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首页> 外文期刊>The Journal of Chemical Physics >Potential of mean force for insertion of antimicrobial peptide melittin into a pore in mixed DOPC/DOPG lipid bilayer by molecular dynamics simulation
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Potential of mean force for insertion of antimicrobial peptide melittin into a pore in mixed DOPC/DOPG lipid bilayer by molecular dynamics simulation

机译：分子动力学模拟将抗菌肽蛋白酶插入混合DOPC / DOPG脂质双层的孔中的平均力的潜力

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摘要

Antimicrobial peptides (AMPs) inactivate microorganisms by forming transmembrane pores in a cell membrane through adsorption and aggregation. Energetics of addition of an AMP to a transmembrane pore is important for evaluation of its formation and growth. Such information is essential for the characterization of pore forming ability of peptides in cell membranes. This study quantifies the potential of mean force through molecular dynamics (MD) simulation for the addition of melittin, a naturally occurring AMP, into a DOPC/DOPG mixed bilayer, a mimic of bacterial membrane, for different extents of insertion into either a bilayer or a pore consisting of three to six transmembrane peptides. The energy barrier for insertion of a melittin molecule into the bilayer was highest in the absence of transmembrane peptides and decreased for the number of transmembrane peptides from three to six, eventually approaching zero. The decrease in free energy for complete insertion of peptide was found to be higher for larger pore size. Water channel formation occurred only for insertion into pores consisting of three or more transmembrane peptides with the radius of water channel being larger for a larger number of transmembrane peptides. The structure of the pore was found to be paraboloid. The estimated free energy barrier for insertion of melittin into an ideal paraboloid pore accounting for different intermolecular interactions was consistent with MD simulation results. The results reported in this manuscript will be useful for the development of a model for nucleation of pores and a rational methodology for selection of synthetic antimicrobial peptides. Published by AIP Publishing.
机译：通过吸附和聚集在细胞膜中形成跨膜孔，抗微生物肽（AMPS）灭活微生物。对跨膜孔添加放大器的精力学对于评估其形成和生长是重要的。这些信息对于肽在细胞膜中的孔形成能力的表征至关重要。本研究量化了通过分子动力学（MD）模拟的平均力的潜力，用于将天然存在的amp，进入DOPC / DOPG混合双层，细菌膜的模拟，用于插入双层或由三到六个跨膜肽组成的孔。在没有跨膜肽的情况下，将熔母分子插入双层的能量屏障在没有跨膜肽的情况下最高，并且对于从三到六个，最终接近零点的跨膜肽的数量降低。对于较大的孔径，发现可用于完全插入肽的自由能量降低。仅用于插入由三个或更多个跨膜肽组成的孔径的孔径形成水通道形成，其水半径为较大数量的跨膜肽。发现孔的结构是抛物面的。将Melittin插入理想的抛物面孔隙算用于不同分子间相互作用的估计的自由能屏障与MD仿真结果一致。在本手稿中报告的结果对于开发孔的成核模型以及选择合成抗微生物肽的理性方法是有用的。通过AIP发布发布。

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