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Wagh MA, Maity R, Bhosale RJ, Semwal D, Tothadi S, Vaidhyanathan R, Sanjayan GJ. Three in One: Triple G-C-T Base-Coded Brahma Nucleobase Amino Acid: Synthesis, Peptide Formation, and Structural Features. J Org Chem 2021; 86:15689-15694. [PMID: 34623156 DOI: 10.1021/acs.joc.1c01228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This note reports the synthesis and peptide formation of a novel triple G-C-T nucleobase amino acid (NBA) building block featuring three recognition faces: DDA (G mimic), DAA (C mimic), and ADA (T mimic). Readily obtainable in multigram scale in a remarkably easy one-step reaction, this unique NBA building block offers scope for wide ranging applications for nucleic acid recognition and nucleic acid peptide/protein interaction studies.
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Affiliation(s)
- Mahendra A Wagh
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road Pashan, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Rahul Maity
- Department of Chemistry and Centre for Energy Science, Indian Institute of Science Education and Research, Dr Homi Bhabha Road Pashan, Pune 411008, India
| | - Rohit J Bhosale
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road Pashan, Pune 411008, India
| | - Divyam Semwal
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road Pashan, Pune 411008, India
| | - Srinu Tothadi
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road Pashan, Pune 411008, India
| | - Ramanathan Vaidhyanathan
- Department of Chemistry and Centre for Energy Science, Indian Institute of Science Education and Research, Dr Homi Bhabha Road Pashan, Pune 411008, India
| | - Gangadhar J Sanjayan
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road Pashan, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
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Takahashi T. Generation of Active Protease Depending on Peptide-Protein Interactions Using Interaction-Dependent Native Chemical Ligation and Protein Trans-Splicing. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tsuyoshi Takahashi
- Chemistry and Chemical Biology, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjincho, Kiryu, Gunma 376-8515, Japan
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3
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Investigation of the Stereochemical-Dependent DNA and RNA Binding of Arginine-Based Nucleopeptides. Symmetry (Basel) 2019. [DOI: 10.3390/sym11040567] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nucleopeptides represent an intriguing class of nucleic acid analogues, in which nucleobases are placed in a peptide structure. The incorporation of D- and/or L-amino acids in nucleopeptide molecules allows the investigation of the role of backbone stereochemistry in determining the formation of DNA and RNA hybrids. Circular Dichroism (CD) spectroscopic studies indicated the nucleopeptide as having fully l-backbone configuration-formed stable hybrid complexes with RNA molecules. Molecular Dynamics (MD) simulations suggested a potential structure of the complex resulting from the interaction between the l-nucleopeptide and RNA strand. From this study, both the backbone (ionics and H-bonds) and nucleobases (pairing and π-stacking) of the chiral nucleopeptide appeared to be involved in the hybrid complex formation, highlighting the key role of the backbone stereochemistry in the formation of the nucleopeptide/RNA complexes.
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Bai X, Talukder P, Daskalova SM, Roy B, Chen S, Li Z, Dedkova LM, Hecht SM. Enhanced Binding Affinity for an i-Motif DNA Substrate Exhibited by a Protein Containing Nucleobase Amino Acids. J Am Chem Soc 2017; 139:4611-4614. [PMID: 28263595 DOI: 10.1021/jacs.6b11825] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Several variants of a nucleic acid binding motif (RRM1) of putative transcription factor hnRNP LL containing nucleobase amino acids at specific positions have been prepared and used to study binding affinity for the BCL2 i-motif DNA. Molecular modeling suggested a number of amino acids in RRM1 likely to be involved in interaction with the i-motif DNA, and His24 and Arg26 were chosen for modification based on their potential ability to interact with G14 of the i-motif DNA. Four nucleobase amino acids were introduced into RRM1 at one or both of positions 24 and 26. The introduction of cytosine nucleobase 2 into position 24 of RRM1 increased the affinity of the modified protein for the i-motif DNA, consistent with the possible Watson-Crick interaction of 2 and G14. In comparison, the introduction of uracil nucleobase 3 had a minimal effect on DNA affinity. Two structurally simplified nucleobase analogues (1 and 4) lacking both the N-1 and the 2-oxo substituents were also introduced in lieu of His24. Again, the RRM1 analogue containing 1 exhibited enhanced affinity for the i-motif DNA, while the protein analogue containing 4 bound less tightly to the DNA substrate. Finally, the modified protein containing 1 in lieu of Arg26 also bound to the i-motif DNA more strongly than the wild-type protein, but a protein containing 1 both at positions 24 and 26 bound to the DNA less strongly than wild type. The results support the idea of using nucleobase amino acids as protein constituents for controlling and enhancing DNA-protein interaction. Finally, modification of the i-motif DNA at G14 diminished RRM1-DNA interaction, as well as the ability of nucleobase amino acid 1 to stabilize RRM1-DNA interaction.
