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Hrabarova E, Belkova M, Koszagova R, Nahalka J. Pull-Down Into Active Inclusion Bodies and Their Application in the Detection of (Poly)-Phosphates and Metal-Ions. Front Bioeng Biotechnol 2022; 10:833192. [PMID: 35299638 PMCID: PMC8921494 DOI: 10.3389/fbioe.2022.833192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Inclusion bodies are typically ignored as they are considered unwanted protein waste generated by prokaryotic host cells during recombinant protein production or harmful protein inclusions in human cell biology. However, these protein particles may have applications for in vivo immobilization in industrial biocatalysis or as cell-tolerable protein materials for the pharmaceuticals industry and clinical development. Thus, there is a need to in vivo “pull-down” (insolubilize) soluble enzymes and proteins into inclusion bodies. Accordingly, in this study, sequences from the short-chain polyphosphatase ygiF were used to design pull-down tags capable of detecting (poly)-phosphates and metal ions. These tags were compared with the entire CHAD domain from Escherichia coli ygiF and SACS2 CHAD from Saccharolobus solfataricus. The results demonstrated that highly soluble green fluorescent protein variants could be pulled down into the inclusion bodies and could have modified sensitivity to metals and di-/tri-inorganic phosphates.
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Affiliation(s)
- Eva Hrabarova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Martina Belkova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Romana Koszagova
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
| | - Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Bratislava, Slovakia
- Institute of Chemistry, Centre of Excellence for White-green Biotechnology, Slovak Academy of Sciences, Nitra, Slovakia
- *Correspondence: Jozef Nahalka,
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Arakawa T, Tokunaga M, Kita Y, Niikura T, Baker RW, Reimer JM, Leschziner AE. Structure Analysis of Proteins and Peptides by Difference Circular Dichroism Spectroscopy. Protein J 2021; 40:867-875. [PMID: 34709521 DOI: 10.1007/s10930-021-10024-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 11/25/2022]
Abstract
Difference circular dichroism (CD) spectroscopy was used here to characterize changes in structure of flexible peptides upon altering their environments. Environmental changes were introduced by binding to a large target structure, temperature shift (or concentration increase) or so-called membrane-mimicking solvents. The first case involved binding of a largely disordered peptide to its target structure associated with chromatin remodeling, leading to a transition into a highly helical structure. The second example was a short 8HD (His-Asp) repeat peptide that can bind metal ions. Both Zn and Ni at μM concentrations resulted in different type of changes in secondary structure, suggesting that these metal ions provide different environments for the peptide to assume unique secondary structures. The third case is related to a few short neuroprotective peptides that were largely disordered in aqueous solution. Increased temperature resulted in induction of significant, though small, β-sheet structures. Last example was the induction of non-helical structures for short neuroprotective peptides by membrane-mimicking solvents, including trifluoroethanol, dodecylphosphocholine and sodium dodecylsulfate. While these agents are known to induce α-helix, none of the neuropeptides underwent transition to a typical helical structure. However, trifluoroethanol did induce α-helix for the first peptide involved in chromatin remodeling described above in the first example.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Road, San Diego, CA, 92130, USA.
| | - Masao Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, 890-0065, Japan
| | - Yoshiko Kita
- Alliance Protein Laboratories, 13380 Pantera Road, San Diego, CA, 92130, USA
| | - Takako Niikura
- Department of Information and Communication Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan
| | - Richard W Baker
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Janice M Reimer
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
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Ahamad T, Naushad M, Eldesoky GE, Alqadami AA, Khan A. Synthesis and characterization of egg-albumen-formaldehyde based magnetic polymeric resin (MPR): Highly efficient adsorbent for Cd(II) ion removal from aqueous medium. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.110951] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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