Dissecting the Binding Mode of Low Affinity Phage Display Peptide Ligands to Protein Targets by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry

Research output: Contribution to journalJournal articleResearchpeer-review

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Dissecting the Binding Mode of Low Affinity Phage Display Peptide Ligands to Protein Targets by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry. / Leurs, Ulrike; Lohse, Brian; Ming, Shonoi A; Cole, Philip A; Clausen, Rasmus P; Kristensen, Jesper L; Rand, Kasper D.

In: Analytical Chemistry, Vol. 86, No. 23, 17.10.2014, p. 11734-11741.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Leurs, U, Lohse, B, Ming, SA, Cole, PA, Clausen, RP, Kristensen, JL & Rand, KD 2014, 'Dissecting the Binding Mode of Low Affinity Phage Display Peptide Ligands to Protein Targets by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry', Analytical Chemistry, vol. 86, no. 23, pp. 11734-11741. https://doi.org/10.1021/ac503137u

APA

Leurs, U., Lohse, B., Ming, S. A., Cole, P. A., Clausen, R. P., Kristensen, J. L., & Rand, K. D. (2014). Dissecting the Binding Mode of Low Affinity Phage Display Peptide Ligands to Protein Targets by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry. Analytical Chemistry, 86(23), 11734-11741. https://doi.org/10.1021/ac503137u

Vancouver

Leurs U, Lohse B, Ming SA, Cole PA, Clausen RP, Kristensen JL et al. Dissecting the Binding Mode of Low Affinity Phage Display Peptide Ligands to Protein Targets by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry. Analytical Chemistry. 2014 Oct 17;86(23):11734-11741. https://doi.org/10.1021/ac503137u

Author

Leurs, Ulrike ; Lohse, Brian ; Ming, Shonoi A ; Cole, Philip A ; Clausen, Rasmus P ; Kristensen, Jesper L ; Rand, Kasper D. / Dissecting the Binding Mode of Low Affinity Phage Display Peptide Ligands to Protein Targets by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry. In: Analytical Chemistry. 2014 ; Vol. 86, No. 23. pp. 11734-11741.

Bibtex

@article{4f6503b7086b4745af7cda7782615b7c,
title = "Dissecting the Binding Mode of Low Affinity Phage Display Peptide Ligands to Protein Targets by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry",
abstract = "Phage display (PD) is frequently used to discover peptides capable of binding to biological protein targets. The structural characterization of peptide-protein complexes is often challenging due to their low binding affinities and high structural flexibility. Here, we investigate the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize interactions of low affinity peptides with their cognate protein targets. The HDX-MS workflow was optimized to accurately detect low-affinity peptide-protein interactions by use of ion mobility, electron transfer dissociation, non-binding control peptides and statistical analysis of replicate data. We show that HDX-MS can identify regions in the two epigenetic regulator proteins KDM4C and KDM1A that are perturbed through weak interactions with PD-identified peptides. Two peptides cause reduced HDX on opposite sides of the active site of KDM4C, indicating distinct binding modes. In contrast, the perturbation site of another PD-selected peptide inhibiting the function of KDM1A maps to a GST-tag. Our results demonstrate that HDX-MS can validate and map weak peptide-protein interactions, and pave the way for understanding and optimizing the binding of peptide scaffolds identified through PD and similar ligand discovery approaches.",
author = "Ulrike Leurs and Brian Lohse and Ming, {Shonoi A} and Cole, {Philip A} and Clausen, {Rasmus P} and Kristensen, {Jesper L} and Rand, {Kasper D}",
year = "2014",
month = "10",
day = "17",
doi = "10.1021/ac503137u",
language = "English",
volume = "86",
pages = "11734--11741",
journal = "Analytical Chemistry",
issn = "0003-2700",
publisher = "American Chemical Society",
number = "23",

}

RIS

TY - JOUR

T1 - Dissecting the Binding Mode of Low Affinity Phage Display Peptide Ligands to Protein Targets by Hydrogen/Deuterium Exchange Coupled to Mass Spectrometry

AU - Leurs, Ulrike

AU - Lohse, Brian

AU - Ming, Shonoi A

AU - Cole, Philip A

AU - Clausen, Rasmus P

AU - Kristensen, Jesper L

AU - Rand, Kasper D

PY - 2014/10/17

Y1 - 2014/10/17

N2 - Phage display (PD) is frequently used to discover peptides capable of binding to biological protein targets. The structural characterization of peptide-protein complexes is often challenging due to their low binding affinities and high structural flexibility. Here, we investigate the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize interactions of low affinity peptides with their cognate protein targets. The HDX-MS workflow was optimized to accurately detect low-affinity peptide-protein interactions by use of ion mobility, electron transfer dissociation, non-binding control peptides and statistical analysis of replicate data. We show that HDX-MS can identify regions in the two epigenetic regulator proteins KDM4C and KDM1A that are perturbed through weak interactions with PD-identified peptides. Two peptides cause reduced HDX on opposite sides of the active site of KDM4C, indicating distinct binding modes. In contrast, the perturbation site of another PD-selected peptide inhibiting the function of KDM1A maps to a GST-tag. Our results demonstrate that HDX-MS can validate and map weak peptide-protein interactions, and pave the way for understanding and optimizing the binding of peptide scaffolds identified through PD and similar ligand discovery approaches.

AB - Phage display (PD) is frequently used to discover peptides capable of binding to biological protein targets. The structural characterization of peptide-protein complexes is often challenging due to their low binding affinities and high structural flexibility. Here, we investigate the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize interactions of low affinity peptides with their cognate protein targets. The HDX-MS workflow was optimized to accurately detect low-affinity peptide-protein interactions by use of ion mobility, electron transfer dissociation, non-binding control peptides and statistical analysis of replicate data. We show that HDX-MS can identify regions in the two epigenetic regulator proteins KDM4C and KDM1A that are perturbed through weak interactions with PD-identified peptides. Two peptides cause reduced HDX on opposite sides of the active site of KDM4C, indicating distinct binding modes. In contrast, the perturbation site of another PD-selected peptide inhibiting the function of KDM1A maps to a GST-tag. Our results demonstrate that HDX-MS can validate and map weak peptide-protein interactions, and pave the way for understanding and optimizing the binding of peptide scaffolds identified through PD and similar ligand discovery approaches.

U2 - 10.1021/ac503137u

DO - 10.1021/ac503137u

M3 - Journal article

C2 - 25325890

VL - 86

SP - 11734

EP - 11741

JO - Analytical Chemistry

JF - Analytical Chemistry

SN - 0003-2700

IS - 23

ER -

ID: 126111855