Imai Kenichiro, Mitaku Shigeki
Department of Applied Physics, Graduate School of Engineering, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8606, Japan.
Biophysics (Nagoya-shi). 2005 Oct 19;1:55-65. doi: 10.2142/biophysics.1.55. eCollection 2005.
Breaking signals of secondary structure put strong limitations on the tertiary structures of proteins. In addition to proline and glycine clusters, which are well-known secondary structure breakers, clusters of amphiphilic residues were found to be a novel type of secondary structure breaker. These secondary structure breakers were found to depend on specific environmental factors. Such conditions included the average hydrophobicity, the helical periodicity, the density of serine and threonine residues, and the presence of tryptophan and tyrosine clusters. Principal component analysis of environmental factors was conducted in order to identify candidate breakers in the secondary structure breaking regions. Predicted breakers were located in breaking regions with an accuracy of 72%. Taking the loop core into consideration, almost 90% of the predicted breakers were located in the loop segments. When the migration effect of the breaking point was taken into account, the loop segments with the predicted breakers covered two thirds of all loop segments. Herein, the possibility of secondary structure prediction based on secondary structure breakers is discussed. The system of the present method is available at the URL: http://bp.nuap.nagoya-u.ac.jp/sosui/sosuibreaker/sosuibreaker_submit.html.
二级结构的断裂信号对蛋白质的三级结构施加了严格限制。除了脯氨酸和甘氨酸簇（众所周知的二级结构破坏者）之外，两亲性残基簇被发现是一种新型的二级结构破坏者。这些二级结构破坏者被发现依赖于特定的环境因素。这些条件包括平均疏水性、螺旋周期性、丝氨酸和苏氨酸残基的密度以及色氨酸和酪氨酸簇的存在。为了识别二级结构断裂区域中的候选破坏者，对环境因素进行了主成分分析。预测的破坏者位于断裂区域，准确率为72%。考虑到环核心，几乎90%的预测破坏者位于环段中。当考虑断裂点的迁移效应时，带有预测破坏者的环段覆盖了所有环段的三分之二。在此，讨论了基于二级结构破坏者进行二级结构预测的可能性。本方法的系统可在以下网址获取：http://bp.nuap.nagoya-u.ac.jp/sosui/sosuibreaker/sosuibreaker_submit.html 。
