1
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Xiong J, Chen G, Lin B, Zhong L, Jiang X, Lu H. Integrative analysis of single-Cell RNA sequencing and experimental validation in the study of abdominal aortic aneurysm progression. Gene 2024; 929:148820. [PMID: 39103059 DOI: 10.1016/j.gene.2024.148820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/13/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Abdominal aortic aneurysm (AAA) is a complex vascular disorder characterized by the progressive dilation of the abdominal aorta, with a high risk of rupture and mortality. Understanding the cellular interactions and molecular mechanisms underlying AAA development is critical for identifying potential therapeutic targets. METHODS This study utilized datasets GSE197748, GSE164678 and GSE183464 from the GEO database, encompassing bulk and single-cell RNA sequencing data from AAA and control samples. We performed principal component analysis, differential expression analysis, and functional enrichment analysis to identify key pathways involved in AAA. Cell-cell interactions were investigated using CellPhoneDB, focusing on fibroblasts, vascular smooth muscle cells (VSMCs), and macrophages. We further validated our findings using a mouse model of AAA induced by porcine pancreatic enzyme infusion, followed by gene expression analysis and co-immunoprecipitation experiments. RESULTS Our analysis revealed significant alterations in gene expression profiles between AAA and control samples, with a pronounced immune response and cell adhesion pathways being implicated. Single-cell RNA sequencing data highlighted an increased proportion of pro-inflammatory macrophages, along with changes in the composition of fibroblasts and VSMCs in AAA. CellPhoneDB analysis identified critical ligand-receptor interactions, notably collagen type I alpha 1 chain (COL1A1)/COL1A2-CD18 and thrombospondin 1 (THBS1)-CD3, suggesting complex communication networks between fibroblasts and VSMCs. In vivo experiments confirmed the upregulation of these genes in AAA mice and demonstrated the functional interaction between COL1A1/COL1A2 and CD18. CONCLUSION The interaction between fibroblasts and VSMCs, mediated by specific ligand-receptor pairs such as COL1A1/COL1A2-CD18 and THBS1-CD3, plays a pivotal role in AAA pathogenesis.
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MESH Headings
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/pathology
- Aortic Aneurysm, Abdominal/metabolism
- Animals
- Mice
- Single-Cell Analysis/methods
- Humans
- Sequence Analysis, RNA/methods
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Macrophages/metabolism
- Disease Progression
- Fibroblasts/metabolism
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Disease Models, Animal
- Male
- Mice, Inbred C57BL
- Gene Expression Profiling/methods
- Cell Communication/genetics
- Collagen Type I/genetics
- Collagen Type I/metabolism
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Affiliation(s)
- Jie Xiong
- Department of Cardiology, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai 519000, China
| | - Guojun Chen
- Department of Cardiology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou 510515, China
| | - Beiyou Lin
- Department of Cardiology, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai 519000, China
| | - Lintao Zhong
- Department of Cardiology, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai 519000, China
| | - Xiaofei Jiang
- Department of Cardiology, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai 519000, China.
| | - Hongyun Lu
- Department of Cardiology, Zhuhai Hospital affiliated with Jinan University (Zhuhai People's Hospital), Zhuhai 519000, China.
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2
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Chun C, Byun JM, Cha M, Lee H, Choi B, Kim H, Hong S, Lee Y, Park H, Koh Y, Yoon TY. Profiling protein-protein interactions to predict the efficacy of B-cell-lymphoma-2-homology-3 mimetics for acute myeloid leukaemia. Nat Biomed Eng 2024:10.1038/s41551-024-01241-3. [PMID: 39025942 DOI: 10.1038/s41551-024-01241-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 06/28/2024] [Indexed: 07/20/2024]
Abstract
B-cell-lymphoma-2 (BCL2) homology-3 (BH3) mimetics are inhibitors of protein-protein interactions (PPIs) that saturate anti-apoptotic proteins in the BCL2 family to induce apoptosis in cancer cells. Despite the success of the BH3-mimetic ABT-199 for the treatment of haematological malignancies, only a fraction of patients respond to the drug and most patients eventually develop resistance to it. Here we show that the efficacy of ABT-199 can be predicted by profiling the rewired status of the PPI network of the BCL2 family via single-molecule pull-down and co-immunoprecipitation to quantify more than 20 types of PPI from a total of only 1.2 × 106 cells per sample. By comparing the obtained multidimensional data with BH3-mimetic efficacies determined ex vivo, we constructed a model for predicting the efficacy of ABT-199 that designates two complexes of the BCL2 protein family as the primary mediators of drug effectiveness and resistance, and applied it to prospectively assist therapeutic decision-making for patients with acute myeloid leukaemia. The characterization of PPI complexes in clinical specimens opens up opportunities for individualized protein-complex-targeting therapies.
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Affiliation(s)
- Changju Chun
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Ja Min Byun
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Minkwon Cha
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
| | - Hongwon Lee
- Department of Biomarker Discovery, PROTEINA Co., Ltd, Seoul, South Korea
| | - Byungsan Choi
- Department of Biomarker Discovery, PROTEINA Co., Ltd, Seoul, South Korea
| | - Hyunwoo Kim
- Department of Biomarker Discovery, PROTEINA Co., Ltd, Seoul, South Korea
| | - Saem Hong
- Department of Biomarker Discovery, PROTEINA Co., Ltd, Seoul, South Korea
| | - Yunseo Lee
- Department of Biomarker Discovery, PROTEINA Co., Ltd, Seoul, South Korea
| | - Hayoung Park
- Department of Biomarker Discovery, PROTEINA Co., Ltd, Seoul, South Korea
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea.
| | - Tae-Young Yoon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.
