Simple model to study insertion of a protein into a membrane.
A simple coarse grained model on a two-dimensional lattice is presented to elucidate the main effects ruling the insertion of a protein into a polar environment such as a lipidic membrane. The amino acids are divided into two classes (hydrophobic or polar), and they behave differently according to their surroundings. In aqueous solution the hydrophobic amino acids are forced to minimize contacts with water, whereas in the apolar environment all the amino acids try to aggregate regardless to their specificity. The lattice is employed in order to perform exact calculations and to generate a fictitious protein data bank. Despite the simplicity of the model, some morphological features of the protein-like lattice structures obtained by our model are compatible with the observed phenomenology of transmembrane proteins. These results seem to corroborate the hypothesis that the number of classes into which the amino acids can be divided that correctly describe the phenomena may be extremely low.
Bonaccini
R
R
INFM, Dipartimento di Fisica, Università di Padova, Via Marzolo 8, 35131 Padova, Italy.
Seno
F
F
D000596:Amino Acids / Q000737:chemistry; D003087:Colicins / Q000737:chemistry*; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008051:Lipid Bilayers / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry*; D008956:Models, Chemical; D011487:Protein Conformation; D017510:Protein Folding; D012995:Solubility; D012996:Solutions / Q000737:chemistry
D000596:Amino Acids; D003087:Colicins; D008051:Lipid Bilayers; D008565:Membrane Proteins; D012996:Solutions