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Front Biol    2012, Vol. 7 Issue (4) : 336-349    https://doi.org/10.1007/s11515-012-1236-9
REVIEW
Functional protein microarray: an ideal platform for investigating protein binding property
Shu-Min ZHOU1,2, Li CHENG1,2, Shu-Juan GUO1,2, Heng ZHU3,4(), Sheng-Ce TAO1,2()
1. Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; 2. State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China; 3. Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; 4. The High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Abstract

Functional protein microarray is an important tool for high-throughput and large-scale systems biology studies. Besides the progresses that have been made for protein microarray fabrication, significant advancements have also been achieved for applying protein microarrays on determining a variety of protein biochemical activities. Among these applications, detection of protein binding properties, such as protein-protein interactions (PPIs), protein-DNA interactions (PDIs), protein-RNA interactions, and antigen-antibody interactions, are straightforward and have substantial impacts on many research fields. In this review, we will focus on the recent progresses in protein-protein, protein-DNA, protein-RNA, protein-small molecule, protein-lipid, protein-glycan, and antigen-antibody interactions. We will also discuss the challenges and future directions of protein microarray technologies. We strongly believe that protein microarrays will soon become an indispensible tool for both basic research and clinical applications.
Keywords lectin microarray      protein microarray      protein-cell interaction      protein-DNA interaction (PDI)      protein-protein interaction (PPI)     
Corresponding Author(s): ZHU Heng,Email:hzhu4@jhmi.edu; TAO Sheng-Ce,Email:taosc@sjtu.edu.cn   
Issue Date: 01 August 2012
 Cite this article:   
Shu-Min ZHOU,Shu-Juan GUO,Heng ZHU, et al. Functional protein microarray: an ideal platform for investigating protein binding property[J]. Front Biol, 2012, 7(4): 336-349.
 URL:  
https://academic.hep.com.cn/fib/EN/10.1007/s11515-012-1236-9
https://academic.hep.com.cn/fib/EN/Y2012/V7/I4/336
Fig.1  Protein microarrays for protein-ligand interaction study. The ligands could be probed on the protein microarray are protein, DNA/RNA, small molecule, glycan, lipid and etc.
Fig.2  Labeling strategies for protein microarray based PPI study. (a) Bound target proteins are recognized by a specific primary antibody followed by a fluorescent secondary antibody or by a biotinylated secondary antibody. (b) The target protein is prepared as a fusion protein with an affinity tag, thus the binding could be readout by a primary antibody specific for the affinity tag followed by a fluorescent secondary antibody. (c) The target protein could be directly labeled by a fluorescent dye when there is no specific antibody and affinity tag available.
Fig.3  Protein microarrays for protein-DNA/RNA interaction study. Generally, DNA or RNA molecules are end-labeled and profiled on a protein microarray. After washing away the non-specific binding DNA/RNA, the interactions between protein and DNA/RNA can be detected and recorded by a laser scanner. A variety types of probes such as damaged DNA, DNA motif and virus shRNA could be used as analyte.
Fig.4  Protein microarrays for protein-small molecule interaction study. Usually, a small molecule such as drug candidate is biotinylated or fluorescent conjugated and probed on a protein microarray. As to overcome the shortcoming of chemically labeling of small molecule prior to probing, MALDI-TOF may be applied as a readout technology. Briefly, a protein microarray is fabricated on a hydrophilic/hydrophobic patterned substrate slide. A mixture of un-labeled small molecules could be probed on this microarray, the results were then readout by MALDI-TOF analysis.
Fig.5  Live cell surface glycan profiling using lectin microarray. Live cells from cell cultures or clinical samples are labeled with a fluorescent dye, such as CFSE. The labeled cells were probed directly on a lectin microarray. After incubation for a while, a mild washing step should be taken to remove the non-specific bindings. The positive binding could be readout and recorded by a high-resolution fluorescence scanner.
Fig.6  Protein microarrays for protein-lipid interaction study. A target lipid is assembled into liposome with a biotinylated DHPC or a fluorescent dye. Except the sample preparation, the protein microarray based procedure for protein-lipid interaction study is similar to that of protein-small molecule study.
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