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Proteomic Applications of Surface Plasmon Resonance Biosensors: Analysis of Protein Arrays

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Proteomic Applications of Surface Plasmon Resonance Biosensors: Analysis of Protein Arrays EXPERIMENTAL and MOLECULAR MEDICINE, Vol. 37, No. 1, 1-10, February 2005 Proteomic applications of surface plasmon resonance biosensors: analysis of protein arrays Jong Seol Yuk1 and Kwon-Soo Ha1,2 (Zhu and Snyder, 2003). Several techniques for the analysis of protein interactions on protein arrays have 1 been reported based on various methods such as Department of Molecular and Cellular Biochemistry fluorescence detection, surface-enhanced laser de- Nano-bio Sensor Research Center sorption/ionization (SELDI) mass spectrometry, atomic Kangwon National University School of Medicine force microscopy (AFM), and surface plasmon re- Chunchon, Kangwon-do 200-701, South Korea sonance (SPR). 2Coressponding author: Tel, 82-33-250-8833; SPR has been used as an optical detection te- Fax, 82-33-250-8807; E-mail, [email protected] chnology since Lidberg et al. (1983) demonstrated its potential to use as biosensors in 1983 (Yuk et al., Accepted 4 February 2005 2004a). SPR-based biosensors have several advant- ages in the analysis of protein interactions compared to other sensors. SPR spectroscopy allows real-time Abbreviations: AFM, atomic force microscopy; MALDI, matrix- measurement of biomolecular interactions without la- assisted laser desorption/ionization; SELDI, surface-enhanced la- beling and with simple optical system device (Zhu and ser desorption/ionization; SPR, surface plasmon resonance Snyder, 2003). There are several examples in which SPR biosensors have been used to characterize the details of biomolecular interactions, and thus the SPR biosensors have emerged as one of the most powerful Abstract tools in biochemical and proteomics researches (My- Proteomics is one of the most important issues szka and Rich, 2000). The success of SPR biosen- sors was indicated by the growing number of com- in the post-genomic area, because it can greatly mercially available instruments. Since Biacore AB (ori- contribute to identifying protein biomarkers for ginally Pharmacia Biosensor AB) launched the first disease diagnosis and drug screening. Protein commercial SPR biosensor on market in 1990, there array is a key technology for proteome research- have been many more competing SPR instruments es and has been analyzed by various methods including IASys (Affinity Sensors), SPR-670 (Nippon including fluorescence, mass spectrometry, atom- Laser Electronics), IBIS (IBIS Technology BV), TI- ic force microscopy and surface plasmon re- SPR (Texas Instruments), etc. (see Table 1). The general versatility of SPR methods, the ease of auto- sonance (SPR). SPR biosensor is a promising mation, and the lack of labeling requirements are able technology in proteomics, since it has various to permit the potential use of the SPR biosensors for advantages including real-time measurement of large-scale screening of proteins (McDonnell, 2001). biomolecular interactions without labeling and In this review, we will discuss trends in protein array the simple optical system for the device. SPR technology and a potential use of SPR biosensors in biosensors have a strong potential for analyzing proteome researches. proteomes by SPR imaging and SPR spectro- scopic imaging, even though the challenge is to produce proteins on a proteomic scale. Significance of protein arrays in proteome analysis Keywords: biosensing techniques; microscopy, atom- ic force; protein array analysis; proteome; proteomics; One of the urgent scientific pursuit of the post-human genome era is the understanding of gene-expressed surface plasmon resonance proteins and their target reactions to distinguish func- tional specificity and preferences in the multi-milieu pots of proteins in the cell enclosure. Proteomics, the Introduction large-scale analysis of proteins, can provide protein biomarkers for disease diagnosis and drug screening Recently, intensive efforts have been put into the field by quantitative analysis of cellular protein expression of proteomics to utilize its great potential in iden- level and protein-protein interactions in signaling net- tifying protein biomarkers for disease diagnosis and works of cells. Extensive studies on various human drug screening. There has been a great demand for proteome reported include human plasma proteome developing efficient protein arrays, since the techn- (Anderson and Anderson, 2002), human liver (Yan et ology allows the large-scale and high-throughput ana- al., 2004), human lung fibroblasts (Durr et al., 2004), lysis of proteomes in cells, tissues and organisms cancers (Simpson and Dorow, 2001), diseases (Ha- 2 Exp. Mol. Med. Vol. 37(1), 1-10, 2005 Table 