General References

Berg, J. M., et al. 2015. Biochemistry, 8th ed. Macmillan.

Nelson, D. L., and M. M. Cox. 2013. Lehninger Principles of Biochemistry, 6th ed. Macmillan.

Web Sites

Entry site into proteins, structures, genomes, and taxonomy: http://www.ncbi.nlm.nih.gov/Entrez/

The protein 3-D structure database: http://www.rcsb.org/

Structural classifications of proteins: http://scop.berkeley.edu/

Sites containing general information about proteins: http://www.expasy.ch/; http://scop.berkeley.edu/

PROSITE database of protein families and domains: http://www.expasy.org/prosite/

Domain organization of proteins and large collection of multiple sequence alignments: http://www.sanger.ac.uk/Software/Pfam/; http://people.cryst.bbk.ac.uk/~ubcg16z/cpn/elmovies.html

MitoCarta: An Inventory of Mammalian Mitochondrial Genes: http://www.broadinstitute.org/pubs/MitoCarta/index.html

Human protein atlas with expression of proteins in different tissues: http://www.proteinatlas.org/

Hierarchical Structure of Proteins

Branden, C., and J. Tooze. 1999. Introduction to Protein Structure. Garland.

Dunker, A. K., et al. 2015. Intrinsically disordered proteins and multicellular organisms. Semin. Cell Dev. Biol. 37:44–55.

Dyson, H. J., and P. E. Wright. 2005. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 6:197–208.

Gimona, M. 2006. Protein linguistics—a grammar for modular protein assembly? Nat. Rev. Mol. Cell Biol. 7:68–73.

Gough, J. 2006. Genomic scale sub-family assignment of protein domains. Nucleic Acids Res. 34:3625–3633.

Koonin, E. V., Y. I. Wolf, and G. P. Karev. 2002. The structure of the protein universe and genome evolution. Nature 420:218–223.

Lesk, A. M. 2001. Introduction to Protein Architecture. Oxford.

Levitt, M. 2009. Nature of the protein universe. P. Natl. Acad. Sci. USA 106:11079–11084.

Orengo, C. A., D. T. Jones, and J. M. Thornton. 1994. Protein superfamilies and domain superfolds. Nature 372:631–634.

Patthy, L. 1999. Protein Evolution. Blackwell Science.

Vogel, C., and C. Chothia. 2006. Protein family expansions and biological complexity. PLoS Comput. Biol. 2(5):e48.

Wlodarski, T., and B. Zagrovic. 2009. Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin. P. Natl. Acad. Sci. USA 106:19346–19351.

Yaffe, M. B. 2006. “Bits” and pieces. Sci. STKE 2006:pe28.

Protein Folding

Brandvold, K. R., and R. I. Morimoto. 2015. The chemical biology of molecular chaperones—implications for modulation of proteostasis. J. Mol. Biol. 427:2931–2947.

Broadley, S. A., and F. U. Hartl. 2009. The role of molecular chaperones in human misfolding diseases. FEBS Lett. 583:2647–2653.

Brodsky, J. L., and G. Chiosis. 2006. Hsp70 molecular chaperones: emerging roles in human disease and identification of small molecule modulators. Curr. Top. Med. Chem. 6:1215–1225.

Bukau, B, J. Weissman, and A. Horwich. 2006. Molecular chaperones and protein quality control. Cell 125:443–451.

Cohen, F. E. 1999. Protein misfolding and prion diseases. J. Mol. Biol. 293:313–320.

Coulson, A. F., and J. Moult. 2002. A unifold, mesofold, and superfold model of protein fold use. Proteins 46:61–71.

Daggett, V, and A. R. Fersht. 2003. Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28:18–25.

Dobson, C. M. 1999. Protein misfolding, evolution, and disease. Trends Biochem. Sci. 24:329–332.

Jackrel, M. E., et al. 2014. Potentiated Hsp104 variants antagonize diverse proteotoxic misfolding events. Cell 156:170–182.

Knowles, T. P., M. Vendruscolo, and C. M. Dobson. 2014. The amyloid state and its association with protein misfolding diseases. Nat. Rev. Mol. Cell Biol. 15:384–396.

Lavery, L. A., et al. 2014. Structural asymmetry in the closed state of mitochondrial Hsp90 (TRAP1) supports a two-step ATP hydrolysis mechanism. Mol. Cell 53:330–343.

Lin, Z., and H. S. Rye. 2006. GroEL-mediated protein folding: making the impossible, possible. Crit. Rev. Biochem. Mol. Biol. 41:211–239.

Rochet, J.-C., and P. T. Landsbury. 2000. Amyloid fibrillogenesis: themes and variations. Curr. Opin. Struc. Biol. 10:60–68.

Saibil, H. 2013. Chaperone machines for protein folding, unfolding and disaggregation. Nat. Rev. Mol. Cell Biol. 14:630–642

Schmidpeter, P. A., and F. X. Schmid. 2015. Prolyl isomerization and its catalysis in protein folding and protein function. J. Mol. Biol. 427:1609–1631.

