化学
回转半径
范德瓦尔斯力
二面角
蒙特卡罗方法
化学物理
平均力势
疏水效应
氢键
静电学
均方根
能源景观
分子动力学
结晶学
计算化学
聚合物
物理化学
分子
物理
统计
数学
生物化学
有机化学
量子力学
作者
Priya Dey,Parbati Biswas
标识
DOI:10.1016/j.bpc.2023.107011
摘要
Coarse-grained Monte Carlo simulations are performed for a disordered protein, amyloid-β 42 to identify the interactions and understand the mechanism of its aggregation. A statistical potential is developed from a selected dataset of intrinsically disordered proteins, which accounts for the respective contributions of the bonded and non-bonded potentials. While, the bonded potential comprises the bond, bend, and dihedral constraints, the nonbonded interactions include van der Waals interactions, hydrogen bonds, and the two-body potential. The two-body potential captures the features of both hydrophobic and electrostatic interactions that brings the chains at a contact distance, while the repulsive van der Waals interactions prevent them from a collapse. Increased two-body hydrophobic interactions facilitate the formation of amorphous aggregates rather than the fibrillar ones. The formation of aggregates is validated from the interchain distances, and the total energy of the system. The aggregate is structurally characterized by the root-mean-square deviation, root-mean-square fluctuation and the radius of gyration. The aggregates are characterized by a decrease in SASA, an increase in the non-local interactions and a distinct free energy minimum relative to that of the monomeric state of amyloid-β 42. The hydrophobic residues help in nucleation, while the charged residues help in oligomerization and aggregation.
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