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Synthetic site-directed ligands.

A B Edmundson1, J N Herron, K R Ely

  • 1Department of Biology, University of Utah, Salt Lake City 84112.

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
|June 12, 1989
PubMed
Summary
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X-ray analysis reveals how immunoglobulin fragments bind diverse molecules. Protein structures adapt to ligands, with binding sites varying in size and shape between different antibody fragments and dimers.

Area of Science:

  • Structural biology
  • Biochemistry
  • Immunology

Background:

  • Immunoglobulin fragments like Fab and Bence-Jones dimers are crucial for molecular recognition.
  • Understanding ligand-protein interactions at atomic resolution is key to drug design and immunology.

Purpose of the Study:

  • To investigate the structural basis of ligand binding to immunoglobulin fragments using X-ray crystallography.
  • To compare the binding sites and conformational changes in different immunoglobulin systems.

Main Methods:

  • X-ray crystallography was used to study complexes of immunoglobulin fragments with nucleotides, peptides, and small molecules.
  • Diffusion of various ligands into protein crystals allowed for co-crystallization and structural analysis.
  • Fourier difference analysis was employed to locate bound ligands within the protein structures.

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Main Results:

  • Fab (BV04-01) showed extensive structural changes upon binding deoxythymidylate oligonucleotides, with co-crystallization occurring in a different space group.
  • The human Mcg Bence-Jones dimer exhibited conformational changes in both ligand and protein upon binding opioid peptides and dinitrophenyl (DNP) derivatives.
  • Tyrosine residues in the dimer's binding cavity acted as flexible "trap-doors" to accommodate ligands, and peptide binding was specific to predicted sites.

Conclusions:

  • Ligand binding induces significant conformational flexibility in some immunoglobulin fragments, while others show more rigid binding pockets.
  • The size and shape of binding sites differ considerably between Fab and Bence-Jones dimer systems, impacting ligand accommodation.
  • X-ray analysis provides detailed insights into the molecular mechanisms of antibody-antigen and related interactions.