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Willardiine and Its Synthetic Analogues: Biological Aspects and Implications in Peptide Chemistry of This Nucleobase Amino Acid. Pharmaceuticals (Basel) 2022; 15:ph15101243. [PMID: 36297355 PMCID: PMC9611319 DOI: 10.3390/ph15101243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 12/16/2022] Open
Abstract
Willardiine is a nonprotein amino acid containing uracil, and thus classified as nucleobase amino acid or nucleoamino acid, that together with isowillardiine forms the family of uracilylalanines isolated more than six decades ago in higher plants. Willardiine acts as a partial agonist of ionotropic glutamate receptors and more in particular it agonizes the non-N-methyl-D-aspartate (non-NMDA) receptors of L-glutamate: ie. the α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) and kainate receptors. Several analogues and derivatives of willardiine have been synthesised in the laboratory in the last decades and these compounds show different binding affinities for the non-NMDA receptors. More in detail, the willardiine analogues have been employed not only in the investigation of the structure of AMPA and kainate receptors, but also to evaluate the effects of receptor activation in the various brain regions. Remarkably, there are a number of neurological diseases determined by alterations in glutamate signaling, and thus, ligands for AMPA and kainate receptors deserve attention as potential neurodrugs. In fact, similar to willardiine its analogues often act as agonists of AMPA and kainate receptors. A particular importance should be recognized to willardiine and its thymine-based analogue AlaT also in the peptide chemistry field. In fact, besides the naturally-occurring short nucleopeptides isolated from plant sources, there are different examples in which this class of nucleoamino acids was investigated for nucleopeptide development. The applications are various ranging from the realization of nucleopeptide/DNA chimeras for diagnostic applications, and nucleoamino acid derivatization of proteins for facilitating protein-nucleic acid interaction, to nucleopeptide-nucleopeptide molecular recognition for nanotechnological applications. All the above aspects on both chemistry and biotechnological applications of willardine/willardine-analogues and nucleopeptide will be reviewed in this work.
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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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3
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Scognamiglio PL, Platella C, Napolitano E, Musumeci D, Roviello GN. From Prebiotic Chemistry to Supramolecular Biomedical Materials: Exploring the Properties of Self-Assembling Nucleobase-Containing Peptides. Molecules 2021; 26:3558. [PMID: 34200901 PMCID: PMC8230524 DOI: 10.3390/molecules26123558] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
Peptides and their synthetic analogs are a class of molecules with enormous relevance as therapeutics for their ability to interact with biomacromolecules like nucleic acids and proteins, potentially interfering with biological pathways often involved in the onset and progression of pathologies of high social impact. Nucleobase-bearing peptides (nucleopeptides) and pseudopeptides (PNAs) offer further interesting possibilities related to their nucleobase-decorated nature for diagnostic and therapeutic applications, thanks to their reported ability to target complementary DNA and RNA strands. In addition, these chimeric compounds are endowed with intriguing self-assembling properties, which are at the heart of their investigation as self-replicating materials in prebiotic chemistry, as well as their application as constituents of innovative drug delivery systems and, more generally, as novel nanomaterials to be employed in biomedicine. Herein we describe the properties of nucleopeptides, PNAs and related supramolecular systems, and summarize some of the most relevant applications of these systems.
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Affiliation(s)
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
- Istituto di Biostrutture e Bioimmagini IBB-CNR, via Tommaso De Amicis 95, I-80145 Naples, Italy
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Roviello GN, Oliviero G, Di Napoli A, Borbone N, Piccialli G. Synthesis, self-assembly-behavior and biomolecular recognition properties of thyminyl dipeptides. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2018.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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5
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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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Musumeci D, Roviello V, Roviello GN. DNA- and RNA-binding ability of oligoDapT, a nucleobase-decorated peptide, for biomedical applications. Int J Nanomedicine 2018; 13:2613-2629. [PMID: 29750033 PMCID: PMC5936014 DOI: 10.2147/ijn.s156381] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Nucleobase-bearing peptides and their interaction with DNA and RNA are an important topic in the development of therapeutic approaches. On one hand, they are highly effective for modulating the nucleic-acid-based biological processes. On the other hand, they permit to overcome some of the main factors limiting the therapeutic efficacy of natural oligonucleotides, such as their rapid degradation by nucleases. Methods and results This article describes the synthesis and characterization of a novel thymine-bearing nucleoamino acid based on the l-diaminopropionic acid (l-Dap) and its solid phase oligomerization to α-peptides (oligoDapT), characterized using mass spectrometry, spectroscopic techniques, and scanning electron microscopy (SEM) analysis. The interaction of the obtained nucleopeptide with DNA and RNA model systems as both single strands (dA12, rA12, and poly(rA)) and duplex structures (dA12/dT12 and poly(rA)/poly(rU)) was investigated by means of circular dichroism (CD) and ultraviolet (UV) experiments. From the analysis of our data, a clear ability of the nucleopeptide to bind nucleic acids emerged, with oligoDapT being able to form stable complexes with both unpaired and double-stranded DNA and RNA. In particular, dramatic changes in the dA12/dT12 and poly(rA)/poly(rU) structures were observed as a consequence of the nucleopeptide binding. CD titrations revealed that multiple peptide units bound all the examined nucleic acid targets, with TLdap/A or TLdap/A:T(U) ratios >4 in case of oligoDapT/DNA and ~2 in oligoDapT/RNA complexes. Conclusion Our findings seem to indicate that Dap-based nucleopeptides are interesting nucleic acid binding-tools to be further explored with the aim to efficiently modulate DNA- and RNA-based biological processes.
