Conformational changes in tertiary structure near the ligand binding site of an integrin I domain

Abstract Localization of epitopes for platelet-associated (PA) anti–GPIIb-IIIa (αIIbβ3) autoantibodies in chronic immune thrombocytopenic purpura remains elusive. Previous studies suggest that PA antibodies recognize the tertiary structure of intact glycoprotein (GP) IIb-IIIa. To localize their epitopes using antigen-capture enzyme-linked immunosorbent assay (ELISA), the reactivity of 34 PA anti–GPIIb-IIIa antibodies was examined with recombinant GPIIb-IIIa having a defect in ligand-binding sites in either GPIIb or GPIIIa, and no major conformational change was induced: KO variant GPIIb-IIIa was attributed to a 2–amino acid insertion between residues 160 and 161 in the W3 4-1 loop in GPIIb, and CAM variant GPIIb-IIIa was attributed to D119Y in GPIIIa. In one third (11 of 34) of the patients, PA antibodies showed a marked decrease (less than 50%) in reactivity with KO compared with wild-type GPIIb-IIIa. Their reactivity was also impaired against GPIIbD163A-IIIa. In sharp contrast, they reacted normally with CAM GPIIb-IIIa. OP-G2, a ligand-mimetic monoclonal antibody, markedly inhibited their binding to GPIIb-IIIa in patients with impaired binding to KO GPIIb-IIIa, but small GPIIb-IIIa antagonists did not. In addition, a newly developed sensitive ELISA indicated that autoantibodies showing impaired binding to KO are more potent inhibitors for fibrinogen binding. The present data suggest that certain PA anti–GPIIb-IIIa autoantibodies recognize epitopes close to the ligand-binding site in GPIIb, but not in GPIIIa.

Download Full-text

Nuclear magnetic resonance studies of hemoglobins. VII. Tertiary structure around ligand binding site in carbonmonoxyhemoglobin

Biochemistry ◽

10.1021/bi00759a023 ◽

1972 ◽

Vol 11 (9) ◽

pp. 1677-1681 ◽

Cited By ~ 73

Author(s):

Ted R. Lindstrom ◽

Ingrid B. E. Noren ◽

Samuel Charache ◽

Hermann Lehmann ◽

Chein Ho

Keyword(s):

Nuclear Magnetic Resonance ◽

Magnetic Resonance ◽

Ligand Binding ◽

Binding Site ◽

Tertiary Structure ◽

Ligand Binding Site ◽

Magnetic Resonance Studies ◽

Nuclear Magnetic

Download Full-text

Conformational changes of loops highlight a potential binding site in Rhodococcus equi VapB

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x2100738x ◽

2021 ◽

Vol 77 (8) ◽

Author(s):

Christina Geerds ◽

Albert Haas ◽

Hartmut H. Niemann

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Conformational Changes ◽

Structural Similarity ◽

Crystal Form ◽

Rhodococcus Equi ◽

Ligand Binding Site ◽

Binding Function ◽

Potential Binding ◽

Associated Proteins

Virulence-associated proteins (Vaps) contribute to the virulence of the pathogen Rhodococcus equi, but their mode of action has remained elusive. All Vaps share a conserved core of about 105 amino acids that folds into a compact eight-stranded antiparallel β-barrel with a unique topology. At the top of the barrel, four loops connect the eight β-strands. Previous Vap structures did not show concave surfaces that might serve as a ligand-binding site. Here, the structure of VapB in a new crystal form was determined at 1.71 Å resolution. The asymmetric unit contains two molecules. In one of them, the loop regions at the top of the barrel adopt a different conformation from other Vap structures. An outward movement of the loops results in the formation of a hydrophobic cavity that might act as a ligand-binding site. This lends further support to the hypothesis that the structural similarity between Vaps and avidins suggests a potential binding function for Vaps.

Download Full-text

Modulation of HIF-2 Function with Small Molecules: Did Nature Beat Us to It?

Blood ◽

10.1182/blood.v118.21.sci-39.sci-39 ◽

2011 ◽

Vol 118 (21) ◽

pp. SCI-39-SCI-39

Author(s):

Richard K. Bruick ◽

Kevin H Gardner ◽

John MacMillan ◽

Uttam Tambar

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Conformational Changes ◽

Conflicts Of Interest ◽

Single Agent ◽

Amino Acid Identity ◽

Ligand Binding Site ◽

Low Oxygen ◽

High Amino Acid

Abstract Abstract SCI-39 Hypoxia inducible factors (HIFs) govern a mammalian cellular hypoxic response, regulating the transcription of hundreds of genes in response to low oxygen levels. Though this pathway performs critical functions under physiological conditions, increased levels of HIFs are also highly correlated with several disease states. As such, the development of artificial compounds that directly and selectively regulate HIF function is of interest. We have used a combination of biophysical, biochemical, and chemical approaches to study the structure and function of the Per-ARNT-Sim (PAS) domains of human HIFs, which serve as critical protein/protein interaction modules in assembling the functional HIF heterodimer. These studies have revealed the presence of a putative ligand-binding site within one of the HIF-2α PAS domains. A series of biased and unbiased approaches were undertaken to identify compounds that bind at this site and trigger conformational changes within the domain, leading to dissociation of the HIF-2 heterodimer in vitro and in living cells. Consequently, the expression of many hypoxia-inducible genes can be coordinately downregulated by a single agent. Despite its high amino acid identity, HIF-1α lacks a comparable ligand-binding site, indicating that these agents will be useful in deciphering differences in the biological roles of the HIF-1 and HIF-2 isoforms. The presence of a preformed cavity within HIF-2α is particularly as exciting as it suggests the potential for direct physiological regulation of HIF-2 by endogenous metabolite(s). Together, these studies offer further insight into HIF function and regulation while providing chemical tools that advance therapeutic applications. Disclosures: No relevant conflicts of interest to declare.

Download Full-text