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Chan KH, Lim J, Jee JE, Aw JH, Lee SS. Peptide-Peptide Co-Assembly: A Design Strategy for Functional Detection of C-peptide, A Biomarker of Diabetic Neuropathy. Int J Mol Sci 2020; 21:ijms21249671. [PMID: 33352955 PMCID: PMC7766332 DOI: 10.3390/ijms21249671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/29/2022] Open
Abstract
Diabetes-related neuropathy is a debilitating condition that may be averted if it can be detected early. One possible way this can be achieved at low cost is to utilise peptides to detect C-peptide, a biomarker of diabetic neuropathy. This depends on peptide-peptide co-assembly, which is currently in a nascent stage of intense study. Instead, we propose a bead-based triple-overlay combinatorial strategy that can preserve inter-residue information during the screening process for a suitable complementary peptide to co-assemble with C-peptide. The screening process commenced with a pentapeptide general library, which revealed histidine to be an essential residue. Further screening with seven tetrapeptide focused libraries led to a table of self-consistent peptide sequences that included tryptophan and lysine at high frequencies. Three complementary nonapeptides (9mer com-peptides), wpkkhfwgq (Trp-D), kwkkhfwgq (Lys-D), and KWKKHFWGQ (Lys-L) (as a negative control) were picked from this table for co-assembly studies with C-peptide. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) and circular dichroism (CD) spectroscopies were utilized to study inter-peptide interactions and changes in secondary structures respectively. ATR-FTIR studies showed that there is indeed inter-peptide interaction between C-peptide and the tryptophan residues of the 9mer com-peptides. CD studies of unaggregated and colloidal C-peptide with the 9mer com-peptides suggest that the extent of co-assembly of C-peptide with Trp-D is greatest, followed by Lys-D and Lys-L. These results are promising and indicate that the presented strategy is viable for designing and evaluating longer complementary peptides, as well as complementary peptides for co-assembly with other polypeptides of interest and importance. We discuss the possibility of designing complementary peptides to inhibit toxic amyloidosis with this approach.
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Affiliation(s)
- Kiat Hwa Chan
- Division of Science, Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore;
- Correspondence: (K.H.C.); (S.S.L.)
| | - Jaehong Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
| | - Joo Eun Jee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
| | - Jia Hui Aw
- Division of Science, Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore;
| | - Su Seong Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
- Correspondence: (K.H.C.); (S.S.L.)
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2
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Kim J, Kim S, Shin DS, Lee YS. Preparation of tri(ethylene glycol) grafted core-shell type polymer support for solid-phase peptide synthesis. J Pept Sci 2017; 24. [PMID: 29235177 DOI: 10.1002/psc.3061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/03/2017] [Accepted: 11/10/2017] [Indexed: 11/10/2022]
Abstract
A core-shell type polymer support for solid-phase peptide synthesis has been developed for high coupling efficiency of peptides and versatile applications such as on-bead bioassays. Although various kinds of polymer supports have been developed, they have their own drawbacks including poor accessibility of reagents and incompatibility in aqueous solution. In this paper, we prepared hydrophilic tri(ethylene glycol) (TEG) grafted core-shell type polymer supports (TEG SURE) for efficient solid-phase peptide synthesis and on-bead bioassays. TEG SURE was prepared by grafting TEG derivative on the surface of AM PS resin via biphasic diffusion control method and subsequent acetylation of amine groups which are located at the core region of AM PS resin. The performance of TEG SURE was evaluated by synthesizing several peptides. Three points can be highlighted: (1) easy control of loading level of TEG, (2) improved efficiency of peptide synthesis compared with the conventional resins, and (3) applicability of on-bead bioassays.
