Economou Lab-Teaching BIO506/BIO408


BIO408/

BIO506

From proteins to molecular machines to proteomes-Protein-protein interactions Molecular Biology and Biomedicine and Protein Biotechnology
lecture
 
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  Recommended Textbooks:  
1.

Golemis, E, ed. (2003) Protein-Protein Interactions: a molecular cloning manual .Cold Spring Harbor Laboratory Press            (home)

 
2. Petsko and Ringe, 2004 Protein structure and function (home)  
3. Branden and Tooze, 1999 Introduction to Protein structure 2nd edition (home)  
4. Simpson RJ, ed.2003 Proteins and Proteomics: a laboratory manual .Cold Spring Harbor Laboratory Press (home) (companion WWW site)  
5. Pollack, 2001 Cells and gels and the engines of life (home)  
6. Stryer, 2003 Biochemistry 5th edition (home); Greek translation 2004; Crete University Press (home)  
7. Alberts et al, 2002 Molecular Biology of the Cell 4th edition (home)  
     

Reading:

(** essential/*recommended)
Integrated Systems Biology
Weiwen Zhang, Feng Li, Lei Nie (2010) Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies. Microbiology 156, 287–301.
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Protein-Protein Interactions

Cooper MA. (2003) Label-free screening of bio-molecular interactions. Anal Bioanal Chem. 377, 834-842.

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**Phizicky E, Bastiaens PI, Zhu H, Snyder M, Fields S. (2003) Protein analysis on a proteomic scale. Nature 422, 208-215.

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**Lakey JH, Raggett EM. (1998) Measuring protein-protein interactions. Curr Opin Struct Biol. 8, 119-123.

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*Phizicky EM, Fields S. (1995) Protein-protein interactions: methods for detection and analysis. Microbiol Rev. 59, 94-123.

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FunctionalGenomix with MS

*Andersen JS, Mann M. (2000) Functional genomics by mass spectrometry. FEBS Lett.480, 25-31

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MolecularCrowding

*Ellis RJ. (2001) Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci.26, 597-604.

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ProteinBioChips

*Zhu H, Snyder M. (2003) Protein chip technology. Curr Opin Chem Biol. 7, 55-63.

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Molecular machines

**Mavroidis C, Dubey A, Yarmush ML. (2004) Molecular machines. Annu Rev Biomed Eng. 2004;6:363-95.

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DrugDiscovery+Diagnostix+Disease

*Miklos GL, Maleszka R. (2004) Microarray reality checks in the context of a complex disease.
Nat Biotechnol. 22. 615-621

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More reading (2007 reviews):
Analytical Ultracentrifugation
Padrick S.B, Deka R.K, Chuang J.L, Wynn R.M, Chuang D.T, Norgard M.V, Rosen M.K, Brautigam C.A.
Determination of protein complex stoichiometry through multisignal sedimentation velocity experiments
.
Analytical Biochemistry 2010 407 89–103.


HardingS.E, Rowe A.J.
Insight into protein–protein interactions from analytical ultracentrifugation.
Biochem. Soc. Trans. 2010 38: 901–907; doi:10.1042/BST0380901

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.

 

Beltrao P, Kiel C, Serrano L.

Structures in systems biology.

Curr Opin Struct Biol. 2007 Jun;17(3):378-84.

 

Rusmini F, Zhong Z, Feijen J.

Protein immobilization strategies for protein biochips.

Biomacromolecules. 2007 Jun;8(6):1775-89.

 

Cox J, Mann M.

Is proteomics the new genomics?

Cell. 2007 Aug 10;130(3):395-8.

 

Berggård T, Linse S, James P.

Methods for the detection and analysis of protein-protein interactions.

Proteomics. 2007 Aug;7(16):2833-42.

 

Zhou M, Veenstra TD.

Proteomic analysis of protein complexes.

Proteomics. 2007 Aug;7(16):2688-97.

 

Righetti PG, Boschetti E.

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.

 

Pham TK, Wright PC.

Proteomic analysis of Saccharomyces cerevisiae.

Expert Rev Proteomics. 2007 Dec;4(6):793-8

 

García Osuna E, Murphy RF.

Automated, systematic determination of protein subcellular location using fluorescence microscopy.

Subcell Biochem. 2007;43:263-76.

 

Collura V, Boissy G.

From protein-protein complexes to interactomics.

Subcell Biochem. 2007;43:135-83.

 

di RP, Moebius J, Sickmann A.

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.

 

Barglow KT, Cravatt BF.

Activity-based protein profiling for the functional annotation of enzymes.

Nat Methods. 2007 Oct;4(10):822-7.

 

Köcher T, Superti-Furga G.

Mass spectrometry-based functional proteomics: from molecular machines to protein networks.

Nat Methods. 2007 Oct;4(10):807-15.

 

Macher BA, Yen TY.

Proteins at membrane surfaces-a review of approaches.

Mol Biosyst. 2007 Oct;3(10):705-13.

 

Lv LL, Liu BC.

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.

 

Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.

The minimum information required for reporting a molecular interaction experiment (MIMIx).

Nat Biotechnol. 2007 Aug;25(8):894-8.

 

Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H.

The minimum information about a proteomics experiment (MIAPE).

Nat Biotechnol. 2007 Aug;25(8):887-93

 

Speers AE, Wu CC.

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

 

Chmelik J.

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

 

Betts MJ, Russell RB.

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.

Hathout Y.

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.

 

Peters R.

Single-molecule fluorescence analysis of cellular nanomachinery components.

Annu Rev Biophys Biomol Struct. 2007;36:371-94.

 

Kustos I, Kocsis B, Kilár F.

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.