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

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 (EHH) aminoacids were chosen from the well-known HP-type models (EHH∈[−4,−3,−2.3,−1]), whereas interaction energies between hydrophobic and hydrophilic aminoacids (EHP) as well as interaction energies between hydrophilic aminoacids (EPP) 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.