This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Human plasminogen, so-called Glu-plasminogen (Glu-Pg), consists of an N-terminal peptide (NTP) Glu1-Val79, followed by five kringle domains and a serine-protease domain at the C-terminal end. Glu-Pg forms a closed structure postulated to result from NTP-kringle binding. There is experimental evidence that the closed conformation of Glu-Pg is maintained via kringle 5 and NTP binding. With the aid of this experimental information, the molecular dynamics (MD) study can be very useful in elucidating detail mechanisms of conformational change of plasminogen in the fibrinolysis. While computational studies can be very helpful to understanding binding mechanisms, it is difficult and tedious to search the entire free energy space to characterize their binding processes. Thus, we will investigate possible binding regions near lysine-binding sites (LBSs) of kringle 5 by approaching Lys50 of NTP. Despite numerous experimental studies, the structure of an entire plasminogen molecule has not been determined. Thus, the rest of unknown structures will be added to crystallographic X-ray structures of some kringles, adjusting entire structures via energy-minimization and equilibration. Equilibrium geometries of five kringes and NTP (541 residues) in water will be determined with chloride/sodium ions and 40,000 TIP3P water molecules placed in an orthorhombic periodic box. CHARMM force field will be used for all MD simulations. During equilibration, ad hoc harmonic constraints on distance between eligible binding sites, will be implemented. This will be done slowly by decreasing force constants associated with the constraints to zero during the first 0.4 ns of the run. After their removal, MD simulations will be continued for an additional 1 ns to trace trajectories of the distances of the binding atom pairs without the constraints. To conduct successfully MD simulations for such a large biosystem, we request 10,000 SU on the PSC BIGBEN platform.
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