Protein crystal’s shape and polymorphism prediction within the limits resulting from the exploration of the Miyazawa–Jernigan matrix

Abstract

A computer study of the prediction of the protein crystal’s shape and polymorphism of crystal’s structures within the limits resulting from the exploration of the Miyazawa–Jernigan matrix is presented. In this study, a coarse-graining procedure was applied to prepare a two-dimensional growth unit, where instead of full atom representation of the protein a two-type (hydrophobic–hydrophilic, HP) aminoacidal representation was used. The interaction energies between hydrophobic ( E HH ) aminoacids were chosen from the well-known HP-type models ( E HH ∈ [ − 4 , − 3 , − 2.3 , − 1 ] ), whereas interaction energies between hydrophobic and hydrophilic aminoacids ( E HP ) as well as interaction energies between hydrophilic aminoacids ( E PP ) were chosen from the range: < − 1 , 1 > , but not all values from this range fulfiled limitations resulting from the exploration of the Miyazawa–Jernigan matrix. Exploring every positively vetted combinations of energy interactions a polymorphism of the unit cell was observed what led to the fact that different final crystal’s shapes were obtained.