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Affiliation(s)
- Jaehi Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seojung Kim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, 100 Cheongpa-ro 47-gil, Yongsan-gu, Seoul, 04310, Republic of Korea
| | - Dong-Sik Shin
- Department of Chemical and Biological Engineering, Sookmyung Women's University, 100 Cheongpa-ro 47-gil, Yongsan-gu, Seoul, 04310, Republic of Korea
| | - Yoon-Sik Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
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3
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Sun K, Chang Y, Zhou B, Wang X, Liu L. Gold nanoparticles-based electrochemical method for the detection of protein kinase with a peptide-like inhibitor as the bioreceptor. Int J Nanomedicine 2017; 12:1905-1915. [PMID: 28331314 PMCID: PMC5352234 DOI: 10.2147/ijn.s127957] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
This article presents a general method for the detection of protein kinase with a peptide-like kinase inhibitor as the bioreceptor, and it was done by converting gold nanoparticles (AuNPs)-based colorimetric assay into sensitive electrochemical analysis. In the colorimetric assay, the kinase-specific aptameric peptide triggered the aggregation of AuNPs in solution. However, the specific binding of peptide to the target protein (kinase) inhibited its ability to trigger the assembly of AuNPs. In the electrochemical analysis, peptides immobilized on a gold electrode and presented as solution triggered together the in situ formation of AuNPs-based network architecture on the electrode surface. Nevertheless, the formation of peptide-kinase complex on the electrode surface made the peptide-triggered AuNPs assembly difficult. Electrochemical impedance spectroscopy was used to measure the change in surface property in the binding events. When a ferrocene-labeled peptide (Fc-peptide) was used in this design, the network of AuNPs/Fc-peptide produced a good voltammetric signal. The competitive assay allowed for the detection of protein kinase A with a detection limit of 20 mU/mL. This work should be valuable for designing novel optical or electronic biosensors and likely lead to many detection applications.
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Affiliation(s)
- Kai Sun
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan, People’s Republic of China
| | - Yong Chang
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan, People’s Republic of China
| | - Binbin Zhou
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan, People’s Republic of China
| | - Xiaojin Wang
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan, People’s Republic of China
| | - Lin Liu
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan, People’s Republic of China
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4
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Na Z, Pan S, Uttamchandani M, Yao SQ. Protein-Protein Interaction Inhibitors of BRCA1 Discovered Using Small Molecule Microarrays. Methods Mol Biol 2017; 1518:139-156. [PMID: 27873205 DOI: 10.1007/978-1-4939-6584-7_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microarray screening technology has transformed the life sciences arena over the last decade. The platform is widely used in the area of mapping interaction networks, to molecular fingerprinting and small molecular inhibitor discovery. The technique has significantly impacted both basic and applied research. The microarray platform can likewise enable high-throughput screening and discovery of protein-protein interaction (PPI) inhibitors. Herein we demonstrate the application of microarray-guided PPI inhibitor discovery, using human BRCA1 as an example. Mutations in BRCA1 have been implicated in ~50 % of hereditary breast cancers. By targeting the (BRCT)2 domain, we showed compound 15a and its prodrug 15b inhibited BRCA1 activities in tumor cells. Unlike previously reported peptide-based PPI inhibitors of BRCA1, the compounds identified could be directly administered to tumor cells, thus making them useful in targeting BRCA1/PARP-related pathways involved in DNA damage and repair response, for cancer therapy.
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Affiliation(s)
- Zhenkun Na
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Mahesh Uttamchandani
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore, Singapore
| | - Shao Q Yao
- Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.
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5
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Wang W, Fang Q, Hu Z. High-Throughput Peptide Screening on a Bimodal Imprinting Chip Through MS-SPRi Integration. Methods Mol Biol 2016; 1352:111-25. [PMID: 26490471 DOI: 10.1007/978-1-4939-3037-1_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Screening of high affinity and high specificity peptide probes towards various targets is important in the biomedical field while traditional peptide screening procedure is manual and tedious. Herein, a bimodal imprinting microarray system to embrace the whole peptide screening process is presented. Surface Plasmon Resonance imaging (SPRi) and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) are combined for both quantitative and qualitative identification of the peptide. The method provides a solution for high efficiency peptide screening.
