Exploring the challenges of computational enzyme design by
rebuilding the active site of a dehalogenase

J 2019

Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase

JINDAL, Garima, Kateřina SLÁNSKÁ, Veselin KOLEV, Jiří DAMBORSKÝ, Zbyněk PROKOP et. al.

Basic information

Original name

Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase

Authors

JINDAL, Garima (356 India), Kateřina SLÁNSKÁ (203 Czech Republic, belonging to the institution), Veselin KOLEV (840 United States of America), Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution), Zbyněk PROKOP (203 Czech Republic, belonging to the institution) and Arieh WARSHEL (840 United States of America)

Edition

Proceedings of the National Academy of Sciences of the United States of America, WASHINGTON, NATL ACAD SCIENCES, 2019, 0027-8424

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 9.412

RIV identification code

RIV/00216224:14310/19:00108175

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1073/pnas.1804979115

UT WoS

000455086900011

Keywords in English

enzyme design; EVB; transient kinetics; dehalogenase; nucleophilic substitution

Abstract

V originále

Rational enzyme design presents a major challenge that has not been overcome by computational approaches. One of the key challenges is the difficulty in assessing the magnitude of the maximum possible catalytic activity. In an attempt to overcome this challenge, we introduce a strategy that takes an active enzyme (assuming that its activity is close to the maximum possible activity), design mutations that reduce the catalytic activity, and then try to restore that catalysis by mutating other residues. Here we take as a test case the enzyme haloalkane dehalogenase (DhlA), with a 1,2-dichloroethane substrate. We start by demonstrating our ability to reproduce the results of single mutations. Next, we design mutations that reduce the enzyme activity and finally design double mutations that are aimed at restoring the activity. Using the computational predictions as a guide, we conduct an experimental study that confirms our prediction in one case and leads to inconclusive results in another case with 1,2-dichloroethane as substrate. Interestingly, one of our predicted double mutants catalyzes dehalogenation of 1,2-dibromoethane more efficiently than the wild-type enzyme.

Links

GA16-07965S, research and development project

Name: Řízená evoluce dynamických elementů v enzymech s využitím mikrofluidních čipů

Investor: Czech Science Foundation

LM2015047, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

LM2015051, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX RI)

Investor: Ministry of Education, Youth and Sports of the CR

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

LO1214, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

JINDAL, Garima, Kateřina SLÁNSKÁ, Veselin KOLEV, Jiří DAMBORSKÝ, Zbyněk PROKOP and Arieh WARSHEL. Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase. Proceedings of the National Academy of Sciences of the United States of America. WASHINGTON: NATL ACAD SCIENCES, 2019, vol. 116, No 2, p. 389-394. ISSN 0027-8424. Available from: https://dx.doi.org/10.1073/pnas.1804979115.

@article{1632620,
   author = {Jindal, Garima and Slánská, Kateřina and Kolev, Veselin and Damborský, Jiří and Prokop, Zbyněk and Warshel, Arieh},
   article_location = {WASHINGTON},
   article_number = {2},
   doi = {http://dx.doi.org/10.1073/pnas.1804979115},
   keywords = {enzyme design; EVB; transient kinetics; dehalogenase; nucleophilic substitution},
   language = {eng},
   issn = {0027-8424},
   journal = {Proceedings of the National Academy of Sciences of the United States of America},
   title = {Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase},
   url = {http://dx.doi.org/10.1073/pnas.1804979115},
   volume = {116},
   year = {2019}
}

TY  - JOUR
ID  - 1632620
AU  - Jindal, Garima - Slánská, Kateřina - Kolev, Veselin - Damborský, Jiří - Prokop, Zbyněk - Warshel, Arieh
PY  - 2019
TI  - Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase
JF  - Proceedings of the National Academy of Sciences of the United States of America
VL  - 116
IS  - 2
SP  - 389-394
EP  - 389-394
PB  - NATL ACAD SCIENCES
SN  - 00278424
KW  - enzyme design
KW  - EVB
KW  - transient kinetics
KW  - dehalogenase
KW  - nucleophilic substitution
UR  - http://dx.doi.org/10.1073/pnas.1804979115
L2  - http://dx.doi.org/10.1073/pnas.1804979115
N2  - Rational enzyme design presents a major challenge that has not been overcome by computational approaches. One of the key challenges is the difficulty in assessing the magnitude of the maximum possible catalytic activity. In an attempt to overcome this challenge, we introduce a strategy that takes an active enzyme (assuming that its activity is close to the maximum possible activity), design mutations that reduce the catalytic activity, and then try to restore that catalysis by mutating other residues. Here we take as a test case the enzyme haloalkane dehalogenase (DhlA), with a 1,2-dichloroethane substrate. We start by demonstrating our ability to reproduce the results of single mutations. Next, we design mutations that reduce the enzyme activity and finally design double mutations that are aimed at restoring the activity. Using the computational predictions as a guide, we conduct an experimental study that confirms our prediction in one case and leads to inconclusive results in another case with 1,2-dichloroethane as substrate. Interestingly, one of our predicted double mutants catalyzes dehalogenation of 1,2-dibromoethane more efficiently than the wild-type enzyme.
ER  -

JINDAL, Garima, Kateřina SLÁNSKÁ, Veselin KOLEV, Jiří DAMBORSKÝ, Zbyněk PROKOP and Arieh WARSHEL. Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase. \textit{Proceedings of the National Academy of Sciences of the United States of America}. WASHINGTON: NATL ACAD SCIENCES, 2019, vol.~116, No~2, p.~389-394. ISSN~0027-8424. Available from: https://dx.doi.org/10.1073/pnas.1804979115.

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