Taipale, M., D. F. Jarosz, and S. Lindquist. 2010. HSP90 at the hub of protein homeostasis: emerging mechanistic insights. Nat. Rev. Mol. Cell Biol. 11:515–528.

Valastyan, J. S., and S. Lindquist. 2014. Mechanisms of protein-folding diseases at a glance. Dis. Model Mech. 7:9–14.

Young, J. C., et al. 2004. Pathways of chaperone-mediated protein folding in the cytosol. Nat. Rev. Mol. Cell Biol. 5:781–791.

Protein Binding and Enzyme Catalysis

Dressler, D. H., and H. Potter. 1991. Discovering Enzymes. Scientific American Library.

Fersht, A. 1999. Enzyme Structure and Mechanism, 3d ed. W. H. Freeman and Company.

Jeffery, C. J. 2004. Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins. Curr. Opin. Struc. Biol. 14:663–668.

Marnett, A. B., and C. S. Craik. 2005. Papa’s got a brand new tag: advances in identification of proteases and their substrates. Trends Biotechnol. 23:59–64.

Martínez Cuesta, S., et al. 2015. The classification and evolution of enzyme function. Biophys. J. 109:1082–1086.

Polgar, L. 2005. The catalytic triad of serine peptidases. Cell. Mol. Life Sci. 62:2161–2172.

Radisky, E. S., et al. 2006. Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates. P. Natl. Acad. Sci. USA 103:6835–6840.

Schenone, M., B. C. Furie, and B. Furie. 2004. The blood coagulation cascade. Curr. Opin. Hematol. 11:272–277.

Schramm, V. L. 2005. Enzymatic transition states and transition state analogues. Curr. Opin. Struc. Biol. 15:604–613.

Regulating Protein Function

Bellelli, A., et al. 2006. The allosteric properties of hemoglobin: insights from natural and site directed mutants. Curr. Prot. Pep. Sci. 7:17–45.

Bochtler, M., et al. 1999. The proteasome. Annu. Rev. Bioph. Biom. 28:295–317.

Burack, W. R., and A. S. Shaw. 2000. Signal transduction: hanging on a scaffold. Curr. Opin. Cell Biol. 12:211–216.

Campbell, M. G., et al. 2015. 2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy. eLife. 10.7554/eLife.06380.

Gallastegui, N., and M. Groll. 2010. The 26S proteasome: assembly and function of a destructive machine. Trends Biochem. Sci. 35:634–642.

Glen, R., et al. 2008. Regulatory monoubiquitination of phosphoenolpyruvate carboxylase in germinating castor oil seeds. J. Biol. Chem. 283:29650–29657.

Glickman, M. H., and A. Ciechanover. 2002. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol. Rev. 82:373–428.

Goldberg, A. L. 2003. Protein degradation and protection against misfolded or damaged proteins. Nature 426:895–899.

Goldberg, A. L, S. J. Elledge, and J. W. Harper. 2001. The cellular chamber of doom. Sci. Am. 284:68–73.

Groll, M., and R. Huber. 2005. Purification, crystallization, and x-ray analysis of the yeast 20S proteasome. Method Enzymol. 398:329–336.

Halling, D. B., P. Aracena-Parks, and S. L. Hamilton. 2006. Regulation of voltage-gated Ca²⁺ channels by calmodulin. Sci. STKE 2005:re15.

Horovitz, A., et al. 2001. Review: allostery in chaperonins. J. Struct. Biol. 135:104–114.

Huang, H., et al. 2010. K33-linked polyubiquitination of T cell receptor-ζ regulates proteolysis-independent T cell signaling. Immunity 33:60–70.

Katz, E. J., M. Isasa, and B. Crosas. 2010. A new map to understand deubiquitination. Biochem. Soc. T. 38:21–28.

Kern, D., and E. R. Zuiderweg. 2003. The role of dynamics in allosteric regulation. Curr. Opin. Struc. Biol. 13:748–757.

Kisselev, A. F., A. Callard, and A. L. Goldberg. 2006. Importance of the different proteolytic sites of the proteasome and the efficacy of inhibitors varies with the protein substrate. J. Biol. Chem. 281:8582–8590.

Lane, K. T., and L. S. Beese. 2006. Thematic review series: lipid posttranslational modifications. Structural biology of protein farnesyltransferase and geranylgeranyltransferase type I. J. Lipid Res. 47:681–699.

Lim, W. A. 2002. The modular logic of signaling proteins: building allosteric switches from simple binding domains. Curr. Opin. Struc. Biol. 12:61–68.

Martin, C., and Y. Zhang. 2005. The diverse functions of histone lysine methylation. Nat. Rev. Mol. Cell Biol. 6:838–849.

Rabl, J., et al. 2008. Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. Mol. Cell 30:360–368.

