Theoretical conformational investigation of thrombin-fibrinogen recognition complex.
Theoretical conformational investigation of the thrombin-fibrinogen recognition complex was fulfilled. At first preliminary study was carried out using space-filling molecular models. At the next stage computer simulation was conducted. For this purpose a package of programs for the theoretical conformational analysis of two interacting molecules has been developed in the framework of atom-atom potentials. The package contains an original algorithm for constructing initial approximation based on assumption that the structure of the complex is determined mainly by the ligand-ligand attraction and Van-der-Vaals repulsion. Complex structure with considerable binding energy was obtained. Molecules of that structure are bound mainly by four oppositely charged pairs of side chain groups. The beta -loop of thrombin in the complex is shown to undergo essential structural transformations. A hypothesis is suggested that this transformation may influence active sites allosterically. Some ways and mechanisms of this influence are discussed as well as an approach to its calculation.
Schechkin
I E
IE
Karabut
L V
LV
Chetyrkina
S N
SN
Sereyskaya
A A
AA
D003198:Computer Simulation; D005340:Fibrinogen / Q000737:chemistry*; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D013816:Thermodynamics; D013917:Thrombin / Q000737:chemistry*
D008024:Ligands; D005340:Fibrinogen; D013917:Thrombin