Summary information

PDB id
8bw5
Class
hydrolase
Method
X-ray (2.8 Å)
Summary
X-ray structure of the complex between human alpha thrombin and the duplex-quadruplex aptamer m08s-1_41mer
Reference
Troisi R, Napolitano V, Rossitto E, Osman W, Nagano M, Wakui K, Popowicz GM, Yoshimoto K, Sica F (2023): "Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide." Nucleic Acids Res., 51, 8880-8890. doi: 10.1093/nar/gkad634.
Abstract
Ligand/protein molecular recognition involves a dynamic process, whereby both partners require a degree of structural plasticity to regulate the binding/unbinding event. Here, we present the characterization of the interaction between a highly dynamic G-rich oligonucleotide, M08s-1, and its target protein, human α-thrombin. M08s-1 is the most active anticoagulant aptamer selected thus far. Circular dichroism and gel electrophoresis analyses indicate that both intramolecular and intermolecular G-quadruplex structures are populated in solution. The presence of thrombin stabilises the antiparallel intramolecular chair-like G-quadruplex conformation, that provides by far the main contribution to the biological activity of the aptamer. The crystal structure of the thrombin-oligonucleotide complex reveals that M08s-1 adopts a kinked structural organization formed by a G-quadruplex domain and a long duplex module, linked by a stretch of five purine bases. The quadruplex motif hooks the exosite I region of thrombin and the duplex region is folded towards the surface of the protein. This structural feature, which has never been observed in other anti-exosite I aptamers with a shorter duplex motif, hinders the approach of a protein substrate to the active site region and may well explain the significant increase in the anticoagulant activity of M08s-1 compared to the other anti-exosite I aptamers.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.550 type=bowl   nts=4 GGGG F.DG14,F.DG27,F.DG22,F.DG19
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.537 type=other  nts=4 GGGG F.DG15,F.DG26,F.DG23,F.DG18

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG F.DG14,F.DG27,F.DG22,F.DG19
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG F.DG15,F.DG26,F.DG23,F.DG18
  step#1  mm(<>,outward)  area=15.66 rise=3.58 twist=13.9
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG F.DG14,F.DG15
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG F.DG27,F.DG26
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG F.DG22,F.DG23
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG F.DG19,F.DG18

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG F.DG14,F.DG27,F.DG22,F.DG19
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG F.DG15,F.DG26,F.DG23,F.DG18
  step#1  mm(<>,outward)  area=15.66 rise=3.58 twist=13.9

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List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG F.DG14,F.DG27,F.DG22,F.DG19
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG F.DG15,F.DG26,F.DG23,F.DG18
  step#1  mm(<>,outward)  area=15.66 rise=3.58 twist=13.9
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG F.DG14,F.DG15
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG F.DG27,F.DG26
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG F.DG22,F.DG23
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG F.DG19,F.DG18
  loop#1 type=lateral   strands=[#1,#4] nts=2 AT F.DA16,F.DT17
  loop#2 type=lateral   strands=[#4,#3] nts=2 GG F.DG20,F.DG21
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT F.DT24,F.DT25

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