Hu W P, Kolinski A, Skolnick J
Scripps Research Institute, Department of Molecular Biology, La Jolla, CA 92037, USA.
Proteins. 1997 Dec;29(4):443-60. doi: 10.1002/(sici)1097-0134(199712)29:4<443::aid-prot5>3.0.co;2-9.
A new and more accurate method has been developed for predicting the backbone U-turn positions (where the chain reverses global direction) and the dominant secondary structure elements between U-turns in globular proteins. The current approach uses sequence-specific secondary structure propensities and multiple sequence information. The latter plays an important role in the enhanced success of this approach. Application to two sets (total 108) of small to medium-sized, single-domain proteins indicates that approximately 94% of the U-turn locations are correctly predicted within three residues, as are 88% of dominant secondary structure elements. These results are significantly better than our previous method (Kolinski et al., Proteins 27:290-308, 1997). The current study strongly suggests that the U-turn locations are primarily determined by local interactions. Furthermore, both global length constraints and local interactions contribute significantly to the determination of the secondary structure types between U-turns. Accurate U-turn predictions are crucial for accurate secondary structure predictions in the current method. Protein structure modeling, tertiary structure predictions, and possibly, fold recognition should benefit from the predicted structural data provided by this new method.
已开发出一种新的、更准确的方法来预测球状蛋白质中主链U型转弯位置（即链改变整体方向的位置）以及U型转弯之间的主要二级结构元件。当前方法使用序列特异性二级结构倾向和多序列信息。后者在该方法的更高成功率中起着重要作用。应用于两组（共108个）中小尺寸单结构域蛋白质表明，约94%的U型转弯位置能在三个残基范围内被正确预测，主要二级结构元件的预测准确率为88%。这些结果明显优于我们之前的方法（科林斯基等人，《蛋白质》27:290 - 308，1997年）。当前研究强烈表明，U型转弯位置主要由局部相互作用决定。此外，整体长度限制和局部相互作用都对U型转弯之间二级结构类型的确定有显著贡献。在当前方法中，准确的U型转弯预测对于准确的二级结构预测至关重要。蛋白质结构建模、三级结构预测以及可能的折叠识别都应受益于这种新方法提供的预测结构数据。
