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Sun B, Xu J, Liu S, Li QX. Characterization of Small Molecule-Protein Interactions Using SPR Method. Methods Mol Biol 2023; 2690:149-159. [PMID: 37450146 DOI: 10.1007/978-1-0716-3327-4_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Surface plasmon resonance (SPR) is an optical phenomenon being used to monitor molecular binding events. With the advantages of being label-free, real-time, and sensitive, SPR assays have become one of the most commonly used techniques to measure binding kinetics, affinity, specificity, and concentration of molecular interactions. In an SPR experiment to measure small molecule-protein interactions, the protein is immobilized on the biosensor surface, while the small molecule flows through the surface of the sensor chip. The interactions between the small molecules and proteins are monitored by subsequent changes in the refractive index and quantified with resonance units. In this chapter, we have utilized an SPR assay to study the interaction of flavonoids and the glucose-regulated protein 78. Assay steps are detailed for immobilization optimization, SPR instrument setup, operation, sample injection, and affinity data analysis.
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Affiliation(s)
- Binmei Sun
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jianmei Xu
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Shaoqun Liu
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA.
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2
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Lian X, Yang X, Yang S, Zhang Z. Current status and future perspectives of computational studies on human-virus protein-protein interactions. Brief Bioinform 2021; 22:6161422. [PMID: 33693490 DOI: 10.1093/bib/bbab029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/19/2022] Open
Abstract
The protein-protein interactions (PPIs) between human and viruses mediate viral infection and host immunity processes. Therefore, the study of human-virus PPIs can help us understand the principles of human-virus relationships and can thus guide the development of highly effective drugs to break the transmission of viral infectious diseases. Recent years have witnessed the rapid accumulation of experimentally identified human-virus PPI data, which provides an unprecedented opportunity for bioinformatics studies revolving around human-virus PPIs. In this article, we provide a comprehensive overview of computational studies on human-virus PPIs, especially focusing on the method development for human-virus PPI predictions. We briefly introduce the experimental detection methods and existing database resources of human-virus PPIs, and then discuss the research progress in the development of computational prediction methods. In particular, we elaborate the machine learning-based prediction methods and highlight the need to embrace state-of-the-art deep-learning algorithms and new feature engineering techniques (e.g. the protein embedding technique derived from natural language processing). To further advance the understanding in this research topic, we also outline the practical applications of the human-virus interactome in fundamental biological discovery and new antiviral therapy development.
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Affiliation(s)
- Xianyi Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaodi Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shiping Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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3
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Dumond J, Tronchet JMJ, Kirkiacharian S, Seman M, Reboud-Ravaux M. Insights into Biophysical Methods to Study Interactions Between HIV-1 Reverse Transcriptase and Non-nucleoside Reverse Transcriptase Inhibitors. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190723121845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:Reverse Transcriptase (RT) of immunodeficiency virus type-1 (HIV-1) remains an essential target for new antiretroviral therapies. Non-nucleoside reverse transcriptase inhibitors (or NNRTIs) constitute a major class of RT inhibitors whose characterization is essential.Introduction:Several biochemical, biological, and biophysical methods have been previously used to analyze the biological effects of NNRTIs. We explored here the use of surface plasmonic resonance to characterize the affinity of RT towards selected NNRTIs and compared the results with those obtained with in vitro and in cellulo assays.Methods:The solubility and stability in buffers of the tested NNRTIs were assessed by spectrophotometry and fluorescence. Surface plasmonic resonance experiments to study direct NNRTIs binding to immobilized RT and intramolecular quenching of RT tryptophan fluorescence were used to determine the KA association constants (= 1/KD) between RT and the inhibitors. The in vitro inhibition constants of RT were determined using kinetics and the effects on three other potential targets (proteasome, HIV-1 integrase, and HIV-1 protease) were analyzed.Results:The results obtained with two typical molecules belonging to our previous N-hydroxyureido acylnucleoside derivatives series using the above biophysical assays matched those obtained in in vitro and previous in cellulo assays.Conclusion:Surface plasmonic resonance provides reliable thermodynamic information on the interaction of RT with NNRTIs and appears as a useful method for understanding their inhibitory mechanism.
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Affiliation(s)
- Julien Dumond
- Sorbonne Universite, CNRS, INSERM, Institut de Biologie Paris Seine, IBPS, Adaptation biologique et Vieillissement, 7 quai Saint Bernard 75252 Paris Cedex 05, France
| | | | - Serge Kirkiacharian
- Faculte de Pharmacie Paris-Sud. Laboratoire de Chimie Therapeutique. 5 rue Jean- Baptiste Clement 92290 Chatenay-Malabry, France
| | - Michel Seman
- Institut National de la Sante et de la Recherche Medicale U905, Pathophysiology Biotherapy of Inflammatory and Autoimmune Diseases, Faculte de Médecine et de Pharmacie de Rouen, 22 Boulevard Gambetta 76183 Rouen Cedex, France
| | - Michèle Reboud-Ravaux
- Sorbonne Universite, CNRS, INSERM, Institut de Biologie Paris Seine, IBPS, Adaptation biologique et Vieillissement, 7 quai Saint Bernard 75252 Paris Cedex 05, France
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4
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Singh V, Singh K, Nand A, Dai H, Wang J, Zhang L, Merino A, Zhu J. Small molecule microarray screening methodology based on surface plasmon resonance imaging. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2014.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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5
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Investigation of cathepsin D–mAb interactions using a combined experimental and computational tool set. Biotechnol Bioeng 2019; 116:1684-1697. [DOI: 10.1002/bit.26968] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/20/2019] [Accepted: 03/14/2019] [Indexed: 12/18/2022]
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6
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Fundamental Principles for Luminescence Sensing Measuring Devices Used for the Detection of Biological Warfare Agents. ACTA ACUST UNITED AC 2017. [PMCID: PMC7122564 DOI: 10.1007/978-94-024-1113-3_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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7
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Wang L, Cheng J, Wang S, Zhang X, Cai, X. Screening of inhibitors of Taenia solium glycogen synthase Kinase-3β. RSC Adv 2017. [DOI: 10.1039/c7ra05873j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A flow chart of the screening of lead compounds.