1. Various commercial SPR biosensors. ꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚꠚ System Manufacturer Website ꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏ BIACORE BIAcore AB (Sweden) www.biacore.com TI-SPR Texas Instruments (TX) www.ti.com/spreeta Kinetics Instrument BioTuL Bio Instruments (Germany) www.biotul.com IASys Affinity Sensors www.affinity-sensors.com SPR-670 Nippon Laser Electronics (Japan) www.rikei.com IBIS IBIS Technology BV (Netherlands) www.ibis-spr.nl OWLS Artificial Sensing Instruments (Switzerland) www.microvacuum.com PWR-400 Aviv (NJ) www.avivinst.com FasTraQ Quantech Ltd (MN) www.quantechltd.com FT-SPR 100 GWC Technologies (WI) www.gwcinstruments.com ꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏꠏ nash, 2003), etc. The human plasma proteome can biomarkers whose expression is related to the par- provide a revolutionary tool in disease diagnosis and ticular diseases. Based on the new biomarkers, pro- therapeutic monitoring, since plasma is the primary tein arrays can provide a powerful tool to diagnose clinical specimen and represents the largest version numerous diseases including cancer, arthritis, or heart of human proteome (Anderson and Anderson, 2002). disease, by a drop of a patient's blood or urine. The plasma, circulating body fluid, contains abund- Beyond diagnosis, protein arrays allow researchers to ance of tissue origin proteins that have been released reveal the network of protein interactions and bioche- and could be used as protein markers along with a mical communication in different cells. In addition, the large number of immunoglobulins pools. Recently, arrays can provide methods to illuminate expression Giot et al. (2004) has reported a protein interaction profile of proteins at a given place and time in cells, map in Drosophila melanogaster based on Yeast two- and to screen drugs by investigating whether test hybrid method and this map can be a systems biology compounds interact with particular proteins on the model for multicellular organisms including humans. arrays. They isolated 10,623 predicted transcripts and screen- ed 4,679 proteins and 4,780 interactions by a com- putational method of rating two-hybrid interaction con- Trends in protein array technology fidence map. Proteomics has used techniques such as two-di- Analysis of protein arrays mensional gel electrophoresis or chromatography, combined with mass spectrometry, to separate and Protein arrays are prepared by the similar way to identify proteins on a large scale (Gershon, 2003; DNA arrays in many cases (Service, 2001). Adaptor Hanash, 2003). Mass spectrometry has been a key molecules bind to specific target proteins, including technology to identify and quantify a large number of proteins, antibodies, peptides, oligonucleotides or ap- proteins from complex samples, and four types of tamers, are arrayed on a solid support, such as glass mass spectrometry such as ion trap, time-of-flight, or plastic. Then, target proteins binding to adaptor quadrupole and Fourier transform ion cyclotron are molecules on the arrays are detected by various currently in use. Mass spectrometry has been suc- methods, such as fluorescence detection, mass spec- cessfully applied to the study of protein-protein in- trometry, AFM, piezoelectric microcantilever or SPR teractions via affinity-based isolations on a small and (Zhavnerko and Ha, 2004). However, getting all the proteome-wide scale, the mapping of numerous or- elements to work is far more difficult than with DNA ganelles, description of malaria parasite proteome and arrays. Analysis of nucleic acid interactions on DNA quantitative protein profiling from several species (see arrays is simple and streamlined, because nucleic review by Aebersold and Mann, 2003). acids have a characteristic and distinct complemen- A quite different approach to monitor activity and tary binding. In contrast, protein interaction is influ- function of proteome is the protein array method. enced by various factors including three-dimensional Protein arrays permit a rapid interaction of proteins structure, chemical interaction and isoelectric points of on a proteomic scale, and are produced by anchoring proteins. Thus, it is essential to array specific adaptor hundreds of proteins or peptides to the solid surface molecules in preparing protein arrays. as a bait to capture a specific interacting proteins (Tyers and Mann, 2003). Recently, many laboratories and proteomics companies have intensively focused Fluorescence detection method on the identification of a novel protein(s) and peptide Detection and quantification of proteins captured on Analysis of protein arrays by SPR biosensors 3 arrays require an additional technique. Fluorescence shows the surface topology of tissue transglutaminase detection method has been widely used,
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