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Peng X, Emiliani F, Smallwood PM, Rattner A, Lei H, Sabbagh MF, Nathans J. Affinity capture of polyribosomes followed by RNAseq (ACAPseq), a discovery platform for protein-protein interactions. eLife 2018; 7:40982. [PMID: 30345971 PMCID: PMC6197854 DOI: 10.7554/elife.40982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/02/2018] [Indexed: 02/05/2023] Open
Abstract
Defining protein-protein interactions (PPIs) is central to the biological sciences. Here, we present a novel platform - Affinity Capture of Polyribosomes followed by RNA sequencing (ACAPseq) - for identifying PPIs. ACAPseq harnesses the power of massively parallel RNA sequencing (RNAseq) to quantify the enrichment of polyribosomes based on the affinity of their associated nascent polypeptides for an immobilized protein 'bait'. This method was developed and tested using neonatal mouse brain polyribosomes and a variety of extracellular domains as baits. Of 92 baits tested, 25 identified one or more binding partners that appear to be biologically relevant; additional candidate partners remain to be validated. ACAPseq can detect binding to targets that are present at less than 1 part in 100,000 in the starting polyribosome preparation. One of the observed PPIs was analyzed in detail, revealing the mode of homophilic binding for Protocadherin-9 (PCDH9), a non-clustered Protocadherin family member.
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Affiliation(s)
- Xi Peng
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Francesco Emiliani
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Philip M Smallwood
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Amir Rattner
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Hong Lei
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Mark F Sabbagh
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Jeremy Nathans
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
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Wang X, Jiang C, Qin Y, Peng Y, Wen G, Liang A, Jiang Z. SERS spectral study of HAuCl 4-cysteine nanocatalytic reaction and its application for detection of heparin sodium with label-free VB4r molecular probe. Sci Rep 2017; 7:45979. [PMID: 28378828 PMCID: PMC5380991 DOI: 10.1038/srep45979] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/07/2017] [Indexed: 12/23/2022] Open
Abstract
In the presence of nanocatalyst, L-cysteine reduce HAuCl4 rapidly to form gold nanoparticles (AuNP), and a quick nanocatalytic preparation procedure was established for Au/AuNP sol with highly active surface enhanced Raman scattering (SERS) effect and good stability. The nanoreaction was also studied by absorption, resonance Rayleigh scattering (RRS), transmission electron microscopy (TEM) and energy spectra. In the selected conditions, the analyte heparin sodium (HS) could react with victoria blue 4 R (VB4r) to form associated complexes which have very weak SERS effect to make the SERS signals decrease. The SERS signals at 1617 cm−1 reduced linearly with HS concentration increasing. Upon addition of FeCl3, it hydrolyzed to form stable Fe(OH)3 sol platform that carried SERS active Au/AuNPs to enhance the sensitivity. Accordingly, we established a SERS quantitative analysis method in the sol substrate of Fe(OH)3-Au/AuNPs, with a linear range of 0.5–75 ng/mL HS and a detection limit of 0.2 ng/mL. HS in real samples was determined, with a relative standard deviation of 2.65–7.63% and a recovery of 99.3–101%.
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Affiliation(s)
- Xiaoliang Wang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection of Ministry Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guangxi Normal University, Guilin 541004, China
| | - Caina Jiang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection of Ministry Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guangxi Normal University, Guilin 541004, China
| | - Yanna Qin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection of Ministry Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guangxi Normal University, Guilin 541004, China
| | - Yutao Peng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection of Ministry Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guangxi Normal University, Guilin 541004, China
| | - Guiqing Wen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection of Ministry Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guangxi Normal University, Guilin 541004, China
| | - Aihui Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection of Ministry Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guangxi Normal University, Guilin 541004, China
| | - Zhiliang Jiang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection of Ministry Education, Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guangxi Normal University, Guilin 541004, China
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