Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

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Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations. / Eildal, Jonas N N; Hultqvist, Greta; Balle, Thomas; Stuhr-Hansen, Nicolai; Padrah, Shahrokh; Gianni, Stefano; Strømgaard, Kristian; Jemth, Per.

In: Journal of the American Chemical Society, Vol. 135, No. 35, 04.09.2013, p. 12998-3007.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Eildal, JNN, Hultqvist, G, Balle, T, Stuhr-Hansen, N, Padrah, S, Gianni, S, Strømgaard, K & Jemth, P 2013, 'Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations', Journal of the American Chemical Society, vol. 135, no. 35, pp. 12998-3007. https://doi.org/10.1021/ja402875h

APA

Eildal, J. N. N., Hultqvist, G., Balle, T., Stuhr-Hansen, N., Padrah, S., Gianni, S., ... Jemth, P. (2013). Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations. Journal of the American Chemical Society, 135(35), 12998-3007. https://doi.org/10.1021/ja402875h

Vancouver

Eildal JNN, Hultqvist G, Balle T, Stuhr-Hansen N, Padrah S, Gianni S et al. Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations. Journal of the American Chemical Society. 2013 Sep 4;135(35):12998-3007. https://doi.org/10.1021/ja402875h

Author

Eildal, Jonas N N ; Hultqvist, Greta ; Balle, Thomas ; Stuhr-Hansen, Nicolai ; Padrah, Shahrokh ; Gianni, Stefano ; Strømgaard, Kristian ; Jemth, Per. / Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations. In: Journal of the American Chemical Society. 2013 ; Vol. 135, No. 35. pp. 12998-3007.

Bibtex

@article{c962d37514eb4cf4aed172c1121ecc7d,
title = "Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations",
abstract = "One of the most frequent protein-protein interaction modules in mammalian cells is the postsynaptic density 95/discs large/zonula occludens 1 (PDZ) domain, involved in scaffolding and signaling and emerging as an important drug target for several diseases. Like many other protein-protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1)). This decrease in affinity was mainly due to an increase in the dissociation rate constant, but a significant decrease in the association rate constant was found for some amide-to-ester mutations suggesting that native hydrogen bonds have begun to form in the transition state of the binding reaction. This study provides a general framework for studying the role of backbone hydrogen bonds in protein-peptide interactions and for the first time specifically addresses these for PDZ domain-peptide interactions.",
author = "Eildal, {Jonas N N} and Greta Hultqvist and Thomas Balle and Nicolai Stuhr-Hansen and Shahrokh Padrah and Stefano Gianni and Kristian Str{\o}mgaard and Per Jemth",
year = "2013",
month = "9",
day = "4",
doi = "10.1021/ja402875h",
language = "English",
volume = "135",
pages = "12998--3007",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
publisher = "ACS Publications",
number = "35",

}

RIS

TY - JOUR

T1 - Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

AU - Eildal, Jonas N N

AU - Hultqvist, Greta

AU - Balle, Thomas

AU - Stuhr-Hansen, Nicolai

AU - Padrah, Shahrokh

AU - Gianni, Stefano

AU - Strømgaard, Kristian

AU - Jemth, Per

PY - 2013/9/4

Y1 - 2013/9/4

N2 - One of the most frequent protein-protein interaction modules in mammalian cells is the postsynaptic density 95/discs large/zonula occludens 1 (PDZ) domain, involved in scaffolding and signaling and emerging as an important drug target for several diseases. Like many other protein-protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1)). This decrease in affinity was mainly due to an increase in the dissociation rate constant, but a significant decrease in the association rate constant was found for some amide-to-ester mutations suggesting that native hydrogen bonds have begun to form in the transition state of the binding reaction. This study provides a general framework for studying the role of backbone hydrogen bonds in protein-peptide interactions and for the first time specifically addresses these for PDZ domain-peptide interactions.

AB - One of the most frequent protein-protein interaction modules in mammalian cells is the postsynaptic density 95/discs large/zonula occludens 1 (PDZ) domain, involved in scaffolding and signaling and emerging as an important drug target for several diseases. Like many other protein-protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1)). This decrease in affinity was mainly due to an increase in the dissociation rate constant, but a significant decrease in the association rate constant was found for some amide-to-ester mutations suggesting that native hydrogen bonds have begun to form in the transition state of the binding reaction. This study provides a general framework for studying the role of backbone hydrogen bonds in protein-peptide interactions and for the first time specifically addresses these for PDZ domain-peptide interactions.

U2 - 10.1021/ja402875h

DO - 10.1021/ja402875h

M3 - Journal article

C2 - 23705582

VL - 135

SP - 12998

EP - 13007

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 35

ER -

ID: 96078999