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首页> 外文期刊>Scientific reports. >Revealing Hidden Conformational Space of LOV Protein VIVID Through Rigid Residue Scan Simulations
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Revealing Hidden Conformational Space of LOV Protein VIVID Through Rigid Residue Scan Simulations

机译：通过刚性残留扫描模拟揭示LOV蛋白的隐藏构象空间

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VIVID(VVD) protein is a Light-Oxygen-Voltage(LOV) domain in circadian clock system. Upon blue light activation, a covalent bond is formed between VVD residue Cys108 and its cofactor flavin adenine dinucleotide(FAD), and prompts VVD switching from Dark state to Light state with significant conformational deviation. However, the mechanism of this local environment initiated global protein conformational change remains elusive. We employed a recently developed computational approach, rigid residue scan(RRS), to systematically probe the impact of the internal degrees of freedom in each amino acid residue of VVD on its overall dynamics by applying rigid body constraint on each residue in molecular dynamics simulations. Key residues were identified with distinctive impacts on Dark and Light states, respectively. All the simulations display wide range of distribution on a two-dimensional(2D) plot upon structural root-mean-square deviations(RMSD) from either Dark or Light state. Clustering analysis of the 2D RMSD distribution leads to 15 representative structures with drastically different conformation of N-terminus, which is also a key difference between Dark and Light states of VVD. Further principle component analyses(PCA) of RRS simulations agree with the observation of distinctive impact from individual residues on Dark and Light states.
机译：生动（VVD）蛋白是昼夜时钟系统的光 - 电压（LOV）域。在蓝光激活时，在VVD残基Cys108及其辅助actOlFavin腺嘌呤二核苷酸（FAD）之间形成共价键，并提示VVD从暗状态切换到具有显着构象偏差的光状态。然而，这种当地环境的机制发起全球蛋白质构象变化仍然难以捉摸。我们采用最近开发的计算方法，刚性残留扫描（RRS），通过在分子动力学模拟中施加对每个残留物的刚体约束来系统地探测VVD的每个氨基酸残基的内部自由度对其整体动力学的影响。鉴定关键残留物分别以暗和光源的独特影响鉴定。所有模拟在结构根部平均方偏差（RMSD）上显示在二维（2D）曲线上的宽范围分布，无论是黑暗还是光线。 2D RMSD分布的聚类分析导致15个代表性结构，其N-末端的巨大不同构象，这也是VVD的黑暗和光源之间的关键差异。 RRS模拟的其他原则分析（PCA）同意观察来自暗和光源的个别残留物的独特影响。

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