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Affiliation(s)
- Xiaoguang Bai
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Poulami Talukder
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Sasha M Daskalova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Basab Roy
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Zhongxian Li
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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Talukder P, Dedkova LM, Ellington AD, Yakovchuk P, Lim J, Anslyn EV, Hecht SM. Synthesis of alanyl nucleobase amino acids and their incorporation into proteins. Bioorg Med Chem 2016; 24:4177-4187. [PMID: 27452282 DOI: 10.1016/j.bmc.2016.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/02/2016] [Accepted: 07/05/2016] [Indexed: 01/13/2023]
Abstract
Proteins which bind to nucleic acids and regulate their structure and functions are numerous and exceptionally important. Such proteins employ a variety of strategies for recognition of the relevant structural elements in their nucleic acid substrates, some of which have been shown to involve rather subtle interactions which might have been difficult to design from first principles. In the present study, we have explored the preparation of proteins containing unnatural amino acids having nucleobase side chains. In principle, the introduction of multiple nucleobase amino acids into the nucleic acid binding domain of a protein should enable these modified proteins to interact with their nucleic acid substrates using Watson-Crick and other base pairing interactions. We describe the synthesis of five alanyl nucleobase amino acids protected in a fashion which enabled their attachment to a suppressor tRNA, and their incorporation into each of two proteins with acceptable efficiencies. The nucleobases studied included cytosine, uracil, thymine, adenine and guanine, i.e. the major nucleobase constituents of DNA and RNA. Dihydrofolate reductase was chosen as one model protein to enable direct comparison of the facility of incorporation of the nucleobase amino acids with numerous other unnatural amino acids studied previously. The Klenow fragment of DNA polymerase I was chosen as a representative DNA binding protein whose mode of action has been studied in detail.
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Affiliation(s)
- Poulami Talukder
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew D Ellington
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Petro Yakovchuk
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Jaebum Lim
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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Uozumi R, Takahashi T, Yamazaki T, Granholm V, Mihara H. Design and conformational analysis of natively folded β-hairpin peptides stabilized by nucleobase interactions. Biopolymers 2011; 94:830-42. [PMID: 20535820 DOI: 10.1002/bip.21464] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To examine stabilizing effects of the base pair interaction on a protein scaffold, various peptides with L-α-amino acids bearing a nucleobase in the side chain (nucleobase amino acids; NBAs) were designed based on a G-peptide β-hairpin structure, and their conformational properties were investigated by circular dichroism and NMR spectroscopy. Thermodynamic analyses based on the chemical shifts showed that adenine-thymine pairing in a diagonal fashion at positions 4 and 15 (2AT) enhanced thermal stability of the peptide conformation by more than 30 K as compared with the wild-type G-peptide. In NOESY spectrum, not only numerous nonadjacent crosspeaks but also long-range crosspeaks between the nucleobases were observed in some peptides with the base pairing. NMR structure calculations of the 2AT peptide confirmed that cross-strand pairing of the nucleobases occurs on the well-defined β-hairpin structure as designed. Taken together, the base pairing in an appropriate position and orientation facilitates folding and stabilization of a native-like β-hairpin structure.
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Affiliation(s)
- Ryuichi Uozumi
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B40 4259 Nagatsuta, Yokohama 226-8501, Japan
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Giraldo R. Amyloid Assemblies: Protein Legos at a Crossroads in Bottom-Up Synthetic Biology. Chembiochem 2010; 11:2347-57. [DOI: 10.1002/cbic.201000412] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Watanabe S, Tomizaki KY, Takahashi T, Usui K, Kajikawa K, Mihara H. Interactions between peptides containing nucleobase amino acids and T7 phages displaying S. cerevisiae proteins. Biopolymers 2007; 88:131-40. [PMID: 17206624 DOI: 10.1002/bip.20662] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The importance of high-throughput analyses of protein abundances and functions is interestingly increasing in genomic/proteomic studies. In such postgenome sequencing era, a protein-detecting chip, in which a large number of molecules specifically capturing target proteins (capturing agents) such as antibodies, recombinant proteins, and small molecules are arrayed onto solid, wet, or semi-wet substrates, enables comprehensive analysis of proteomes by a single experiment. However, whole proteomes are generally complicated for comprehensive analyses so that alternative approaches to subproteome analysis categorized by protein functions and binding properties (focused proteome) would be effective. Approaching the goal of development of designed peptide chip for protein analysis, diversity increases in peptide structures and validation of target proteins are needed. We herein describe design and synthesis of nucleobase amino acid (NBA)-containing peptides, selection of nucleic acid-related proteins derived from S. cerevisiae, and detection of interactions between NBA-containing peptides and T7 phages displaying proteins by both enzyme-linked immunosorbent assays (ELISA) and label-free anomalous reflection of gold (AR) measurements. Twenty-eight phage clones were obtained by the phage-display method and sequenced. Ten of 28 clones were expected to be nucleic acid-related proteins including initiation factor, TYB protein, ribosomal proteins, elongation factor, ATP synthase subunit, GTP-binding protein, and ribonuclease. Other phage clones encoded several classes of enzymes such as reductase, oxidase, aldolase, metalloprotease, and hexokinase. Both ELISA and AR measurements suggested that the methodology of in vitro selection for recognition of the NBA-containing peptide presented in this study was successfully established. Such a combination of NBA and phage display technologies would be potential to efficiently confirm valuable target proteins binding specifically to capturing agents, to be arrayed onto solid surfaces to develop the designed peptide chip.
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Affiliation(s)
- Sinya Watanabe
- The COE21 Program and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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