- Department of Biomarker Discovery, PROTEINA Co., Ltd, Seoul, South Korea.
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3
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Kim SH, Chun C, Yoon TY. Profiling of BCLxL Protein Complexes in Non-Small Cell Lung Cancer Cells via Multiplexed Single-Molecule Pull-Down and Co-Immunoprecipitation. Anal Chem 2024; 96:8932-8941. [PMID: 38728439 DOI: 10.1021/acs.analchem.3c05801] [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: 05/12/2024]
Abstract
We introduce multiplexed single-molecule pull-down and co-immunoprecipitation, named m-SMPC, an analysis tool for profiling multiple protein complexes within a single reaction chamber using single-molecule fluorescence imaging. We employed site-selective conjugation of biotin and fluorescent dye directly onto the monoclonal antibodies, which completed an independent sandwich immunoassay without the issue of host cross-reactivity. We applied this technique to profile endogenous B-cell lymphoma extra-large (BCLxL) complexes in non-small cell lung cancer (NSCLC) cells. Up to three distinct BCLxL complexes were successfully detected simultaneously within a single reaction chamber without fluorescence signal crosstalk. Notably, the NSCLC cell line EBC-1 exhibited high BCLxL-BAX and BCLxL-BAK levels, which closely paralleled a strong response to the BCLxL inhibitor A-1331852. This streamlined method offers the potential for quantitative biomarkers derived from protein complex profiling, paving the way for their application in protein complex-targeted therapies.
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Affiliation(s)
- Shi Ho Kim
- Department of Biomarker Discovery, PROTEINA Co., Ltd, Seoul 08826, South Korea
| | - Changju Chun
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
- Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Tae-Young Yoon
- Department of Biomarker Discovery, PROTEINA Co., Ltd, Seoul 08826, South Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
- Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
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4
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Duran E, Schmidt A, Welty R, Jalihal AP, Pitchiaya S, Walter NG. Utilizing functional cell-free extracts to dissect ribonucleoprotein complex biology at single-molecule resolution. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1787. [PMID: 37042458 PMCID: PMC10524090 DOI: 10.1002/wrna.1787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/06/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Cellular machineries that drive and regulate gene expression often rely on the coordinated assembly and interaction of a multitude of proteins and RNA together called ribonucleoprotein complexes (RNPs). As such, it is challenging to fully reconstitute these cellular machines recombinantly and gain mechanistic understanding of how they operate and are regulated within the complex environment that is the cell. One strategy for overcoming this challenge is to perform single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts. This strategy enables elucidation of the interaction and kinetic behavior of specific fluorescently labeled biomolecules within RNPs under conditions that approximate native cellular environments. In this review, we describe single molecule fluorescence microcopy approaches that dissect RNP-driven processes within cellular extracts, highlighting general strategies used in these methods. We further survey biological advances in the areas of pre-mRNA splicing and transcription regulation that have been facilitated through this approach. Finally, we conclude with a summary of practical considerations for the implementation of the featured approaches to facilitate their broader future implementation in dissecting the mechanisms of RNP-driven cellular processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Elizabeth Duran
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Andreas Schmidt
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Ameya P Jalihal
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, Department of Pathology, Department of Urology, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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5
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Hsu CF, Chang KC, Chen YL, Hsieh PS, Lee AI, Tu JY, Chen YT, Wen JD. Formation of frameshift-stimulating RNA pseudoknots is facilitated by remodeling of their folding intermediates. Nucleic Acids Res 2021; 49:6941-6957. [PMID: 34161580 PMCID: PMC8266650 DOI: 10.1093/nar/gkab512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/27/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Programmed –1 ribosomal frameshifting is an essential regulation mechanism of translation in viruses and bacteria. It is stimulated by mRNA structures inside the coding region. As the structure is unfolded repeatedly by consecutive translating ribosomes, whether it can refold properly each time is important in performing its function. By using single-molecule approaches and molecular dynamics simulations, we found that a frameshift-stimulating RNA pseudoknot folds sequentially through its upstream stem S1 and downstream stem S2. In this pathway, S2 folds from the downstream side and tends to be trapped in intermediates. By masking the last few nucleotides to mimic their gradual emergence from translating ribosomes, S2 can be directed to fold from the upstream region. The results show that the intermediates are greatly suppressed, suggesting that mRNA refolding may be modulated by ribosomes. Moreover, masking the first few nucleotides of S1 favors the folding from S2 and yields native pseudoknots, which are stable enough to retrieve the masked nucleotides. We hypothesize that translating ribosomes can remodel an intermediate mRNA structure into a stable conformation, which may in turn stimulate backward slippage of the ribosome. This supports an interactive model of ribosomal frameshifting and gives an insightful account addressing previous experimental observations.
