Abstract：
Several simple secondary structures could form complex and diverse functional proteins, meaning that secondary structures may contain a lot of hidden information and are arranged according to certain principles, to carry enough information of functional specificity and diversity. However, these inner information and principles have not been understood systematically. In our study, we designed a structure-function alphabet of helix based on reduced amino acid clusters to describe the typical features of helices and delve into the information. Firstly, we selected 480 typical helices from membrane proteins, zymoproteins, transcription factors, and other proteins to define and calculate the interval range, and the helices are classified in terms of hydrophilicity, charge and length: (1) hydrophobic helix (≤43%), amphiphilic helix (43%∼71%), and hydrophilic helix (≥71%). (2) positive helix, negative helix, electrically neutral helix and uncharged helix. (3) short helix (≤8 aa), medium-length helix (9-28 aa), and long helix (≥29 aa). Then, we designed an alphabet containing 36 triplet codes according to the above classification, so that the main features of each helix can be represented by only three letters. This alphabet not only preliminarily defined the helix characteristics, but also greatly reduced the informational dimension of protein structure. Finally, we present an application example to demonstrate the value of the structure-function alphabet in protein functional determination and differentiation.
摘要：
几个简单的二级结构可以形成复杂多样的功能蛋白，意味着二级结构可能包含大量隐藏信息，并按照一定的原则排列，携带足够的功能特异性和多样性信息。然而,这些内部信息和原则还没有被系统地理解。在我们的研究中,我们基于简化的氨基酸簇设计了螺旋的结构-功能字母，以描述螺旋的典型特征并深入研究信息。首先,我们从膜蛋白中选择了480个典型的螺旋，酶蛋白，转录因子，和其他蛋白质来定义和计算间隔范围，螺旋根据亲水性进行分类，电荷和长度：（1）疏水螺旋（≤43％），两亲性螺旋(43%~71%)，和亲水螺旋（≥71％）。（2）正螺旋，负螺旋,电中性螺旋和不带电螺旋。（3）短螺旋（≤8aa），中等长度螺旋（9-28aa），和长螺旋（≥29aa）。然后，我们根据上述分类设计了一个包含36个三元组代码的字母，这样每个螺旋的主要特征只能用三个字母表示。这个字母不仅初步定义了螺旋特征，而且大大降低了蛋白质结构的信息维度。最后,我们提供了一个应用实例来证明结构-功能字母在蛋白质功能测定和分化中的价值。
