Home / Publications / Identification of the precursor cluster in thermolysin crystallization solution by molecular dynamics methods

Identification of the precursor cluster in thermolysin crystallization solution by molecular dynamics methods

Yuliya Vladimirovna Kordonskaya 1, 2
Yuliya Vladimirovna Kordonskaya
, 
Vladimir Igorevich Timofeev 2
Vladimir Igorevich Timofeev
, 
Yulia Alekseevna Dyakova 1
Yulia Alekseevna Dyakova
, 
Margarita Aleksandrovna Marchenkova 2
Margarita Aleksandrovna Marchenkova
, 
Yury Vladimirovich Pisarevsky 2
Yury Vladimirovich Pisarevsky
, 
Svetlana Yu Silvestrova 3
Svetlana Yu Silvestrova
, 
Mikhail Valentinovich Kovalchuk 1, 2
Mikhail Valentinovich Kovalchuk
1 National Research Centre 'Kurchatov Institute', Moscow, Russian Federation
2 A.V. Shubnikov Institute of Crystallography, FSRC ‘Crystallography and Photonics', Russian Academy of Sciences, Moscow, Russian Federaion
3 A.S. Loginov Moscow Clinical Scientific Center, Moscow, Russian Federation
10.1016/j.mencom.2023.02.024
Published 2023-02-13
Communication , Volume 33, Issue 2, 225-227
6
Share
Cite this
GOST
 | 
Cite this
GOST Copy
Kordonskaya Y. V. et al. Identification of the precursor cluster in thermolysin crystallization solution by molecular dynamics methods // Mendeleev Communications. 2023. Vol. 33. No. 2. pp. 225-227.
GOST all authors (up to 50) Copy
Kordonskaya Y. V., Timofeev V. I., Dyakova Y. A., Marchenkova M. A., Pisarevsky Y. V., Silvestrova S. Yu., Kovalchuk M. V. Identification of the precursor cluster in thermolysin crystallization solution by molecular dynamics methods // Mendeleev Communications. 2023. Vol. 33. No. 2. pp. 225-227.
RIS
 | 
Cite this
RIS Copy
TY - JOUR
DO - 10.1016/j.mencom.2023.02.024
UR - https://mendcomm.colab.ws/publications/10.1016/j.mencom.2023.02.024
TI - Identification of the precursor cluster in thermolysin crystallization solution by molecular dynamics methods
T2 - Mendeleev Communications
AU - Kordonskaya, Yuliya Vladimirovna
AU - Timofeev, Vladimir Igorevich
AU - Dyakova, Yulia Alekseevna
AU - Marchenkova, Margarita Aleksandrovna
AU - Pisarevsky, Yury Vladimirovich
AU - Silvestrova, Svetlana Yu
AU - Kovalchuk, Mikhail Valentinovich
PY - 2023
DA - 2023/02/13
PB - Mendeleev Communications
SP - 225-227
IS - 2
VL - 33
ER -
BibTex
 | 
Cite this
BibTex (up to 50 authors) Copy
@article{2023_Kordonskaya,
author = {Yuliya Vladimirovna Kordonskaya and Vladimir Igorevich Timofeev and Yulia Alekseevna Dyakova and Margarita Aleksandrovna Marchenkova and Yury Vladimirovich Pisarevsky and Svetlana Yu Silvestrova and Mikhail Valentinovich Kovalchuk},
title = {Identification of the precursor cluster in thermolysin crystallization solution by molecular dynamics methods},
journal = {Mendeleev Communications},
year = {2023},
volume = {33},
publisher = {Mendeleev Communications},
month = {Feb},
url = {https://mendcomm.colab.ws/publications/10.1016/j.mencom.2023.02.024},
number = {2},
pages = {225--227},
doi = {10.1016/j.mencom.2023.02.024}
}
MLA
Cite this
MLA Copy
Kordonskaya, Yuliya Vladimirovna, et al. “Identification of the precursor cluster in thermolysin crystallization solution by molecular dynamics methods.” Mendeleev Communications, vol. 33, no. 2, Feb. 2023, pp. 225-227. https://mendcomm.colab.ws/publications/10.1016/j.mencom.2023.02.024.