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Affiliation(s)
- Domenica Musumeci
- CNR-Institute of Biostructure and Bioimaging, Naples, Italy.,Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Valentina Roviello
- Analytical Chemistry for the Environment and Centro Servizi Metereologici Avanzati, University of Naples Federico II, Naples, Italy
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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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8
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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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Syahir A, Tomizaki KY, Kajikawa K, Mihara H. Anomalous Reflection of Gold: A Novel Platform for Biochips. Methods Mol Biol 2015; 1352:97-110. [PMID: 26490470 DOI: 10.1007/978-1-4939-3037-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The importance of protein detection system for protein functions analyses in recent post-genomic era is rising with the emergence of label-free protein detection methods. We are focusing on a simple and practical label-free optical-detection method called anomalous reflection (AR) of gold. When a molecular layer forms on the gold surface, significant reduction in reflectivity can be observed at wavelengths of 400-500 nm. This allows the detection of molecular interactions by monitoring changes in reflectivity. In this chapter, we describe the AR method with three different application platforms: (1) gold, (2) gold containing alloy/composite (AuAg2O), and (3) metal-insulator-metal (MIM) thin layers. The AuAg2O composite and MIM are implemented as important concepts for signal enhancement process for the AR technique. Moreover, the observed molecular adsorption and activity is aided by a three-dimensional surface geometry, performed using poly(amidoamine) or PAMAM dendrimer modification. The described system is suitable to be used as a platform for high-throughput detection system in a chip format.
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Affiliation(s)
- Amir Syahir
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400, Malaysia.
| | - Kin-ya Tomizaki
- Department of Materials Chemistry, Ryukoku University, Seta-Oe, Otsu, 520-2194, Japan
| | - Kotaro Kajikawa
- Department of Electronics and Applied Physics, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama, 226-8502, Japan
| | - Hisakazu Mihara
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
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Label and Label-Free Detection Techniques for Protein Microarrays. MICROARRAYS 2015; 4:228-44. [PMID: 27600222 PMCID: PMC4996399 DOI: 10.3390/microarrays4020228] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/10/2015] [Accepted: 04/17/2015] [Indexed: 02/02/2023]
Abstract
Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano-biological events.
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Syahir A, Kajikawa K, Mihara H. Sensitive Detection of Small Molecule–Protein Interactions on a Metal–Insulator–Metal Label‐Free Biosensing Platform. Chem Asian J 2012; 7:1867-74. [DOI: 10.1002/asia.201200138] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 04/03/2012] [Indexed: 12/16/2022]
Affiliation(s)
- Amir Syahir
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226‐8501 (Japan), Fax: (+81) 45‐924‐5756
| | - Kotaro Kajikawa
- Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama 226‐8502 (Japan)
| | - Hisakazu Mihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226‐8501 (Japan), Fax: (+81) 45‐924‐5756
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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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Berrade L, Garcia AE, Camarero JA. Protein microarrays: novel developments and applications. Pharm Res 2010; 28:1480-99. [PMID: 21116694 PMCID: PMC3137928 DOI: 10.1007/s11095-010-0325-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 11/08/2010] [Indexed: 02/05/2023]
Abstract
Protein microarray technology possesses some of the greatest potential for providing direct information on protein function and potential drug targets. For example, functional protein microarrays are ideal tools suited for the mapping of biological pathways. They can be used to study most major types of interactions and enzymatic activities that take place in biochemical pathways and have been used for the analysis of simultaneous multiple biomolecular interactions involving protein-protein, protein-lipid, protein-DNA and protein-small molecule interactions. Because of this unique ability to analyze many kinds of molecular interactions en masse, the requirement of very small sample amount and the potential to be miniaturized and automated, protein microarrays are extremely well suited for protein profiling, drug discovery, drug target identification and clinical prognosis and diagnosis. The aim of this review is to summarize the most recent developments in the production, applications and analysis of protein microarrays.
