Multi-particle Brownian Dynamics software ProKSim for protein-protein interactions modeling

“…We used BD calculations to obtain structures of Pc–cyt f encounter complexes with the threshold of electrostatic attractive energy values of 8.2 × 10 −21 kJ molecule ‐1 (2 kT ), 1.6 × 10 −20 kJ molecule ‐1 (4 kT ) and 3.3 × 10 −20 kJ molecule ‐1 (8 kT ). We used the ProKSim (Protein Kinetics Simulator) software (Kovalenko et al , Kovalenko et al , Khrushchev et al ) for BD simulations of the protein motion and the formation of energetically favorable orientations in the way it was described in our previous paper (Khruschev et al ).…”

Section: Methodsmentioning

confidence: 99%

Comparative analysis of plastocyanin–cytochrome f complex formation in higher plants, green algae and cyanobacteria

Fedorov

Kovalenko

Khruschev

et al. 2019

Physiologia Plantarum

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Mechanisms of the complex formation between plastocyanin and cytochrome f in higher plants (Spinacia oleracea and Brassica rapa), green microalgae Chlamydomonas reinhardtii and two species of cyanobacteria (Phormidium laminosum and Nostoc sp.) were investigated using combined Brownian and molecular dynamics simulations and hierarchical cluster analysis. In higher plants and green algae, electrostatic interactions force plastocyanin molecule close to the heme of cytochrome f. In the subsequent rotation of plastocyanin molecule around the point of electrostatic contact in the vicinity of cytochrome f, copper (Cu) atom approaches cytochrome heme forming a stable configuration where cytochrome f molecule behaves as a rather rigid body without conformational changes. In Nostoc plastocyanin molecule approaches cytochrome f in a different orientation (head‐on) where the stabilization of the plastocyanin–cytochrome f complex is accompanied by the conformational changes of the G188E189D190 loop that stabilizes the whole complex. In cyanobacterium P. laminosum, electrostatic preorientation of the approaching molecules was not detected, thus indicating that random motions rather than long‐range electrostatic interactions are responsible for the proper mutual orientation. We demonstrated that despite the structural similarity of the investigated electron transport proteins in different photosynthetic organisms, the complexity of molecular mechanisms of the complex formation increases in the following sequence: non‐heterocystous cyanobacteria – heterocystous cyanobacteria – green algae – flowering plants.

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“…To reveal in detail the mechanisms of encounter complex formation, the classical approach of Brownian dynamics was used, namely multiple computational experiments on the convergence of two molecules. The protein movement was simulated by the software ProKSim -Protein Kinetic Simulator [15]. The analysis of molecular trajectories in such experiments makes it possible to identify highly frequent types of their mutual arrangement that form most often during the approach of diffusive molecules to estimate the interaction energy between molecules and the rate constant of the protein association reaction.…”

Section: Productive and Non-productive Encounter Complexesmentioning

confidence: 99%

“…To determine the electrostatic potential grid around each molecule Poisson-Boltzmann calculations [13] were used as described in [14]. For simulation of multiparticle BD original software ProKSim [15,16] was used. The program is available by request.…”

Section: Introductionmentioning

confidence: 99%

Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling

et al. 2019

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The paper presents the review of works on modeling the interaction of photosynthetic proteins using the multiparticle Brownian dynamics method developed at the Department of Biophysics, Biological Faculty, Lomonosov Moscow State University. The method describes the displacement of individual macromolecules – mobile electron carriers, and their electrostatic interactions between each other and with pigment-protein complexes embedded in photosynthetic membrane. Three-dimensional models of the protein molecules were constructed on the basis of the data from the Protein Data Bank. We applied the Brownian methods coupled to molecular dynamic simulations to reveal the role of electrostatic interactions and conformational motions in the transfer of an electron from the cytochrome complex Cyt b6f) membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and to the molecule of the mobile carrier plastocyanin (Pc) in plants, green algae and cyanic bacteria. Taking into account the interior of photosynthetic membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and Cyt b6f, embedded in photosynthetic membrane, electron transfer and complex dissociation. Multiparticle Brownian simulation method can be used to consider the processes of protein interactions in subcellular systems in order to clarify the role of individual stages and the biophysical mechanisms of these processes.

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Multi-particle Brownian Dynamics software ProKSim for protein-protein interactions modeling

Cited by 15 publications

References 35 publications

Influence of sodium alginate on the formation of the structure of the products from chopped and minced meat

Influence of sodium alginate on the formation of the structure of the products from chopped and minced meat

Comparative analysis of plastocyanin–cytochrome f complex formation in higher plants, green algae and cyanobacteria

Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling

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