Development of α-Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction

Jo, Hyunil; Meinhardt, Nataline; Wu, Yibing; Kulkarni, Swapnil; Hu, Xiaozhen; Low, Kristin E.; Davies, Peter L.; DeGrado, William F.; Greenbaum, Doron C.

doi:10.1021/ja307599z

Cited by 261Calpain Protease Function and RegulationChemical Synthesis and AnalysisProtein Structure and Dynamics

Development of α-Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction

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Jo, Hyunil, Meinhardt, Nataline, Wu, Yibing, Kulkarni, Swapnil, Hu, Xiaozhen, Low, Kristin E., Davies, Peter L., DeGrado, William F. +1 more·2012·Journal of the American Chemical Society

DOI 10.1021/ja307599zPMC PMC3523126

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Abstract

We have designed a highly specific inhibitor of calpain by mimicking a natural protein-protein interaction between calpain and its endogenous inhibitor calpastatin. To enable this goal we established a new method of stabilizing an α-helix in a small peptide by screening 24 commercially available cross-linkers for successful cysteine alkylation in a model peptide sequence. The effects of cross-linking on the α-helicity of selected peptides were examined by CD and NMR spectroscopy, and revealed structurally rigid cross-linkers to be the best at stabilizing α-helices. We applied this strategy to the design of inhibitors of calpain that are based on calpastatin, an intrinsically unstable polypeptide that becomes structured upon binding to the enzyme. A two-turn α-helix that binds proximal to the active site cleft was stabilized, resulting in a potent and selective inhibitor for calpain. We further expanded the utility of this inhibitor by developing irreversible calpain family activity-based probes (ABPs), which retained the specificity of the stabilized helical inhibitor. We believe the inhibitor and ABPs will be useful for future investigation of calpains, while the cross-linking technique will enable exploration of other protein-protein interactions.

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Authors: Jo, H., Meinhardt, N., Wu, Y., Kulkarni, S., Hu, X., Low, K. E., Davies, P. L., DeGrado, W. F., & Greenbaum, D. C.
Affiliations: University of California, San Francisco (US)
University of Pennsylvania (US)
Queen's University (CA)
Corresponding author: DeGrado, William F.
Greenbaum, Doron C.
ORCID: Jo, Hyunil
Wu, Yibing
Hu, Xiaozhen
Low, Kristin E.
Davies, Peter L.
DeGrado, William F.
Venue: Journal of the American Chemical Society
Publisher: American Chemical Society (ACS)
Published: 2012-10-11
Volume: 134
Issue: 42
Pages: 17704-17713
ISSN: 0002-7863 (ISSN-L)
1520-5126
DOI: 10.1021/ja307599z
PMC: PMC3523126
OpenAlex: W1982782947
Cited by: 261
References: 98
Citations by year: 2026: 8 · 2025: 12 · 2024: 15 · 2023: 14 · 2022: 11 · 2021: 23 · 2020: 24 · 2019: 19 · 2018: 29 · 2017: 28 · 2016: 25 · 2015: 23 · 2014: 23 · 2013: 7
FWCI: 8.02
Type: journal article
Language: en
Open access: green
europepmc.org
Locations: Journal of the American Chemical Society (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: Canadian Institutes of Health Research
National Institute of General Medical Sciences (R37GM054616, GM-54616, R01GM054616, T32GM071339)
National Institute of Allergy and Infectious Diseases (R01AI097273)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Calpain Protease Function and Regulation
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords: calpain inhibitors, calpastatin, alpha-helix stabilization, crosslinking agents, cysteine alkylation, activity-based probes, peptide helicity
MeSH terms: Calcium-Binding Proteins, Calpain, Models, Molecular, Protein Binding, Structure-Activity Relationship, Molecular Structure, Cysteine Proteinase Inhibitors, Protein Structure, Secondary

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Development of α-Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction

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