COMPUTER MODEL OF BIOPOLYMER CRYSTAL GROWTH AND AGGREGATION BY ADDITION OF MACROMOLECULAR UNITS — A COMPARATIVE STUDY

J. Siódmiak () and A. Gadomski
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J. Siódmiak: Institute of Mathematics and Physics, University of Technology and Agriculture, 85-796 Bydgoszcz, Poland
A. Gadomski: Institute of Mathematics and Physics, University of Technology and Agriculture, 85-796 Bydgoszcz, Poland

International Journal of Modern Physics C (IJMPC), 2006, vol. 17, issue 07, 1037-1053

Abstract: We discuss the results of a computer simulation of the biopolymer crystal growth and aggregation based on the 2D lattice Monte Carlo technique and the HP approximation of the biopolymers. As a modeled molecule (growth unit) we comparatively consider the previously studied non-mutant lysozyme protein, Protein Data Bank (PDB) ID: 193L, which forms, under a certain set of thermodynamic-kinetic conditions, the tetragonal crystals, and an amyloidogenic variant of the lysozyme, PDB ID: 1LYY, which is known as fibril-yielding and prone-to-aggregation agent. In our model, the site-dependent attachment, detachment and migration processes are involved. The probability of growth unit motion, attachment and detachment to/from the crystal surface are assumed to be proportional to the orientational factor representing the anisotropy of the molecule. Working within a two-dimensional representation of the truly three-dimensional process, we also argue that the crystal grows in a spiral way, whereby one or more screw dislocations on the crystal surface give rise to a terrace. We interpret the obtained results in terms of known models of crystal growth and aggregation such as B-C-F (Burton-Cabrera-Frank) dislocation driven growth and M-S (Mullins-Sekerka) instability concept, with stochastic aspects supplementing the latter. We discuss the conditions under which crystalsvsnon-crystalline protein aggregates appear, and how the process depends upon difference in chemical structure of the protein molecule seen as the main building block of the elementary crystal cell.

Keywords: Protein; lysozyme; MC simulation; HP model; coarse-graining; non-Kossel crystal; spiral growth; 02.50.Ng; 68.35.Bs; 81.10.-h; 87.15.Kg; 87.15.Nn (search for similar items in EconPapers)
Date: 2006
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DOI: 10.1142/S0129183106009643

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