Economou Lab-Teaching BIO506/BIO408
Reading: (** essential/*recommended) Protein-Protein Interactions Cooper MA. (2003) Label-free screening of bio-molecular interactions. Anal Bioanal Chem. 377, 834-842. **Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. (2003) Protein analysis on a proteomic scale. Nature 422, 208-215. **Lakey JH, Raggett EM. (1998) Measuring protein-protein interactions. Curr Opin Struct Biol. 8, 119-123. *Phizicky EM, Fields S. (1995) Protein-protein interactions: methods for detection and analysis. Microbiol Rev. 59, 94-123. FunctionalGenomix with MS *Andersen JS, Mann M. (2000) Functional genomics by mass spectrometry. FEBS Lett.480, 25-31 MolecularCrowding *Ellis RJ. (2001) Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci.26, 597-604. ProteinBioChips *Zhu H, Snyder M. (2003) Protein chip technology. Curr Opin Chem Biol. 7, 55-63. Molecular machines **Mavroidis C, Dubey A, Yarmush ML. (2004) Molecular machines. Annu Rev Biomed Eng. 2004;6:363-95. DrugDiscovery+Diagnostix+Disease *Miklos GL, Maleszka R. (2004) Microarray reality checks in the context of a complex disease. More reading (2007 reviews):
Cravatt BF, Simon GM, Yates JR 3rd. The biological impact of mass-spectrometry-based proteomics. Nature. 2007 Dec 13;450(7172):991-1000.
Gingras AC, Gstaiger M, Raught B, Aebersold R. Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol. 2007 Aug;8(8):645-54.
Structures in systems biology. Curr Opin Struct Biol. 2007 Jun;17(3):378-84.
Protein immobilization strategies for protein biochips. Biomacromolecules. 2007 Jun;8(6):1775-89.
Is proteomics the new genomics? Cell. 2007 Aug 10;130(3):395-8.
Methods for the detection and analysis of protein-protein interactions. Proteomics. 2007 Aug;7(16):2833-42.
Proteomic analysis of protein complexes. Proteomics. 2007 Aug;7(16):2688-97.
Sherlock Holmes and the proteome--a detective story. FEBS J. 2007 Feb;274(4):897-905.
Robinson CV, Sali A, Baumeister W. The molecular sociology of the cell. Nature. 2007 Dec 13;450(7172):973-82.
Proteomic analysis of Saccharomyces cerevisiae. Expert Rev Proteomics. 2007 Dec;4(6):793-8
Automated, systematic determination of protein subcellular location using fluorescence microscopy. Subcell Biochem. 2007;43:263-76.
From protein-protein complexes to interactomics. Subcell Biochem. 2007;43:135-83.
Two-dimensional BAC/SDS-PAGE for membrane proteomics. Subcell Biochem. 2007;43:13-20.
Cornett DS, Reyzer ML, Chaurand P, Caprioli RM. MALDI imaging mass spectrometry: molecular snapshots of biochemical systems. Nat Methods. 2007 Oct;4(10):828-33.
Activity-based protein profiling for the functional annotation of enzymes. Nat Methods. 2007 Oct;4(10):822-7.
Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat Methods. 2007 Oct;4(10):807-15.
Proteins at membrane surfaces-a review of approaches. Mol Biosyst. 2007 Oct;3(10):705-13.
High-throughput antibody microarrays for quantitative proteomic analysis. Expert Rev Proteomics. 2007 Aug;4(4):505-13
Au CE, Bell AW, Gilchrist A, Hiding J, Nilsson T, Bergeron JJ. Organellar proteomics to create the cell map. Curr Opin Cell Biol. 2007 Aug;19(4):376-85.
Gevaert K, Van Damme P, Ghesquière B, Impens F, Martens L, Helsens K, Vandekerckhove J. A la carte proteomics with an emphasis on gel-free techniques. Proteomics. 2007 Aug;7(16):2698-718.
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007 Aug;25(8):894-8.
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007 Aug;25(8):887-93
Proteomics of integral membrane proteins--theory and application. Chem Rev. 2007 Aug;107(8):3687-714.
Braun RJ, Kinkl N, Beer M, Ueffing M. Two-dimensional electrophoresis of membrane proteins. Anal Bioanal Chem. 2007 Oct;389(4):1033-45.
Fournier ML, Gilmore JM, Martin-Brown SA, Washburn MP. Multidimensional separations-based shotgun proteomics. Chem Rev. 2007 Aug;107(8):3654-86
Xia Q, Hendrickson EL, Wang T, Lamont RJ, Leigh JA, Hackett M. Protein abundance ratios for global studies of prokaryotes. Proteomics. 2007 Aug;7(16):2904-19
Applications of field-flow fractionation in proteomics: presence and future. Proteomics. 2007 Aug;7(16):2719-28
Nice EC, Rothacker J, Weinstock J, Lim L, Catimel B. Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomics analysis. J Chromatogr A. 2007 Oct 19;1168(1-2):190-210
The hard cell: from proteomics to a whole cell model. FEBS Lett. 2007 Jun 19;581(15):2870-6.
Simpson JC, Mateos A, Pepperkok R. Maturation of the mammalian secretome. Genome Biol. 2007;8(4):211.
Villalobos V, Naik S, Piwnica-Worms D. Current state of imaging protein-protein interactions in vivo with genetically encoded reporters. Annu Rev Biomed Eng. 2007;9:321-49. Approaches to the study of the cell secretome. Expert Rev Proteomics. 2007 Apr;4(2):239-48
Falk R, Ramström M, Ståhl S, Hober S. Approaches for systematic proteome exploration. Biomol Eng. 2007 Jun;24(2):155-68.
Dobrovetsky E, Menendez J, Edwards AM, Koth CM. A robust purification strategy to accelerate membrane proteomics. Methods. 2007 Apr;41(4):381-7.
Single-molecule fluorescence analysis of cellular nanomachinery components. Annu Rev Biophys Biomol Struct. 2007;36:371-94.
Bacterial outer membrane protein analysis by electrophoresis and microchip technology. Expert Rev Proteomics. 2007 Feb;4(1):91-106. Lebowitz J, Lewis M.S, Schuck P. Modern analytical ultracentrifugation in protein science: A tutorial review. Protein Science 2002 11:2067–2079. |
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