Keywords

crystallization solution.
molecular dynamics
molecular modeling
precursor cluster
protein crystallization
thermolysin crystal

Abstract

An analysis of the crystal structure of thermolysin revealed four possible precursor clusters (hexamers) of its crystal. Using the method of molecular dynamics and plots of root mean square fluctuation, root mean square deviation and radius of gyration, the most stable hexamer, which is a precursor cluster,was determined. The importance of the established structure of the thermolysin precursor cluster for determining the mechanism of crystal formation is shown.

References

.
GROMACS: Fast, flexible, and free
Van Der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., Berendsen H.J.
Journal of Computational Chemistry, 2005
.
Improved side-chain torsion potentials for the Amber ff99SB protein force field
Lindorff-Larsen K., Piana S., Palmo K., Maragakis P., Klepeis J.L., Dror R.O., Shaw D.E.
Proteins: Structure, Function and Genetics, 2010
.
ACPYPE - AnteChamber PYthon Parser interfacE
Sousa da Silva A.W., Vranken W.F.
BMC Research Notes, 2012
.
Molecular dynamics with coupling to an external bath
Berendsen H.J., Postma J.P., van Gunsteren W.F., DiNola A., Haak J.R.
Journal of Chemical Physics, 1984
.
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
Dolinsky T.J., Nielsen J.E., McCammon J.A., Baker N.A.
Nucleic Acids Research, 2004
.
A Leap-frog Algorithm for Stochastic Dynamics
Van Gunsteren W.F., Berendsen H.J.
Molecular Simulation, 1988
.
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
Horn H.W., Swope W.C., Pitera J.W., Madura J.D., Dick T.J., Hura G.L., Head-Gordon T.
Journal of Chemical Physics, 2004
.
Investigation of the Initial Crystallization Stage in Lysozyme Solutions by Small-Angle X-ray Scattering
Kovalchuk M.V., Blagov A.E., Dyakova Y.A., Gruzinov A.Y., Marchenkova M.A., Peters G.S., Pisarevsky Y.V., Timofeev V.I., Volkov V.V.
Crystal Growth and Design, 2016
.
Pre-crystallization phase formation of thermolysin hexamers in solution close to crystallization conditions
Kovalchuk M.V., Boikova A.S., Dyakova Y.A., Ilina K.B., Konarev P.V., Kryukova A.E., Marchenkova M.A., Pisarevsky Y.V., Timofeev V.I.
Journal of Biomolecular Structure and Dynamics, 2018
.
Dodecamers derived from the crystal structure were found in the pre-crystallization solution of the transaminase from the thermophilic bacterium Thermobaculum terrenum by small-angle X-ray scattering
Marchenkova M.A., Konarev P.V., Rakitina T.V., Timofeev V.I., Boikova A.S., Dyakova Y.A., Ilina K.B., Korzhenevskiy D.A., Yu Nikolaeva A., Pisarevsky Y.V., Kovalchuk M.V.
Journal of Biomolecular Structure and Dynamics, 2019
.
Investigation of the Pre-crystallization Stage of Proteinase K in Solution (Influence of Temperature and Precipitant Type) by Small-Angle X-Ray Scattering
Boikova A.S., D’yakova Y.A., Il’ina K.B., Konarev P.V., Kryukova A.E., Marchenkova M.A., Pisarevskii Y.V., Koval’chuk M.V.
Crystallography Reports, 2018
.
Study of the Behavior of Lysozyme Oligomers in Solutions by the Molecular Dynamics Method
Kordonskaya Y.V., Timofeev V.I., Dyakova Y.A., Marchenkova M.A., Pisarevsky Y.V., Podshivalov D.D., Kovalchuk M.V.
Crystallography Reports, 2018
.
Strain fluctuations and elastic constants
Parrinello M., Rahman A.
Journal of Chemical Physics, 1982