α/β类蛋白折叠中π-π相互作用的特异性

doi:10.7503/cjcu20140389

摘要/Abstract

摘要：

以α/β类蛋白的2种典型折叠类型为研究对象, 对205个低相似度蛋白样本中的π-π相互作用进行统计分析. 计算结果表明, (α/β)₈-barrel折叠中π-π相互作用的分布密度高于经典Rossmann折叠, 且在关键的局部区域的差异更加显著; 芳香族氨基酸在(α/β)₈-barrel结构中更容易形成π-π相互作用; 色氨酸对应的3种π-π相互作用组合在(α/β)₈-barrel折叠中出现的几率显著高于经典Rossmann折叠; (α/β)₈-barrel折叠中π-π相互作用形成复杂π网络的能力强于经典Rossmann折叠. 上述结果表明, π-π相互作用在α/β类蛋白的不同折叠类型中存在特异性, 其在稳定(α/β)₈-barrel结构中的作用强于经典Rossmann折叠.

关键词: (α/β)₈-barrel折叠, Rossmann折叠, π-π相互作用, π-网络, 非经典相互作用

Abstract:

Protein folding study is one of the main ways to investigate structural stability and mechanism of proteins. π-π Interaction has been focused much attention on its role in the stability of protein structure and functions. In this paper, two typical protein folds of α/β protein were selected for the research, π-π interactions of 205 low similarity protein samples were statistically analyzed. The results showed that the distribution density of π-π interactions in (α/β)₈-barrel fold was higher than those of classical Rossmann fold and the difference was more significant in the critical local area, aromatic amino acids easily form π-π interactions in (α/β)₈-barrel, the three π-π interaction combinations corresponding to Trp appearing in (α/β)₈-barrel were significantly higher than classic Rossmann and (α/β)₈-barrel fold had greater ability to form complex π-network than classical Rossmann fold. In a word, π-π interactions in different folding types of α/β protein exist specificity. π-π Interaction effects the stability of (α/β)₈-barrel stronger than the classical Rossmann.

Key words: (α/β)₈-Barrel fold, Rossmann fold, π-π Interaction, π-Network, Non-classical interaction

中图分类号:

O641.3

TrendMD:

王勤, 李晓琴, 马帅. α/β类蛋白折叠中π-π相互作用的特异性. 高等学校化学学报, 2014, 35(12): 2674.

WANG Qin, LI Xiaoqin, MA Shuai. Specificity of π-π Interactions in α/β Protein Folding^†. Chem. J. Chinese Universities, 2014, 35(12): 2674.

图/表 6

Fig.1 Topological structures of (α/β)8-barrel fold(A) and classical Rossmann fold(B)

Table 1 Distribution density of π-π interaction(%)

Fold type	s		d
Fold type	Mean value	Confidence interval	Mean value	Confidence interval
(α/β)₈-barrel	4.21	3.69—4.73	41.53	38.27—44.79
Classical Rossmann	1.71	1.31—2.11	22.29	18.65—25.94

Table 2 Participation rate of π-π interacting residues(%)

Amino acid	$com p π - π (i)$ in (α/β)₈-barrel		$com p π - π (i)$ in classical Rossmann		Preference
Amino acid	Mean value	Confidence interval	Mean value	Confidence interval	Preference
Phe	91.45	83.48—99.42	52.04	42.17—61.91	1.75
Tyr	68.96	62.19—75.72	40.78	32.19—49.38	1.69
Trp	95.59	83.33—107.85	34.48	21.47—47.50	2.77

Table 2 Participation rate of π-π interacting residues(%)

Amino acid	$com p π - π (i)$ in (α/β)₈-barrel		$com p π - π (i)$ in classical Rossmann		Preference
Amino acid	Mean value	Confidence interval	Mean value	Confidence interval	Preference
Phe	91.45	83.48—99.42	52.04	42.17—61.91	1.75
Tyr	68.96	62.19—75.72	40.78	32.19—49.38	1.69
Trp	95.59	83.33—107.85	34.48	21.47—47.50	2.77

Table 3 Distribution of different π-π interacting pairs(%)

Type	(α/β)₈-barrel		Classical Rossmann
Type	Mean value	Confidence interval	Mean value	Confidence interval
Phe-Phe	25.05	21.29—28.41	25.78	18.29—33.28
Phe-Trp	17.74	14.84—20.46	8.55	4.65—12.45
Phe-Tyr	29.44	26.11—32.77	37.60	28.77—46.43
Trp-Trp	2.38	1.33—3.43	0.11	0.11—0.32
Trp-Tyr	13.23	10.98—15.47	6.55	2.84—10.26
Tyr-Tyr	9.22	8.02—11.83	7.32	3.61—11.04
X-Trp^*	33.35	29.21—37.49	15.21	9.79—20.62

Table 4 Distribution(%) of the π-network

Fold type	Number of one residue involved in interacting pairs
Fold type	2π	3π	4π	5π	6π	7π	8π	9π
(α/β)₈-barrel	67.30	17.77	8.13	4.16	1.13	0.57	0.57	0.37
Classical Rossmann	81.73	8.89	7.46	1.68	0.24	0	0	0

Table 5 Distribution(%) of the number of one residue involved in interacting pairs

Fold type	Number of one residue involved in interacting pairs
Fold type	1	2	3	4	5
(α/β)₈-barrel	55.94	29.64	11.11	2.79	0.52
Classical Rossmann	75.61	18.78	5.37	0.24	0

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