Residue Specific Force Field ff14IDPsrs for Sampling Intrinsically Disordered Proteins

来源 :第四届国际分子模拟大会(The International Conference on Molecular Simula | 被引量 : 0次 | 上传用户:liguiming321
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  Intrinsically disordered proteins(IDPs)are proteins which lack of specific tertiary structure and unable to fold spontaneously without the partner binding.These IDPs are found to associate with various diseases,such as diabetes,cancer,and neurodegenerative diseases.However,current widely used force fields,such as ff99SB,ff14SB,OPLS/AA,and Charmm27 are insufficient in sampling the conformational characters of IDPs.In this study,the CMAP method was used to correct the φ/ψ distributions of amino acids and these parameters were named residue specific force field(ff14IDPsrs).The simulation results show that the force filed can better improve the φ/ψ Distributions of the amino acids,with RMSD less than 0.15%relative to the benchmark data of IDPs.Further test suggests that the calculated secondary chemical shifts under ff14IDPsrs force field are in quantitative agreement with the data of NMR experiment for five tested systems.In addition,the simulation results show that ff14IDPsrs can still be used to model structural proteins,such as tested lysozyme and ubiquitin,with better performance in coil regions than the original version force field ff14IDPs.These findings confirm that the newly developed Amber ff14IDPsrs force field is a robust model for improving the conformation sampling of IDPs.
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