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Affiliation(s)
- Chiung-Fang Hsu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Kai-Chun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Lan Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Po-Szu Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - An-I Lee
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Jui-Yun Tu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Ting Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
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6
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Ziegler SJ, Mallinson SJ, St. John PC, Bomble YJ. Advances in integrative structural biology: Towards understanding protein complexes in their cellular context. Comput Struct Biotechnol J 2020; 19:214-225. [PMID: 33425253 PMCID: PMC7772369 DOI: 10.1016/j.csbj.2020.11.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/26/2023] Open
Abstract
Microorganisms rely on protein interactions to transmit signals, react to stimuli, and grow. One of the best ways to understand these protein interactions is through structural characterization. However, in the past, structural knowledge was limited to stable, high-affinity complexes that could be crystallized. Recent developments in structural biology have revolutionized how protein interactions are characterized. The combination of multiple techniques, known as integrative structural biology, has provided insight into how large protein complexes interact in their native environment. In this mini-review, we describe the past, present, and potential future of integrative structural biology as a tool for characterizing protein interactions in their cellular context.
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Key Words
- CLEM, correlated light and electron microscopy
- Crosslinking mass spectrometry
- Cryo-electron microscopy
- Cryo-electron tomography
- EPR, electron paramagnetic resonance
- FRET, Forster resonance energy transfer
- ISB, Integrative structural biology
- Integrative structural biology
- ML, machine learning
- MR, molecular replacement
- MSAs, multiple sequence alignments
- MX, macromolecular crystallography
- NMR, nuclear magnetic resonance
- PDB, Protein Data Bank
- Protein docking
- Protein structure prediction
- Quinary interactions
- SAD, single-wavelength anomalous dispersion
- SANS, small angle neutron scattering
- SAXS, small angle X-ray scattering
- X-ray crystallography
- XL-MS, cross-linking mass spectrometry
- cryo-EM SPA, cryo-EM single particle analysis
- cryo-EM, cryo-electron microscopy
- cryo-ET, cryo-electron tomography
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Affiliation(s)
- Samantha J. Ziegler
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Sam J.B. Mallinson
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Peter C. St. John
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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7
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Choi B, Cha M, Eun GS, Lee DH, Lee S, Ehsan M, Chae PS, Heo WD, Park Y, Yoon TY. Single-molecule functional anatomy of endogenous HER2-HER3 heterodimers. eLife 2020; 9:53934. [PMID: 32267234 PMCID: PMC7176432 DOI: 10.7554/elife.53934] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
Human epidermal growth factor receptors (HERs) are the primary targets of many directed cancer therapies. However, the reason a specific dimer of HERs generates a stronger proliferative signal than other permutations remains unclear. Here, we used single-molecule immunoprecipitation to develop a biochemical assay for endogenously-formed, entire HER2-HER3 heterodimers. We observed unexpected, large conformational fluctuations in juxta-membrane and kinase domains of the HER2-HER3 heterodimer. Nevertheless, the individual HER2-HER3 heterodimers catalyze tyrosine phosphorylation at an unusually high rate, while simultaneously interacting with multiple copies of downstream signaling effectors. Our results suggest that the high catalytic rate and multi-tasking capability make a concerted contribution to the strong signaling potency of the HER2-HER3 heterodimers.
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Affiliation(s)
- Byoungsan Choi
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.,Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Minkwon Cha
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Gee Sung Eun
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | | | - Seul Lee
- Proteina Co. Ltd., Seoul, Republic of Korea
| | - Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, Ansan, Republic of Korea
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Ansan, Republic of Korea
| | - Won Do Heo
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Tae-Young Yoon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
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8
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Shin JW, Kim S, Ha S, Choi B, Kim S, Im SA, Yoon TY, Chung J. The HER2 S310F Mutant Can Form an Active Heterodimer with the EGFR, Which Can Be Inhibited by Cetuximab but Not by Trastuzumab as well as Pertuzumab. Biomolecules 2019; 9:E629. [PMID: 31635022 PMCID: PMC6843359 DOI: 10.3390/biom9100629] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 12/17/2022] Open
Abstract
G309 or S310 mutations on the HER2 extracellular domain II induce receptor activation. Clinically, S310F is most frequent among HER2 extracellular domain mutations and patients with the S310F mutation without HER2 amplification responded to trastuzumab with or without the pertuzumab combination. However, the ability of S310F mutant to form homodimers or heterodimers with wild-type HER2 and other HER receptors, or their reactivity to trastuzumab and pertuzumab treatments, has not been reported. We overexpressed S310F as well as G309A, G309E and S310Y HER2 mutants and tested their reactivity to trastuzumab and pertuzumab. All mutants reacted to trastuzumab, but S310F mutant did not react to pertuzumab along with S310Y or G309E mutants. Thereafter, we tested the effects of trastuzumab and pertuzumab on 5637 cell line expressing both wild-type HER2 and S310F mutant. The ligand-independent HER2 homodimerization blocking antibody, trastuzumab, did not inhibit the activation of the HER2 receptor, suggesting that the S310F HER2 mutant did not form homodimers or heterodimers with wild-type HER2. Because 5637 cells overexpressed the EGFR, the effects of cetuximab and gefitinib were determined, and both inhibited the activation of HER2 and significantly reduced cell growth. Because pertuzumab did not inhibit the phosphorylation of HER2 while it bound to wild-type HER2, EGFR-mediated phosphorylation is expected to occur on the S310F mutant. To confirm whether the S310F mutant HER2 retained its affinity to the EGFR, single molecule interaction analyses using TIRF microscopy were performed, which showed that S310F mutant successfully formed complexes with EGFR. In conclusion, HER2 S310F mutant can form an active heterodimer with the EGFR and it can be inhibited by cetuximab, but not by trastuzumab in combination with pertuzumab.