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Affiliation(s)
- Weizhi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No.11. Beiyitiao Zhongguancun, Beijing, 100190, China
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No.11. Beiyitiao Zhongguancun, Beijing, 100190, China.
| | - Zhiyuan Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No.11. Beiyitiao Zhongguancun, Beijing, 100190, China.
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6
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Wang W, Li M, Wei Z, Wang Z, Bu X, Lai W, Yang S, Gong H, Zheng H, Wang Y, Liu Y, Li Q, Fang Q, Hu Z. Bimodal Imprint Chips for Peptide Screening: Integration of High-Throughput Sequencing by MS and Affinity Analyses by Surface Plasmon Resonance Imaging. Anal Chem 2014; 86:3703-7. [DOI: 10.1021/ac500465e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Weizhi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Menglin Li
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Zewen Wei
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zihua Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Xiangli Bu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Wenjia Lai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Shu Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - He Gong
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Hui Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Yuqiao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Ying Liu
- Beijing
Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Qin Li
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zhiyuan Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
- Beijing
Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
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7
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Trinh TB, Xiao Q, Pei D. Profiling the substrate specificity of protein kinases by on-bead screening of peptide libraries. Biochemistry 2013; 52:5645-55. [PMID: 23848432 DOI: 10.1021/bi4008947] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A robust, high-throughput method has been developed to screen one-bead-one-compound peptide libraries to systematically profile the sequence specificity of protein kinases. Its ability to provide individual sequences of the preferred substrates permits the identification of sequence contextual effects and nonpermissive residues. Application of the library method to kinases Pim1, MKK6, and Csk revealed that Pim1 and Csk are highly active toward peptide substrates and recognize specific sequence motifs, whereas MKK6 has little activity or sequence selectivity against peptide substrates. Pim1 recognizes peptide substrates of the consensus RXR(H/R)X(S/T); it accepts essentially any amino acid at the S/T-2 and S/T+1 positions, but strongly disfavors acidic residues (Asp or Glu) at the S/T-2 position and a proline residue at the S/T+1 position. The selected Csk substrates show strong sequence covariance and fall into two classes with the consensus sequences of (D/E)EPIYϕXϕ and (D/E)(E/D)S(E/D/I)YϕXϕ (where X is any amino acid and ϕ is a hydrophobic amino acid). Database searches and in vitro kinase assays identified phosphatase PTP-PEST as a Pim1 substrate and phosphatase SHP-1 as a potential Csk substrate. Our results demonstrate that the sequence specificity of protein kinases is defined not only by favorable interactions between permissive residue(s) on the substrate and their cognate binding site(s) on the kinase but also by repulsive interactions between the kinase and nonpermissive residue(s).
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Affiliation(s)
- Thi B Trinh
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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8
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Lee JH, Song E, Lee SG, Kim BG. High-throughput screening for transglutaminase activities using recombinant fluorescent proteins. Biotechnol Bioeng 2013; 110:2865-73. [PMID: 23740563 DOI: 10.1002/bit.24970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/28/2013] [Accepted: 05/28/2013] [Indexed: 01/20/2023]
Abstract
Since detailed evaluation of specific transglutaminases (TGs) from various species requires identification of their substrate specificities, rapid substrate screening method by measurement of their relative activities is in great demand. Here, a novel evaluation method of TG activity was developed using two recombinant fluorescent proteins (FPs), that is, eYFP and DsRed, tagged with TG substrate peptides. By cross-linking the two FPs based on the tagged target peptide sequences at their C-terminus, the expression of co-transformed TG allows quenching of the yellow fluorescence intensities. It was shown that the degree of in vivo fluorescent quenching by the TG activity agrees well with its in vitro reaction data, suggesting that this system can be used to identify relative substrate specificity of TGs for target peptide sequences. Using this method, the lysine substrates of TGs from Bacillus species (BTG) were evaluated, and the newly selected pentapeptide, KTKTN showed almost the same reactivity with the well-known hexa-lysine (K₆) substrate for BTG reaction.
