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Qiu Z, Nakamura S, Fujimoto K. Reversible photo-cross-linking of the GCN4 peptide containing 3-cyanovinylcarbazole amino acid to double-stranded DNA. Org Biomol Chem 2019; 17:6277-6283. [PMID: 31192345 DOI: 10.1039/c9ob00372j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Interaction analysis in vivo greatly promotes the analyses and understanding of biological functions. The interaction between DNA and peptides or proteins is very important in terms of readout and amplifying information from genomic DNA. In this study, we designed and synthesized a photo-cross-linkable amino acid, l-3-cyanovinlycarbazole amino acid (l-CNVA), to double-stranded DNA. Reversible photo-cross-linking between DNA and peptides containing CNVA, having 3-cyanovinylcarbazole moieties capable of photo-cross-linking to nucleic acids, was demonstrated. As a result, it was shown that the GCN4 peptide, containing CNVA, can be photo-cross-linked to DNA, and its adduct was photo-split into the original peptide and DNA with 312 nm-irradiation. This is the first report that reversibly manipulates photo-crosslinking between double stranded DNA and peptides. In addition, this reversible photo-cross-linking, using l-CNVA, is faster and with higher yield than that using diazirine and psoralen.
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Affiliation(s)
- Zhiyong Qiu
- School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology. Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan.
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Chow HK, Xu J, Shahravan SH, De Jong AT, Chen G, Shin JA. Hybrids of the bHLH and bZIP protein motifs display different DNA-binding activities in vivo vs. in vitro. PLoS One 2008; 3:e3514. [PMID: 18949049 PMCID: PMC2568859 DOI: 10.1371/journal.pone.0003514] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 10/02/2008] [Indexed: 12/18/2022] Open
Abstract
Minimalist hybrids comprising the DNA-binding domain of bHLH/PAS (basic-helix-loop-helix/Per-Arnt-Sim) protein Arnt fused to the leucine zipper (LZ) dimerization domain from bZIP (basic region-leucine zipper) protein C/EBP were designed to bind the E-box DNA site, CACGTG, targeted by bHLHZ (basic-helix-loop-helix-zipper) proteins Myc and Max, as well as the Arnt homodimer. The bHLHZ-like structure of ArntbHLH-C/EBP comprises the Arnt bHLH domain fused to the C/EBP LZ: i.e. swap of the 330 aa PAS domain for the 29 aa LZ. In the yeast one-hybrid assay (Y1H), transcriptional activation from the E-box was strong by ArntbHLH-C/EBP, and undetectable for the truncated ArntbHLH (PAS removed), as detected via readout from the HIS3 and lacZ reporters. In contrast, fluorescence anisotropy titrations showed affinities for the E-box with ArntbHLH-C/EBP and ArntbHLH comparable to other transcription factors (K(d) 148.9 nM and 40.2 nM, respectively), but only under select conditions that maintained folded protein. Although in vivo yeast results and in vitro spectroscopic studies for ArntbHLH-C/EBP targeting the E-box correlate well, the same does not hold for ArntbHLH. As circular dichroism confirms that ArntbHLH-C/EBP is a much more strongly alpha-helical structure than ArntbHLH, we conclude that the nonfunctional ArntbHLH in the Y1H must be due to misfolding, leading to the false negative that this protein is incapable of targeting the E-box. Many experiments, including protein design and selections from large libraries, depend on protein domains remaining well-behaved in the nonnative experimental environment, especially small motifs like the bHLH (60-70 aa). Interestingly, a short helical LZ can serve as a folding- and/or solubility-enhancing tag, an important device given the focus of current research on exploration of vast networks of biomolecular interactions.