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Affiliation(s)
- Jung Won Shin
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul National University, Seoul 03080, Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul National University, Seoul 03080, Korea.
| | - Soohyun Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul National University, Seoul 03080, Korea.
- Department of Cancer Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
| | - Suji Ha
- Cancer Research Institute, Seoul National University College of Medicine, Seoul National University, Seoul 03080, Korea.
- Department of Cancer Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
| | - Byungsan Choi
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Seongyeong Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul National University, Seoul 03080, Korea.
| | - Seock-Ah Im
- Cancer Research Institute, Seoul National University College of Medicine, Seoul National University, Seoul 03080, Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea.
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea.
| | - Tae-Young Yoon
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea.
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul National University, Seoul 03080, Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul National University, Seoul 03080, Korea.
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9
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Struk S, Jacobs A, Sánchez Martín-Fontecha E, Gevaert K, Cubas P, Goormachtig S. Exploring the protein-protein interaction landscape in plants. PLANT, CELL & ENVIRONMENT 2019; 42:387-409. [PMID: 30156707 DOI: 10.1111/pce.13433] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.
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Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Anse Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Elena Sánchez Martín-Fontecha
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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10
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Macdonald PJ, Ruan Q, Tetin SY. Direct single-molecule counting for immunoassay applications. Anal Biochem 2018; 566:139-145. [PMID: 30496720 DOI: 10.1016/j.ab.2018.11.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022]
Abstract
Single-molecule methods offer specificity in studying complex systems and dynamics, but they also offer high sensitivity for basic enumeration. We apply single-molecule TIRF to immunoassays by counting the number of target molecules captured on a streptavidin surface. We demonstrate the utility of using single-molecule counting on eluted detection conjugate, following the capture and sandwich formation portions of the assay having been completed on microparticles. This approach is simple and effective, and creates the opportunity for a universal detection platform that can be used to perform a variety of diagnostic and blood screening assays. We take advantage of the low volume requirements of single-molecule detection and apply a sample reloading approach to concentrate sample onto the detection surface. Due to the high affinity of the streptavidin-biotin reaction, concentration through reloading is both quick and robust. These findings are demonstrated on a model system and in an HIV p24 antigen assay. Single-molecule detection techniques do not need to be complex to exhibit power and flexibility, and so can become valuable in the field of immunoassay diagnostics.
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Affiliation(s)
- Patrick J Macdonald
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, 60064, USA
| | - Qiaoqiao Ruan
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, 60064, USA
| | - Sergey Y Tetin
- Applied Research and Technology, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL, 60064, USA.
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11
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Sung MS, Jung JH, Jeong C, Yoon TY, Park JH. Single-Molecule Co-Immunoprecipitation Reveals Functional Inheritance of EGFRs in Extracellular Vesicles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802358. [PMID: 30239124 DOI: 10.1002/smll.201802358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/09/2018] [Indexed: 06/08/2023]
Abstract
Cancer cells actively release extracellular vesicles (EVs) as important carriers of cellular information to tumor microenvironments. Although the composition and quantity of the proteins contained in EVs are characterized, it remains unknown how these proteins in EVs are related to those in the original cells at the functional level. With epidermal growth factor receptor (EGFR) in lung adenocarcinoma cells as a model oncoprotein, it is studied how distinct types of EVs, microvesicles and exosomes, represent their original cells at the protein and protein-protein interaction (PPI) level. Using the recently developed single-molecule immunolabeling and co-immunoprecipitation schemes, the quantity and PPI strengths of EGFRs derived from EVs and the original lung adenocarcinoma cells are determined. It is found that the microvesicles exhibit higher correlations with the original cells than the exosomes in terms of the EGFR levels and their PPI patterns. In spite of these detailed differences between the microvesicles and exosomes, the EGFR PPI strengths measured for EVs generally show a tight correlation with those determined for the original cells. The results suggest that EGFRs contained in EVs closely reflect the cellular EGFR in terms of their downstream signaling capacity.
