Flap dynamics of plasmepsin proteases: insight into proposed parameters and molecular dynamics

Abstract

Herein, for the first time, we report the flap opening and closing in Plasmepsin proteases - plasmepsin II (PlmII) was used as a prototype model. We proposed different combined parameters to define the asymmetric flap motion; the distance, d1, between the flap tip residues (Val78 and Leu292); the dihedral angle, ϕ; in addition to TriCα angles Val78-Asp34-Leu292, θ1, and Val78-Asp214-Leu292, θ2. Only three combined parameters, the distance, d1, the dihedral angle, ϕ, and the TriCα angle, θ1, were found to appropriately define the observed "twisting' motion during the flap opening and closing. The coordinated motions of the proline-rich loop adjacent to the binding cavity rim appeared to exert steric hindrance on the flap residues, driving the flap away from the active site cavity. This loop may also have increased movements around the catalytic dyad residue, Asp214, making TriCα, θ2, unreliable in describing the flap motion. The full flap opening at d1, 23.6 Å, corresponded to the largest TriCα angle, θ1, at 78.6° on a ∼46 ns time scale. Overall the average θ1 and θ2 for the bound was ∼46° and ∼53°, respectively, compared to ∼50° and ∼59° for the Apo PlmII, indicating a drastic increase in TriCα as the active site cavity opens. Similar trends in the distance, d1, and the dihedral angle, ϕ, were observed during the simulation. The asymmetrical opening of the binding cavity was best described by the large shift in ϕ from -33.91° to +21.00° corresponding to the partial opening of the flap in the range of 22-31 ns. Though, the dihedral angle described the twisting of the flap, the extent of flap opening can appropriately be defined by combining d1 and θ1. The results presented here, on the combined parameters, will certainly augment current efforts in designing potent structure-based inhibitors against plasmepsins.

Investigation of flap flexibility of β-secretase using molecular dynamic simulations

“…Calculating the fluctuation of TriCα angles, θ 1 and θ 2 has emerged as a useful strategy to understand the extent of the flap opening in the case of plasmepsin (17). Calculating θ 1 (Thr72-Asp32-Ser325) and θ 2 (Thr72-Asp228-Ser325) proved to be a useful parameter in values showed a similar trend that of d 1 (Figure 8D).…”

“…The flap dynamics in HIV protease is one such example, which highlights the importance of defining the appropriate parameters that best describe specific dynamics associated with the inhibitor binding to the binding cavity. In one of our recent studies, we proposed similar parameters in order to understand the extent of flap opening and closing in the case of plasmepsin II (Plm II) (17). The study highlighted that in case of Plm II, the distance between flap tip residues Val78 and Leu292, and the angle between Val78, Asp214 and Leu292, will describe the opening and closing phenomena of flaps to a great extent.…”

“…The distance (d 1 ) between the flap tip residues and dihedral angle (ϕ), taking into account the flap tip residues and the catalytic dyads, emerged as the conventional strategy to understand the extent of the flap opening and twisting phenomena in HIV protease and plasmepsin (17).…”

“…For instance, flap dynamics is a distinctive motion observed amongst aspartate proteases e.g. HIV protease (16), cathepsin and plasmepsins (17). Flaps have been shown to regulate entry to the active site of proteases by providing access for substrate and/or inhibitors binding (15,18).…”

Modeling and resistant alleles explain the selectivity of antimalarial compound 49c towards apicomplexan aspartyl proteases

“…Previous studies have reported on the importance of the flap in regulating the opening and closing of the enzyme and thereby providing access or not, to the active site (Karubiu et al, 2015). In apicomplexans, the aspartyl proteases exhibit several characteristics including two conserved catalytic motifs DTGS or DTGS/DSGT/DTGT, optimal for activity in acidic pH conditions, as well as a polyproline loop and a flap predicted to close over the active site, thereby influencing substrate specificity.…”