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Affiliation(s)
- Jae-Hun Lee
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Kwanak-Gu, Seoul, South Korea; Institute of Bioengineering, Seoul National University, Kwanak-Gu, Seoul, South Korea
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9
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Xue L, Tao WA. Current technologies to identify protein kinase substrates in high throughput. ACTA ACUST UNITED AC 2013; 8:216-227. [PMID: 25110472 DOI: 10.1007/s11515-013-1257-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Since the discovery of protein phosphorylation as an important modulator of many cellular processes, the involvement of protein kinases in diseases, such as cancer, diabetes, cardiovascular diseases, and central nervous system pathologies, has been extensively documented. Our understanding of many disease pathologies at the molecular level, therefore, requires the comprehensive identification of substrates targeted by protein kinases. In this review, we focus on recent techniques for kinase substrate identification in high throughput, in particular on genetic and proteomic approaches. Each method with its inherent advantages and limitations is discussed.
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Affiliation(s)
- Liang Xue
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA ; Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA ; Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA ; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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10
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Lee JH, Song C, Kim DH, Park IH, Lee SG, Lee YS, Kim BG. Glutamine (Q)-peptide screening for transglutaminase reaction using mRNA display. Biotechnol Bioeng 2012; 110:353-62. [DOI: 10.1002/bit.24622] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 05/16/2012] [Accepted: 07/26/2012] [Indexed: 11/06/2022]
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11
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Kim DH, Shin DS, Lee YS. Determination of protease subsite preference on SPOT peptide array by fluorescence quenching-based assay. J Pept Sci 2012; 18:394-9. [DOI: 10.1002/psc.2409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 02/25/2012] [Accepted: 03/02/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Do-Hyun Kim
- School of Chemical and Biological Engineering; Seoul National University; Seoul; 151-747; Korea
| | - Dong-Sik Shin
- School of Chemical and Biological Engineering; Seoul National University; Seoul; 151-747; Korea
| | - Yoon-Sik Lee
- School of Chemical and Biological Engineering; Seoul National University; Seoul; 151-747; Korea
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12
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Cha J, Lim J, Zheng Y, Tan S, Ang YL, Oon J, Ang MW, Ling J, Bode M, Lee SS. Process Automation toward Ultra-High-Throughput Screening of Combinatorial One-Bead-One-Compound (OBOC) Peptide Libraries. ACTA ACUST UNITED AC 2012; 17:186-200. [DOI: 10.1177/2211068211433503] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Hwang S, Choi CH, Lee CS. Regioselective surface modification of pdms microfluidic device for the generation of monodisperse double emulsions. Macromol Res 2012. [DOI: 10.1007/s13233-012-0048-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Kim M, Shin DS, Kim J, Lee YS. Substrate screening of protein kinases: detection methods and combinatorial peptide libraries. Biopolymers 2011; 94:753-62. [PMID: 20564046 DOI: 10.1002/bip.21506] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The study of protein kinases has become a matter of great importance in the development of new drugs for the treatment of diseases, including cancer and inflammation. Substrate screening is the first step in the fundamental investigation of protein kinases and the development of inhibitors for use in drug discovery. Towards this goal, various studies have been reported regarding the development of phospho-peptide detection methods and the screening of phosphorylated peptide sites by protein kinases. This review introduces the detection methods for phosphorylation events using the reagents with (γ(32)P)ATP, ligand-linked ATP, phospho-peptide-specific antibodies and metal chelating compounds. Chemical modification methods using β-elimination for the detection of phospho-Ser/Thr peptides are introduced as well. In addition, the implementations of combinatorial peptide libraries for screening peptide substrates of protein kinases are discussed. The phage display approach has been suggested as an alternative method of using synthetic peptides for screening the substrate specificities of protein kinase. However, a solid phase assay using a peptide library-bound polymer resin or a peptide-arrayed glass chip is preferred for high throughput screening (HTS).