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Affiliation(s)
- Mi Sook Sung
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, 30722, South Korea
- Yonsei-IBS Institute, Yonsei University, Seoul, 30722, South Korea
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea
| | - Jik-Han Jung
- Department of Bio and Brain Engineering and KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
| | - Cherlhyun Jeong
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul, 02447, South Korea
| | - Tae-Young Yoon
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, 30722, South Korea
- Yonsei-IBS Institute, Yonsei University, Seoul, 30722, South Korea
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea
| | - Ji-Ho Park
- Department of Bio and Brain Engineering and KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
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12
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Iqbal MS, Siddiqui AA, Banerjee C, Nag S, Mazumder S, De R, Saha SJ, Karri SK, Bandyopadhyay U. Detection of retromer assembly in Plasmodium falciparum by immunosensing coupled to Surface Plasmon Resonance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:722-730. [PMID: 29654975 DOI: 10.1016/j.bbapap.2018.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/02/2018] [Accepted: 04/06/2018] [Indexed: 12/23/2022]
Abstract
Retromer complex plays a crucial role in intracellular protein trafficking and is conserved throughout the eukaryotes including malaria parasite, Plasmodium falciparum, where it is partially conserved. The assembly of retromer complex in RBC stages of malarial parasite is extremely difficult to explore because of its complicated physiology, small size, and intra-erythrocytic location. Nonetheless, understanding of retromer assembly may pave new ways for the development of novel antimalarials targeting parasite-specific protein trafficking pathways. Here, we investigated the assembly of retromer complex in P. falciparum, by an immunosensing method through highly sensitive Surface Plasmon Resonance (SPR) technique. After taking leads from the bioinformatics search and literature, different interacting proteins were identified and specific antibodies were raised against them. The sensor chip was prepared by covalently linking antibody specific to one component and the whole cell lysate was passed through it in order to trap the interacting complex. Antibodies raised against other interacting components were used to detect them in the trapped complex on the SPR chip. We were able to detect three different components in the retromer complex trapped by the immobilized antibody specific against a different component on a sensor chip. The assay was reproduced and validated in a different two-component CD74-MIF system in mammalian cells. We, thus, illustrate the assembly of retromer complex in P. falciparum through a bio-sensing approach that combines SPR with immunosensing requiring a very small amount of sample from the native source.
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Affiliation(s)
- Mohd Shameel Iqbal
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Somnath Mazumder
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Rudranil De
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Shubhra Jyoti Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Suresh Kumar Karri
- Central Instrumentation Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India.
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13
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Lee HW, Choi B, Kang HN, Kim H, Min A, Cha M, Ryu JY, Park S, Sohn J, Shin K, Yun MR, Han JY, Shon MJ, Jeong C, Chung J, Lee SH, Im SA, Cho BC, Yoon TY. Profiling of protein–protein interactions via single-molecule techniques predicts the dependence of cancers on growth-factor receptors. Nat Biomed Eng 2018; 2:239-253. [DOI: 10.1038/s41551-018-0212-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 02/23/2018] [Indexed: 02/04/2023]
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14
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Fareh M, Joo C. Probing RNA-Protein Interactions with Single-Molecule Pull-Down Assays. Methods Mol Biol 2018; 1814:267-285. [PMID: 29956238 DOI: 10.1007/978-1-4939-8591-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recent advances in single-molecule techniques allow for dynamic observations of the interactions between various protein assemblies and RNA molecules with high spatiotemporal resolution. However, it remains challenging to obtain functional eukaryotic protein complexes and cost-effective fluorescently labeled RNAs to study their interactions at the single-molecule level. Here, we describe protocols combining single-molecule fluorescence with various protein complex pull-down techniques to determine the function of RNA-interacting protein complexes of interest. We provide step-by-step guidance for using novel single-molecule techniques including RNA labeling, protein complexes purification, and single-molecule imaging. As a proof-of-concept of the utility of our single-molecule approaches, we show how human Dicer and its cofactor TRBP orchestrate the biogenesis of microRNA in real time. These single-molecule pull-down and fluorescence assays provide sub-second time resolution and can be applied to various ribonucleoprotein complexes that are essential for cellular processes.
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Affiliation(s)
- Mohamed Fareh
- Department of BioNanoScience, Kavli Institute of NanoScience, Delft University of Technology, Building 58, vander Maasweg 9, Delft, 2629 HZ, The Netherlands.
- Cancer Immunology Program, Peter MacCallum Cancer Center, East Melbourne, Victoria,Australia. Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of NanoScience, Delft University of Technology, Building 58, vander Maasweg 9, Delft, 2629 HZ, The Netherlands
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15
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New method of detecting hydrophobic interaction between C-terminal binding domain and biomacromolecules. J Biotechnol 2018; 265:101-108. [DOI: 10.1016/j.jbiotec.2017.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 10/16/2017] [Accepted: 11/17/2017] [Indexed: 01/29/2023]
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16
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Abstract
Complex immunoprecipitation (Co-IP) is a powerful technique for precipitating an intact protein complex out of solution and cell lysates using an antibody that specifically binds to a particular protein in a large complex of proteins. Mass spectrometry (MS) is used to identify, sequence, and quantify proteins. RNA-induced silencing complexes (RISCs), Ago2 centered protein assemblies, are essential for miRNA mediated RNA decay and gene expression regulation; however, the complete list of RISCs is unknown. Here we describe methods used to combine IP and MS to identify new components of RISCs.
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17
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Kim SH, Kim KR, Ahn DR, Lee JE, Yang EG, Kim SY. Reversible Regulation of Enzyme Activity by pH-Responsive Encapsulation in DNA Nanocages. ACS NANO 2017; 11:9352-9359. [PMID: 28846390 DOI: 10.1021/acsnano.7b04766] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Reversible regulation of enzyme activity by chemical and physical stimuli is often achieved by incorporating stimuli-responsive domains in the enzyme of interest. However, this method is suitable for a limited number of enzymes with well-defined structural and conformational changes. In this study, we present a method to encapsulate enzymes in a DNA cage that could transform its conformation depending on the pH, allowing reversible control of the accessibility of the enzyme to the surrounding environment. This enabled us to regulate various properties of the enzyme, such as its resistance to protease-dependent degradation, binding affinity to the corresponding antibody, and most importantly, enzyme activity. Considering that the size and pH responsiveness of the DNA cage can be easily adjusted by the DNA length and sequence, our method provides a broad-impact platform for controlling enzyme functions without modifying the enzyme of interest.
