Structural and thermodynamic insights into the recognition of native proteins by anti-peptide antibodies

Anthonya Armstrong, James Hildreth, L. Mario Amzel

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

The mechanism by which antibodies elicited against protein-derived peptides achieve cross-reactivity with their cognate proteins remains unknown. To address this question, we have carried out the complete thermodynamic characterization of the association of a monoclonal antibody (260.33.12) raised against a peptide (SNpep) derived from staphylococcal nuclease (SNase) with both eliciting peptide and cognate protein. Although both ligands bind with similar affinity (Kd = 0.42 μM and 0.30 μM for protein and peptide, respectively), protein and peptide binding have highly different thermodynamic signatures: peptide binding is characterized by a large enthalpic contribution (ΔH = - 7.7 kcal/mol) whereas protein binding is dominated by a large entropic contribution (- TΔS = - 7.2 kcal/mol). The structure of the SNpep:Fab complex, determined by X-ray diffraction, reveals that the bound conformation of the peptide differs from the conformation of the corresponding loop region in crystal structures of free SNase. The energy difference, estimated by molecular dynamics simulations between native SNase and a model in which the Ω-loop is built in the conformation of the Fab-bound peptide, shows that the energetic cost of adopting this conformation is compatible with the enthalpic cost of binding the protein vis-à-vis the peptide. These results are compatible with a mechanism by which the anti-peptide antibody recognizes the cognate protein: high affinity is maintained upon binding a non-native conformation by offsetting enthalpic penalties with reduced entropic losses. These findings provide potentially useful guidelines for the identification of linear epitopes within protein sequences that are well suited for the development of synthetic peptide vaccines.

Original languageEnglish (US)
Pages (from-to)2027-2038
Number of pages12
JournalJournal of Molecular Biology
Volume425
Issue number11
DOIs
StatePublished - Jun 12 2013
Externally publishedYes

Fingerprint

Thermodynamics
Anti-Idiotypic Antibodies
Peptides
Micrococcal Nuclease
Proteins
Protein Binding
Costs and Cost Analysis
Synthetic Vaccines
Subunit Vaccines
Molecular Dynamics Simulation
X-Ray Diffraction
Epitopes
Carrier Proteins
Monoclonal Antibodies
Guidelines
Ligands
Antibodies

Keywords

  • antibody
  • isothermal titration calorimetry
  • peptide vaccine
  • protein crystallography

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Structural and thermodynamic insights into the recognition of native proteins by anti-peptide antibodies. / Armstrong, Anthonya; Hildreth, James; Amzel, L. Mario.

In: Journal of Molecular Biology, Vol. 425, No. 11, 12.06.2013, p. 2027-2038.

Research output: Contribution to journalArticle

@article{d32d01b557ea4b62aa80bc8a769fd7cc,
title = "Structural and thermodynamic insights into the recognition of native proteins by anti-peptide antibodies",
abstract = "The mechanism by which antibodies elicited against protein-derived peptides achieve cross-reactivity with their cognate proteins remains unknown. To address this question, we have carried out the complete thermodynamic characterization of the association of a monoclonal antibody (260.33.12) raised against a peptide (SNpep) derived from staphylococcal nuclease (SNase) with both eliciting peptide and cognate protein. Although both ligands bind with similar affinity (Kd = 0.42 μM and 0.30 μM for protein and peptide, respectively), protein and peptide binding have highly different thermodynamic signatures: peptide binding is characterized by a large enthalpic contribution (ΔH = - 7.7 kcal/mol) whereas protein binding is dominated by a large entropic contribution (- TΔS = - 7.2 kcal/mol). The structure of the SNpep:Fab complex, determined by X-ray diffraction, reveals that the bound conformation of the peptide differs from the conformation of the corresponding loop region in crystal structures of free SNase. The energy difference, estimated by molecular dynamics simulations between native SNase and a model in which the Ω-loop is built in the conformation of the Fab-bound peptide, shows that the energetic cost of adopting this conformation is compatible with the enthalpic cost of binding the protein vis-{\`a}-vis the peptide. These results are compatible with a mechanism by which the anti-peptide antibody recognizes the cognate protein: high affinity is maintained upon binding a non-native conformation by offsetting enthalpic penalties with reduced entropic losses. These findings provide potentially useful guidelines for the identification of linear epitopes within protein sequences that are well suited for the development of synthetic peptide vaccines.",
keywords = "antibody, isothermal titration calorimetry, peptide vaccine, protein crystallography",
author = "Anthonya Armstrong and James Hildreth and Amzel, {L. Mario}",
year = "2013",
month = "6",
day = "12",
doi = "10.1016/j.jmb.2013.02.031",
language = "English (US)",
volume = "425",
pages = "2027--2038",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "11",