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Affiliation(s)
- Li Wang
- College of Veterinary Medicine
- Jilin University
- Changchun 130062
- China
- State Key Laboratory of Veterinary Etiological Biology
| | - Jiagao Cheng
- Shanghai Key Laboratory of Chemical Biology
- School of Pharmacy
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Shuai Wang
- State Key Laboratory of Veterinary Etiological Biology
- Lanzhou Veterinary Research Institute
- Chinese Academy of Agricultural Sciences
- Lanzhou 730046
- China
| | - Xichen Zhang
- College of Veterinary Medicine
- Jilin University
- Changchun 130062
- China
| | - Xuepeng Cai,
- College of Veterinary Medicine
- Jilin University
- Changchun 130062
- China
- State Key Laboratory of Veterinary Etiological Biology
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8
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Abera MB, Xiao J, Nofziger J, Titus S, Southall N, Zheng W, Moritz KE, Ferrer M, Cherry JJ, Androphy EJ, Wang A, Xu X, Austin C, Fischbeck KH, Marugan JJ, Burnett BG. ML372 blocks SMN ubiquitination and improves spinal muscular atrophy pathology in mice. JCI Insight 2016; 1:e88427. [PMID: 27882347 DOI: 10.1172/jci.insight.88427] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease and one of the leading inherited causes of infant mortality. SMA results from insufficient levels of the survival motor neuron (SMN) protein, and studies in animal models of the disease have shown that increasing SMN protein levels ameliorates the disease phenotype. Our group previously identified and optimized a new series of small molecules, with good potency and toxicity profiles and reasonable pharmacokinetics, that were able to increase SMN protein levels in SMA patient-derived cells. We show here that ML372, a representative of this series, almost doubles the half-life of residual SMN protein expressed from the SMN2 locus by blocking its ubiquitination and subsequent degradation by the proteasome. ML372 increased SMN protein levels in muscle, spinal cord, and brain tissue of SMA mice. Importantly, ML372 treatment improved the righting reflex and extended survival of a severe mouse model of SMA. These results demonstrate that slowing SMN degradation by selectively inhibiting its ubiquitination can improve the motor phenotype and lifespan of SMA model mice.
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Affiliation(s)
- Mahlet B Abera
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hebert School of Medicine, Bethesda, Maryland, USA
| | - Jingbo Xiao
- NIH Chemical Genomics Center, Discovery Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Jonathan Nofziger
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Steve Titus
- NIH Chemical Genomics Center, Discovery Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Noel Southall
- NIH Chemical Genomics Center, Discovery Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Wei Zheng
- NIH Chemical Genomics Center, Discovery Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Kasey E Moritz
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hebert School of Medicine, Bethesda, Maryland, USA
| | - Marc Ferrer
- NIH Chemical Genomics Center, Discovery Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Jonathan J Cherry
- Department of Dermatology,, School of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Elliot J Androphy
- Department of Dermatology,, School of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Amy Wang
- NIH Chemical Genomics Center, Discovery Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Xin Xu
- NIH Chemical Genomics Center, Discovery Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Christopher Austin
- NIH Chemical Genomics Center, Discovery Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Juan J Marugan
- NIH Chemical Genomics Center, Discovery Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Barrington G Burnett
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, F. Edward Hebert School of Medicine, Bethesda, Maryland, USA
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9
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Choi HJ, Chung BH, Kim Y. Analysis of Protein-Protein Interactions by Surface Plasmon Resonance Imaging-based Microwell and Microfluidic Chip. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hyun-Ju Choi
- Institute of General Education; Kyungnam University; Changwon-si Republic of Korea
| | - Bong Hyun Chung
- Department of Science Education; Kyungnam University; Changwon-si Republic of Korea
| | - Yongseong Kim
- BioNanotechnology Research Center; Korea Research Institute of Bioscience and Biotechnology (KRIBB); Daejeon 305-806 Republic of Korea
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10
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Walgama C, Al Mubarak ZH, Zhang B, Akinwale M, Pathiranage A, Deng J, Berlin KD, Benbrook DM, Krishnan S. Label-Free Real-Time Microarray Imaging of Cancer Protein–Protein Interactions and Their Inhibition by Small Molecules. Anal Chem 2016; 88:3130-5. [DOI: 10.1021/acs.analchem.5b04234] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Doris M. Benbrook
- Department
of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
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11
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Singh V, Li Z, Zhou X, Xu X, Xu J, Nand A, Wen H, Li H, Zhu J, Zhang J. High-throughput measurement of drug–cyclodextrin kinetic rate constants by a small molecule microarray using surface plasmon resonance imaging. RSC Adv 2016. [DOI: 10.1039/c5ra21298g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A high-throughput methodology for the measurement of drug–CD kinetic rate constants.
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12
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Surface plasmon resonance: a versatile technique for biosensor applications. SENSORS 2015; 15:10481-510. [PMID: 25951336 PMCID: PMC4481982 DOI: 10.3390/s150510481] [Citation(s) in RCA: 567] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/24/2015] [Accepted: 04/28/2015] [Indexed: 02/07/2023]
Abstract
Surface plasmon resonance (SPR) is a label-free detection method which has emerged during the last two decades as a suitable and reliable platform in clinical analysis for biomolecular interactions. The technique makes it possible to measure interactions in real-time with high sensitivity and without the need of labels. This review article discusses a wide range of applications in optical-based sensors using either surface plasmon resonance (SPR) or surface plasmon resonance imaging (SPRI). Here we summarize the principles, provide examples, and illustrate the utility of SPR and SPRI through example applications from the biomedical, proteomics, genomics and bioengineering fields. In addition, SPR signal amplification strategies and surface functionalization are covered in the review.