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Affiliation(s)
- Seong Ho Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST) , Seoul, Republic of Korea 02792
| | - Kyoung-Ran Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
| | - Dae-Ro Ahn
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST) , Seoul, Republic of Korea 02792
| | - Ji Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
| | - Eun Gyeong Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
| | - So Yeon Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST) , Seoul, Republic of Korea 02792
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18
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Oligomerization of the tetramerization domain of p53 probed by two- and three-color single-molecule FRET. Proc Natl Acad Sci U S A 2017; 114:E6812-E6821. [PMID: 28760960 DOI: 10.1073/pnas.1700357114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe a method that combines two- and three-color single-molecule FRET spectroscopy with 2D FRET efficiency-lifetime analysis to probe the oligomerization process of intrinsically disordered proteins. This method is applied to the oligomerization of the tetramerization domain (TD) of the tumor suppressor protein p53. TD exists as a monomer at subnanomolar concentrations and forms a dimer and a tetramer at higher concentrations. Because the dissociation constants of the dimer and tetramer are very close, as we determine in this paper, it is not possible to characterize different oligomeric species by ensemble methods, especially the dimer that cannot be readily separated. However, by using single-molecule FRET spectroscopy that includes measurements of fluorescence lifetime and two- and three-color FRET efficiencies with corrections for submillisecond acceptor blinking, we show that it is possible to obtain structural information for individual oligomers at equilibrium and to determine the dimerization kinetics. From these analyses, we show that the monomer is intrinsically disordered and that the dimer conformation is very similar to that of the tetramer but the C terminus of the dimer is more flexible.
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19
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Chen YT, Chang KC, Hu HT, Chen YL, Lin YH, Hsu CF, Chang CF, Chang KY, Wen JD. Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot. Nucleic Acids Res 2017; 45:6011-6022. [PMID: 28334864 PMCID: PMC5449628 DOI: 10.1093/nar/gkx134] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 12/28/2022] Open
Abstract
Frameshifting is an essential process that regulates protein synthesis in many viruses. The ribosome may slip backward when encountering a frameshift motif on the messenger RNA, which usually contains a pseudoknot structure involving tertiary base pair interactions. Due to the lack of detailed molecular explanations, previous studies investigating which features of the pseudoknot are important to stimulate frameshifting have presented diverse conclusions. Here we constructed a bimolecular pseudoknot to dissect the interior tertiary base pairs and used single-molecule approaches to assess the structure targeted by ribosomes. We found that the first ribosome target stem was resistant to unwinding when the neighboring loop was confined along the stem; such constrained conformation was dependent on the presence of consecutive adenosines in this loop. Mutations that disrupted the distal base triples abolished all remaining tertiary base pairs. Changes in frameshifting efficiency correlated with the stem unwinding resistance. Our results demonstrate that various tertiary base pairs are coordinated inside a highly efficient frameshift-stimulating RNA pseudoknot and suggest a mechanism by which mechanical resistance of the pseudoknot may persistently act on translocating ribosomes.
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Affiliation(s)
- Yu-Ting Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Kai-Chun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Hao-Teng Hu
- Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Yi-Lan Chen
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - You-Hsin Lin
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Chiung-Fang Hsu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Cheng-Fu Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Kung-Yao Chang
- Institute of Biochemistry, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
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20
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Chen YF, Lin HC, Chuang KN, Lin CH, Yen HCS, Yeang CH. A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons. PLoS Comput Biol 2017; 13:e1005367. [PMID: 28178267 PMCID: PMC5323020 DOI: 10.1371/journal.pcbi.1005367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 02/23/2017] [Accepted: 01/18/2017] [Indexed: 12/20/2022] Open
Abstract
Ambiguity in genetic codes exists in cases where certain stop codons are alternatively used to encode non-canonical amino acids. In selenoprotein transcripts, the UGA codon may either represent a translation termination signal or a selenocysteine (Sec) codon. Translating UGA to Sec requires selenium and specialized Sec incorporation machinery such as the interaction between the SECIS element and SBP2 protein, but how these factors quantitatively affect alternative assignments of UGA has not been fully investigated. We developed a model simulating the UGA decoding process. Our model is based on the following assumptions: (1) charged Sec-specific tRNAs (Sec-tRNASec) and release factors compete for a UGA site, (2) Sec-tRNASec abundance is limited by the concentrations of selenium and Sec-specific tRNA (tRNASec) precursors, and (3) all synthesis reactions follow first-order kinetics. We demonstrated that this model captured two prominent characteristics observed from experimental data. First, UGA to Sec decoding increases with elevated selenium availability, but saturates under high selenium supply. Second, the efficiency of Sec incorporation is reduced with increasing selenoprotein synthesis. We measured the expressions of four selenoprotein constructs and estimated their model parameters. Their inferred Sec incorporation efficiencies did not correlate well with their SECIS-SBP2 binding affinities, suggesting the existence of additional factors determining the hierarchy of selenoprotein synthesis under selenium deficiency. This model provides a framework to systematically study the interplay of factors affecting the dual definitions of a genetic codon. The “code book” of protein translation maps 43 = 64 triplets of RNA sequences (codons) into 20 canonical amino acids and the stop signal. This code book is universal in almost all organisms on earth. Selenoproteins consist of selenium-containing amino acids–selenocysteines (Sec)–that are not among the 20 canonical amino acids. The cells “borrow” a stop codon UGA to translate selenocysteines. Since UGA maps to two possible outcomes, the translation machinery can synthesize both full-length selenoproteins (when UGA encodes selenocysteine) and truncated peptide chains (when UGA encodes translational termination). Despite extensive study about selenoprotein synthesis mechanisms, a quantitative model for how cells allocate resources to synthesize each species is yet to appear. We propose a quantitative model that can explain the dependency of experimental observables such as protein stability and Sec incorporation efficiency by various factors such as selenium concentration and mRNA levels. Saturation of those quantities implies the existence of limiting factors such as mRNA transcripts and Sec-specific tRNAs. The match between model simulations and experimental data suggests that the cellular decision making of synthesizing the two species of proteins may follow simple first-order kinetics.
