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Okuda A, Shimizu M, Inoue R, Urade R, Sugiyama M. Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance. Angew Chem Int Ed Engl 2023; 62:e202214412. [PMID: 36347766 DOI: 10.1002/anie.202214412] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 11/10/2022]
Abstract
Three domain fragments of a multi-domain protein, ER-60, were ligated in two short linker regions using asparaginyl endopeptidase not involving denaturation. To identify appropriate ligation sites, by selecting several potential ligation sites with fewer mutations around two short linker regions, their ligation efficiencies and the functions of the ligated ER-60s were examined experimentally. To evaluate the dependence of ligation efficiencies on the ligation sites computationally, steric hinderances around the sites for the ligation were calculated through molecular dynamics simulations. Utilizing the steric hindrance, a site-dependent ligation potential index was introduced as reproducing the experimental ligation efficiency. Referring to this index, the reconstruction of ER-60 was succeeded by the ligation of the three domains for the first time. In addition, the new ligation potential index well-worked for application to other domain ligations. Therefore, the index may serve as a more time-effective tool for multi-site ligations.
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Affiliation(s)
- Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
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Boyko KV, Rosenkranz EA, Smith DM, Miears HL, Oueld es cheikh M, Lund MZ, Young JC, Reardon PN, Okon M, Smirnov SL, Antos JM. Sortase-mediated segmental labeling: A method for segmental assignment of intrinsically disordered regions in proteins. PLoS One 2021; 16:e0258531. [PMID: 34710113 PMCID: PMC8553144 DOI: 10.1371/journal.pone.0258531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
A significant number of proteins possess sizable intrinsically disordered regions (IDRs). Due to the dynamic nature of IDRs, NMR spectroscopy is often the tool of choice for characterizing these segments. However, the application of NMR to IDRs is often hindered by their instability, spectral overlap and resonance assignment difficulties. Notably, these challenges increase considerably with the size of the IDR. In response to these issues, here we report the use of sortase-mediated ligation (SML) for segmental isotopic labeling of IDR-containing samples. Specifically, we have developed a ligation strategy involving a key segment of the large IDR and adjacent folded headpiece domain comprising the C-terminus of A. thaliana villin 4 (AtVLN4). This procedure significantly reduces the complexity of NMR spectra and enables group identification of signals arising from the labeled IDR fragment, a process we refer to as segmental assignment. The validity of our segmental assignment approach is corroborated by backbone residue-specific assignment of the IDR using a minimal set of standard heteronuclear NMR methods. Using segmental assignment, we further demonstrate that the IDR region adjacent to the headpiece exhibits nonuniform spectral alterations in response to temperature. Subsequent residue-specific characterization revealed two segments within the IDR that responded to temperature in markedly different ways. Overall, this study represents an important step toward the selective labeling and probing of target segments within much larger IDR contexts. Additionally, the approach described offers significant savings in NMR recording time, a valuable advantage for the study of unstable IDRs, their binding interfaces, and functional mechanisms.
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Affiliation(s)
- Kristina V. Boyko
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Erin A. Rosenkranz
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Derrick M. Smith
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Heather L. Miears
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Melissa Oueld es cheikh
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Micah Z. Lund
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - Jeffery C. Young
- Department of Biology, Western Washington University, Bellingham, Washington, United States of America
| | - Patrick N. Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, Oregon, United States of America
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Serge L. Smirnov
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
| | - John M. Antos
- Department of Chemistry, Western Washington University, Bellingham, Washington, United States of America
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Vogl DP, Conibear AC, Becker CFW. Segmental and site-specific isotope labelling strategies for structural analysis of posttranslationally modified proteins. RSC Chem Biol 2021; 2:1441-1461. [PMID: 34704048 PMCID: PMC8496066 DOI: 10.1039/d1cb00045d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
Posttranslational modifications can alter protein structures, functions and locations, and are important cellular regulatory and signalling mechanisms. Spectroscopic techniques such as nuclear magnetic resonance, infrared and Raman spectroscopy, as well as small-angle scattering, can provide insights into the structural and dynamic effects of protein posttranslational modifications and their impact on interactions with binding partners. However, heterogeneity of modified proteins from natural sources and spectral complexity often hinder analyses, especially for large proteins and macromolecular assemblies. Selective labelling of proteins with stable isotopes can greatly simplify spectra, as one can focus on labelled residues or segments of interest. Employing chemical biology tools for modifying and isotopically labelling proteins with atomic precision provides access to unique protein samples for structural biology and spectroscopy. Here, we review site-specific and segmental isotope labelling methods that are employed in combination with chemical and enzymatic tools to access posttranslationally modified proteins. We discuss illustrative examples in which these methods have been used to facilitate spectroscopic studies of posttranslationally modified proteins, providing new insights into biology.
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Affiliation(s)
- Dominik P Vogl
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
| | - Anne C Conibear
- The University of Queensland, School of Biomedical Sciences St Lucia Brisbane 4072 QLD Australia
| | - Christian F W Becker
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
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