Free energy calculations on the stability of the 14-3-3 zeta
protein

J 2018

Free energy calculations on the stability of the 14-3-3 zeta protein

JANDOVA, Z., Zuzana TROŠANOVÁ, Veronika WEISOVÁ, C. OOSTENBRINK, Jozef HRITZ et. al.

Basic information

Original name

Free energy calculations on the stability of the 14-3-3 zeta protein

Authors

JANDOVA, Z. (203 Czech Republic), Zuzana TROŠANOVÁ (703 Slovakia, belonging to the institution), Veronika WEISOVÁ (703 Slovakia, belonging to the institution), C. OOSTENBRINK (40 Austria) and Jozef HRITZ (703 Slovakia, guarantor, belonging to the institution)

Edition

Biochimica et Biophysica Acta - Proteins and Proteomics, Amsterdam, The Netherlands, Elsevier, 2018, 1570-9639

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.540

RIV identification code

RIV/00216224:14740/18:00100854

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1016/j.bbapap.2017.11.012

UT WoS

000425201900005

Keywords in English

14-3-3 protein; Protein stability; Molecular dynamics simulation; Differential scanning calorimetry; Free energy calculation; Thermodynamic integration

Abstract

V originále

Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3 zeta was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naive expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.

Links

GF15-34684L, research and development project

Name: Efektivní výpočty volných energií a konfiguračního vzorkování protein-‐proteinových interakcí

Investor: Czech Science Foundation, Partner Agency (Austria)

LM2015043, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

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

Citovat

JANDOVA, Z., Zuzana TROŠANOVÁ, Veronika WEISOVÁ, C. OOSTENBRINK and Jozef HRITZ. Free energy calculations on the stability of the 14-3-3 zeta protein. Biochimica et Biophysica Acta - Proteins and Proteomics. Amsterdam, The Netherlands: Elsevier, 2018, vol. 1866, No 3, p. 442-450. ISSN 1570-9639. Available from: https://dx.doi.org/10.1016/j.bbapap.2017.11.012.

@article{1410442,
   author = {Jandova, Z. and Trošanová, Zuzana and Weisová, Veronika and Oostenbrink, C. and Hritz, Jozef},
   article_location = {Amsterdam, The Netherlands},
   article_number = {3},
   doi = {http://dx.doi.org/10.1016/j.bbapap.2017.11.012},
   keywords = {14-3-3 protein; Protein stability; Molecular dynamics simulation; Differential scanning calorimetry; Free energy calculation; Thermodynamic integration},
   language = {eng},
   issn = {1570-9639},
   journal = {Biochimica et Biophysica Acta - Proteins and Proteomics},
   title = {Free energy calculations on the stability of the 14-3-3 zeta protein},
   url = {https://www.sciencedirect.com/science/article/pii/S1570963917302807?via%3Dihub},
   volume = {1866},
   year = {2018}
}

TY  - JOUR
ID  - 1410442
AU  - Jandova, Z. - Trošanová, Zuzana - Weisová, Veronika - Oostenbrink, C. - Hritz, Jozef
PY  - 2018
TI  - Free energy calculations on the stability of the 14-3-3 zeta protein
JF  - Biochimica et Biophysica Acta - Proteins and Proteomics
VL  - 1866
IS  - 3
SP  - 442-450
EP  - 442-450
PB  - Elsevier
SN  - 15709639
KW  - 14-3-3 protein
KW  - Protein stability
KW  - Molecular dynamics simulation
KW  - Differential scanning calorimetry
KW  - Free energy calculation
KW  - Thermodynamic integration
UR  - https://www.sciencedirect.com/science/article/pii/S1570963917302807?via%3Dihub
L2  - https://www.sciencedirect.com/science/article/pii/S1570963917302807?via%3Dihub
N2  - Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3 zeta was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naive expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.
ER  -

JANDOVA, Z., Zuzana TROŠANOVÁ, Veronika WEISOVÁ, C. OOSTENBRINK and Jozef HRITZ. Free energy calculations on the stability of the 14-3-3 zeta protein. \textit{Biochimica et Biophysica Acta - Proteins and Proteomics}. Amsterdam, The Netherlands: Elsevier, 2018, vol.~1866, No~3, p.~442-450. ISSN~1570-9639. Available from: https://dx.doi.org/10.1016/j.bbapap.2017.11.012.

Detailed Information on Publication Record