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Affiliation(s)
- Yen-Fu Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Chuan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Kai-Neng Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Chih-Hsu Lin
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Hsueh-Chi S. Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- * E-mail: (HCSY); (CHY)
| | - Chen-Hsiang Yeang
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- * E-mail: (HCSY); (CHY)
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21
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Yoo J, Lee TS, Choi B, Shon MJ, Yoon TY. Observing Extremely Weak Protein-Protein Interactions with Conventional Single-Molecule Fluorescence Microscopy. J Am Chem Soc 2016; 138:14238-14241. [PMID: 27758101 DOI: 10.1021/jacs.6b09542] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Extremely weak protein-protein interactions (PPIs), signified by micromolar or even millimolar dissociation constants, are one of the keys to understanding the rapid responses of cellular systems. Although single-molecule methods are particularly useful in determining kinetics of biological processes, their application is largely limited to rather strong interactions because of the diffraction-limited observation volume. In this study, we report a single-molecule method that allows the characterization of PPIs using a prey concentration 4 orders of magnitude lower than the dissociation constant. Instead of increasing the concentration of diffusing molecules, which is inevitably limited by the optical diffraction limit, we employed an increased density of surface bait protein. The low occupancy of the surface baits permitted determination of the kinetics with single-molecule resolution. We used this approach to study a PPI network consisting of Ras and its downstream proteins including full-length Rafs and catalytic subunits of phosphoinositide 3-kinase.
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Affiliation(s)
- Janghyun Yoo
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141, South Korea.,Center for Nanomedicine, Institute for Basic Science (IBS), Yonsei University , Seoul 30722, South Korea.,Yonsei-IBS Institute, Yonsei University , Seoul 30722, South Korea
| | - Tae-Sun Lee
- Center for Nanomedicine, Institute for Basic Science (IBS), Yonsei University , Seoul 30722, South Korea.,Yonsei-IBS Institute, Yonsei University , Seoul 30722, South Korea
| | - Byungsan Choi
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141, South Korea.,Center for Nanomedicine, Institute for Basic Science (IBS), Yonsei University , Seoul 30722, South Korea.,Yonsei-IBS Institute, Yonsei University , Seoul 30722, South Korea
| | - Min Ju Shon
- Center for Nanomedicine, Institute for Basic Science (IBS), Yonsei University , Seoul 30722, South Korea.,Yonsei-IBS Institute, Yonsei University , Seoul 30722, South Korea
| | - Tae-Young Yoon
- Center for Nanomedicine, Institute for Basic Science (IBS), Yonsei University , Seoul 30722, South Korea.,Yonsei-IBS Institute, Yonsei University , Seoul 30722, South Korea
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22
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Single-molecule fluorescence microscopy of native macromolecular complexes. Curr Opin Struct Biol 2016; 41:225-232. [PMID: 27662375 DOI: 10.1016/j.sbi.2016.09.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/06/2016] [Accepted: 09/07/2016] [Indexed: 12/11/2022]
Abstract
Macromolecular complexes consisting of proteins, lipids, and/or nucleic acids are ubiquitous in biological processes. Their composition, stoichiometry, order of assembly, and conformations can be heterogeneous or can change dynamically, making single-molecule studies best suited to measure these properties accurately. Recent single-molecule pull-down and other related approaches have combined the principles of conventional co-immunoprecipitation assay with single-molecule fluorescence microscopy to probe native macromolecular complexes. In this review, we present the advances in single-molecule pull-down methods and biological systems that have been investigated in such semi vivo manner.
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23
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Fareh M, Loeff L, Szczepaniak M, Haagsma AC, Yeom KH, Joo C. Single-molecule pull-down for investigating protein-nucleic acid interactions. Methods 2016; 105:99-108. [PMID: 27017911 DOI: 10.1016/j.ymeth.2016.03.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/26/2016] [Accepted: 03/24/2016] [Indexed: 12/30/2022] Open
Abstract
The genome and transcriptome are constantly modified by proteins in the cell. Recent advances in single-molecule techniques allow for high spatial and temporal observations of these interactions between proteins and nucleic acids. However, due to the difficulty of obtaining functional protein complexes, it remains challenging to study the interactions between macromolecular protein complexes and nucleic acids. Here, we combined single-molecule fluorescence with various protein complex pull-down techniques to determine the function and stoichiometry of ribonucleoprotein complexes. Through the use of three examples of protein complexes from eukaryotic cells (Drosha, Dicer, and TUT4 protein complexes), we provide step-by-step guidance for using novel single-molecule techniques. Our single-molecule methods provide sub-second and nanometer resolution and can be applied to other nucleoprotein complexes that are essential for cellular processes.