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Affiliation(s)
- Hiu-Kwan Chow
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Jing Xu
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - S. Hesam Shahravan
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Antonia T. De Jong
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Gang Chen
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Jumi A. Shin
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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Shahravan SH, Qu X, Chan IS, Shin JA. Enhancing the specificity of the enterokinase cleavage reaction to promote efficient cleavage of a fusion tag. Protein Expr Purif 2008; 59:314-9. [PMID: 18406169 DOI: 10.1016/j.pep.2008.02.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 02/21/2008] [Accepted: 02/27/2008] [Indexed: 10/22/2022]
Abstract
In our work with designed minimalist proteins based on the bZIP motif, we have found our His-tagged proteins to be prone to inclusion body formation and aggregation; we suspect this problem is largely due to the His tag, known to promote aggregation. Using AhR6-C/EBP, a hybrid of the AhR basic region and C/EBP leucine zipper, as representative of our bZIP-like protein family, we attempted removal of the His tag with enterokinase (EK) but obtained the desired cleavage product in very small yield. EK is known for proteolysis at noncanonical sites, and most cleavage occurred at unintended sites. We manipulated experimental conditions to improve specificity of proteolysis and analyzed the cleavage products; no effect was observed after changing pH, temperature, or the amount of EK. We then suspected the accessibility of the EK site was impeded due to protein aggregation. We found that the easily implemented strategy of addition of urea (1-4 M) greatly improved EK cleavage specificity at the canonical site and reduced adventitious cleavage. We believe that this enhancement in specificity is due to a more "open" protein structure, in which the now accessible canonical target can compete effectively with adventitious cleavage sites of related sequence.
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Affiliation(s)
- S Hesam Shahravan
- Department of Chemistry, University of Toronto, Mississauga, Ont., Canada L5L 1C6
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Joshi NS, Whitaker LR, Francis MB. A Three-Component Mannich-Type Reaction for Selective Tyrosine Bioconjugation. J Am Chem Soc 2004; 126:15942-3. [PMID: 15584710 DOI: 10.1021/ja0439017] [Citation(s) in RCA: 248] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new selective bioconjugation reaction is described for the modification of tyrosine residues on protein substrates. The reaction uses imines formed in situ from aldehydes and electron-rich anilines to modify phenolic side chains through a Mannich-type electrophilic aromatic substitution pathway. The reaction takes place under mild pH and temperature conditions and can modify protein substrates at concentrations as low as 20 muM. Using an efficient fluorescence-based assay, we demonstrated the reaction using a number of aldehydes and protein targets. Importantly, proteins lacking surface-accessible tyrosines remained unmodified. It was also demonstrated that enzymatic activity is preserved under the mild reaction conditions. This strategy represents one of the first carbon-carbon bond-forming reactions for protein modification and provides an important complement to more commonly used lysine- and cysteine-based methods.
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Affiliation(s)
- Neel S Joshi
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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Bird GH, Lajmi AR, Shin JA. Sequence-specific recognition of DNA by hydrophobic, alanine-rich mutants of the basic region/leucine zipper motif investigated by fluorescence anisotropy. Biopolymers 2002; 65:10-20. [PMID: 12209468 DOI: 10.1002/bip.10205] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We generated minimalist proteins capable of sequence-specific, high-affinity binding of DNA to probe how proteins are used and can be used to recognize DNA. In order to quantify binding affinities and specificities in our protein-DNA system, we used fluorescence anisotropy to measure in situ the thermodynamics of binding of alanine-rich mutants of the GCN4 basic region/leucine zipper (bZIP) domain to DNA duplexes containing target sites AP-1 (5'-TGACTCA-3') or ATF/CREB (5'-TGACGTCA-3'). We simplified the alpha-helical bZIP molecular recognition scaffold by alanine substitution: 4A, 11A, and 18A contain four, eleven, and eighteen alanine mutations in their DNA-binding basic regions, respectively. DNase I footprinting analysis demonstrates that all bZIP mutants retain the sequence-specific DNA-binding function of native GCN4 bZIP. Titration of fluorescein-labeled oligonucleotide duplexes with increasing amounts of protein yielded low nanomolar dissociation constants for all bZIP mutants in complex with the AP-1 and ATF/CREB sites: binding to the nonspecific control duplex was > 1000-fold weaker. Remarkably, the most heavily mutated protein 18A, containing 24 alanines in its 27-residue basic region, still binds AP-1 and ATF/CREB with dissociation constants of 15 and 7.8 nM, respectively. Similarly, wild-type bZIP binds these sites with K(d) values of 9.1 and 14 nM. 11A also displays low nanomolar dissociation constants for AP-1 and ATF/CREB, while 4A binds these sites with approximately 10-fold weaker K(d) values. Thus, both DNA-binding specificity and affinity are maintained in all our bZIP derivatives. This Ala-rich scaffold may be useful in design and synthesis of small alpha-helical proteins with desired DNA-recognition properties capable of serving as therapeutics targeting transcription.