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13
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Serrano M, Kombrink E, Meesters C. Considerations for designing chemical screening strategies in plant biology. FRONTIERS IN PLANT SCIENCE 2015; 6:131. [PMID: 25904921 PMCID: PMC4389374 DOI: 10.3389/fpls.2015.00131] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/18/2015] [Indexed: 05/03/2023]
Abstract
Traditionally, biologists regularly used classical genetic approaches to characterize and dissect plant processes. However, this strategy is often impaired by redundancy, lethality or pleiotropy of gene functions, which prevent the isolation of viable mutants. The chemical genetic approach has been recognized as an alternative experimental strategy, which has the potential to circumvent these problems. It relies on the capacity of small molecules to modify biological processes by specific binding to protein target(s), thereby conditionally modifying protein function(s), which phenotypically resemble mutation(s) of the encoding gene(s). A successful chemical screening campaign comprises three equally important elements: (1) a reliable, robust, and quantitative bioassay, which allows to distinguish between potent and less potent compounds, (2) a rigorous validation process for candidate compounds to establish their selectivity, and (3) an experimental strategy for elucidating a compound's mode of action and molecular target. In this review we will discuss details of this general strategy and additional aspects that deserve consideration in order to take full advantage of the power provided by the chemical approach to plant biology. In addition, we will highlight some success stories of recent chemical screenings in plant systems, which may serve as teaching examples for the implementation of future chemical biology projects.
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Affiliation(s)
- Mario Serrano
- Plant Biology, Department of Biology, University of FribourgFribourg, Switzerland
| | - Erich Kombrink
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding ResearchKöln, Germany
| | - Christian Meesters
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding ResearchKöln, Germany
- Department of Chemical Biology, Faculty of Biology, Center for Medical Biotechnology, University of Duisburg-EssenEssen, Germany
- *Correspondence: Christian Meesters, Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Köln, Germany
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14
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Singh V, Nand A, Sarita S. Universal screening platform using three-dimensional small molecule microarray based on surface plasmon resonance imaging. RSC Adv 2015. [DOI: 10.1039/c5ra15637h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Herein we report a potent methodology for drug screening on a three-dimensional (3D) surface using a carbene based photo-cross-linking reaction.
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Affiliation(s)
- Vikramjeet Singh
- Center for Drug Delivery System
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
- China
| | - Amita Nand
- National Center for Nanoscience and Technology
- Beijing 100190
- People’s Republic of China
- University of Chinese Academy
- of Sciences
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15
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Lee KH, Kim DM. Applications of cell-free protein synthesis in synthetic biology: Interfacing bio-machinery with synthetic environments. Biotechnol J 2013; 8:1292-300. [DOI: 10.1002/biot.201200385] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/16/2013] [Accepted: 09/12/2013] [Indexed: 11/08/2022]
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16
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Rusnati M, Chiodelli P, Bugatti A, Urbinati C. Bridging the past and the future of virology: surface plasmon resonance as a powerful tool to investigate virus/host interactions. Crit Rev Microbiol 2013; 41:238-60. [PMID: 24059853 DOI: 10.3109/1040841x.2013.826177] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Despite decades of antiviral drug research and development, viruses still remain a top global healthcare problem. Compared to eukaryotic cells, viruses are composed by a limited numbers of proteins that, nevertheless, set up multiple interactions with cellular components, allowing the virus to take control of the infected cell. Each virus/host interaction can be considered as a therapeutical target for new antiviral drugs but, unfortunately, the systematic study of a so huge number of interactions is time-consuming and expensive, calling for models overcoming these drawbacks. Surface plasmon resonance (SPR) is a label-free optical technique to study biomolecular interactions in real time by detecting reflected light from a prism-gold film interface. Launched 20 years ago, SPR has become a nearly irreplaceable technology for the study of biomolecular interactions. Accordingly, SPR is increasingly used in the field of virology, spanning from the study of biological interactions to the identification of putative antiviral drugs. From the literature available, SPR emerges as an ideal link between conventional biological experimentation and system biology studies functional to the identification of highly connected viral or host proteins that act as nodal points in virus life cycle and thus considerable as therapeutical targets for the development of innovative antiviral strategies.
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Affiliation(s)
- Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia , Brescia , Italy
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17
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Chandrasekhar S, Iyer LK, Panchal JP, Topp EM, Cannon JB, Ranade VV. Microarrays and microneedle arrays for delivery of peptides, proteins, vaccines and other applications. Expert Opin Drug Deliv 2013; 10:1155-70. [PMID: 23662940 DOI: 10.1517/17425247.2013.797405] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Peptide and protein microarray and microneedle array technology provides direct information on protein function and potential drug targets in drug discovery and delivery. Because of this unique ability, these arrays are well suited for protein profiling, drug target identification/validation and studies of protein interaction, biochemical activity, immune responses, clinical prognosis and diagnosis and for gene, protein and drug delivery. AREAS COVERED The aim of this review is to describe and summarize past and recent developments of microarrays in their construction, characterization and production and applications of microneedles in drug delivery. The scope and limitations of various technologies in this respect are discussed. EXPERT OPINION This article offers a review of microarray/microneedle technologies and possible future directions in targeting and in the delivery of pharmacologically active compounds for unmet needs in biopharmaceutical research. A better understanding of the production and use of microarrays and microneedles for delivery of peptides, proteins and vaccines is needed.
