An All-Atom Molecular Dynamics Study

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An All-Atom Molecular Dynamics Study J. Phys. Chem. B 2010, 114, 1004–1009 Effects of the RGTFEGKF Inhibitor on the Structures of the Transmembrane Fragment 70 86 of Glycophorin A: An All-Atom Molecular Dynamics Study Huiyu Li, Yin Luo , and Guanghong Wei Department of physics Fudan University,Shanghai 200433 China Abstract There is experimental evidence that the transmembrane fragment spanning amino acids70—86 of glycophorin-A, GpA70-86, forms amyloid fibrils and the inhibitor RGTFEGKF prevents GpA70-86 fibrilformation at an equimolar ratio. To explore the intrinsic, early interaction and inhibition mechanism ,we have determined the structures of GpA70-86 in the absence and the presence of the inhibitor by means of extensive molecular dynamics simulations in explicit solvent. Consistent with experiments of the fibrils, our simulation show that the inhibitor has a sigmificant impact on the global structure of the GpA70-86. Simulation models and Methods 1.Protein model: Glycophorin A(70-86) monomer, Glycophorin A(70-86) with inhibitor 2.Water model: simple point charge (SPC) model 3.Simulation method: The Molecular Dynamic simulations are performed using GROMACS software package and GROMOS96 force field at a constant temperature of 310 K.. Results Figure1. The initial states o f MD runs:(A)for the isolated GpA70 86 peptide; (B, C) for the GpA70 86-inhibitor complex, and (D) for the isolated Figure 2. Contact map probability averaged over all 100-300 ns MD conformations of the GpA70-86-inhibitor complex for the(A) Main-chain-main-chain and (B) side-chain-side-chain interactions. Fig 4. Distribution of the angle between vectors G79-83 And G2-G6 in the GpA-inhibitor system. Fig 3. Equillibrium conformations of GpA70-86 and the GpA70-86-inhibitor in complex. Conclusion Based on our simulations, we can propose that GpA is essentially random coil in aqueous solution.There are multiple binding modes of the inhibitor to the GpA70-86. In all of process, The GxxxG motif in GpA play an important role in the aggregation of Amyloid Fibrils.