Structure Prediction and Screening of Oligonucleotide Aptamers Target Cε3-Cε4 Protein†

doi:10.7503/cjcu20180428

Abstract

Abstract:

The prediction and selection of binding sites between aptamers and targets are the key steps in SELEX process, however, the conventional screening process is complicated. As a new convenient screening method, the virtual screening based on computer has widely used in aptamers screening. The nucleic acid-protein dock(NPDock) program was used to predict and screen the binding site of Cε3-Cε4 protein and its aptamer A1 based on their molecular docking, and the key site of binding to Cε3-Cε4 protein was screened. According to the amino acid residues and bases in the binding interface between the protein and the DNA complexes by virtual docking, the results showed that the amino acid in the binding interface is most capable of enriching the base G, followed by the ability of enriching the base T and the base C. An efficient optimization method was established based on NPDock docking, which would provide an experimental reference for related researches.

Key words: Cε3-Cε4 protein ;, Nucleic acid-protein dock program, Molecular docking, Aptamers screening

CLC Number:

O621

TrendMD:

LIU Zhongcheng, LIU Shifang, ZHANG Su, YANG Yanlei, LI Fei, ZHANG Nan, YUAN Xin, ZHANG Yanfen. Structure Prediction and Screening of Oligonucleotide Aptamers Target Cε3-Cε4 Protein^†[J]. Chem. J. Chinese Universities, 2019, 40(1): 83.

Figures/Tables 11

Fig.1 3D structure of Cε3-Cε4 protein

Table 1 Sequences for DNA aptamers

No.	Sequence(5'-3')	No.	Sequence(5'-3')
1	ACCGACCGT	25	TGTCTTGTCTTTAATGGTATCCACA
2	CCGACCGTGCTGG	26	TGTCTTTAATGGTATCCACA
3	CCGTGCTGG	27	CTTGTCTTTAATGGTATCCACAG
4	CGACCG	28	TTGTCTTTAA
5	ACCGT	29	TGTCTTTAATGGTATCCA
6	GACCGTGCTGGACTC	30	GTCTTTAATGGTATCCA
7	CGTGCTGGACTCTGCCCCG	31	TCTTTAATGGTATCCACAGTATGA
8	GTGCTGGAC	32	CTTTAATGGTATCCACAG
9	GCTGGACTCTGC	33	TTTAA
10	TGGACTCTGCCCCGCTGCCTTGCA	34	TAATGGTA
11	GGACTCTGCCCC	35	ATGGTAT
12	GGACTCTGCC	36	GGTATCC
13	GACTCTGCCCCGCTGCCTTGCATC	37	GTATCCAC
14	ACTCTGCCCCGCTGCCTTGCATCTGT	38	TATCCACAGTA
15	GCCCCGC	39	ATCCACAGTAT
16	GCCCCGCTGC	40	TCCACAGTATGA
17	GCTGCCTTGC	41	CACAGTATG
18	TGCCTTGCA	42	CAGTATG
19	CATCTG	43	GCGAGC
20	TTGCATCTGTCTTGTCTTTAA	44	GCGAGCGTTGC
21	CATCTGTCTTG	45	CGAGCG
22	ATCTGTCTTGTCTTTAAT	46	CGAGCGTTGCG
23	TGTCTTGTCTTTAATGGTATCCA	47	GCGTTGC
24	GTCTTGTCTTTAATGGTATCCACAG	48	CGTTGCG

Fig.2 3D structures prediction of DNA short hairpin(A)—(F) 3D structures of sequences 4, 10, 18, 21, 22, 29 by MMB; (G)—(L) 3D structures of sequences 4, 10, 18, 21, 22, 29 by RNA composer.

Fig.3 3D conformation of DNA short hairpins and Cε3-Cε4 protein interaction predicted by NPDock(A)—(C) 3D visualization of the 4, 18, 21 best scored complex.

Fig.4 Plot illustrating score changes during a simulation

Fig.5 Scoring statistic of DNA fragments and Cε3-Cε4 protein docking results

Table 2 Best sequences of DNA aptamers from docking results

No.	Sequence	Score	No.	Sequence	Score
6	GACCGTGCTGGACTC	4.08	22	ATCTGTCTTGTCTTTAAT	4.17
11	GGACTCTGCCCC	3.87	23	TGTCTTGTCTTTAATGGTATCCA	3.72
12	GGACTCTGCC	4.85	25	TGTCTTGTCTTTAATGGTATCCACA	3.97
20	TTGCATCTGTCTTGTCTTTAA	3.72	31	TCTTTAATGGTATCCACAGTATGA	3.82

Fig.6 Predictions for protein-DNA complexes(A) The site of interaction of sequence 11 protein complex, the purple are the amino acid residues Thr, Ser, Asp, Lys and His. The cyan are the base T, C and G. (B) The site of interaction of sequence 22-protein complex, the purple are the amino acid residues Ala, Arg, Val, Lys, Glu and Arg. The cyan are the base A, T, C and G.

Fig.7 Frequency of amino acid usage at the site of complex interactiona. Thr; b.Arg; c. Ser; d. Gln; e. Lys; f. Val; g. Asp; h. Pro; i. Glu; j. Phe; k. Ala; l. Asn; m. His; n. Ile; o. Leu; p. Met; q. Tyr.

Fig.8 Binding patterns between the amino acid-nucleotide pairs

Fig.9 Distribution of the frequency of the interaction between each of the amino acids and each of the four nucleotides

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