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Affiliation(s)
- Gregory H Bird
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Bird GH, Shin JA. MALDI-TOF mass spectrometry characterization of recombinant hydrophobic mutants containing the GCN4 basic region/leucine zipper motif. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1597:252-9. [PMID: 12044903 DOI: 10.1016/s0167-4838(02)00303-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to characterize hydrophobic, alanine-rich mutants of the basic region/leucine zipper (bZIP) protein GCN4. These bacterially expressed proteins were generated to probe how small, alpha-helical proteins bind specific DNA sites. Enzymatic digestion mapping combined with MALDI-TOF MS characterization of protein fragments allowed us to resolve mass discrepancies between the expected and observed molecular mass measurements. Changes in mass were attributed to posttranslational modifications (PTMs) by proteolytic cleavage of the initiating methionine residue, carbamylation at the amino terminus, oxidation of histidine side chains, and oxidative addition of beta-mercaptoethanol (BME) at the cysteine side chain. Proteins can undergo a wide variety of co-translational modifications and PTMs during growth, isolation, and purification. Such changes in mass can only be detected by a high-resolution technique such as MALDI, which in conjunction with enzymatic digestion mapping, becomes a powerful methodology for characterization of protein structure.
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Affiliation(s)
- Gregory H Bird
- Department of Chemistry, Faculty of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Lajmi AR, Lovrencic ME, Wallace TR, Thomlinson RR, Shin JA. Minimalist, Alanine-Based, Helical Protein Dimers Bind to Specific DNA Sites. J Am Chem Soc 2000. [DOI: 10.1021/ja993025a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ajay R. Lajmi
- Department of Chemistry, University of Pittsburgh Pittsburgh, Pennsylvania 15260
| | - Michael E. Lovrencic
- Department of Chemistry, University of Pittsburgh Pittsburgh, Pennsylvania 15260
| | - Timothy R. Wallace
- Department of Chemistry, University of Pittsburgh Pittsburgh, Pennsylvania 15260
| | - Robyn R. Thomlinson
- Department of Chemistry, University of Pittsburgh Pittsburgh, Pennsylvania 15260
| | - Jumi A. Shin
- Department of Chemistry, University of Pittsburgh Pittsburgh, Pennsylvania 15260
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Lajmi AR, Wallace TR, Shin JA. Short, hydrophobic, alanine-based proteins based on the basic region/leucine zipper protein motif: overcoming inclusion body formation and protein aggregation during overexpression, purification, and renaturation. Protein Expr Purif 2000; 18:394-403. [PMID: 10733895 DOI: 10.1006/prep.2000.1209] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
GCN4 is a yeast transcriptional regulatory protein; its DNA-binding domain is a basic region/leucine zipper (bZIP) structure that comprises a dimer of alpha-helices capable of high-affinity, sequence-specific recognition of the DNA major groove. We are exploiting what nature has evolved by manipulating the bZIP motif as a molecular recognition scaffold; thus we reduced the elegantly minimal bZIP to an even more simplified structure by substitution with alanine residues-hence, a generic, Ala-based, helical scaffold. These Ala-based mutants are unusual proteins for expression as they are short ( approximately 100 amino acids) and hydrophobic (Ala-mutated basic regions, leucine-zipper dimerization domains). Hydrophobicity posed a major problem throughout the expression, isolation, and purification stages; inclusion body formation and protein aggregation were significant hurdles throughout protein production. We describe measures that solved these problems, including use of high concentrations of denaturant in all steps of protein isolation and purification and use of temperature-dependent renaturing techniques to obtain folded, functional protein. Despite these difficulties, we ultimately retrieved 5-10 mg/L of broth of active, correctly folded protein after the complete purification procedure. Homogeneity of the proteins was established by chromatography, electrophoresis, and mass spectrometry. Furthermore, characterization by circular dichroism and DNase footprinting analysis demonstrates that these alanine-based mutants retain the structure and function of the native GCN4 DNA-binding domain. Remarkably, the most heavily mutated protein, containing 24 alanines of 27 total amino acids in the DNA-binding basic region, still binds the AP-1 site, the target of native GCN4.
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Affiliation(s)
- A R Lajmi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
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