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Affiliation(s)
- Luis Berrade
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, PSC 616, Los Angeles, California 90033, USA
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Tomizaki KY, Usui K, Mihara H. Protein-protein interactions and selection: array-based techniques for screening disease-associated biomarkers in predictive/early diagnosis. FEBS J 2010; 277:1996-2005. [PMID: 20412053 DOI: 10.1111/j.1742-4658.2010.07626.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There has been considerable interest in recent years in the development of miniaturized and parallelized array technology for protein-protein interaction analysis and protein profiling, namely 'protein-detecting microarrays'. Protein-detecting microarrays utilize a wide variety of capture agents (antibodies, fusion proteins, DNA/RNA aptamers, synthetic peptides, carbohydrates, and small molecules) immobilized at high spatial density on a solid surface. Each capture agent binds selectively to its target protein in a complex mixture, such as serum or cell lysate samples. Captured proteins are subsequently detected and quantified in a high-throughput fashion, with minimal sample consumption. Protein-detecting microarrays were first described by MacBeath and Schreiber in 2000, and the number of publications involving this technology is rapidly increasing. Furthermore, the first multiplex immunoassay systems have been cleared by the US Food and Drug Administration, signaling recognition of the usefulness of miniaturized and parallelized array technology for protein detection in predictive/early diagnosis. Although genetic tests still predominate, with further development protein-based diagnosis will become common in clinical use within a few years.
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Affiliation(s)
- Kin-ya Tomizaki
- Innovative Materials and Processing Research Center and Department of Materials Chemistry, Ryukoku University, Otsu, Japan
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Syahir A, Mihara H, Kajikawa K. A new optical label-free biosensing platform based on a metal-insulator-metal structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:6053-6057. [PMID: 20158170 DOI: 10.1021/la903794b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A new label-free biosensing platform is proposed based on a metal-insulator-metal (MIM) structure. This platform allows us to perform biosensing by a simple reflectivity measurement at normal incidence illumination without using any bulky optical setup. Theoretical calculation was made to find optimized MIM structural parameters, and experimental results on the label-free biosensing using the MIM platform are presented. This platform has greater sensitivity and mass resolution with respect to the anomalous reflection method, which is a label-free biosensing platform previously proposed by us. Hence, it is suitable for high throughput analysis of biomolecular detection in a microarray format.
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Affiliation(s)
- Amir Syahir
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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Zhang K, He J, Yang M, Yen M, Yin J. Identifying natural product biosynthetic genes from a soil metagenome by using T7 phage selection. Chembiochem 2010; 10:2599-606. [PMID: 19780075 DOI: 10.1002/cbic.200900297] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Keya Zhang
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, GCIS E505A, Chicago, IL 60637, USA
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Syahir A, Tomizaki KY, Kajikawa K, Mihara H. Poly(amidoamine)-dendrimer-modified gold surfaces for anomalous reflection of gold to detect biomolecular interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:3667-3674. [PMID: 19227984 DOI: 10.1021/la8028275] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Label-free protein detecting chip technology has encouraged a number of discoveries, as it is a powerful analytical tool in the postgenomic era. In particular, we have focused on a unique characteristic of anomalous reflection of gold (AR) as a new class of label-free detection method for a protein chip system. In this paper, in order to improve the sensitivity of detection of biomolecular interactions by the AR method, we have constructed three-dimensional (3D) nanostructures on gold surfaces with a series of well-defined structures of poly(amidoamine) dendrimers (PAMAMs) from generation 2 to 4 (G2, G3, and G4) tethering biotin moieties as capturing agents for avidin and antibiotin IgG. Comparison of features of such 3D nanostructured surfaces with a diamine-modified flat-like surface revealed a 2-fold increase in the amount of avidin for 3D surfaces relative to the flat surface, and surface-assisted nonspecific interactions were significantly suppressed. We thus obtained 91% coverage for avidin detection on the PAMAM G4-modified surface, indicating a theoretically maximum attainable absorption considering a hexagonal-packed arrangement as a saturated monomolecular layer. In the antibiotin IgG assay, the PAMAM G4-modified surface clearly improved the amount of proteins captured compared to that for the flat surface, indicating that an appropriate density of capturing agents played a more important role in the interaction of larger molecular-sized proteins such as antibiotin IgG, which requires more space for interaction than the medium-sized avidin. These findings should assist in the development of a simple and practical tool for high-throughput protein detection, particularly with the AR method.
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Affiliation(s)
- Amir Syahir
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Tomizaki K, Usui K, Mihara H. ELECTROCHEMISTRY 2007; 75:981-986. [DOI: 10.5796/electrochemistry.75.981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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