Rechsteiner, M., and C. P. Hill. 2005. Mobilizing the proteolytic machine: cell biological roles of proteasome activators and inhibitors. Trends Cell Biol. 15:27–33.

Sahtoe, D. D., and T. K. Sixma. 2015. Layers of DUB regulation. Trends Biochem. Sci., in press.

Sawyer, T. K., et al. 2005. Protein phosphorylation and signal transduction modulation: chemistry perspectives for small-molecule drug discovery. Med. Chem. 1:293–319.

Sowa, M. E., et al. 2009. Defining the human deubiquitinating enzyme interaction landscape. Cell 138:389–403.

Xia, Z., and D. R. Storm. 2005. The role of calmodulin as a signal integrator for synaptic plasticity. Nat. Rev. Neurosci. 6:267–276.

Yap, K. L., et al. 1999. Diversity of conformational states and changes within the EF-hand protein superfamily. Proteins 37:499–507.

Zeng, W., et al. 2010. Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity. Cell 141:315–330.

Zhou, P. 2006. REGgamma: a shortcut to destruction. Cell 124:256–257.

Zolk, O., C. Schenke, and A. Sarikas. 2006. The ubiquitin-proteasome system: focus on the heart. Cardiovasc. Res. 70:410–421.

Purifying, Detecting, and Characterizing Proteins

Domon, B., and R. Aebersold. 2006. Mass spectrometry and protein analysis. Science 312:212–217.

Encarnacion, S., et al. 2005. Comparative proteomics using 2-D gel electrophoresis and mass spectrometry as tools to dissect stimulons and regulons in bacteria with sequenced or partially sequenced genomes. Biol. Proc. Online 7:117–135.

Engen, J. R., et al. 2013. Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry. Int. Rev. Phys. Chem. 32:96–127.

Hames, B. D. A Practical Approach. Oxford University Press. A methods series that describes protein purification methods and assays.

Liao, M., et al. 2014. Single particle electron cryo-microscopy of a mammalian ion channel. Curr. Opin. Struc. Biol. 27:1–7.

Nogales, E., and S. H. Scheres. 2015. Cryo-EM: a unique tool for the visualization of macromolecular complexity. Mol. Cell 58:677–689.

O’Connell, M. R., R. Gamsjaeger, and J. P. Mackay. 2009. The structural analysis of protein-protein interactions by NMR spectroscopy. Proteomics 9:5224–5232.

Patton, W. F. 2002. Detection technologies in proteome analysis. J. Chromatogr. B. Analyt. Technol. Biomed. Life Sci. 771:3–31.

Rosenzweig, R., and L. E. Kay. 2014. Bringing dynamic molecular machines into focus by methyl-TROSY NMR. Annu. Rev. Biochem. 83:291–315.

Zhang, G., et al. 2014. Overview of peptide and protein analysis by mass spectrometry. Curr. Prot. Mol. Biol. 108:10.21.1–10.21.30.

Proteomics

Azimifar, S. B., et al. 2014. Cell-type-resolved quantitative proteomics of murine liver. Cell Metab. 20:1076–1087.

Calvo, S. E., and V. K. Mootha. 2010. The mitochondrial proteome and human disease. Annu. Rev. Genomics Hum. Genet. 11:25–34.

Cox, J., and M. Mann. 2011. Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev. Biochem. 80:273–299.

Foster, L. J., et al. 2006. A mammalian organelle map by protein correlation profiling. Cell 125:187–199.

Fu, Q., and J. E. Van Eyk. 2006. Proteomics and heart disease: identifying biomarkers of clinical utility. Expert Rev. Proteomics 3:237–249.

Gavin, A. C., et al. 2006. Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631–636.

Kellie, J. F., et al. 2010. The emerging process of Top Down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput. Mol. Biosyst. 6:1532–1539.

Kislinger, T., et al. 2006. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 125:173–186.

Kolker, E., R. Higdon, and J. M. Hogan. 2006. Protein identification and expression analysis using mass spectrometry. Trends Microbiol. 14:229–235.

Krogan, N. J., et al. 2006. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637–643.

Ong, S. E., and M. Mann. 2005. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1:252–262.

Rifai, N., M. A. Gillette, and S. A. Carr. 2006. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nature Biotech. 24:971–983.

Roux, P. P., and P. Thibault. 2013. The coming of age of phosphoproteomics—from large data sets to inference of protein functions. Mol. Cell Proteomics 12:3453–3464.

Thakur, D., et al. 2011. Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry. J. Chromatogr. A 1218:8168–8174.

Walther, T. C., and M. Mann. 2010. Mass spectrometry-based proteomics in cell biology. J. Cell Biol. 190:491–500.

White, I. R., et al. 2004. A statistical comparison of silver and SYPRO Ruby staining for proteomic analysis. Electrophoresis 25:3048–3054.

Zhou, M., and C. V. Robinson. 2010. When proteomics meets structural biology. Trends Biochem. Sci. 35:522–539.