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Callahan N, Siegall WB, Bergonzo C, Marino JP, Kelman Z. Contributions from ClpS surface residues in modulating N-terminal peptide binding and their implications for NAAB development. Protein Eng Des Sel 2023; 36:gzad007. [PMID: 37498171 DOI: 10.1093/protein/gzad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/20/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023] Open
Abstract
Numerous technologies are currently in development for use in next-generation protein sequencing platforms. A notable published approach employs fluorescently-tagged binding proteins to identity the N-terminus of immobilized peptides, in-between rounds of digestion. This approach makes use of N-terminal amino acid binder (NAAB) proteins, which would identify amino acids by chemical and shape complementarity. One source of NAABs is the ClpS protein family, which serve to recruit proteins to bacterial proteosomes based on the identity of the N-terminal amino acid. In this study, a Thermosynechococcus vestitus (also known as Thermosynechococcus elongatus) ClpS2 protein was used as the starting point for direct evolution of an NAAB with affinity and specificity for N-terminal leucine. Enriched variants were analyzed and shown to improve the interaction between the ClpS surface and the peptide chain, without increasing promiscuity. Interestingly, interactions were found that were unanticipated which favor different charged residues located at position 5 from the N-terminus of a target peptide.
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Affiliation(s)
- Nicholas Callahan
- Institute for Bioscience and Biotechnology Research (IBBR), National Institute of Standards & Technology (NIST) and the University of Maryland (UMD), 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - William B Siegall
- Institute for Bioscience and Biotechnology Research (IBBR), National Institute of Standards & Technology (NIST) and the University of Maryland (UMD), 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Christina Bergonzo
- Institute for Bioscience and Biotechnology Research (IBBR), National Institute of Standards & Technology (NIST) and the University of Maryland (UMD), 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards & Technology (NIST), 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research (IBBR), National Institute of Standards & Technology (NIST) and the University of Maryland (UMD), 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards & Technology (NIST), 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research (IBBR), National Institute of Standards & Technology (NIST) and the University of Maryland (UMD), 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards & Technology (NIST), 100 Bureau Drive, Gaithersburg, MD 20899, USA
- Biomolecular Labeling Laboratory, IBBR, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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Tullman J, Marino JP, Kelman Z. Leveraging nature's biomolecular designs in next-generation protein sequencing reagent development. Appl Microbiol Biotechnol 2020; 104:7261-71. [PMID: 32617618 DOI: 10.1007/s00253-020-10745-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 01/18/2023]
Abstract
Next-generation approaches for protein sequencing are now emerging that could have the potential to revolutionize the field in proteomics. One such sequencing method involves fluorescence-based imaging of immobilized peptides in which the N-terminal amino acid of a polypeptide is readout sequentially by a series of fluorescently labeled biomolecules. When selectively bound to a specific N-terminal amino acid, the NAAB (N-terminal amino acid binder) affinity reagent identifies the amino acid through its associated fluorescence tag. A key technical challenge in implementing this fluoro-sequencing approach is the need to develop NAAB affinity reagents with the high affinity and selectivity for specific N-terminal amino acids required for this biotechnology application. One approach to develop such a NAAB affinity reagent is to leverage naturally occurring biomolecules that bind amino acids and/or peptides. Here, we describe several candidate biomolecules that could be considered for this purpose and discuss the potential for developability of each. Key points • Next-generation sequencing methods are emerging that could revolutionize proteomics. • Sequential readout of N-terminal amino acids by fluorescent-tagged affinity reagents. • Native peptide/amino acid binders can be engineered into affinity reagents. • Protein size and structure contribute to feasibility of reagent developability.
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