Gestation of a Glu Plasminogen Supra Fold via Molecular Dynamics Simulation

Abstract

Plasminogen (Pgn) is the precursor of plasmin, a proteinase that plays key roles in tissue remodeling, cell migration, fibrinolysis, etc. Pgn, Mr ∼92 kD, is structured by seven in-tandem globular domains: an N-terminal preactivation peptide (PAN, 77 aa), five kringle (K) repeats (∼ 80 aa each), and a trypsinogen-like serine protease zymogen (243 aa). Upon activation, Pgn undergoes a conformational change such that binding sites in kringles become accessible and able to interact with fatty acids and exposed lysyl side-chains. Via molecular dynamics (MD) simulations, we have investigated changes in inter-domain interactions that reflect supra-fold of Pgn. A model structure built by connecting sequential domains with fully extended flexible linkers was placed in a box of 282487 explicit water molecules and allowed to equilibrate for 420 ns via NAMD under CHARMM force field. During the MD, the protein folds as monitored by its radius of gyration (RG) that decreases from 157 A to 34 A, in good agreement with experimental observations (Mangel WF, Lin BH, Ramakrishnan V. Science 1990;248:69-73; Ponting CP, Holland SK, Cederholm-Williams SA, et al. Biochim Biophys Acta 1992;1159:155-161). The equilibrated structure is compact with a spiral spatial configurations of the in-tandem domains, as reported for the crystal (Law RHP, Caradoc-Davies T, Cowieson N, et al. Cell Reports 2012;1:185-190). By reversing the time course of the trajectory, dynamics insights are gained for the unfolding that accompanies the Pgn conformational change in the process of fibrinolysis. The PAN-K5 interaction was analyzed via free energy calculations as a function of relevant key inter-atomic distances. Two energy minima unveil configurations that exhibit strong and weak interactions between the PAN Lys 50 and the Asp516/Asp518 loci at the canonical K5 lysine binding site.