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 (E(HH)) aminoacids were chosen from the well-known HP-type models (E(HH)in[-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.
Siódmiak
Jacek
J
Department of Modeling of Physicochemical Processes, Institute of Mathematics and Physics, University of Technology and Life Sciences, Bydgoszcz, Poland.
D003460:Crystallization; D008956:Models, Chemical; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins; D009113:Muramidase