蛋白质三级结构对蛋白质内部形成紧密接触对速率的影响

Effect of protein structure on the rate of intra-molecular contact formation in proteins

通过蛋白质分子内两残基间距的概率分布函数P(r),计算了641个蛋白质分子内近程和远程紧密接触对的形成速率.分析了不同蛋白质结构,不同紧密接触对半径以及DNA的绑定对速率的影响.结果表明:不同结构类型蛋白近程和远程紧密接触对的形成速率的变化趋势恰好相反.近程紧密接触对的形成速率kS随着n(n=|j-i|)的增大而增大,远程紧密接触对的形成速率kL随着n的增大而减小,并且远程紧密接触对的形成速率kL满足kL(n)∝n-γ的关系.γ值随着紧密接触对半径a的增大而变小,当a=0.6 nm时,全α蛋白的γ值等于0.382,α/β蛋白的γ值等于0.343,全β和α+β蛋白的γ值等于0.218.DNA的绑定使蛋白质分子内近程和远程紧密接触对的形成速率都减小.

The rate of short-rang （ks） and long-range （kL） contacts formation in 641 protein was calculated according to the probability distribution P（r） of the residue-residue distance, and the influence of different protein structural class, contact radius a and protein binding in ks and kL on contacts formation rate was analyzed. It was found that the value of ks increases with distance n （n= ｜j--i｜ ） between two residues for all different folding types of protein. On the contrary, the value of kL decreases with n and follows the scaling relationship of kL （n） ∝ n-γ. The value of γ is related to the contact radius. The value of γ decreases with increasing a for all protein. The value of γ is 0. 382, 0. 343, 0. 218 , 0. 218 for all-α,α/β, all-β , and α＋β classes of protein with a ≡ 0.6 nm, respectively. The binding up of DNA in protein decreases the value of ks and kL.