skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

This work reports on 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 suggests 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.

Authors:
 [1];  [2]; ORCiD logo [2]; ORCiD logo [3]
  1. Univ. of California, Berkeley, CA (United States)
  2. Max-Planck-Institut fur Kohlenforschung (Germany)
  3. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); German Research Foundation (DFG)
OSTI Identifier:
1532319
Grant/Contract Number:  
[AC02-05CH11231]
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
Additional Journal Information:
[ Journal Volume: 122; Journal Issue: 21]; Journal ID: ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Belsare, Saurabh, Pattni, Viren, Heyden, Matthias, and Head-Gordon, Teresa. Solvent Entropy Contributions to Catalytic Activity in Designed and Optimized Kemp Eliminases. United States: N. p., 2017. Web. doi:10.1021/acs.jpcb.7b07526.
Belsare, Saurabh, Pattni, Viren, Heyden, Matthias, & Head-Gordon, Teresa. Solvent Entropy Contributions to Catalytic Activity in Designed and Optimized Kemp Eliminases. United States. doi:10.1021/acs.jpcb.7b07526.
Belsare, Saurabh, Pattni, Viren, Heyden, Matthias, and Head-Gordon, Teresa. Tue . "Solvent Entropy Contributions to Catalytic Activity in Designed and Optimized Kemp Eliminases". United States. doi:10.1021/acs.jpcb.7b07526. https://www.osti.gov/servlets/purl/1532319.
@article{osti_1532319,
title = {Solvent Entropy Contributions to Catalytic Activity in Designed and Optimized Kemp Eliminases},
author = {Belsare, Saurabh and Pattni, Viren and Heyden, Matthias and Head-Gordon, Teresa},
abstractNote = {This work reports on 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 suggests 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.},
doi = {10.1021/acs.jpcb.7b07526},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = [21],
volume = [122],
place = {United States},
year = {2017},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

Figures / Tables:

Figure 1 Figure 1: (A) Kemp Eliminase KE07 enzyme and (B) the targeted catalytic reaction. The catalytic (red) and additional stabilizing residues (cyan) create the designed KE07 enzyme. The mutations introduced by laboratory directed evolution (orange) result in an improved variant R7.2 with an increased catalytic turnover rate. The substrate is shownmore » in dark blue.« less

Save / Share:
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.