Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A

Abstract

Molecular simulations were used to design large scale loop motions in the enzyme cyclophilin A and NMR and biophysical methods were employed to validate the models.

Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes

“…We followed the same minimization and equilibration protocols previously reported. 77 In brief, each system was energy minimized combining steepest descent and conjugate gradient (4500 and 500 iterations respectively) minimisation. Systems were then heated from 0 K to 250 K in 150 ps in the NVT ensemble using a time step of 0.5 fs, and from 250 to 298 K in 300 ps using a timestep of 1 fs.…”

“…80 The resulting pool of trajectories was used to construct a Markov State Model (MSM) using the pyEMMA 2.3.0 software package, 81 following our previously described protocol to build MSMs for this system. 77 In brief, the RMSD of the 70s loop with respect to the X-ray structure 1AK4 82 (residues Gly65 to Gly77) was used to monitor the movement of this loop. The movement of the 100s loop (residues Met100 to Ser110) was described monitoring simultaneously the RMSD of the loop, and the distance between the COM of the loop and the COM of the -helix defined by residues Pro30 to Thr41.…”

“…The 100s loop undergoes a flapping movement that maps upward and downward movements of the loop onto similar RMSD values. Following previous work, 77 we multiply RSMD values by -1 when the distance described above is shorter than that observed in the X-ray structure (14.0 Å) to separate both loop motions along this collective variable.…”

“…To allow the most direct comparison with our previously reported model, we also used the same clustering algorithm (K-means) and the same number of microstates (100) from our previous work 77 for the MSM construction. Different lagtimes were used to compute implied timescales of the dominant eigenvectors, and the resulting implied timescale plots are shown in Figure S1.…”

“…We have recently reported an all-atom computational model of the conformational change that occurs between the native state and a transient state of the protein Cyclophilin A (CypA), a key enzyme for the life cycle of the HIV virus. 77 (Figure 4c). This suggests that eMD-VR generated pathways are suitable to generate molecular design hypotheses.…”