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Affiliation(s)
- Saradha Chandrasekhar
- Purdue University, Department of Industrial and Physical Pharmacy, West Lafayette, IN 47907, USA
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18
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Mohr J, Chuan YP, Wu Y, Lua LHL, Middelberg APJ. Virus-like particle formulation optimization by miniaturized high-throughput screening. Methods 2013; 60:248-56. [PMID: 23639868 DOI: 10.1016/j.ymeth.2013.04.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 12/19/2022] Open
Abstract
Virus-like particles (VLPs) are non-infectious and immunogenic virus-mimicking protein assemblies that are increasingly researched as vaccine candidates. Stability against aggregation is an important determinant dictating the viability of a pipeline VLP product, making multivariable stability data highly desirable especially in early product development stages. However, comprehensive formulation studies are challenging due to low sample availability early in developability assessment. This issue is exacerbated by industry-standard analytical techniques which are low-throughput and/or sample-consuming. This study presents a miniaturized high-throughput screening (MHTS) methodology for VLP formulation by integrating dynamic light scattering (DLS) and asymmetrical flow field-flow fractionation (AF4) in a formulation funnel analysis. Using only 2 μg of sample and 100 s per measurement, a DLS plate reader was deployed to effectively pre-screen a large experimental space, allowing a smaller set of superior formulation conditions to be interrogated at high-resolution with AF4. The stabilizing effects of polysorbate 20, sucrose, trehalose, mannitol and sorbitol were investigated. MHTS data showed that addition of 0.5% w/v polysorbate 20 together with either 40% w/v sucrose or 40% w/v sorbitol could stabilize VLPs at elevated temperatures up to 58 °C. AF4 data further confirmed that the formulation containing 40% w/v sorbitol and 0.5% w/v polysorbate 20 effectively protected VLPs during freeze-thawing and freeze-drying, increasing recoveries from these processes by 80 and 50 percentage points, respectively. The MHTS strategy presented here could be used to rapidly explore a large formulation development space using reduced amounts of sample, without sacrificing the analytical resolution needed for quality control. Such a method paves the way for rapid formulation development and could potentially hasten the commercialization of new VLP vaccines.
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Affiliation(s)
- Johannes Mohr
- The University of Queensland, Australian Institute for Bioengineering and Nanotechnology, St Lucia, QLD 4072, Australia
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20
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Worsham MJ, Ali H, Dragovic J, Schweitzer VP. Molecular characterization of head and neck cancer: how close to personalized targeted therapy? Mol Diagn Ther 2012; 16:209-22. [PMID: 22873739 DOI: 10.2165/11635330-000000000-00000] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Molecular targeted therapy in head and neck squamous cell carcinoma (HNSCC) continues to make strides, and holds much promise. Cetuximab remains the sole US FDA-approved molecular targeted therapy available for HNSCC, though several new biologic agents targeting the epidermal growth factor receptor (EGFR) and other pathways are currently in the regulatory approval pipeline. While targeted therapies have the potential to be personalized, their current use in HNSCC is not personalized. This is illustrated for EGFR-targeted drugs, where EGFR as a molecular target has yet to be individualized for HNSCC. Future research needs to identify factors that correlate with response (or lack of one) and the underlying genotype-phenotype relationship that dictates this response. Comprehensive exploration of genetic and epigenetic landscapes in HNSCC is opening new frontiers to further enlighten and mechanistically inform newer as well as existing molecular targets, and to set a course for eventually translating these discoveries into therapies for patients. This opinion offers a snapshot of the evolution of molecular subtyping in HNSCC and its current clinical applicability, as well as new emergent paradigms with implications for controlling this disease in the future.
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Affiliation(s)
- Maria J Worsham
- Department of OtolaryngologyHead and Neck Surgery, Henry Ford Health System, Detroit, MI 48202, USA.
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21
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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22
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Seefeld TH, Halpern AR, Corn RM. On-chip synthesis of protein microarrays from DNA microarrays via coupled in vitro transcription and translation for surface plasmon resonance imaging biosensor applications. J Am Chem Soc 2012; 134:12358-61. [PMID: 22793370 DOI: 10.1021/ja304187r] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein microarrays are fabricated from double-stranded DNA (dsDNA) microarrays by a one-step, multiplexed enzymatic synthesis in an on-chip microfluidic format and then employed for antibody biosensing measurements with surface plasmon resonance imaging (SPRI). A microarray of dsDNA elements (denoted as generator elements) that encode either a His-tagged green fluorescent protein (GFP) or a His-tagged luciferase protein is utilized to create multiple copies of mRNA (mRNA) in a surface RNA polymerase reaction; the mRNA transcripts are then translated into proteins by cell-free protein synthesis in a microfluidic format. The His-tagged proteins diffuse to adjacent Cu(II)-NTA microarray elements (denoted as detector elements) and are specifically adsorbed. The net result is the on-chip, cell-free synthesis of a protein microarray that can be used immediately for SPRI protein biosensing. The dual element format greatly reduces any interference from the nonspecific adsorption of enzyme or proteins. SPRI measurements for the detection of the antibodies anti-GFP and antiluciferase were used to verify the formation of the protein microarray. This convenient on-chip protein microarray fabrication method can be implemented for multiplexed SPRI biosensing measurements in both clinical and research applications.
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Affiliation(s)
- Ting H Seefeld
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, United States
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Battle CH, Jayawickramarajah J. Supramolecular Approaches for Inhibition of Protein-Protein and Protein-DNA Interactions. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kim YE, Yi SY, Lee CS, Jung Y, Chung BH. Gold patterned biochips for on-chip immuno-MALDI-TOF MS: SPR imaging coupled multi-proteinMS analysis. Analyst 2012; 137:386-92. [DOI: 10.1039/c1an15659d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chung CW, Witherington J. Progress in the discovery of small-molecule inhibitors of bromodomain--histone interactions. ACTA ACUST UNITED AC 2011; 16:1170-85. [PMID: 21956175 DOI: 10.1177/1087057111421372] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bromodomains are structurally conserved protein modules present in a large number of chromatin-associated proteins and in many nuclear histone acetyltransferases. The bromodomain functions as an acetyl-lysine binding domain and has been shown to be pivotal in regulating protein-protein interactions in chromatin-mediated cellular gene transcription, cell proliferation, and viral transcriptional activation. Structural analyses of these modules in complex with acetyl-lysine peptide ligands provide insights into the molecular basis for recognition and ligand selectivity within this epigenetic reader family. However, there are significant challenges in configuring assays to identify inhibitors of these proteins. This review focuses on the progress made in developing methods to identify peptidic and small-molecule ligands using biophysical label-free and biochemical approaches. The advantage of each technique and the results reported are summarized, highlighting the potential applicably to other reader domains and the caveats in translation from simple in vitro systems to a biological context.
