes: A Case Study with Kemp Eliminase. , 2017, Journal of the American Chemical Society.

[25]  Andrea J. Snyder,et al.  Mechanism of Chorismate Mutase: Contribution of Conformational Restriction to Catalysis in the Claisen Rearrangement , 1999 .

[26]  Margaret E. Johnson,et al.  Hydration water dynamics near biological interfaces. , 2009, The journal of physical chemistry. B.

[27]  A. Wand,et al.  Site-Resolved Measurement of Water-Protein Interactions by Solution NMR , 2010, Nature Structural &Molecular Biology.

[28]  William A. Goddard,et al.  The two-phase model for calculating thermodynamic properties of liquids from molecular dynamics: Validation for the phase diagram of Lennard-Jones fluids , 2003 .

[29]  Arieh Warshel,et al.  Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase , 2010, Proceedings of the National Academy of Sciences.

[30]  David Baker,et al.  Evaluation and ranking of enzyme designs , 2010, Protein science : a publication of the Protein Society.

[31]  Mikhail Dzugutov,et al.  A universal scaling law for atomic diffusion in condensed matter , 1996, Nature.