Exploring the Binding Mechanism between Human Profilin (PFN1) and Polyproline-10 through Binding Mode Screening

Leili Zhang; David R. Bell; Binquan Luan; Ruhong Zhou

MD simulations were performed with GROMACS 5.1.2 package 24 . The 11 PFN1-P10 binding modes were evaluated in simulations using the OPLS-AA force field 25 with virtual sites for hydrogen atoms. Following similar protocols in our previous studies [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] , all systems were solvated in 8×8×8 nm 3 TIP3P water boxes with 150 mM NaCl. Steepest descent method was used to minimize the solvated PFN1-P10 complexes for 10000 steps. The electrostatic interactions were calculated with particle mesh Ewald (PME) method, while the van der Waals (VDW) interactions were handled with smooth cutoffs with the cutoff distance set to 1 nm. For each mode, a 50 ps of isochoric-isothermic (NVT, 310K) simulation with 1 fs timestep were then performed to equilibrate the systems. A series of 400 ns isobaric-isothermic (NPT, 310K, 1bar) simulations with 4 fs timestep were performed during production runs.