蛋白質鹽橋結構分析與熱穩定性之應用

Abstract

在生物醫學與酵素工業上，蛋白質的熱穩定性一直扮演著非常重要性的角色。儘管之前的研究顯示，影響蛋白質熱穩定性的因子很多，但鹽橋 （Salt-bridge）仍是扮演其中最主要的角色之一。如何有效設計新鹽橋鍵結的形成，仍是一大挑戰。本研究從6,493 X-光結構蛋白質，分析出位於蛋白質表面上共有10,556個鹽橋，利用不同幾何特徵分析，如二級結構、暴露面積、Cα-Cα距離和角度等，發現鹽橋有其構型上的特異性。進一步將其特異數值轉換成不同的比重，設計一種靜電吸引權重的計算模式，並搭配氨基酸在結構上振動幅度（B-factor）、堆積密度（Weighted Contact Number, WCN）和序列保留度，成功地應用在中溫蛋白酵素（β-glucosidase）上。本研究的結果可使對鹽橋的構型特徵有更進一步的了解，並對未來建立較好的模型提供有利的資訊。

The Protein thermal stability is an important factor considered in medical and industrial applications. Many structural characteristics related to protein thermal stability have been elucidated, and increasing salt bridges is considered as one of the most efficient strategies to increase protein thermal stability. However, the accurate simulation of salt bridges remains difficult. In this study, based on the statistical analysis of 10,556 surface salt bridges on 6,493 X-ray protein structures, these salt bridges were first categorized depending on pairing residues, secondary structure locations, and Cα-Cα distances. Furthermore, a novel method was designed by pairing preferences to construct a salt-bridge pair index and used in a weighted electrostatic attraction model to find the effective pairings for designing salt bridges. The model was also coupled with B-factor, weighted contact number (WCN), relative solvent accessibility (RSA), and conservation prescreening to determine the positions appropriate for the thermal adaptive design of salt bridges. According to our method, the putative salt-bridges were successfully designed on a mesophilic β-glucosidase. Thus, this study demonstrated an effective method for the thermal adaptive design of salt bridges through inference of suitable positions and substitutions.