IgG aptamer

Apr 18, 2024 • Zhizhong Lu, Ying Ao

Timeline

Description

In June 2008, Matsumura, H. et al selected RNA aptamers targeting the Fc portion of the human IgG1 subclass (hIgG1 - Fc) from an RNA sequence library. This selection process employed a modified Systematic Evolution of Ligands by EXponential enrichment (SELEX) method, incorporating 2′-fluoro pyrimidines. Subsequently, in October 2008, Nakamura, Y., and Matsumura, H. successfully resolved the crystal structure of an RNA aptamer bound to hIgG1-Fc. The X-rays diffracted to a resolution of 2.2 Å. Moreover, in 2010, they determined the 2.15 Å crystal structure of the Fc fragment of human IgG1 (hFc1) in complex with an anti-Fc RNA aptamer^[1,2,3].

SELEX

In 2008, Matsumura, H. et al used a modified SELEX method and RNA aptamers against the Fc portion of human IgG1 subclass (hIgG1-Fc) were selected from a library of 5 × 10¹⁴ different RNA molecules randomized over 40 nucleotides (40N RNA pool) with 2′-fluoro pyrimidines. After 10 rounds of selection, we obtained six sets of RNA sequences of 71–74 nucleotides (nt) long, Apt1 through Apt6^[1].

Detailed information are accessible on SELEX page.

Structure

2D representation

Here we use ribodraw to complete the figure, through the 3D structure information. Apt8 aptamer was the aptamer sequence studied in SELEX article. And it was named by Matsumura, H^[1,3].

5'-GGGAACAAAGCUGAAGUACUUACCC-3'

3D visualisation

Nakamura, Y., and Matsumura, H. determined the crystal structure of the Apt8-2 aptamer bound to the Fc fragment of human IgG1 at a resolution of 2.15 Å. The Protein Data Bank (PDB) ID for this structure is 3AGV. The final model within an asymmetric unit consists of homodimeric hFc1 residues: for chain A, residues 241–262, 272–296, 302–321, and 334–443; for chain B, residues 237–444. Additionally, it includes two RNA aptamer molecules (with sequences G1-C11, G16-C23, and G1-A24), two carbohydrate chains, two Ca²⁺ ions, and 254 water molecules^[3].

Additional available structures that have been solved and detailed information are accessible on Structures page.

Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 3AGV at 2.15 Å resolution. the Fc fragment of human IgG1 (shown in vacuumm electrostatics), blue is positive charge, red is negative charge. Right: The hydrogen bonds of binding sites of the aptamer bound with the Fc fragment of human IgG1.

Ligand information

SELEX ligand

Yamazaki, S., & Nakamura, Y. used the BIAcore 2000 to conduct surface plasmon resonance (SPR) detection for the affinity of the selected aptamers to hIgG1-Fc. The direct affinity constant (KD) value was not recorded in this article. Therefore, we selected the association rate constant 1 (Ka1) and dissociation rate constant 1 (Kd1) from the article to calculate the affinity constant (KD)^[1]. This result is for reference only.

Structure ligand

The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set, C1-set, C2-set and I-set. Structural studies have shown that these domains share a common core Greek-key β-sandwich structure, with the types differing in the number of strands in the β-sheets as well as in their sequence patterns.-----From Pfam

UniProt ID: uniquely identifies protein sequences in the UniProt database, a resource for protein information.

Pfam: a widely recognised database of protein families and domains.

GenBank: maintained by NCBI(National Center for Biotechnology Information), is a database of nucleotide sequences from various organisms, vital for genetic and molecular biology research.

Mass: an intrinsic property of a body.

Uniprot ID	Pfam	Mass	Protein sequence	PDB ID	GenBank
P01857	PF07654	23.89 KDa	GGPYLQ ...... GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK	1FC1	AAC82527.1

Similar compound

We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation.

Dail server website: a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB).

Z-score: a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious.

RMSD: (Root Mean Square Deviation) is used to measure the degree to which atoms deviate from the alignment position.

PDB: PDB ID+ chain name.

PDB	Z-score	RMSD	Description
3AGV-B	31.6	0	Ig gamma-1 chain c region
1OQO-A	29.2	0.5	Immunoglobulin gamma-1 heavy
7Q3P-B	29.1	0.6	IgG1-Fc-MST-HH
5D4Q-A	29	0.7	Ig gamma-1 chain c region
5IW6-A	29	0.7	Ig gamma-1 chain c region
3AVE-B	29	0.7	Ig gamma-1 chain c region
6FGO-A	29	0.7	Immunoglobulin gamma-1 heavy
6GFE-H	29	0.8	Immunoglobulin gamma-4 heavy
4KU1-B	28.9	0.9	Ig gamma-1 chain c region
5U4Y-A	28.9	0.6	IgG1 Fc

References

[1] Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G.
Miyakawa, S., Nomura, Y., Sakamoto, T., Yamaguchi, Y., Kato, K., Yamazaki, S., & Nakamura, Y.
RNA (New York, N.Y.), 14(6), 1154–1163. (2008)
[2] Crystallization and preliminary X-ray diffraction studies of an RNA aptamer in complex with the human IgG Fc fragment.
Sugiyama, S., Nomura, Y., Sakamoto, T., Kitatani, T., Kobayashi, A., Miyakawa, S., Takahashi, Y., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Nakamura, Y., & Matsumura, H.
Acta crystallographica. Section F, Structural biology and crystallization communications, 64(Pt 10), 942–944. (2008)
[3] Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex.
Nomura, Y., Sugiyama, S., Sakamoto, T., Miyakawa, S., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Nakamura, Y., & Matsumura, H.
Nucleic acids research, 38(21), 7822–7829. (2010)
[4] Engineered synthetic polymer nanoparticles as IgG affinity ligands.
Lee, S. H., Hoshino, Y., Randall, A., Zeng, Z., Baldi, P., Doong, R. A., & Shea, K. J.
Journal of the American Chemical Society, 134(38), 15765–15772. (2012)
[5] Target replacement strategy for selection of DNA aptamers against the Fc region of mouse IgG.
Ma, J., Wang, M. G., Mao, A. H., Zeng, J. Y., Liu, Y. Q., Wang, X. Q., Ma, J., Tian, Y. J., Ma, N., Yang, N., Wang, L., & Liao, S. Q.
Genetics and molecular research : GMR, 12(2), 1399–1410. (2013)