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Affiliation(s)
- Mira Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 151-744 Korea
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15
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Kim M, Park YS, Shin DS, Kim J, Kim BG, Lee YS. Antibody-free peptide substrate screening of serine/threonine kinase (protein kinase A) with a biotinylated detection probe. Anal Biochem 2011; 413:30-5. [PMID: 21310143 DOI: 10.1016/j.ab.2011.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 01/07/2011] [Accepted: 02/02/2011] [Indexed: 01/27/2023]
Abstract
Being different from anti-phosphotyrosine antibodies, anti-phosphoserine- or anti-phosphothreonine-specific antibodies with high affinity for the detection of serine/threonine kinase substrates are not readily available. Therefore, chemical modification methods were developed for the detection of phosphoserine or threonine in the screening of protein kinase substrates based on β-elimination and Michael addition. We have developed a biotin-based detection probe for identification of the phosphorylated serine or threonine residue. A biotin derivative induced a color reaction using alkaline phosphate-conjugated streptavidin that amplified the signal. It was effective for the detection and separation of the target peptide on the resin. The detection probe was successfully used in identifying PKA substrates from peptide libraries on resin beads. The peptide library was prepared as a ladder-type, such that the active peptides on the colored resin beads were readily sequenced with the truncated peptide fragments by MALDI-TOF/MS analysis after releasing the peptides from the resin bead through photolysis.
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Affiliation(s)
- Mira Kim
- School of Chemical and Biological Engineering, Seoul National University, San 56-1, Shilim-dong, Kwnak-gu, Seoul 151-744, South Korea.
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16
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Wu H, Ge J, Uttamchandani M, Yao SQ. Small molecule microarrays: the first decade and beyond. Chem Commun (Camb) 2011; 47:5664-5670. [DOI: 10.1039/c1cc11464f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Molecular Bits and Chips: Profiling and discovering the next generation of small molecule ligands.
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Affiliation(s)
- Hao Wu
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Jingyan Ge
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Mahesh Uttamchandani
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Department of Biological Sciences
- National University of Singapore
| | - Shao Q. Yao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Department of Biological Sciences
- National University of Singapore
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17
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Kim EM, Kim J, Kim YG, Lee P, Shin DS, Kim M, Hahn JS, Lee YS, Kim BG. Development of high-throughput phosphorylation profiling method for identification of Ser/Thr kinase specificity. J Pept Sci 2010; 17:392-7. [DOI: 10.1002/psc.1312] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 09/07/2010] [Accepted: 09/14/2010] [Indexed: 01/21/2023]
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18
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Lee SS, Lim J, Tan S, Cha J, Yeo SY, Agnew HD, Heath JR. Accurate MALDI-TOF/TOF sequencing of one-bead-one-compound peptide libraries with application to the identification of multiligand protein affinity agents using in situ click chemistry screening. Anal Chem 2010; 82:672-9. [PMID: 20000699 PMCID: PMC2829877 DOI: 10.1021/ac902195y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Combinatorial one-bead-one-compound (OBOC) peptide libraries are widely used for affinity screening, and the sequencing of peptides from hit beads is a key step in the process. For rapid sequencing, CNBr cleavage of the peptides from the beads, followed by de novo sequencing by MALDI-TOF/TOF, is explored. We report on a semiautomated sequencing algorithm and validate it through comparison against Edman degradation sequencing. The initial 44% sequencing success rate of the standard de novo sequencing software was improved to nearly 100%. The sequencing algorithm incorporates existing knowledge of amino acid chemistry and a new strategy for differentiating isobaric amino acids. We tested the algorithm by using MALDI-TOF/TOF to identify a peptide biligand affinity agent against the protein bovine carbonic anhydrase II, starting from comprehensive one-bead-one-compound peptide libraries comprised of non-natural and artificial amino acid components and using the strategy of in situ click/OBOC library screening.
