Karubiu Wilson, Bhakat Soumendranath, McGillewie Lara, Soliman Mahmoud E S
School of Health Sciences, University of KwaZulu-Natal, Westville, Durban-4000, South Africa.
Mol Biosyst. 2015 Apr;11(4):1061-6. doi: 10.1039/c4mb00631c.
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.
在此，我们首次报道了疟原虫天冬氨酸蛋白酶中瓣片的打开和关闭情况——以疟原虫天冬氨酸蛋白酶II（PlmII）作为原型模型。我们提出了不同的组合参数来定义不对称瓣片运动；瓣片尖端残基（Val78和Leu292）之间的距离d1；二面角ϕ；此外还有Val78-Asp34-Leu292的TriCα角θ1和Val78-Asp214-Leu292的TriCα角θ2。结果发现，只有三个组合参数，即距离d1、二面角ϕ和TriCα角θ1，能够恰当地定义在瓣片打开和关闭过程中观察到的“扭转”运动。与结合腔边缘相邻的富含脯氨酸的环的协同运动似乎对瓣片残基产生空间位阻，驱使瓣片远离活性位点腔。该环也可能在催化二元残基Asp214周围有更多运动，使得TriCα角θ2在描述瓣片运动时不可靠。在d1为23.6 Å时瓣片完全打开，在约46 ns的时间尺度上对应最大的TriCα角θ1为78.6°。总体而言，结合态的平均θ1和θ2分别约为46°和约53°，而游离态PlmII的分别约为50°和约59°，这表明随着活性位点腔打开，TriCα急剧增加。在模拟过程中，距离d1和二面角ϕ也观察到类似趋势。结合腔的不对称打开最好用ϕ从-33.91°大幅转变为+21.00°来描述，这对应于瓣片在22 - 31 ns范围内的部分打开。虽然二面角描述了瓣片的扭转，但瓣片打开的程度可以通过结合d1和θ1来恰当地定义。这里给出的关于组合参数的结果，必将增强目前针对疟原虫天冬氨酸蛋白酶设计有效基于结构的抑制剂的努力。
