Microfluidic large scale integration of viral-host interaction analysis.

Viral-host interactions represent potential drug targets for novel antiviral strategies (Flisiak et al., Hepatology, 2008, 47, 817-26). Hence, it is important to establish an adequate platform for identifying and analyzing such interactions. In this review, we discuss bottlenecks in conventional protein-protein interaction methodologies and present the contribution of innovative microfluidic-based technologies towards a solution to these problems with respect to viral-host proteomics.

[1]  Ingrid Remy,et al.  A cDNA library functional screening strategy based on fluorescent protein complementation assays to identify novel components of signaling pathways. , 2004, Methods.

[2]  A. Barabasi,et al.  High-Quality Binary Protein Interaction Map of the Yeast Interactome Network , 2008, Science.

[3]  S. Quake,et al.  Highly parallel measurements of interaction kinetic constants with a microfabricated optomechanical device. , 2009, Applied physics letters.

[4]  John B. Shoven,et al.  I , Edinburgh Medical and Surgical Journal.

[5]  M. Kay,et al.  A Prenylation Inhibitor Prevents Production of Infectious Hepatitis Delta Virus Particles , 2002, Journal of Virology.

[6]  A. Grigoriev On the number of protein-protein interactions in the yeast proteome. , 2003, Nucleic acids research.

[7]  W. Marsden I and J , 2012 .

[8]  J. Wojcik,et al.  Functional proteomics mapping of a human signaling pathway. , 2004, Genome research.

[9]  H. Ohno,et al.  Adaptor protein complexes as the key regulators of protein sorting in the post-Golgi network. , 2003, Cell structure and function.

[10]  Anne-Claude Gavin,et al.  Recent advances in charting protein-protein interaction: mass spectrometry-based approaches. , 2011, Current opinion in biotechnology.

[11]  John H. Morris,et al.  Global landscape of HIV–human protein complexes , 2011, Nature.

[12]  A. Vazquez,et al.  Epstein–Barr virus and virus human protein interaction maps , 2007, Proceedings of the National Academy of Sciences.

[13]  M. Vidal,et al.  Protein interaction mapping in C. elegans using proteins involved in vulval development. , 2000, Science.

[14]  S. L. Wong,et al.  A Map of the Interactome Network of the Metazoan C. elegans , 2004, Science.

[15]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[16]  Stephen R Quake,et al.  Proteome-wide protein interaction measurements of bacterial proteins of unknown function , 2012, Proceedings of the National Academy of Sciences.

[17]  S. Quake,et al.  A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors , 2007, Science.

[18]  Tobias M. Fischer,et al.  Monitoring regulated protein-protein interactions using split TEV , 2006, Nature Methods.

[19]  Michele Tinti,et al.  VirusMINT: a viral protein interaction database , 2008, Nucleic Acids Res..

[20]  Howard Y. Chang,et al.  Systematic reconstruction of RNA functional motifs with high-throughput microfluidics , 2012, Nature Methods.

[21]  S. L. Wong,et al.  Towards a proteome-scale map of the human protein–protein interaction network , 2005, Nature.

[22]  Sourav Bandyopadhyay,et al.  Evolutionarily Conserved Herpesviral Protein Interaction Networks , 2009, PLoS pathogens.

[23]  Sean R. Collins,et al.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.

[24]  James R. Knight,et al.  A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.

[25]  H. Kräusslich,et al.  Ultrastructural Analysis of ESCRT Proteins Suggests a Role for Endosome‐Associated Tubular–Vesicular Membranes in ESCRT Function , 2006, Traffic.

[26]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[27]  S. Quake,et al.  Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis , 2008, Nature Biotechnology.

[28]  P. Vidalain,et al.  Benchmarking a luciferase complementation assay for detecting protein complexes , 2011, Nature Methods.

[29]  Uwe Schlattner,et al.  Yeast Two-Hybrid, a Powerful Tool for Systems Biology , 2009, International journal of molecular sciences.

[30]  Peter Uetz,et al.  Improving yeast two-hybrid screening systems. , 2008, Briefings in functional genomics & proteomics.

[31]  B. Berger,et al.  Herpesviral Protein Networks and Their Interaction with the Human Proteome , 2006, Science.

[32]  Stephen R Quake,et al.  An in vitro microfluidic approach to generating protein-interaction networks , 2009, Nature Methods.

[33]  R. Chanet,et al.  Protein interaction mapping: a Drosophila case study. , 2005, Genome research.

[34]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Y. Jacob,et al.  Identification and Targeting of an Interaction between a Tyrosine Motif within Hepatitis C Virus Core Protein and AP2M1 Essential for Viral Assembly , 2012, PLoS pathogens.

[36]  R. Crabbé,et al.  The cyclophilin inhibitor Debio‐025 shows potent anti–hepatitis C effect in patients coinfected with hepatitis C and human immunodeficiency virus , 2008, Hepatology.

[37]  Jodi R Parrish,et al.  Yeast two-hybrid contributions to interactome mapping. , 2006, Current opinion in biotechnology.

[38]  P. Mitchell A perspective on protein microarrays , 2002, Nature Biotechnology.

[39]  Gary Hardiman,et al.  Protein microarrays: challenges and promises. , 2002, Pharmacogenomics.

[40]  James R. Knight,et al.  A Protein Interaction Map of Drosophila melanogaster , 2003, Science.

[41]  H. Lehrach,et al.  A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome , 2005, Cell.

[42]  J. Hudson,et al.  C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression , 2003, Nature Genetics.

[43]  Joel S. Bader,et al.  Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps , 2007, PLoS Comput. Biol..

[44]  Cheng Huang,et al.  Novel Nuclear Export Signal-Interacting Protein, NESI, Critical for the Assembly of Hepatitis Delta Virus , 2005, Journal of Virology.

[45]  Wesley I. Sundquist,et al.  Tsg101 and the Vacuolar Protein Sorting Pathway Are Essential for HIV-1 Budding , 2001, Cell.

[46]  P. Legrain,et al.  Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens , 1997, Nature Genetics.