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Affiliation(s)
- Su Seong Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Jaehong Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Sylvia Tan
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Junhoe Cha
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Shi Yun Yeo
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | - Heather D. Agnew
- Division of Chemistry and Chemical Engineering, Caltech. MC 127-72, Pasadena, CA 911125
| | - James R. Heath
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
- Division of Chemistry and Chemical Engineering, Caltech. MC 127-72, Pasadena, CA 911125
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González-Vera JA, Luković E, Imperiali B. A rapid method for generation of selective Sox-based chemosensors of Ser/Thr kinases using combinatorial peptide libraries. Bioorg Med Chem Lett 2009; 19:1258-60. [PMID: 19157873 PMCID: PMC2838374 DOI: 10.1016/j.bmcl.2008.12.090] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 12/12/2008] [Indexed: 10/21/2022]
Abstract
A novel screening method to identify selective Sox-based fluorescent probes for Ser/Thr kinases has been developed. Peptide libraries were exposed to a kinase of interest and the products of the timed reaction were analyzed by MALDI-TOF. To demonstrate the potential of this methodology, a selective substrate for Aurora A kinase was identified that showed a 7-fold improvement in catalytic efficiency over the best substrate described to date in the literature.
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Affiliation(s)
- Juan A González-Vera
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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20
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Sheridan DL, Kong Y, Parker SA, Dalby KN, Turk BE. Substrate discrimination among mitogen-activated protein kinases through distinct docking sequence motifs. J Biol Chem 2008; 283:19511-20. [PMID: 18482985 DOI: 10.1074/jbc.m801074200] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitogen-activated protein kinases (MAPKs) mediate cellular responses to a wide variety of extracellular stimuli. MAPK signal transduction cascades are tightly regulated, and individual MAPKs display exquisite specificity in recognition of their target substrates. All MAPK family members share a common phosphorylation site motif, raising questions as to how substrate specificity is achieved. Here we describe a peptide library screen to identify sequence requirements of the DEF site (docking site for ERK FXF), a docking motif separate from the phosphorylation site. We show that MAPK isoforms recognize DEF sites with unique sequences and identify two key residues on the MAPK that largely dictate sequence specificity. Based on these observations and computational docking studies, we propose a revised model for MAPK interaction with substrates containing DEF sites. Variations in DEF site sequence requirements provide one possible mechanism for encoding complex target specificity among MAPK isoforms.
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Affiliation(s)
- Douglas L Sheridan
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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21
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Seo JH, Park HY, Kim J, Lee BS, Kim BG. Exploring sequence space: Profile analysis and protein-ligand docking to screen ω-aminotransferases with expanded substrate specificity. Biotechnol J 2008; 3:676-86. [DOI: 10.1002/biot.200700264] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Turk BE. Understanding and exploiting substrate recognition by protein kinases. Curr Opin Chem Biol 2008; 12:4-10. [PMID: 18282484 DOI: 10.1016/j.cbpa.2008.01.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 01/15/2008] [Indexed: 10/22/2022]
Abstract
Protein kinases play a virtually universal role in cellular regulation and are emerging as an important class of new drug targets, yet the cellular functions of most human kinases largely remain obscure. Aspects of substrate recognition common to all kinases in the ATP nucleotide binding site have been exploited in the generation of analog-specific mutants for exploring kinase function and discovering novel protein substrates. Likewise, understanding interactions with the protein substrate, which differ substantially between kinases, can also help to identify substrates and to produce tools for studying kinase pathways, including fluorescent biosensors. Principles of kinase substrate recognition are particularly valuable in guiding bioinformatics and phosphoproteomics approaches that impact our understanding of signaling pathways and networks on a global scale.
