Protein-like copolymers: computer simulation

Alexei R. Khokhlov and Pavel G. Khalatur

Physica A: Statistical Mechanics and its Applications, 1998, vol. 249, issue 1, 253-261

Abstract: The notion of protein-like AB copolymers is introduced. Such copolymers can be generated with the help of the “instant image” of a dense homopolymer globule by assigning that the monomeric units closer to the globular surface are of A type, while the core is formed by the B type units. After that the primary structure of the chain is fixed, and one introduces different interaction potentials for A and B units. In doing so, we have in mind mainly aqueous systems and analogy with globular proteins, therefore A units are regarded as hydrophilic, and B units as hydrophobic. By means of Monte Carlo simulation using the bond fluctuation model we study the coil–globule transition for a protein-like copolymer upon the increase of attraction of hydrophobic B units, and compare the results with those for random AB copolymers. From the analysis of the primary structure of protein-like copolymers one can see that the “degree of blockiness” of the protein-like sequence is higher than for random copolymers, therefore the copolymers with the “random-block” primary structure are generated for comparison as well (the average length of A and B sequences being the same as for protein-like copolymers). It is shown that the coil–globule transition in protein-like copolymers occurs at higher temperatures, is more abrupt and has faster kinetics than for random copolymers with the same A/B composition and for random-block copolymers with the same A/B composition and “degree of blockiness”. The globules of protein-like copolymers exhibit a dense micelle-like core of hydrophobic B units stabilized by the long dangling loops of hydrophilic A units. Apparently, a protein-like copolymer “inherits” some of the properties of the “parent globule” which is reflected in the special long-range correlations in primary structure.

Date: 1998
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:249:y:1998:i:1:p:253-261

DOI: 10.1016/S0378-4371(97)00473-1

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