Computer Simulation of Protein-Protein Association in Photosynthesis

I.B. Kovalenko; A.M. Abaturova; A.N. Diakonova; O.S. Knyazeva; D.M. Ustinin; S.S. Khruschev; G.Yu. Riznichenko; A.B. Rubin

Mathematical Modelling of Natural Phenomena (2011)

  • Volume: 6, Issue: 7, page 39-54
  • ISSN: 0973-5348

Abstract

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The paper is devoted to the method of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. Using this method we have studied kinetic characteristics of protein-protein complex formation for four pairs of proteins involved in photosynthesis at a variety of ionic strength values. Computer simulations describe non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Calculations confirm that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in “wrong” orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer.

How to cite

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Kovalenko, I.B., et al. "Computer Simulation of Protein-Protein Association in Photosynthesis." Mathematical Modelling of Natural Phenomena 6.7 (2011): 39-54. <http://eudml.org/doc/222344>.

@article{Kovalenko2011,
abstract = {The paper is devoted to the method of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. Using this method we have studied kinetic characteristics of protein-protein complex formation for four pairs of proteins involved in photosynthesis at a variety of ionic strength values. Computer simulations describe non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Calculations confirm that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in “wrong” orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer.},
author = {Kovalenko, I.B., Abaturova, A.M., Diakonova, A.N., Knyazeva, O.S., Ustinin, D.M., Khruschev, S.S., Riznichenko, G.Yu., Rubin, A.B.},
journal = {Mathematical Modelling of Natural Phenomena},
keywords = {Brownian dynamics; computer simulation; protein, photosynthesis; electrostatic interaction},
language = {eng},
month = {6},
number = {7},
pages = {39-54},
publisher = {EDP Sciences},
title = {Computer Simulation of Protein-Protein Association in Photosynthesis},
url = {http://eudml.org/doc/222344},
volume = {6},
year = {2011},
}

TY - JOUR
AU - Kovalenko, I.B.
AU - Abaturova, A.M.
AU - Diakonova, A.N.
AU - Knyazeva, O.S.
AU - Ustinin, D.M.
AU - Khruschev, S.S.
AU - Riznichenko, G.Yu.
AU - Rubin, A.B.
TI - Computer Simulation of Protein-Protein Association in Photosynthesis
JO - Mathematical Modelling of Natural Phenomena
DA - 2011/6//
PB - EDP Sciences
VL - 6
IS - 7
SP - 39
EP - 54
AB - The paper is devoted to the method of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. Using this method we have studied kinetic characteristics of protein-protein complex formation for four pairs of proteins involved in photosynthesis at a variety of ionic strength values. Computer simulations describe non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Calculations confirm that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in “wrong” orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer.
LA - eng
KW - Brownian dynamics; computer simulation; protein, photosynthesis; electrostatic interaction
UR - http://eudml.org/doc/222344
ER -

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