Significant structural and functional change of an antigen-binding site by a distant amino acid substitution: Proposal of a structural mechanism

N. C. Chien, V. A. Roberts, A. M. Giusti, Matthew D. Scharff, E. D. Getzoff

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Abstract

To study the molecular basis for antibody diversity and the structural basis for antigen binding, we have characterized the loss of phosphocholine (P-Cho) binding both experimentally and computationally in U10, a somatic mutant of the antibody S107. Nucleotide sequencing of U10 shows a single base change in J(H)1, substituting Asp-101 with Ala, over 9 Å distant from the P-Cho-binding pocket. Probing with anti-idiotypic antibodies suggests local, not global, conformational changes. Computational results support a specific structural mechanism for the loss of P-Cho binding. The U10 mutation eliminates the charged interaction between Asp-101 and Arg-94, which allows the Arg-94 side chain to disrupt P-Cho binding sterically and electrostatically by folding into the P-Cho-binding site. These results specifically show the importance of the Arg-94 to Asp-101 side chain salt bridge in the heavy-chain CDR3 conformation and suggest that residues distant from the binding site play an important role in antibody diversity and inducible complementarity.

Original languageEnglish (US)
Pages (from-to)5532-5536
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume86
Issue number14
StatePublished - 1989

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Phosphorylcholine
Amino Acid Substitution
Binding Sites
Antigens
Antibody Diversity
Anti-Idiotypic Antibodies
Nucleotides
Salts
Mutation
Antibodies

ASJC Scopus subject areas

  • General
  • Genetics

Cite this

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title = "Significant structural and functional change of an antigen-binding site by a distant amino acid substitution: Proposal of a structural mechanism",
abstract = "To study the molecular basis for antibody diversity and the structural basis for antigen binding, we have characterized the loss of phosphocholine (P-Cho) binding both experimentally and computationally in U10, a somatic mutant of the antibody S107. Nucleotide sequencing of U10 shows a single base change in J(H)1, substituting Asp-101 with Ala, over 9 {\AA} distant from the P-Cho-binding pocket. Probing with anti-idiotypic antibodies suggests local, not global, conformational changes. Computational results support a specific structural mechanism for the loss of P-Cho binding. The U10 mutation eliminates the charged interaction between Asp-101 and Arg-94, which allows the Arg-94 side chain to disrupt P-Cho binding sterically and electrostatically by folding into the P-Cho-binding site. These results specifically show the importance of the Arg-94 to Asp-101 side chain salt bridge in the heavy-chain CDR3 conformation and suggest that residues distant from the binding site play an important role in antibody diversity and inducible complementarity.",
author = "Chien, {N. C.} and Roberts, {V. A.} and Giusti, {A. M.} and Scharff, {Matthew D.} and Getzoff, {E. D.}",
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T1 - Significant structural and functional change of an antigen-binding site by a distant amino acid substitution

T2 - Proposal of a structural mechanism

AU - Chien, N. C.

AU - Roberts, V. A.

AU - Giusti, A. M.

AU - Scharff, Matthew D.

AU - Getzoff, E. D.

PY - 1989

Y1 - 1989

N2 - To study the molecular basis for antibody diversity and the structural basis for antigen binding, we have characterized the loss of phosphocholine (P-Cho) binding both experimentally and computationally in U10, a somatic mutant of the antibody S107. Nucleotide sequencing of U10 shows a single base change in J(H)1, substituting Asp-101 with Ala, over 9 Å distant from the P-Cho-binding pocket. Probing with anti-idiotypic antibodies suggests local, not global, conformational changes. Computational results support a specific structural mechanism for the loss of P-Cho binding. The U10 mutation eliminates the charged interaction between Asp-101 and Arg-94, which allows the Arg-94 side chain to disrupt P-Cho binding sterically and electrostatically by folding into the P-Cho-binding site. These results specifically show the importance of the Arg-94 to Asp-101 side chain salt bridge in the heavy-chain CDR3 conformation and suggest that residues distant from the binding site play an important role in antibody diversity and inducible complementarity.

AB - To study the molecular basis for antibody diversity and the structural basis for antigen binding, we have characterized the loss of phosphocholine (P-Cho) binding both experimentally and computationally in U10, a somatic mutant of the antibody S107. Nucleotide sequencing of U10 shows a single base change in J(H)1, substituting Asp-101 with Ala, over 9 Å distant from the P-Cho-binding pocket. Probing with anti-idiotypic antibodies suggests local, not global, conformational changes. Computational results support a specific structural mechanism for the loss of P-Cho binding. The U10 mutation eliminates the charged interaction between Asp-101 and Arg-94, which allows the Arg-94 side chain to disrupt P-Cho binding sterically and electrostatically by folding into the P-Cho-binding site. These results specifically show the importance of the Arg-94 to Asp-101 side chain salt bridge in the heavy-chain CDR3 conformation and suggest that residues distant from the binding site play an important role in antibody diversity and inducible complementarity.

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