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 language | English (US) |
|---|---|
| Pages (from-to) | 2027-2038 |
| Number of pages | 12 |
| Journal | Journal of Molecular Biology |
| Volume | 425 |
| Issue number | 11 |
| DOIs | |
| State | Published - Jun 12 2013 |
| Externally published | Yes |
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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 journal › Article
}
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 -