User:Andrew Perry

Contact Info

Andrew Perry

• Andrew Perry
• Department of Biochemistry and Molecular Biology
• Monash University, Clayton Campus,
• PO Box 13d, VIC, 3800, Australia.

• Email me through OpenWetWare

I'm currently a Postdoctoral Fellow in the Whisstock Lab, Department of Biochemistry and Molecular Biology, Monash University. Previously I worked in the Lithgow Lab when they were at the University of Melbourne; this group has since moved and is now one of the labs in the Host-Pathogen Molecular Biology Unit 'supergroup' at Monash University. I did my PhD under the supervision of Paul Gooley, doing NMR spectroscopy of proteins for structure determination.

I was an advisor and coordinator for the 2010 Monash iGEM team.

Online

• I keep a (sometimes neglected) personal blog about science, bioinformatics and the web.
• I tweet under @pansapiens. It's mostly unprofessional.

Education

• 2006, PhD, University of Melbourne
• 2001, BSc(Hon), University of Melbourne

Research interests

General techniques

1. Structural bioinformatics
2. Structural biology, NMR spectroscopy and X-ray crystallography
3. Outer membrane protein purification, refolding, etc

Specific areas

1. Outer mitochondrial and bacterial protein structure
2. Mitochondrial protein import
3. Beta-barrel membrane protein transport, folding, insertion and assembly
4. Web application development, and new technologies for scientific collaboration and information dissemination

Areas I haven't published in, but would like to do some work in

1. Synthetic biology (esp. compartmentalization of in vitro systems and directed evolution)
2. DNA computing and "in vivo" computation
3. Protein engineering
4. probably lots of other stuff .... gotta stay focused :) !!

Publications

See my Mendeley profile or my ResearcherID profile

1. Clements A, Bursac D, Gatsos X, Perry AJ, Civciristov S, Celik N, Likic VA, Poggio S, Jacobs-Wagner C, Strugnell RA, and Lithgow T. The reducible complexity of a mitochondrial molecular machine. Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15791-5. DOI:10.1073/pnas.0908264106 |
2. Gatsos X, Perry AJ, Anwari K, Dolezal P, Wolynec PP, Likić VA, Purcell AW, Buchanan SK, and Lithgow T. Protein secretion and outer membrane assembly in Alphaproteobacteria. FEMS Microbiol Rev. 2008 Nov;32(6):995-1009. DOI:10.1111/j.1574-6976.2008.00130.x |
3. Perry AJ, Rimmer KA, Mertens HD, Waller RF, Mulhern TD, Lithgow T, and Gooley PR. Structure, topology and function of the translocase of the outer membrane of mitochondria. Plant Physiol Biochem. 2008 Mar;46(3):265-74. DOI:10.1016/j.plaphy.2007.12.012 |
4. Hulett JM, Lueder F, Chan NC, Perry AJ, Wolynec P, Likić VA, Gooley PR, and Lithgow T. The transmembrane segment of Tom20 is recognized by Mim1 for docking to the mitochondrial TOM complex. J Mol Biol. 2008 Feb 22;376(3):694-704. DOI:10.1016/j.jmb.2007.12.021 |
5. Gentle IE, Perry AJ, Alcock FH, Likić VA, Dolezal P, Ng ET, Purcell AW, McConnville M, Naderer T, Chanez AL, Charrière F, Aschinger C, Schneider A, Tokatlidis K, and Lithgow T. Conserved motifs reveal details of ancestry and structure in the small TIM chaperones of the mitochondrial intermembrane space. Mol Biol Evol. 2007 May;24(5):1149-60. DOI:10.1093/molbev/msm031 |
6. Likić VA, Perry A, Hulett J, Derby M, Traven A, Waller RF, Keeling PJ, Koehler CM, Curran SP, Gooley PR, and Lithgow T. Patterns that define the four domains conserved in known and novel isoforms of the protein import receptor Tom20. J Mol Biol. 2005 Mar 18;347(1):81-93. DOI:10.1016/j.jmb.2004.12.057 |
7. Perry AJ, Hulett JM, Likić VA, Lithgow T, and Gooley PR. Convergent evolution of receptors for protein import into mitochondria. Curr Biol. 2006 Feb 7;16(3):221-9. DOI:10.1016/j.cub.2005.12.034 |
8. Perry AJ, Hulett JM, Lithgow T, and Gooley PR. 1H, 13C and 15N resonance assignments of the cytosolic domain of Tom20 from Arabidopsis thaliana. J Biomol NMR. 2005 Nov;33(3):198. DOI:10.1007/s10858-005-2325-8 |
9. Perry AJ and Lithgow T. Protein targeting: entropy, energetics and modular machines. Curr Biol. 2005 Jun 7;15(11):R423-5. DOI:10.1016/j.cub.2005.05.031 |

More publications

Procter, J.B., Perry, A.J., Torda, A.E.a Comparing Objects of Different Sizes: Treating Proteins as Strings Australian Journal of Chemistry 2001 54(6) 367-373 doi:10.1071/CH01053

Some links to useful OWW (and other) resources

• Open writing projects/Beginning Python for Bioinformatics ... a great resource in the making.
• University of Chicago:NMR Software Guide ... it's a bit like "NMRPipe: the missing manual".
• NMRWiki and NMR Q&A Forum ... a growing NMR knowledge base and a "Stack Overflow"-style Q&A community.
• North East Structural Genomics Consortium (NESG) NMR wiki ... for sharing experimental protocols as well as training in structural biology and biomolecular NMR.
• MajorGroove .. a "Stack Overflow"-style Q&A community for biologists, with a bias toward researchers using biomolecular crystallography.
• BioStar .. "Stack Overflow"-style community for bioinformatics, computational genomics and systems biology.
• E._coli_genotypes .. a really useful list of genotypes for E. coli strains in common use in many labs.
• User:Andrew Perry/Web2.0 For Scientists -- "Emerging Tools for Scientific Collaboration Online". Some rough notes for a talk I may give one day.
• User:Andrew_Perry/Other_Bioscience_Wikis -- a list of other bioscience wikis and some commentary.
• User:Andrew_Perry/Lesser_Known_Methods_in_Bacterial_Protein_Expression -- every man and his dog expresses their proteins in bacteria using poly-histidine, GST, Nus or MBP tags. Here are a few lesser known techniques that have been published.
• User:Andrew_Perry/Protocols -- I'm starting to compile my own versions of some molecular biology protocols on OpenWetWare.

Generic OWW links

• Introductory tutorial
• OpenWetWare help pages