论文标题
沿蛋白质序列和共同折叠的结构不对称
Structural asymmetry along protein sequences and co-translational folding
论文作者
论文摘要
蛋白质从N-转换为C端,提出了这种先天方向如何影响其进化的基本问题。为了探讨这个问题,我们分析了蛋白质数据库(PDB)的16,200个结构。我们发现在C末端的$α$ - 螺旋和N末端的$β$ strands的富集。此外,此$α$ - $β$不对称性与序列长度和接触顺序相关,这是折叠率的决定因素,暗示了可能的链接到共倾斜折叠(CTF)。因此,我们提出了“最慢的”方案,蛋白质序列进化了结构不对称以加速CTF:合作折叠段的最慢段位于N末端附近,因此在翻译过程中它们有更多的折叠时间。一个现象学模型预测,当折叠时间与翻译时间相称时,CTF可以通过不对称性加速,最高速度加倍。对PDB的分析表明,在该方案中,结构不对称确实是最大的。原核生物中这种对应关系更大,通常需要更快的蛋白质产生。总之,这表明加速CTF是一种实质性的进化力,其与稳定性和功能的相互作用是按序列不对称编码的。
Proteins are translated from the N- to the C-terminus, raising the basic question of how this innate directionality affects their evolution. To explore this question, we analyze 16,200 structures from the protein data bank (PDB). We find remarkable enrichment of $α$-helices at the C terminus and $β$-strands at the N terminus. Furthermore, this $α$-$β$ asymmetry correlates with sequence length and contact order, both determinants of folding rate, hinting at possible links to co-translational folding (CTF). Hence, we propose the 'slowest-first' scheme, whereby protein sequences evolved structural asymmetry to accelerate CTF: the slowest of the cooperatively-folding segments are positioned near the N terminus so they have more time to fold during translation. A phenomenological model predicts that CTF can be accelerated by asymmetry, up to double the rate, when folding time is commensurate with translation time; analysis of the PDB reveals that structural asymmetry is indeed maximal in this regime. This correspondence is greater in prokaryotes, which generally require faster protein production. Altogether, this indicates that accelerating CTF is a substantial evolutionary force whose interplay with stability and functionality is encoded in sequence asymmetry.