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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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Miears HL, Gruber DR, Horvath NM, Antos JM, Young J, Sigurjonsson JP, Klem ML, Rosenkranz EA, Okon M, McKnight CJ, Vugmeyster L, Smirnov SL. Plant Villin Headpiece Domain Demonstrates a Novel Surface Charge Pattern and High Affinity for F-Actin. Biochemistry 2018; 57:1690-1701. [PMID: 29444403 DOI: 10.1021/acs.biochem.7b00856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plants utilize multiple isoforms of villin, an F-actin regulating protein with an N-terminal gelsolin-like core and a distinct C-terminal headpiece domain. Unlike their vertebrate homologues, plant villins have a much longer linker polypeptide connecting the core and headpiece. Moreover, the linker-headpiece connection region in plant villins lacks sequence homology to the vertebrate villin sequences. It is unknown to what extent the plant villin headpiece structure and function resemble those of the well-studied vertebrate counterparts. Here we present the first solution NMR structure and backbone dynamics characterization of a headpiece from plants, villin isoform 4 from Arabidopsis thaliana. The villin 4 headpiece is a 63-residue domain (V4HP63) that adopts a typical headpiece fold with an aromatics core and a tryptophan-centered hydrophobic cap within its C-terminal subdomain. However, V4HP63 has a distinct N-terminal subdomain fold as well as a novel, high mobility loop due to the insertion of serine residue in the canonical sequence that follows the variable length loop in headpiece sequences. The domain binds actin filaments with micromolar affinity, like the vertebrate analogues. However, the V4HP63 surface charge pattern is novel and lacks certain features previously thought necessary for high-affinity F-actin binding. Utilizing the updated criteria for strong F-actin binding, we predict that the headpiece domains of all other villin isoforms in A. thaliana have high affinity for F-actin.
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Affiliation(s)
- Heather L Miears
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - David R Gruber
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - Nicholas M Horvath
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - John M Antos
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - Jeff Young
- Department of Biology , Western Washington University , 516 High Street , Bellingham , Washington 98225-9160 , United States
| | - Johann P Sigurjonsson
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - Maya L Klem
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - Erin A Rosenkranz
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories , University of British Columbia , Vancouver , British Columbia V6T 1Z3 , Canada
| | - C James McKnight
- Department of Physiology and Biophysics , Boston University School of Medicine , 700 Albany Street , Boston , Massachusetts 02118-2526 , United States
| | - Liliya Vugmeyster
- Department of Chemistry , University of Colorado at Denver , Denver , Colorado 80204 , United States
| | - Serge L Smirnov
- Department of Chemistry , Western Washington University , 516 High Street , Bellingham , Washington 98225-9150 , United States
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