The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics

Abstract

The simulation of membrane proteins requires compatible protein and lipid force fields that reproduce the properties of both the protein and the lipid bilayer. Cytochrome P450 enzymes are bitopic membrane proteins with a transmembrane helical anchor and a large cytosolic globular domain that dips into the membrane. As such, they are representative and challenging examples of membrane proteins for simulations, displaying features of both peripheral and integral membrane proteins. We performed molecular dynamics simulations of three cytochrome P450 isoforms (2C9, 2C19 and 1A1) in a 2-oleoyl-1-palmitoyl-sn-glycerol-3-phosphocholine bilayer using two AMBER force field combinations: GAFF-LIPID with ff99SB for the protein, and LIPID14 with ff14SB for the protein. Comparison of the structural and dynamic properties of the proteins, the lipids and the protein-membrane interactions shows differing sensitivity of the cytochrome P450 isoforms to the choice of force field, with generally better agreement with experiment for the LIPID14 + ff14SB combination.

An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase

“…All four chains (A-D) of the asymmetric unit were used in BD simulations. For the full protein, the TM-helix in CYP 1A1 was assigned to residues 6-27 and the flexible linker and TM-helix were modeled as described previously 57,82 . The structure of an open conformation of human CPR was modeled on the basis of the crystal structures of the N-terminally truncated rat CPR in an open conformation (PDB ID: 3ES9 chain B; 3.4 Å resolution) 62 and the closed form of the N-terminally truncated human CPR (PDB ID: 3QE2; 1.75 Å resolution) 83 .…”

“…We previously developed a protocol for inserting the full-length structure of a CYP into a membrane bilayer without predetermining the orientation or insertion depth 16 . Hence, we superimposed the CYP domain of the CYP globular-domain -CPR FMN-domain complexes onto a modeled structure of the membrane-bound full-length CYP 1A1 in a POPC membrane 82 . Next, we replaced the globular domain of CYP 1A1 with each CYP globular-domain -CPR FMN-domain complex and connected the TM-helix and the linker region (residues 1-50) from the membrane-bound CYP 1A1 simulated in the absence of CPR with residue H51 of CYP 1A1 in the CYP globular-domain -CPR FMN-domain complex 89 .…”

PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking

“…Sixthly, under constant temperature and pressure conditions (ntb = 2, ntp = 1), through six consecutive stages, the constraints on the protein backbone were gradually reduced and removed, and MD without constraints was run for 10 ns. In the process of operation, SHAKE constraints were used for hydrogen atoms (ntc = 2, ntf = 2), and the temperature was controlled by a time step of 2fs and Langevin dynamics (ntt = 3, gamma_ln = 2.0) [ 74 ]. The generated trajectory file was analyzed using Amber16's cpptraj program, and the optimized optimal structure model was obtained by calculating temperature, density, total energy, and RMSD.…”

Single nucleotide polymorphism induces divergent dynamic patterns in CYP3A5: a microsecond scale biomolecular simulation of variants identified in Sub-Saharan African populations

“…Parameters for the CYP3A5 amino acid residues are derived from the AMBER ff14SB force field which is in better agreement with experimental results to simulate cytochrome P450 proteins [24]. General Amber Force Field (GAFF) [38] atom types were assigned to the heme group and parameters from Shahrokh et al, [32] were used to account for the bonded configuration between the Cys 441 sulphur atom and the Fe metal ion as well as the particular electronic state of the heme group.…”