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Heeres JT, Hergenrother PJ. High-throughput screening for modulators of protein–protein interactions: use of photonic crystal biosensors and complementary technologies. Chem Soc Rev 2011; 40:4398-410. [DOI: 10.1039/b923660k] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Berrade L, Garcia AE, Camarero JA. Protein microarrays: novel developments and applications. Pharm Res 2010; 28:1480-99. [PMID: 21116694 PMCID: PMC3137928 DOI: 10.1007/s11095-010-0325-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 11/08/2010] [Indexed: 02/05/2023]
Abstract
Protein microarray technology possesses some of the greatest potential for providing direct information on protein function and potential drug targets. For example, functional protein microarrays are ideal tools suited for the mapping of biological pathways. They can be used to study most major types of interactions and enzymatic activities that take place in biochemical pathways and have been used for the analysis of simultaneous multiple biomolecular interactions involving protein-protein, protein-lipid, protein-DNA and protein-small molecule interactions. Because of this unique ability to analyze many kinds of molecular interactions en masse, the requirement of very small sample amount and the potential to be miniaturized and automated, protein microarrays are extremely well suited for protein profiling, drug discovery, drug target identification and clinical prognosis and diagnosis. The aim of this review is to summarize the most recent developments in the production, applications and analysis of protein microarrays.
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Affiliation(s)
- Luis Berrade
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, PSC 616, Los Angeles, California 90033, USA
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Abstract
IMPORTANCE OF THE FIELD Head and neck squamous cell carcinoma (HNSCC) is the eighth leading cause of cancer death worldwide. Despite advances in surgery and chemoradiation therapy, there has been little improvement in survival rates over the past 4 decades. Additionally, surgery and chemoradiotherapy have serious side effects. The development of agents with greater efficacy and tolerability is needed. AREAS COVERED IN THIS REVIEW EGFR is the only proven molecular target for HNSCC therapy. Cetuximab, the sole FDA-approved molecular targeted HNSCC therapy, and other potential targeted therapies are being evaluated in preclinical, clinical and post-marketing studies. Here, we review the emerging targets for biological agents in HNSCC and the rationale for their selection. WHAT THE READER WILL GAIN Key information in the development of new drug targets and the emergence of new biomarkers are discussed. Readers will gain insight regarding the limitations of current therapies, the impact of recently approved targeted therapies and the influence that predictive biomarkers will have on drug development. TAKE HOME MESSAGE The head and neck cancer drug market is rapidly evolving. Coordination between drug and biomarker development efforts may soon yield targeted therapies that can achieve the promise of personalized cancer medicine.
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Affiliation(s)
- Christopher Fung
- University of Pittsburgh and University of Pittsburgh Cancer Institute, Department of Otolaryngology, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh School of Medicine, Physician-Scientist Training Program, Pittsburgh, Pennsylvania, USA
- Howard Hughes Medical Institute, Medical Fellows Program, Chevy Chase, Maryland, USA
| | - Jennifer R Grandis
- University of Pittsburgh and University of Pittsburgh Cancer Institute, Department of Otolaryngology, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh and University of Pittsburgh Cancer Institute, Department of Pharmacology, Pittsburgh, Pennsylvania, USA
- Eye and Ear Institute, 200 Lothrop St., Suite 500, Pittsburgh, Pennsylvania, USA
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Tomizaki KY, Usui K, Mihara H. Protein-protein interactions and selection: array-based techniques for screening disease-associated biomarkers in predictive/early diagnosis. FEBS J 2010; 277:1996-2005. [PMID: 20412053 DOI: 10.1111/j.1742-4658.2010.07626.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There has been considerable interest in recent years in the development of miniaturized and parallelized array technology for protein-protein interaction analysis and protein profiling, namely 'protein-detecting microarrays'. Protein-detecting microarrays utilize a wide variety of capture agents (antibodies, fusion proteins, DNA/RNA aptamers, synthetic peptides, carbohydrates, and small molecules) immobilized at high spatial density on a solid surface. Each capture agent binds selectively to its target protein in a complex mixture, such as serum or cell lysate samples. Captured proteins are subsequently detected and quantified in a high-throughput fashion, with minimal sample consumption. Protein-detecting microarrays were first described by MacBeath and Schreiber in 2000, and the number of publications involving this technology is rapidly increasing. Furthermore, the first multiplex immunoassay systems have been cleared by the US Food and Drug Administration, signaling recognition of the usefulness of miniaturized and parallelized array technology for protein detection in predictive/early diagnosis. Although genetic tests still predominate, with further development protein-based diagnosis will become common in clinical use within a few years.
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Affiliation(s)
- Kin-ya Tomizaki
- Innovative Materials and Processing Research Center and Department of Materials Chemistry, Ryukoku University, Otsu, Japan
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Kyu Kim S, Cho H, Park HJ, Kwon D, Min Lee J, Hyun Chung B. Nanogap biosensors for electrical and label-free detection of biomolecular interactions. NANOTECHNOLOGY 2009; 20:455502. [PMID: 19822932 DOI: 10.1088/0957-4484/20/45/455502] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We demonstrate nanogap biosensors for electrical and label-free detection of biomolecular interactions. Parallel fabrication of nanometer distance gaps has been achieved using a silicon anisotropic wet etching technique on a silicon-on-insulator (SOI) wafer with a finely controllable silicon device layer. Since silicon anisotropic wet etching resulted in a trapezoid-shaped structure whose end became narrower during the etching, the nanogap structure was simply fabricated on the device layer of a SOI wafer. The nanogap devices were individually addressable and a gap size of less than 60 nm was obtained. We demonstrate that the nanogap biosensors can electrically detect biomolecular interactions such as biotin/streptavidin and antigen/antibody pairs. The nanogap devices show a current increase when the proteins are bound to the surface. The current increases proportionally depending upon the concentrations of the molecules in the range of 100 fg ml(-1)-100 ng ml(-1) at 1 V bias. It is expected that the nanogap developed here could be a highly sensitive biosensor platform for label-free detection of biomolecular interactions.
