J 2018

Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization

BEERENS, Koen, Stanislav MAZURENKO, Antonín KUNKA, Sérgio Manuel MARQUES, N. HANSEN et. al.

Basic information

Original name

Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization

Authors

BEERENS, Koen (56 Belgium, belonging to the institution), Stanislav MAZURENKO (643 Russian Federation, belonging to the institution), Antonín KUNKA (203 Czech Republic, belonging to the institution), Sérgio Manuel MARQUES (620 Portugal, belonging to the institution), N. HANSEN (276 Germany), Miloš MUSIL (203 Czech Republic, belonging to the institution), Radka CHALOUPKOVÁ (203 Czech Republic, belonging to the institution), Jitka WATERMAN (203 Czech Republic), Jan BREZOVSKÝ (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) and Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution)

Edition

ACS Catalysis, WASHINGTON, AMER CHEMICAL SOC, 2018, 2155-5435

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:

Impact factor

Impact factor: 12.221

RIV identification code

RIV/00216224:14310/18:00101752

Organization unit

Faculty of Science

DOI

UT WoS

000447224100051

Keywords in English

protein stabilization; thermostability; evolutionary analysis; force-field calculations; computational tools; entropy; enthalpy; thermodynamic integration
Změněno: 23/4/2024 14:20, Mgr. Michal Petr

Abstract

V originále

Stability is one of the most important characteristics of proteins employed as biocatalysts, biotherapeutics, and biomaterials, and the role of computational approaches in modifying protein stability is rapidly expanding. We have recently identified stabilizing mutations in haloalkane dehalogenase DhaA using phylogenetic analysis but were not able to reproduce the effects of these mutations using force-field calculations. Here we tested four different hypotheses to explain the molecular basis of stabilization using structural, biochemical, biophysical, and computational analyses. We demonstrate that stabilization of DhaA by the mutations identified using the phylogenetic analysis is driven by both entropy and enthalpy contributions, in contrast to primarily enthalpy-driven stabilization by mutations designed by the force-field Comprehensive bioinformatics analysis revealed that more than half (53%) of 1 099 evolution-based stabilizing mutations would be evaluated as destabilizing by force-field calculations. Thermodynamic integration considers both folded and unfolded states and can describe the entropic component of stabilization, yet it is not suitable for predictive purposes due to its high computational demands. Altogether, our results strongly suggest that energetic calculations should be complemented by a phylogenetic analysis in protein-stabilization endeavors.

Links

EE2.3.30.0037, research and development project
Name: Zaměstnáním nejlepších mladých vědců k rozvoji mezinárodní spolupráce
GAP503/12/0572, research and development project
Name: Konstrukce syntetické metabolické dráhy pro degradaci důležitého environmentálního polutantu proteinovým a metabolickým inženýrstvím
Investor: Czech Science Foundation
GA17-24321S, research and development project
Name: Studium hydratace a flexibility enzymů pomocí pokročilých strukturních a biofyzikálních metod
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
4SGA8519, interní kód MU
Name: Rational design and engineering of enzyme gates (Acronym: BIOGATE)
Investor: South-Moravian Region, Incoming grants