Specificity of π-π Interactions in α/β Protein Folding†

doi:10.7503/cjcu20140389

Abstract

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

CLC Number:

O641.3

TrendMD:

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

Figures/Tables 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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