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Affiliation(s)
- Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, P.O. Box 208066, 333 Cedar Street, New Haven, CT 06520, United States.
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23
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Kim YG, Shin DS, Yang YH, Gil GC, Park CG, Mimura Y, Cooper DK, Rudd PM, Dwek RA, Lee YS, Kim BG. High-Throughput Screening of Glycan-Binding Proteins Using Miniature Pig Kidney N-Glycan-Immobilized Beads. ACTA ACUST UNITED AC 2008; 15:215-23. [DOI: 10.1016/j.chembiol.2008.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2007] [Revised: 01/27/2008] [Accepted: 02/05/2008] [Indexed: 12/14/2022]
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24
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Kappel JC, Fan YC, Lam KS. Global Transformation of OBOC Combinatorial Peptide Libraries into OBOC Polyamine and Small Molecule Libraries. ACTA ACUST UNITED AC 2008; 10:333-42. [DOI: 10.1021/cc700165s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Joseph C. Kappel
- Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Cancer Center, 4501 X Street, Sacramento, California 95817
| | - Yi C. Fan
- Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Cancer Center, 4501 X Street, Sacramento, California 95817
| | - Kit S. Lam
- Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Cancer Center, 4501 X Street, Sacramento, California 95817
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25
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Pouchain D, Díaz-Mochón JJ, Bialy L, Bradley M. A 10,000 member PNA-encoded peptide library for profiling tyrosine kinases. ACS Chem Biol 2007; 2:810-8. [PMID: 18154268 DOI: 10.1021/cb700199k] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A 10,000 member peptide nucleic acid (PNA) encoded peptide library was prepared, treated with the Abelson tyrosine kinase (Abl), and decoded using a DNA microarray and a fluorescently labeled secondary antiphosphotyrosine antibody. A dual-color approach ensured internal referencing for each and every member of the library and the generation of robust data sets. Analysis identified 155 peptides (out of 10,000) that were strongly phosphorylated by Abl in full agreement with known Abl specificities. BLAST analysis identified known cellular Abl substrates such as c-Jun amino-terminal kinase as well as new potential target proteins such as the G-protein coupled receptor kinase 6 and diacylglycerol kinase gamma. To illustrate the generalization of this approach, two other tyrosine kinases, human epidermal growth factor 2 (Her2) and vascular endothelial growth factor receptor 2/kinase insert domain protein receptor (VEGFR2/KDR), were profiled allowing characterization of specific peptide sequences known to interact with these kinases; under these conditions Her2 was demonstrated to have a marked preference for D-proline perhaps offering a unique means of targeting and inhibiting this kinase.
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Affiliation(s)
- Delphine Pouchain
- EaStCHEM, School of Chemistry, University of Edinburgh,
Joseph Black Building, West Mains Road, Edinburgh EH9 3JJ, U.K
| | - Juan J. Díaz-Mochón
- EaStCHEM, School of Chemistry, University of Edinburgh,
Joseph Black Building, West Mains Road, Edinburgh EH9 3JJ, U.K
| | - Laurent Bialy
- EaStCHEM, School of Chemistry, University of Edinburgh,
Joseph Black Building, West Mains Road, Edinburgh EH9 3JJ, U.K
| | - Mark Bradley
- EaStCHEM, School of Chemistry, University of Edinburgh,
Joseph Black Building, West Mains Road, Edinburgh EH9 3JJ, U.K
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26
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Shin DS, Kim YG, Kim EM, Kim M, Park HY, Kim JH, Lee BS, Kim BG, Lee YS. Solid-phase peptide library synthesis on HiCore resin for screening substrate specificity of Brk protein tyrosine kinase. ACTA ACUST UNITED AC 2007; 10:20-3. [PMID: 18052331 DOI: 10.1021/cc7001217] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dong-Sik Shin
- School of Chemical and Biological Engineering and Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Kwanak Gu, Seoul 151-744, Korea
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