}

TY - JOUR

T1 - Structural and thermodynamic insights into the recognition of native proteins by anti-peptide antibodies

AU - Armstrong, Anthonya

AU - Hildreth, James

AU - Amzel, L. Mario

PY - 2013/6/12

Y1 - 2013/6/12

N2 - The mechanism by which antibodies elicited against protein-derived peptides achieve cross-reactivity with their cognate proteins remains unknown. To address this question, we have carried out the complete thermodynamic characterization of the association of a monoclonal antibody (260.33.12) raised against a peptide (SNpep) derived from staphylococcal nuclease (SNase) with both eliciting peptide and cognate protein. Although both ligands bind with similar affinity (Kd = 0.42 μM and 0.30 μM for protein and peptide, respectively), protein and peptide binding have highly different thermodynamic signatures: peptide binding is characterized by a large enthalpic contribution (ΔH = - 7.7 kcal/mol) whereas protein binding is dominated by a large entropic contribution (- TΔS = - 7.2 kcal/mol). The structure of the SNpep:Fab complex, determined by X-ray diffraction, reveals that the bound conformation of the peptide differs from the conformation of the corresponding loop region in crystal structures of free SNase. The energy difference, estimated by molecular dynamics simulations between native SNase and a model in which the Ω-loop is built in the conformation of the Fab-bound peptide, shows that the energetic cost of adopting this conformation is compatible with the enthalpic cost of binding the protein vis-à-vis the peptide. These results are compatible with a mechanism by which the anti-peptide antibody recognizes the cognate protein: high affinity is maintained upon binding a non-native conformation by offsetting enthalpic penalties with reduced entropic losses. These findings provide potentially useful guidelines for the identification of linear epitopes within protein sequences that are well suited for the development of synthetic peptide vaccines.

AB - The mechanism by which antibodies elicited against protein-derived peptides achieve cross-reactivity with their cognate proteins remains unknown. To address this question, we have carried out the complete thermodynamic characterization of the association of a monoclonal antibody (260.33.12) raised against a peptide (SNpep) derived from staphylococcal nuclease (SNase) with both eliciting peptide and cognate protein. Although both ligands bind with similar affinity (Kd = 0.42 μM and 0.30 μM for protein and peptide, respectively), protein and peptide binding have highly different thermodynamic signatures: peptide binding is characterized by a large enthalpic contribution (ΔH = - 7.7 kcal/mol) whereas protein binding is dominated by a large entropic contribution (- TΔS = - 7.2 kcal/mol). The structure of the SNpep:Fab complex, determined by X-ray diffraction, reveals that the bound conformation of the peptide differs from the conformation of the corresponding loop region in crystal structures of free SNase. The energy difference, estimated by molecular dynamics simulations between native SNase and a model in which the Ω-loop is built in the conformation of the Fab-bound peptide, shows that the energetic cost of adopting this conformation is compatible with the enthalpic cost of binding the protein vis-à-vis the peptide. These results are compatible with a mechanism by which the anti-peptide antibody recognizes the cognate protein: high affinity is maintained upon binding a non-native conformation by offsetting enthalpic penalties with reduced entropic losses. These findings provide potentially useful guidelines for the identification of linear epitopes within protein sequences that are well suited for the development of synthetic peptide vaccines.

KW - antibody

KW - isothermal titration calorimetry

KW - peptide vaccine

KW - protein crystallography

UR - http://www.scopus.com/inward/record.url?scp=84877700145&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84877700145&partnerID=8YFLogxK

U2 - 10.1016/j.jmb.2013.02.031

DO - 10.1016/j.jmb.2013.02.031

M3 - Article

C2 - 23473830

AN - SCOPUS:84877700145

VL - 425

SP - 2027

EP - 2038

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 11

ER -