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Affiliation(s)
- Mohamed Fareh
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Luuk Loeff
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Malwina Szczepaniak
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Anna C Haagsma
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Kyu-Hyeon Yeom
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629HZ, The Netherlands.
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24
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Ryu JK, Min D, Rah SH, Kim SJ, Park Y, Kim H, Hyeon C, Kim HM, Jahn R, Yoon TY. Spring-loaded unraveling of a single SNARE complex by NSF in one round of ATP turnover. Science 2015; 347:1485-9. [PMID: 25814585 DOI: 10.1126/science.aaa5267] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
During intracellular membrane trafficking, N-ethylmaleimide-sensitive factor (NSF) and alpha-soluble NSF attachment protein (α-SNAP) disassemble the soluble NSF attachment protein receptor (SNARE) complex for recycling of the SNARE proteins. The molecular mechanism by which NSF disassembles the SNARE complex is largely unknown. Using single-molecule fluorescence spectroscopy and magnetic tweezers, we found that NSF disassembled a single SNARE complex in only one round of adenosine triphosphate (ATP) turnover. Upon ATP cleavage, the NSF hexamer developed internal tension with dissociation of phosphate ions. After latent time measuring tens of seconds, NSF released the built-up tension in a burst within 20 milliseconds, resulting in disassembly followed by immediate release of the SNARE proteins. Thus, NSF appears to use a "spring-loaded" mechanism to couple ATP hydrolysis and unfolding of substrate proteins.
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Affiliation(s)
- Je-Kyung Ryu
- National Creative Research Initiative Center for Single-Molecule Systems Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea. Department of Physics, KAIST, Daejeon 305-701, South Korea
| | - Duyoung Min
- National Creative Research Initiative Center for Single-Molecule Systems Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea. Department of Physics, KAIST, Daejeon 305-701, South Korea
| | - Sang-Hyun Rah
- National Creative Research Initiative Center for Single-Molecule Systems Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea. Department of Physics, KAIST, Daejeon 305-701, South Korea
| | - Soo Jin Kim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 305-701, South Korea
| | - Yongsoo Park
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Haesoo Kim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 305-701, South Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 130-722, South Korea
| | - Ho Min Kim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 305-701, South Korea
| | - Reinhard Jahn
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - Tae-Young Yoon
- National Creative Research Initiative Center for Single-Molecule Systems Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea. Department of Physics, KAIST, Daejeon 305-701, South Korea.
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25
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Skinner JP, Tetin SY. Rapid single-molecule imaging in cyclic olefin copolymer channels. Microsc Res Tech 2015; 78:309-16. [PMID: 25704038 DOI: 10.1002/jemt.22476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/15/2015] [Indexed: 01/10/2023]
Abstract
Rapid preparation of high quality capture surfaces is a major challenge for surface-based single-molecule protein binding assays. Here we introduce a simple method to activate microfluidic chambers made from cyclic olefin copolymer for single-molecule imaging with total internal reflection fluorescence microscopy. We describe a surface coating protocol and demonstrate single-molecule imaging in off-the-shelf microfluidic parts that can be activated for binding assays within a few minutes. As the first example, biotinylated protein directly captured on the neutravidin-coated surface was detected using fluorescently labeled antibody. We then showed detection of a fusion construct containing green fluorescence protein and verified its single fluorophore behavior by observing stepwise photobleaching events. Finally, a target protein was identified in the crude cell lysate using antibody-sandwich complex formation. In all experiments, controls were completed to ensure that nonspecific binding to the surface was minimal. Based on our results, we conclude that the simple surface preparation described in this paper enables single-molecule imaging assays without time-consuming coating procedures.
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Affiliation(s)
- Joseph P Skinner
- Diagnostics Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, 60064
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Gust A, Zander A, Gietl A, Holzmeister P, Schulz S, Lalkens B, Tinnefeld P, Grohmann D. A starting point for fluorescence-based single-molecule measurements in biomolecular research. Molecules 2014; 19:15824-65. [PMID: 25271426 PMCID: PMC6271140 DOI: 10.3390/molecules191015824] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 01/24/2023] Open
Abstract
Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET) experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.
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Affiliation(s)
- Alexander Gust
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Adrian Zander
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Andreas Gietl
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Phil Holzmeister
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Sarah Schulz
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Birka Lalkens
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Philip Tinnefeld
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany.
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Affiliation(s)
- Vasudha Aggarwal
- Center for Biophysics and Computational Biology; University of Illinois Urbana Champaign; Urbana IL USA
| | - Taekjip Ha
- Center for Biophysics and Computational Biology; University of Illinois Urbana Champaign; Urbana IL USA
- Department of Physics; University of Illinois Urbana Champaign; Urbana IL USA
- Howard Hughes Medical Institute; Urbana IL USA
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