FireProt: Energy- and Evolution-Based Computational Design of
Thermostable Multiple-Point Mutants

J 2015

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants

BEDNÁŘ, David; Koen BEERENS; Eva ŠEBESTOVÁ; Jaroslav BENDL; S. KHARE et al.

Základní údaje

Originální název

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants

Autoři

BEDNÁŘ, David; Koen BEERENS; Eva ŠEBESTOVÁ; Jaroslav BENDL; S. KHARE; Radka CHALOUPKOVÁ; Zbyněk PROKOP; Jan BREZOVSKÝ; D. BAKER a Jiří DAMBORSKÝ

Vydání

PLOS COMPUTATIONAL BIOLOGY, 2015, 1553-734X

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.587

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/15:00081399

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

FireProt;haloalkane dehalogenase

Štítky

AKR, rivok

Změněno: 21. 3. 2017 07:46, prof. Mgr. Jiří Damborský, Dr.

Anotace

V originále

There is great interest in increasing proteins’ stability to enhance their utility as biocatalysts, therapeutics, diagnostics and nanomaterials. Directed evolution is a powerful, but experimentally strenuous approach. Computational methods offer attractive alternatives. However, due to the limited reliability of predictions and potentially antagonistic effects of substitutions, only single-point mutations are usually predicted in silico, experimentally verified and then recombined in multiple-point mutants. Thus, substantial screening is still required. Here we present FireProt, a robust computational strategy for predicting highly stable multiple-point mutants that combines energy- and evolution-based approaches with smart filtering to identify additive stabilizing mutations. FireProt’s reliability and applicability was demonstrated by validating its predictions against 656 mutations from the ProTherm database. We demonstrate that thermostability of the model enzymes haloalkane dehalogenase DhaA and gama-hexachlorocyclohexane dehydrochlorinase LinA can be substantially increased (Tm = 24°C and 21°C) by constructing and characterizing only a handful of multiple-point mutants. FireProt can be applied to any protein for which a tertiary structure and homologous sequences are available, and will facilitate the rapid development of robust proteins for biomedical and biotechnological applications.

Návaznosti

EE2.3.30.0037, projekt VaV

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GAP503/12/0572, projekt VaV

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Investor: Grantová agentura ČR, Konstrukce syntetické metabolické dráhy pro degradaci důležitého environmentlního polutantu proteinovým a metabolickým inženýrstvím

LH14027, projekt VaV

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Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Nové koncepty a nástroje pro racionální design enzymů

LM2010005, projekt VaV

Název: Velká infrastruktura CESNET (Akronym: VI CESNET)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Velká infrastruktura CESNET

LO1214, projekt VaV

Název: Centrum pro výzkum toxických látek v prostředí (Akronym: RECETOX)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Centrum pro výzkum toxických látek v prostředí

Citovat

BEDNÁŘ, David; Koen BEERENS; Eva ŠEBESTOVÁ; Jaroslav BENDL; S. KHARE; Radka CHALOUPKOVÁ; Zbyněk PROKOP; Jan BREZOVSKÝ; D. BAKER a Jiří DAMBORSKÝ. FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PLOS COMPUTATIONAL BIOLOGY. 2015, roč. 11, č. 11, s. "nestrankovano", 20 s. ISSN 1553-734X. Dostupné z: https://doi.org/10.1371/journal.pcbi.1004556.

@article{1322952,
   author = {Bednář, David and Beerens, Koen and Šebestová, Eva and Bendl, Jaroslav and Khare, S. and Chaloupková, Radka and Prokop, Zbyněk and Brezovský, Jan and Baker, D. and Damborský, Jiří},
   article_number = {11},
   doi = {https://doi.org/10.1371/journal.pcbi.1004556},
   keywords = {FireProt;haloalkane dehalogenase},
   language = {eng},
   issn = {1553-734X},
   journal = {PLOS COMPUTATIONAL BIOLOGY},
   title = {FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants},
   url = {http://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2015/11/Bednar_2015ploscb1.pdf},
   volume = {11},
   year = {2015}
}

TY  - JOUR
ID  - 1322952
AU  - Bednář, David - Beerens, Koen - Šebestová, Eva - Bendl, Jaroslav - Khare, S. - Chaloupková, Radka - Prokop, Zbyněk - Brezovský, Jan - Baker, D. - Damborský, Jiří
PY  - 2015
TI  - FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants
JF  - PLOS COMPUTATIONAL BIOLOGY
VL  - 11
IS  - 11
SP  - "nestrankovano"
EP  - "nestrankovano"
SN  - 1553734X
KW  - FireProt;haloalkane dehalogenase
UR  - http://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2015/11/Bednar_2015ploscb1.pdf
L2  - http://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2015/11/Bednar_2015ploscb1.pdf
N2  - There is great interest in increasing proteins’ stability to enhance their utility as biocatalysts, therapeutics, diagnostics and nanomaterials. Directed evolution is a powerful, but experimentally strenuous approach. Computational methods offer attractive alternatives. However, due to the limited reliability of predictions and potentially antagonistic effects of substitutions, only single-point mutations are usually predicted in silico, experimentally verified and then recombined in multiple-point mutants. Thus, substantial screening is still required. Here we present FireProt, a robust computational strategy for predicting highly stable multiple-point mutants that combines energy- and evolution-based approaches with smart filtering to identify additive stabilizing mutations. FireProt’s reliability and applicability was demonstrated by validating its predictions against 656 mutations from the ProTherm database. We demonstrate that thermostability of the model enzymes haloalkane dehalogenase DhaA and gama-hexachlorocyclohexane dehydrochlorinase LinA can be substantially increased (Tm = 24°C and 21°C) by constructing and characterizing only a handful of multiple-point mutants. FireProt can be applied to any protein for which a tertiary structure and homologous sequences are available, and will facilitate the rapid development of robust proteins for biomedical and biotechnological applications.
ER  -

BEDNÁŘ, David; Koen BEERENS; Eva ŠEBESTOVÁ; Jaroslav BENDL; S. KHARE; Radka CHALOUPKOVÁ; Zbyněk PROKOP; Jan BREZOVSKÝ; D. BAKER a Jiří DAMBORSKÝ. FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. \textit{PLOS COMPUTATIONAL BIOLOGY}. 2015, roč.~11, č.~11, s.~''nestrankovano'', 20 s. ISSN~1553-734X. Dostupné z: https://doi.org/10.1371/journal.pcbi.1004556.

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