Gong Haipeng, Shen Yang, Rose George D
T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA.
Protein Sci. 2007 Aug;16(8):1515-21. doi: 10.1110/ps.072988407.
We have been analyzing the extent to which protein secondary structure determines protein tertiary structure in simple protein folds. An earlier paper demonstrated that three-dimensional structure can be obtained successfully using only highly approximate backbone torsion angles for every residue. Here, the initial information is further diluted by introducing a realistic degree of experimental uncertainty into this process. In particular, we tackle the practical problem of determining three-dimensional structure solely from backbone chemical shifts, which can be measured directly by NMR and are known to be correlated with a protein's backbone torsion angles. Extending our previous algorithm to incorporate these experimentally determined data, clusters of structures compatible with the experimentally determined chemical shifts were generated by fragment assembly Monte Carlo. The cluster that corresponds to the native conformation was then identified based on four energy terms: steric clash, solvent-squeezing, hydrogen-bonding, and hydrophobic contact. Currently, the method has been applied successfully to five small proteins with simple topology. Although still under development, this approach offers promise for high-throughput NMR structure determination.
我们一直在分析在简单蛋白质折叠中蛋白质二级结构决定蛋白质三级结构的程度。较早的一篇论文表明，仅使用每个残基高度近似的主链扭转角就能成功获得三维结构。在此，通过在这个过程中引入实际程度的实验不确定性，初始信息被进一步稀释。特别是，我们解决了仅从主链化学位移确定三维结构的实际问题，主链化学位移可通过核磁共振直接测量，并且已知与蛋白质的主链扭转角相关。将我们之前的算法扩展以纳入这些实验确定的数据，通过片段组装蒙特卡罗方法生成了与实验确定的化学位移兼容的结构簇。然后基于四个能量项确定对应于天然构象的簇：空间冲突、溶剂挤压、氢键和疏水接触。目前，该方法已成功应用于五个具有简单拓扑结构的小蛋白质。尽管仍在开发中，但这种方法为高通量核磁共振结构测定带来了希望。