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Affiliation(s)
- Sang Kyu Kim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, PO Box 115, Yuseong, Daejeon 305-600, Republic of Korea
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Ishi K, Sugawara F. A facile method to screen inhibitors of protein-protein interactions including MDM2-p53 displayed on T7 phage. Biochem Pharmacol 2008; 75:1743-50. [PMID: 18384755 DOI: 10.1016/j.bcp.2008.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 01/04/2008] [Accepted: 01/28/2008] [Indexed: 12/29/2022]
Abstract
Protein-protein interactions are essential in many biological processes including cell cycle and apoptosis. It is currently of great medical interest to inhibit specific protein-protein interactions in order to treat a variety of disease states. Here, we describe a facile multiwell plate assay method using T7 phage display to screen for candidate inhibitors of protein-protein interactions. Because T7 phage display is an effective method for detecting protein-protein interactions, we aimed to utilize this technique to screen for small-molecule inhibitors that disrupt these types of interaction. We used the well-characterized interaction between p53 and MDM2 and an inhibitor of this interaction, nutlin 3, as a model system to establish a new screening method. Phage particles displaying p53 interacted with GST-MDM2 immobilized on 96-well plates, and the interaction was inhibited by nutlin 3. Multiwell plate assay was then performed using a natural product library, which identified dehydroaltenusin as a candidate inhibitor of the p53-MDM2 interaction. We discuss the potential applications of this novel T7 phage display methodology, which we propose to call 'reverse phage display'.
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Affiliation(s)
- Kazutomo Ishi
- Genome and Drug Research Center, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Kim SW, Kim MG, Kim J, Lee HS, Ro HS. Detection of the mycovirus OMSV in the edible mushroom, Pleurotus ostreatus, using an SPR biosensor chip. J Virol Methods 2008; 148:120-4. [DOI: 10.1016/j.jviromet.2007.10.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 10/23/2007] [Accepted: 10/26/2007] [Indexed: 11/16/2022]
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Chaffey BT, Mitchell E, Birch MA, Lakey JH. A generic expression system to produce proteins that co-assemble with alkane thiol SAM. Int J Nanomedicine 2008; 3:287-93. [PMID: 18990938 PMCID: PMC2626940 DOI: 10.2147/ijn.s2655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Surface biology aims to observe and control biological processes by combining bio-, surface, and physical chemistry. Self-assembled monolayers (SAM) on gold surfaces have provided excellent methods for nanoscale surface preparation for such studies. However, extension of this work requires the specific immobilization of whole protein domains and the direct incorporation of recombinant proteins into SAM is still problematic. In this study a short random coil peptide has been designed to insert into thioalkane layers by formation of a hydrophobic helix. Surface plasmon resonance (SPR) studies show that specific immobilization via the internal cysteine is achieved. Addition of the peptide sequence to the terminus of a protein at the genetic level enables the production of a range of recombinant fusion-proteins with good yield. SPR shows that the proteins display the same gold-binding behavior as the peptide. It is shown that cell growth control can be achieved by printing the proteins using soft lithography with subsequent infilling with thio-alkanes The expression plasmid is constructed so that any stable protein domain can be easily cloned, expressed, purified and immobilized.
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Affiliation(s)
| | | | - Mark A Birch
- The School of Surgical and Reproductive Sciences, The Medical School, Framlington Place, The University of Newcastle-upon-Tyne, Newcastle-upon-Tyne, Great Britain
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Wang Z, Wilkop T, Xu D, Dong Y, Ma G, Cheng Q. Surface plasmon resonance imaging for affinity analysis of aptamer-protein interactions with PDMS microfluidic chips. Anal Bioanal Chem 2007; 389:819-25. [PMID: 17673982 DOI: 10.1007/s00216-007-1510-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 07/02/2007] [Accepted: 07/12/2007] [Indexed: 01/03/2023]
Abstract
We report on the use of PDMS multichannels for affinity studies of DNA aptamer-human Immunoglobulin E (IgE) interactions by surface plasmon resonance imaging (SPRi). The sensing surface was prepared with thiol-terminated aptamers through a self-assembling process in the PDMS channels defined on a gold substrate. Cysteamine was codeposited with the thiol aptamers to promote proper spatial arrangement of the aptamers and thus maintain their optimal binding efficiencies. Four aptamers with different nucleic acid sequences were studied to test their interaction affinity toward IgE, and the results confirmed that aptamer I (5'-SH-GGG GCA CGT TTA TCC GTC CCT CCT AGT GGC GTG CCC C-3') has the strongest binding affinity. Control experiments were conducted with a PEG-functionalized surface and IgG was used to replace IgE in order to verify the selective binding of aptamer I to the IgE molecules. A linear concentration-dependent relationship between IgE and aptamer I was obtained, and a 2-nM detection limit was achieved. SPRi data were further analyzed by global fitting, and the dissociation constant of aptamer I-IgE complex was found to be 2.7 x 10(-7) M, which agrees relatively well with the values reported in the literature. Aptamer affinity screening by SPR imaging demonstrates marked advantages over competing methods because it does not require labeling, can be used in real-time, and is potentially high-throughput. The ability to provide both qualitative and quantitative results on a multichannel chip further establishes SPRi as a powerful tool for the study of biological interactions in a multiplexed format.
