論蛋白質與核酸之作用–結合結構和演化之研究

Abstract

基於比較蛋白質胺基酸保留程度和胺基酸周圍密度，某些酵素粗略的胺基酸保留程度已能從蛋白質結構中得到。胺基酸周圍密度是藉由加權接觸數模型 (weighted contact number model) 產生。然而蛋白質也會我們推測有些酵素與其它酵素相比，這些酵素可能與其結合之蛋白有較強的演化關係。然而蛋白質除了與其他蛋白質作用也會與核酸作用。那麼與核酸結合的蛋白質之演化資訊是否能從蛋白質與核酸的複合體結構中得到呢？對於蛋白質與核酸的複合體中之蛋白質，計算它的胺基酸周圍密度有兩種方式，分別為忽略或考慮核酸結構的存在。在本篇論文我們挑選129個蛋白質與核酸的複合體。我們發現蛋白質的胺基酸保留程度相似其胺基酸周圍密度。對於76%的非同源蛋白而言，它們胺基酸保留程度與胺基酸周圍密度的相關性大於0.5。我們的結果指出對於與核酸結合的蛋白質，從蛋白質與核酸的複合體結構中能得到其粗略的胺基酸保留程度。大部份的蛋白質之胺基酸保留程度較相似於考慮到核酸的影響所算的胺基酸周圍密度。對於其他蛋白質而言，這種情況是相反的。產生不同的情況也許與蛋白質是否和核酸有共演化情形有關。本篇論文擴展了加權接觸數模型的可用性。

Based on comparison of the sequence conservation and the packing density profiles of proteins, some enzymes have been found that their coarse-grained sequence conservation can be derived from protein structures. The packing density profile is generated through the weighted contact number model. However, proteins also have specific interactions with nucleic acids besides other proteins. There is a question whether the evolutionary information of a nucleic acid-binding protein can be derived from a protein-nucleic acid structure. For a protein of a protein-nucleic acid complex, there are two ways to compute it’s packing density. One ignores and the other considers the presences of the structures of nucleic acids. Here we selected 129 protein-nucleic acid complexes. We found that the packing density profiles of proteins look like their sequence conservation profiles. For 76% (98/129) of non-homologous proteins, the correlation coefficients between two profiles are greater than 0.5. Our results indicate that a protein-nucleic acid structure can derive coarse-grained sequence conservation of a nucleic acid-binding protein. The sequence conservation profiles of most proteins are more similar to their packing density profiles computed considering the contributions from nucleic acids. For other proteins, this situation is reversed. Different situations may be related to coevolution between proteins and nucleic acids. This study extends the availability of the weighted contact number model.