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Lysozyme dimerization: brownian dynamics simulation

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Abstract

The lysozyme dimerization reaction has been studied within the framework of encounter-complex (EC) formation theory using the MacroDox software package. Two types of energetically favorite ECs were determined. In the first of them, active-center amino acids of lysozyme take part in the complex formation or the second molecule blocks accessibility to active center sterically. Epitope amino-acid residues are involved in the complex of type II. The existence of both types of complexes does not contradict experimental data. Dimer-formation rate constants for different kinds of EC were calculated. Increasing the pH from 2.0 to 10.0 decreases the total positive lysozyme charge and eliminates the unfavorable repulsive electrostatic interaction. The rate constant of EC formation is inversely proportional to the protein total charge. The association rate constant was also enhanced by an increase of ionic strength that screened repulsive electrostatic interaction between positively charged proteins.

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Acknowledgements

The author is very grateful to Dr. S. Northrup for providing her with the MacroDox package programs and Dr. I. Nesmelova (Minnesota University) for critical reading of this manuscript. This work was supported by the Russian Foundation for Basic Research grant 03-04-96276p2003tatarstan and NIOKR AN RT grant 03.3-10.227.

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  1. Kazan Institute of Biochemistry and Biophysics RAS, 420111, Kazan, P.O. Box 30, Russia

    Elena Ermakova

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  1. Elena Ermakova
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Correspondence to Elena Ermakova.

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Ermakova, E. Lysozyme dimerization: brownian dynamics simulation. J Mol Model 12, 34–41 (2005). https://doi.org/10.1007/s00894-005-0001-2

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  • DOI: https://doi.org/10.1007/s00894-005-0001-2

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