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Affiliation(s)
- Zhuangzhi Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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Mahmoud KA, Kraatz HB. A Bioorganometallic Approach for the Electrochemical Detection of Proteins: A Study on the Interaction of Ferrocene–Peptide Conjugates with Papain in Solution and on Au Surfaces. Chemistry 2007; 13:5885-95. [PMID: 17455185 DOI: 10.1002/chem.200601878] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this paper, a new bioorganometallic approach for the detection of proteins using surface-bound ferrocene-peptide conjugates is presented. Specifically, a series of peptide conjugates of 1'-aminoferrocene-1-carboxylic acid (ferrocene amino acid, Fca) is synthesized: Boc-Fca-Gly-Gly-Tyr(Bzl)-Arg(NO2)-OMe (2), Thc-Fca-Gly-Gly-Tyr(Bzl)-Arg(NO2)-OMe (3), Thc-Fca-Gly-Gly-Tyr(Bzl)-Arg(NO2)-OH (4), Boc-Fca-Gly-Gly-Arg(Mtr)-Tyr-OMe (7), Thc-Fca-Gly-Gly-Arg(Mtr)-Tyr-OMe (8), Thc-Fca-Gly-Gly-Arg(Mtr)-Tyr-OH (9), Thc-Fca-Gly-Gly-Arg-Tyr-OH (10). The peptide is conjugated to the C-terminal side of Fca and compounds 4, 7-10 possess a thiostic acid linked to the N-terminal side of Fca in order to facilitate formation of thin films on gold substrates. Competitive inhibition towards papain was determined for Thc-Fca-Gly-Gly-Tyr(Bzl)-Arg(NO2)-OH (4), Thc-Fca-Gly-Gly-Arg(Mtr)-Tyr-OH (9) and Thc-Fca-Gly-Gly-Arg-Tyr-OH (10). The binding interaction between the peptide modified substrates and papain enzyme was studied using real-time surface plasmon resonance (SPR) imaging. Peptide 10 showed the strongest binding affinity to papain. Adsorption/desorption rate constants were ka = 1.75+/-0.05 x 10(5) M(-1) s(-1) and kd = 2.90 +/- 0.05 x 10(-2) s(-1). Interactions of papain with Fca-peptide 10 were investigated by cyclic voltammetry. The interaction results were also verified by measuring the electrochemical response of the peptide-papain interaction as function of increasing enzyme concentration. A linear relationship was observed for papain concentration of up to 80 nM. Shifting to higher potentials as well as decrease in the overall signal intensity was observed. The detection limit was 4 x 10(-9) M.
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Affiliation(s)
- Khaled A Mahmoud
- Department of Chemistry, University Of Saskatchewan, Saskatoon, SK S7N 5C9, Canada
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Lee KH, Joung HA, Ahn JH, Kim KO, Oh IS, Shin YB, Kim MG, Kim DM. Real-time monitoring of cell-free protein synthesis on a surface plasmon resonance chip. Anal Biochem 2007; 366:170-4. [PMID: 17543877 DOI: 10.1016/j.ab.2007.04.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 04/23/2007] [Accepted: 04/25/2007] [Indexed: 10/23/2022]
Abstract
Taking advantage of the "open" nature of cell-free protein synthesis, this study investigated the direct analysis of protein expression using a surface plasmon resonance sensor. During the on-chip incubation of the reaction mixture for cell-free protein synthesis, the expressed protein molecules were immobilized onto the surface of the chip, giving rise to a sensorgram signal, which enabled on-line monitoring of protein expression. In addition, we found that the expression of the aggregation-prone proteins could be effectively monitored. The ability to monitor these proteins was most likely through the instant isolation of the expressed protein molecules onto the solid surface of the chip.
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Affiliation(s)
- Kyung-Ho Lee
- Department of Fine Chemical Engineering and Chemistry, Chungnam National University, Daejeon 305-764, Korea
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Kim TS, Kim SJ, Chung BH, Yoo KH, Park SH. The Korean research & development program on micro-electro-mechanical systems (MEMS) in medical applications. MINIM INVASIV THER 2007; 16:109-19. [PMID: 17474054 DOI: 10.1080/13645700701267071] [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: 10/23/2022]
Abstract
Non or minimally invasive approaches for medical applications are very important for the alleviation of patient complaints. The miniaturization of medical devices using micro & nano technologies might be one of the possible solutions. Several national research and development (R&D) programs have been launched by the Korean government to further the development of biological & medical micro/nano devices in this country. This paper gives an overview of the current status of national R&D programs which are related to the development of micro-electro-mechanical systems (MEMS)/Nano technology in biological and medical applications and discusses the main activities of each program.
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Affiliation(s)
- Tae Song Kim
- Intelligent Microsystem Center, Korean Institute of Science & Technology (KIST), Seoul, Korea.
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Abstract
With the growth of the "-omics" such as functional genomics and proteomics, one of the foremost challenges in biotechnologies has become the development of novel methods to monitor biological process and acquire the information of biomolecular interactions in a systematic manner. To fully understand the roles of newly discovered genes or proteins, it is necessary to elucidate the functions of these molecules in their interaction network. Microarray technology is becoming the method of choice for such a task. Although protein microarray can provide a high throughput analytical platform for protein profiling and protein-protein interaction, most of the current reports are limited to labeled detection using fluorescence or radioisotope techniques. These limitations deflate the potential of the method and prevent the technology from being adapted in a broader range of proteomics applications. In recent years, label-free analytical approaches have gone through intensified development and have been coupled successfully with protein microarray. In many examples of label-free study, the microarray has not only offered the high throughput detection in real time, but also provided kinetics information as well as in situ identification. This article reviews the most significant label-free detection methods for microarray technology, including surface plasmon resonance imaging, atomic force microscope, electrochemical impedance spectroscopy and MS and their applications in proteomics research.
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Affiliation(s)
- Xiaobo Yu
- Department of Biochemistry, Beijing Institute of Radiation Medicine, Beijing Proteome Research Center, Beijing, PR China
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Ha TH, Park MR, Park HJ, Choi JS, Kim G, Hyun MS, Chung BH. Photoreactive immobilization of 11-(2,4-dinitro-5-fluorobenzene)undecenamide on a hydrogenated silicon (100) surface for protein immobilizations. Chem Commun (Camb) 2007:1611-3. [PMID: 17530076 DOI: 10.1039/b617443d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Several nucleophiles such as proteins or poly(ethyleneimine) could be easily conjugated with a 11-(2,4-dinitro-5-fluorobenzene)undecenamide (DFUA) monolayer photochemically prepared on a silicon (100) surface.
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Affiliation(s)
- Tai Hwan Ha
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea.
