Molecular dynamics study of the membrane interaction of a membranotropic dengue virus C protein-derived peptide

Dengue virus C protein, essential in the dengue virus life cycle, possesses a segment, peptide PepC, known to bind membranes composed of negatively charged phospholipids. To characterize its interaction with the membrane, we have used the molecular dynamics HMMM membrane model system. This approach is capable of achieving a stable system and sampling the peptide/lipid interactions which determine the orientation and insertion of the peptide upon membrane binding. We have been able to demonstrate spontaneous binding of PepC to the 1,2-divaleryl-sn-glycero-3-phosphate/1,2-divaleryl-sn-glycero-3-phosphocholine membrane model system, whereas no binding was observed at all for the 1,2-divaleryl-sn-glycero-3-phosphocholine one. PepC, adopting an α-helix profile, did not insert into the membrane but did bind to its surface through a charge anchor formed by its three positively charged residues. PepC, maintaining its three-dimensional structure along the whole simulation, presented a nearly parallel orientation with respect to the membrane when bound to it. The positively charged amino acid residues Arg-2, Lys-6, and Arg-16 are mainly responsible for the peptide binding to the membrane stabilizing the structure of the bound peptide. The segment of dengue virus C protein where PepC resides is a fundamental protein–membrane interface which might control protein/membrane interaction, and its positive amino acids are responsible for membrane binding defining its specific location in the bound state. These data should help in our understanding of the molecular mechanism of DENV life cycle as well as making possible the future development of potent inhibitor molecules, which target dengue virus C protein structures involved in membrane binding.登革病毒C蛋白（Dengue virus C protein）是登革病毒生命周期中不可或缺的关键组分，其包含一段名为PepC的肽段，该肽段已被证实可与带负电荷的磷脂所构成的膜结构结合。为表征该肽段与膜的相互作用机制，本研究采用了分子动力学HMMM膜模型系统。该模拟方法可构建稳定的模拟体系，并对肽-脂相互作用进行充分采样，进而明确肽段结合膜后的取向与插入状态。本研究成功观测到PepC可自发结合至1,2-二戊酰-sn-甘油-3-磷酸/1,2-二戊酰-sn-甘油-3-磷酸胆碱膜模型系统，而仅含1,2-二戊酰-sn-甘油-3-磷酸胆碱的膜体系则未观测到任何结合现象。呈现α螺旋构象的PepC并未插入膜内部，而是通过其三个带正电荷残基构成的电荷锚定区域结合于膜表面。在整个模拟过程中，PepC始终维持其三维空间结构，结合至膜时与膜平面呈现近乎平行的取向。带正电荷的氨基酸残基Arg-2、Lys-6与Arg-16是介导该肽段与膜结合的主要基团，同时可稳定结合态肽段的空间结构。登革病毒C蛋白中PepC所在的区段是关键的蛋白-膜相互作用界面，其可调控蛋白与膜的结合过程，而该区段的带正电荷氨基酸负责介导膜结合，并决定肽段在结合态下的精准定位。本研究所得数据不仅有助于深入解析登革病毒（DENV）生命周期的分子机制，同时可为未来开发靶向登革病毒C蛋白膜结合相关结构的强效抑制剂分子提供理论支撑。