Detailed Information on Publication Record
2021
Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers
MARKOVÁ, Klára, Antonín KUNKA, Klaudia CHMELOVÁ, Martin HAVLÁSEK, Petra BABKOVÁ et. al.Basic information
Original name
Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers
Authors
MARKOVÁ, Klára (203 Czech Republic, belonging to the institution), Antonín KUNKA (203 Czech Republic, belonging to the institution), Klaudia CHMELOVÁ (703 Slovakia, belonging to the institution), Martin HAVLÁSEK (203 Czech Republic, belonging to the institution), Petra BABKOVÁ (203 Czech Republic, belonging to the institution), Sérgio Manuel MARQUES (620 Portugal, belonging to the institution), Michal VAŠINA (203 Czech Republic, belonging to the institution), Joan PLANAS IGLESIAS (724 Spain, belonging to the institution), Radka CHALOUPKOVÁ (203 Czech Republic, belonging to the institution), David BEDNÁŘ (203 Czech Republic, belonging to the institution), Zbyněk PROKOP (203 Czech Republic, belonging to the institution), Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution) and Martin MAREK (203 Czech Republic, belonging to the institution)
Edition
ACS Catalysis, WASHINGTON, AMER CHEMICAL SOC, 2021, 2155-5435
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10403 Physical chemistry
Country of publisher
United States of America
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
Impact factor
Impact factor: 13.700
RIV identification code
RIV/00216224:14310/21:00124052
Organization unit
Faculty of Science
UT WoS
000716773800006
Keywords in English
protein folding; protein design; alpha/beta-hydrolase; haloalkane dehalogenase; domain swapping; energy landscape; oligonicrization; catalytic efficiency; substrate inhibition
Tags
Tags
International impact, Reviewed
Změněno: 15/2/2023 23:13, Mgr. Michaela Hylsová, Ph.D.
Abstract
V originále
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.
Links
EF17_043/0009632, research and development project |
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LM2015047, research and development project |
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LM2018121, research and development project |
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LM2018127, research and development project |
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LM2018140, research and development project |
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MUNI/H/1561/2018, interní kód MU |
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792772, interní kód MU |
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814418, interní kód MU |
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857560, interní kód MU (CEP code: EF17_043/0009632) |
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