Uncovering quantitative protein interaction networks for mouse PDZ domains using protein microarrays.

Journal of the American Chemical Society
Michael A StifflerGavin MacBeath

Abstract

One of the principal challenges in systems biology is to uncover the networks of protein-protein interactions that underlie most biological processes. To date, experimental efforts directed at this problem have largely produced only qualitative networks that are replete with false positives and false negatives. Here, we describe a domain-centered approach--compatible with genome-wide investigations--that enables us to measure the equilibrium dissociation constant (K(D)) of recombinant PDZ domains for fluorescently labeled peptides that represent physiologically relevant binding partners. Using a pilot set of 22 PDZ domains, 4 PDZ domain clusters, and 20 peptides, we define a gold standard dataset by determining the K(D) for all 520 PDZ-peptide combinations using fluorescence polarization. We then show that microarrays of PDZ domains identify interactions of moderate to high affinity (K(D) < or = 10 microM) in a high-throughput format with a false positive rate of 14% and a false negative rate of 14%. By combining the throughput of protein microarrays with the fidelity of fluorescence polarization, our domain/peptide-based strategy yields a quantitative network that faithfully recapitulates 85% of previously reported interaction...Continue Reading

References

Feb 12, 1998·Proceedings of the National Academy of Sciences of the United States of America·J J GrootjansG David
Aug 11, 1998·Nature Genetics·V A LettsW N Frankel
Oct 27, 1998·Genomics·H G Laverty, J B Wilson
Mar 3, 1999·Nature Biotechnology·S SchneiderC M Hovens
Apr 20, 2000·The Journal of Biological Chemistry·J J GrootjansG David
Jun 17, 2000·Trends in Cell Biology·C C GarnerR L Huganir
Sep 8, 2000·Science·D J Rogers, S E Randolph
Nov 23, 2000·Proceedings of the National Academy of Sciences of the United States of America·J R NewmanP S Kim
Jan 3, 2001·American Journal of Human Genetics·C F BoerkoelJ R Lupski
Apr 3, 2001·Annual Review of Neuroscience·M Sheng, C Sala
Apr 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·T ItoY Sakaki
Aug 30, 2001·Trends in Genetics : TIG·D Bilder
Jan 24, 2002·Nature·Alexander A Ischenko, Murat K Saparbaev
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Friedhelm BladtTony Pawson
Jun 25, 2002·Nature Structural Biology·Jose ReinaCayetano Gonzalez
Jul 16, 2002·Molecular & Cellular Proteomics : MCP·Charlotte M DeaneDavid Eisenberg
Oct 22, 2002·FEBS Letters·Patrick Aloy, Robert B Russell
Mar 5, 2003·Journal of Molecular Biology·Jia-Fu LongMingjie Zhang
Mar 14, 2003·Nature·Eric PhizickyStanley Fields
Apr 24, 2003·Science's STKE : Signal Transduction Knowledge Environment·Claire NourryJean-Paul Borg
Jan 6, 2004·Science·Siming LiMarc Vidal
Jan 6, 2004·Nature Biotechnology·Joel S BaderJohn Chant
Apr 6, 2004·Methods in Molecular Biology·John C Obenauer, Michael B Yaffe
Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Dec 21, 2004·Nucleic Acids Research·T HubbardE Birney
Mar 15, 2005·FEBS Letters·Gianni CesareniMaria Victoria Schneider
Jul 12, 2005·Oncogene·Jorrit J HornbergHans V Westerhoff

❮ Previous
Next ❯

Citations

Dec 14, 2006·ACS Chemical Biology·Mark R Spaller
Aug 20, 2008·Nature Biotechnology·Jiunn R ChenGavin MacBeath
Apr 3, 2010·Nature Protocols·Alexis KaushanskyGavin MacBeath
Jan 1, 2010·The Journal of Biological Chemistry·Shibani BhattacharyaZimei Bu
Jul 21, 2007·Science·Michael A StifflerGavin MacBeath
Jul 2, 2010·BMC Bioinformatics·Sibel KalyoncuAttila Gursoy
Jun 1, 2010·Cell Communication and Signaling : CCS·Ho-Jin Lee, Jie J Zheng
Jul 26, 2013·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Daniel R ZamzowKathy R Magnusson
Dec 22, 2010·Biointerphases·M Uttamchandani, S Moochhala
Apr 24, 2013·Biochimica Et Biophysica Acta·Songyot NakariyakulLuonan Chen
Nov 1, 2007·Expert Opinion on Drug Discovery·Krishnanand D Kumble
Feb 20, 2016·Analytical and Bioanalytical Chemistry·Michael D SinzingerRoland Brock
Aug 8, 2009·Current Opinion in Chemical Biology·Alejandro Wolf-YadlinGavin MacBeath
Sep 17, 2014·Annals of Neurology·Andrea K VaagsBerge A Minassian
Aug 15, 2006·Trends in Pharmacological Sciences·Peter Day, Brian Kobilka
Jun 12, 2013·Journal of Proteomics·Michael D SinzingerRoland Brock
Dec 28, 2006·Molecular & Cellular Proteomics : MCP·Oda StoevesandtRoland Brock
Jul 20, 2018·ELife·Victor H Salinas, Rama Ranganathan
Aug 18, 2010·Chembiochem : a European Journal of Chemical Biology·Wendy S Iskenderian-Epps, Barbara Imperiali
Jul 28, 2019·The Journal of Biological Chemistry·Zakir KhanMonique Lafon
Feb 7, 2007·Chembiochem : a European Journal of Chemical Biology·Marcin PaduchJacek Otlewski
Sep 14, 2016·Current Protocols in Chemical Biology·Nathan Moerke, Mohammad Fallahi-Sichani
Oct 3, 2020·The Journal of Cell Biology·Ryan BaumertPierre D McCrea
Jan 17, 2021·Scientific Reports·Miroslav JurásekRobert Vácha
May 14, 2009·Accounts of Chemical Research·Mahesh UttamchandaniShao Q Yao
Oct 6, 2007·Journal of the American Chemical Society·Mahesh UttamchandaniShao Q Yao
Aug 30, 2007·The Journal of Physical Chemistry. B·Fabio CecconiFrancesco Piazza
Oct 19, 2006·Journal of the American Chemical Society·Andrew Gordus, Gavin MacBeath

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.