Applicability of the MARTINI coarse-grained force field for simulations of protein oligomers in crystallization solution

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Abstract

The molecular dynamics of two types of lysozyme octamers was simulated under crystallization conditions in the MARTINI coarse-grained force field. Comparative analysis of the obtained results with the simulation data for the same octamers modelled in the all-atom field Amber99sb-ildn showed that octamer “A” demonstrates greater stability compared to octamer “B” in both force fields. Thus, the results of molecular dynamics simulations of octamers using both force fields are consistent. Despite several differences in the behavior of the protein in different fields, they do not affect the validity of the data obtained using MARTINI. This confirms the applicability of the MARTINI force field for studying crystallization solutions of proteins.

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About the authors

Y. V. Kordonskaya

National Research Centre "Kurchatov Institute"

Author for correspondence.
Email: yukord@mail.ru
Russian Federation, 123182 Moscow

V. I. Timofeev

National Research Centre "Kurchatov Institute"; Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics of NRC “Kurchatov Institute”

Email: yukord@mail.ru
Russian Federation, 123182 Moscow; Moscow

M. A. Marchenkova

National Research Centre "Kurchatov Institute"; Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics of NRC “Kurchatov Institute”

Email: yukord@mail.ru
Russian Federation, 123182 Moscow; Moscow

Y. V. Pisarevsky

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics of NRC “Kurchatov Institute”

Email: yukord@mail.ru
Russian Federation, Moscow

Y. A. Dyakova

National Research Centre "Kurchatov Institute"

Email: yukord@mail.ru
Russian Federation, 123182 Moscow

M. V. Kovalchuk

National Research Centre "Kurchatov Institute"; Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics of NRC “Kurchatov Institute”

Email: yukord@mail.ru
Russian Federation, 123182 Moscow; Moscow

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Supplementary files

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2. Fig. 1. The correspondence of the atomistic and coarse-grained (in the MARTINI field) structure of the amino acid residues of arginine (a) and tryptophan (b). For clarity, the hydrogen atoms are hidden. Translucent spheres show the particles in MARTINI: BB (Backbone) belong to the main chain of the protein, and SC (Side Chain) – to the side.

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3. Fig. 2. The structure of octamers A (left) and B (right) at the beginning (top) and at the end (bottom) of modeling in full-atomic (Amber99sb-ildn) and coarse-grained (MARTINI) force fields. In Amber99sb-ildn, one sphere corresponds to one atom, in MARTINI – to a group of atoms. One molecule contains 1022 atoms in Amber99sb-ildnand 304 grains in MARTINI. The pairwise RMSD between the initial and final structure are shown below. It is clearly shown that in both fields, octamer B decays, while octamer A remains more stable.

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4. Fig. 3. Stability of octamers A and B in crystallization solution during molecular dynamics modeled in different force fields: the ”full-atomic" Amber99sb-ildnfield (left) and the coarse-grained MARTINI field (right). Stability was assessed using the characteristics of RMSF (a, b), RMSD (c, d) and Rg (e, e). In all graphs (a–e), octamer A is more stable than octamer B, which indicates the consistency of the simulation results in the Amber99sb-ildn and MARTINI force fields.

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