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Abstract
BACKGROUND The "inverse" problem is related to the determination of unknown causes on the bases of the observation of their effects. This is the opposite of the corresponding "direct" problem, which relates to the prediction of the effects generated by a complete description of some agencies. The solution of an inverse problem entails the construction of a mathematical model and takes the moves from a number of experimental data. In this respect, inverse problems are often ill-conditioned as the amount of experimental conditions available are often insufficient to unambiguously solve the mathematical model. Several approaches to solving inverse problems are possible, both computational and experimental, some of which are mentioned in this article. In this work, we will describe in details the attempt to solve an inverse problem which arose in the study of an intracellular signaling pathway. RESULTS Using the Genetic Algorithm to find the sub-optimal solution to the optimization problem, we have estimated a set of unknown parameters describing a kinetic model of a signaling pathway in the neuronal cell. The model is composed of mass action ordinary differential equations, where the kinetic parameters describe protein-protein interactions, protein synthesis and degradation. The algorithm has been implemented on a parallel platform. Several potential solutions of the problem have been computed, each solution being a set of model parameters. A sub-set of parameters has been selected on the basis on their small coefficient of variation across the ensemble of solutions. CONCLUSION Despite the lack of sufficiently reliable and homogeneous experimental data, the genetic algorithm approach has allowed to estimate the approximate value of a number of model parameters in a kinetic model of a signaling pathway: these parameters have been assessed to be relevant for the reproduction of the available experimental data.
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Affiliation(s)
- Ivan Arisi
- European Brain Research Institute, Via Fosso del Fiorano 64, Roma, Italy
| | - Antonino Cattaneo
- European Brain Research Institute, Via Fosso del Fiorano 64, Roma, Italy
- Lay Line Genomics SpA, S.Raffaele Science Park, Castel Romano, Italy
- International School of Advanced Studies (SISSA/ISAS), Biophysics Dept., Via Beirut 2-4, Trieste, Italy
| | - Vittorio Rosato
- ENEA, Casaccia Research Center, Computing and Modelling Unit, Via Anguillarese 301, S.Maria di Galeria, Italy
- Ylichron Srl, c/o ENEA, Casaccia Research Center, Via Anguillarese 301, S.Maria di Galeria, Italy
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Kim M, Lee SY, Choi H, Shin YB, Jung SO, Kim MG, Chung BH. On-chip Escherichia coli culture, purification, and detection of expressed proteins. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 35:655-62. [PMID: 16724194 DOI: 10.1007/s00249-006-0072-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Revised: 04/17/2006] [Accepted: 04/21/2006] [Indexed: 10/24/2022]
Abstract
In a recent study, we reported the results of a rapid high-throughput expression analysis of the affinity-tagged proteins present in total cell lysates, using a surface plasmon resonance (SPR) imaging protein chip system. In this paper, we describe a novel method, which is able to sequentially carry out a recombinant Escherichia coli culture, as well as the detection and purification of the expressed proteins on a single microwell chip, fabricated on a two-dimensional thin gold film. Following the induction of the protein on the microwell chip, the E. coli cells were lysed on the chip via the addition of lysozymes, and the expressed glutathione S-transferase-fused green fluorescent protein (GST-GFP) was then purified on the chip via affinity interaction with the glutathionylated gold surface of the chip. Finally, the expressed protein was directly detected using the surface plasmon resonance (SPR) imaging system. This system saves a substantial amount of time, experimental resources, and labor, by allowing for the complicated and labor-intensive procedures inherent to the production of recombinant proteins to be conducted on a single microwell chip, simply and economically.
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Affiliation(s)
- Moonil Kim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 115, Yuseong, Daejeon, South Korea
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Kim M, Park K, Jeong EJ, Shin YB, Chung BH. Surface plasmon resonance imaging analysis of protein–protein interactions using on-chip-expressed capture protein. Anal Biochem 2006; 351:298-304. [PMID: 16510110 DOI: 10.1016/j.ab.2006.01.042] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Revised: 01/18/2006] [Accepted: 01/25/2006] [Indexed: 10/25/2022]
Abstract
A surface plasmon resonance (SPR) imaging system, combined with a microwell gold chip for on-chip cell cultivation, was used to monitor protein-protein interactions. In particular, we developed an on-chip microscale cell cultivation system that integrates cell culture and on-chip analysis of protein-protein interactions on a single microwell chip in a time- and labor-saving manner. To assess the performance of this system in the analysis of protein-protein interactions, we conducted a series of protein-protein interaction analyses by measuring the binding of the yeast GAL4 dimerization domain (GAL4DD) to the GAL11 protein (GAL11P). Our system was found to enable the simple and rapid analysis of protein-protein interactions, requiring no special cell culturing equipment or recombinant protein expression prior to the immobilization of the purified proteins onto the chip. Our results demonstrate that the combination of an on-chip cell cultivation system and an SPR imaging system can be a useful tool to study protein-protein interactions without the need for time-consuming and labor-intensive protein preparation steps as well as fluorescent or other labeling of the interactants.
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Affiliation(s)
- Moonil Kim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-600, Republic of Korea
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Kim M, Jung SO, Park K, Jeong EJ, Joung HA, Kim TH, Seol DW, Chung BH. Detection of Bax protein conformational change using a surface plasmon resonance imaging-based antibody chip. Biochem Biophys Res Commun 2005; 338:1834-8. [PMID: 16288712 DOI: 10.1016/j.bbrc.2005.10.155] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Accepted: 10/18/2005] [Indexed: 01/30/2023]
Abstract
We describe an antibody chip technology that uses a surface plasmon resonance (SPR) imaging system to examine the conformational change of a protein. In this study, we used Bax protein, a pro-apoptotic member of the Bcl-2 family of proteins, as a model protein to investigate the conformational alteration triggered by a TNF-related apoptosis-inducing ligand (TRAIL), a potent inducer of apoptosis. To develop the antibody chip for detecting the Bax conformational change, we immobilized Bax monoclonal antibody 6A7, which recognizes only a conformationally changed Bax protein on a gold surface. The resultant immobilized Bax antibodies provided specific and accurate measurements of the active conformation-specific epitope in the apoptotic cancer cells treated with the TRAIL; these measurements corresponded to the data obtained by immunoprecipitation analysis using an active conformation-specific Bax antibody (6A7). The results of our study indicated that TRAIL-induced Bax structural change could be monitored quickly and simply using an SPR imaging system, thus demonstrating the potential for using such a system for the analysis of conformational properties of target proteins.
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Affiliation(s)
- Moonil Kim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, P.O. Box 115, Yuseong, Daejeon 305-600, Republic of Korea
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