| MARKOVÁ, Klára, Antonín KUNKA, Klaudia CHMELOVÁ, Martin HAVLÁSEK, Petra BABKOVÁ, Sérgio Manuel MARQUES, Michal VAŠINA, Joan PLANAS IGLESIAS, Radka CHALOUPKOVÁ, David BEDNÁŘ, Zbyněk PROKOP, Jiří DAMBORSKÝ and Martin MAREK. Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2021, vol. 11, No 21, p. 12864-12885. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.1c03343. |
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@article{1831417,
author = {Marková, Klára and Kunka, Antonín and Chmelová, Klaudia and Havlásek, Martin and Babková, Petra and Marques, Sérgio Manuel and Vašina, Michal and Planas Iglesias, Joan and Chaloupková, Radka and Bednář, David and Prokop, Zbyněk and Damborský, Jiří and Marek, Martin},
article_location = {WASHINGTON},
article_number = {21},
doi = {http://dx.doi.org/10.1021/acscatal.1c03343},
keywords = {protein folding; protein design; alpha/beta-hydrolase; haloalkane dehalogenase; domain swapping; energy landscape; oligonicrization; catalytic efficiency; substrate inhibition},
language = {eng},
issn = {2155-5435},
journal = {ACS Catalysis},
title = {Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers},
url = {https://pubs.acs.org/doi/10.1021/acscatal.1c03343},
volume = {11},
year = {2021}
}
TY - JOUR
ID - 1831417
AU - Marková, Klára - Kunka, Antonín - Chmelová, Klaudia - Havlásek, Martin - Babková, Petra - Marques, Sérgio Manuel - Vašina, Michal - Planas Iglesias, Joan - Chaloupková, Radka - Bednář, David - Prokop, Zbyněk - Damborský, Jiří - Marek, Martin
PY - 2021
TI - Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers
JF - ACS Catalysis
VL - 11
IS - 21
SP - 12864-12885
EP - 12864-12885
PB - AMER CHEMICAL SOC
SN - 21555435
KW - protein folding
KW - protein design
KW - alpha/beta-hydrolase
KW - haloalkane dehalogenase
KW - domain swapping
KW - energy landscape
KW - oligonicrization
KW - catalytic efficiency
KW - substrate inhibition
UR - https://pubs.acs.org/doi/10.1021/acscatal.1c03343
N2 - The functionality of an enzyme depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encoded algorithms are increasingly employed to stabilize native proteins for use in research and biotechnology applications. Here, we reveal a unique example where the computational stabilization of a monomeric alpha/beta-hydrolase enzyme (T-m = 73.5 degrees C; Delta T-m > 23 degrees C) affected the protein folding energy landscape. The introduction of eleven single-point stabilizing mutations based on force field calculations and evolutionary analysis yielded soluble domain-swapped intermediates trapped in local energy minima. Crystallographic structures revealed that these stabilizing mutations might (i) activate cryptic hinge-loop regions and (ii) establish secondary interfaces, where they make extensive noncovalent interactions between the intertwined protomers. The existence of domain-swapped dimers in a solution is further confirmed experimentally by data obtained from small-angle X-ray scattering (SAXS) and cross-linking mass spectrometry. Unfolding experiments showed that the domain-swapped dimers can be irreversibly converted into native-like monomers, suggesting that the domain swapping occurs exclusively in vivo. Crucially, the swapped-dimers exhibited advantageous catalytic properties such as an increased catalytic rate and elimination of substrate inhibition. These findings provide additional enzyme engineering avenues for next-generation biocatalysts.
ER -
MARKOVÁ, Klára, Antonín KUNKA, Klaudia CHMELOVÁ, Martin HAVLÁSEK, Petra BABKOVÁ, Sérgio Manuel MARQUES, Michal VAŠINA, Joan PLANAS IGLESIAS, Radka CHALOUPKOVÁ, David BEDNÁŘ, Zbyněk PROKOP, Jiří DAMBORSKÝ and Martin MAREK. Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. \textit{ACS Catalysis}. WASHINGTON: AMER CHEMICAL SOC, 2021, vol.~11, No~21, p.~12864-12885. ISSN~2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.1c03343.
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