Abstract

Biological membranes are essential to preserve structural integrity and regulate functional properties through the permeability of nutrients, pharmaceutical drugs, and neurotransmitters of a living cell. The movement of acetylated and amidated phenylalanine (NAFA) across 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane bilayers is investigated to probe physical transport. The rate of transport is measured experimentally applying parallel artificial membrane permeation assay (PAMPA). At the physiological temperature, 310 K, the measured time constants in the neutral pH were ∼6 h in DOPC and ∼3 h in POPC, while in a more acidic condition, at a pH 4.8, the time constants were ∼8 h in both lipids. Computationally, we have expanded our transport study of three aromatic dipeptides across a bilayer composed of DOPC¹⁸. In this study, we have examined the effects of lipid composition and bilayer size on the passive transport of NAFA by simulating the dipeptide in three different bilayers, with 50 DOPC lipids, 50 POPC lipids, and 40 POPC molecules. Specifically, atomistic molecular dynamics simulations with umbrella sampling were used to calculate the potential of mean force for the passive permeation of NAFA across the bilayers. Diffusion constants were then calculated by numerically solving the Smoluchowski equation. Permeability coefficients and mean first passage times were then calculated. Structural properties – Ramachandran plots, sidechain torsions, peptide insertion angles, radial distribution functions, and proximal peptide water molecules – were also examined to determine the effect of system size and lipid type. In terms of systems size, we observed a small decrease in the highest barrier of the potential of mean force and fewer sampled sidechain dihedral angle conformations with 40 versus 50 POPC lipids due to weaker membrane deformations within a smaller lipid bilayer. In terms of lipid type, DOPC contains two monounsaturated acyl chains compared to only one such acyl chain in POPC; therefore, DOPC bilayers are less ordered and more easily deformed, as seen by a much broader potential of mean force profile. The NAFA in DOPC lipid also transitioned to an internally hydrogen-bonded backbone conformation at lower membrane depths than in POPC. Similarly, as for other aromatic dipeptides, NAFA tends to insert into the membrane sidechain-first, remains mostly desolvated in the membrane center, and exhibits slow reorientations within the bilayer in both DOPC and POPC. With a joint experimental and computational study we have gained a new insight into the rate of transport and the underlying microscopic mechanism in different lipid bilayer conditions of the simplest hydrophobic aromatic dipeptide.

Communicated by Ramaswamy H. Sarma

摘要

生物膜对于通过营养物质、药物和活细胞的神经递质的渗透性来保持结构完整性和调节功能特性至关重要。乙酰化和酰胺化苯丙氨酸 (NAFA) 在 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) 和 1-palmitoyl-2-oleoyl- sn中的运动研究了-glycero-3-phosphocholine (POPC) 膜双层以探测物理转运。应用平行人工膜渗透测定法 (PAMPA) 通过实验测量传输速率。在生理温度 310 K 下，在中性 pH 值中测得的时间常数在 DOPC 中约为 6 小时，在 POPC 中约为 3 小时，而在更酸性的条件下，在 pH 值 4.8 时，两者的时间常数均为 8 小时脂质。在计算上，我们扩展了对三种芳香二肽在由 DOPC ^{18组成的双层中的转运研究}. 在这项研究中，我们通过模拟三种不同双层中的二肽（50 种 DOPC 脂质、50 种 POPC 脂质和 40 种 POPC 分子）来检查脂质组成和双层大小对 NAFA 被动转运的影响。具体来说，使用伞形采样的原子分子动力学模拟来计算 NAFA 被动渗透穿过双层的平均力的潜力。然后通过数值求解 Smoluchowski 方程计算扩散常数。然后计算渗透系数和平均首次通过时间。还检查了结构特性——Ramachandran 图、侧链扭转、肽插入角度、径向分布函数和近端肽水分子——以确定系统大小和脂质类型的影响。就系统规模而言，我们观察到平均力的最高势垒略有下降，并且由于较小的脂质双层内的膜变形较弱，因此具有 40 对 50 种 POPC 脂质的采样侧链二面角构象较少。就脂质类型而言，DOPC含有两条单不饱和酰基链，而POPC中只有一条这样的酰基链；因此，从更广泛的平均力分布潜力可以看出，DOPC 双层的有序性较低且更容易变形。DOPC 脂质中的 NAFA 在比 POPC 更低的膜深度处也转变为内部氢键骨架构象。类似地，对于其他芳香族二肽，NAFA 倾向于首先插入膜侧链，在膜中心大部分保持去溶剂化，并且在 DOPC 和 POPC 的双层内表现出缓慢的重新定向。

由 Ramaswamy H. Sarma 传达