蛋白質單一結構所蘊含之演化訊息

Abstract

蛋白質序列上保留性高的氨基酸可能在功能上或結構上扮演這重要的角色，並在演化的過程中會給予保留下來。找出保留性高的氨基酸有助於我們暸解化學反應的機制或是蛋白質摺疊的資訊。欲得知序列上各氨基酸彼此間在演化過程中的保留程度一般會收集足量同源性的蛋白質進行序列比對。本篇論文提供了只需要蛋白質單一結構且不需序列氨基酸資訊即可推估在演化過程中此蛋白質序列上各氨基酸保留性，其原因在於我們發現在蛋白質結構中氨基酸於所處周圍含有其他氨基酸多寡與其保留性有著高度相關。 本研究利用554個不同源的酵素並各自比較其周圍氨基酸密度與保留性有著74%相關性大於0.5。其後我們發現考慮同一蛋白質中計算包含不同subunits與序列保留性比較可能可以用來推估在各自蛋白質中subunits之間的結合於演化上重要的程度。

Protein residues that are critical for structure and function that are expect-ing to be conserved throughout evolution. Finding the conserved residues might be helpful in understanding the mechanism of chemical reaction or information of protein folding. Generating the conservation profile of a sequence requires aligning families of homologous sequences and having knowledge of their evo-lutionary relationships. Here, we report that the conservation profile at the resi-due level can be quantitatively derived from a single protein structure with only backbone information. We found that the reciprocal packing density profiles of protein structures closely resemble their sequence conservation profiles. For a set of 554 non-homologous enzymes, 74% (408/554) of the proteins have a cor-relation coefficient > 0.5 between these two profiles. Our main result is the es-tablishment of a close correlation between a protein’s conservation profile and its packing density profile on the level of individual proteins. Later, We found that the elucidation of the evolutionary coupling among subunits based on the comparison of two profiles. Finally, we made a discussion on why evolutionary information could be derived from only a single protein structure.