SELECTED READINGS

B1

Chapter 2

Where to Start

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Doolittle, R. F. 1985. Proteins. Sci. Am. 253(4):88–99.

Richards, F. M. 1991. The protein folding problem. Sci. Am. 264(1):54–57.

Weber, A. L., and Miller, S. L. 1981. Reasons for the occurrence of the twenty coded protein amino acids. J. Mol. Evol. 17:273–284.

Petsko, G. A., and Ringe, D. 2004. Protein Structure and Function. New Science Press.

Tanford, C., and Reynolds, J. 2004. Nature’s Robots: A History of Proteins. Oxford.

Branden, C., and Tooze, J. 1999. Introduction to Protein Structure (2d ed.). Garland.

Creighton, T. E. 1992. Proteins: Structures and Molecular Principles (2d ed.). W. H. Freeman and Company.

Smock, R. G., and Gierasch, L. M. 2009. Sending signals dynamically. Science 324:198–203.

Tokuriki, N., and Tawfik, D. S. 2009. Protein dynamism and evolvability. Science 324:203–207.

Pace, C. N., Grimsley, G. R., and Scholtz, J. M. 2009. Protein ionizable groups: pK values and their contribution to protein stability and solubility. J. Biol. Chem. 284:13285–13289.

Breslow, R., and Cheng, Z.-L. 2009. On the origin of terrestrial homochirality for nucleosides and amino acids. Proc. Natl. Acad. Sci. U.S.A. 106:9144–9146.

Shoulders, M. D., and Raines, R. T. 2009. Collagen structure and stability. Annu. Rev. Biochem. 78:929–958.

O’Neil, K. T., and DeGrado, W. F. 1990. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250:646–651.

Zhang, C., and Kim, S. H. 2000. The anatomy of protein beta-sheet topology. J. Mol. Biol. 299:1075–1089.

Regan, L. 1994. Protein structure: Born to be beta. Curr. Biol. 4:656–658.

Srinivasan, R., and Rose, G. D. 1999. A physical basis for protein secondary structure. Proc. Natl. Acad. Sci. U.S.A. 96:14258–14263.

Galea, C. A., Wang, Y., Sivakolundu, S. G., and Kriwacki, R. W. 2008. Regulation of cell division by intrinsically unstructured proteins: Intrinsic flexibility, modularity, and signaling conduits. Biochemistry 47:7598–7609.

Raychaudhuri, S., Dey, S., Bhattacharyya, N. P., and Mukhopadhyay, D. 2009. The role of intrinsically unstructured proteins in neurodegenerative diseases. PLoS One 4:e5566.

Tompa, P., and Fuxreiter, M. 2008. Fuzzy complexes: Polymorphism and structural disorder in protein–protein interactions. Trends Biochem. Sci. 33:2–8.

Tuinstra, R. L., Peterson, F. C., Kutlesa, E. S., Elgin, S., Kron, M. A., and Volkman, B. F. 2008. Interconversion between two unrelated protein folds in the lymphotactin native state. Proc. Natl. Acad. Sci. U.S.A. 105:5057–5062.

Jin, J., Xie, X., Chen, C., Park, J. G., Stark, C., James, D. A., Olhovsky, M., Lindinger, R., Mao, Y., and Pawson, T. 2009. Eukaryotic protein domains as functional units of cellular evolution. Sci. Signal. 2:ra76.

Bennett, M. J., Choe, S., and Eisenberg, D. 1994. Domain swapping: Entangling alliances between proteins. Proc. Natl. Acad. Sci. U.S.A. 91:3127–3131.

Bergdoll, M., Eltis, L. D., Cameron, A. D., Dumas, P., and Bolin, J. T. 1998. All in the family: Structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly. Protein Sci. 7:1661–1670.

Hopfner, K. P., Kopetzki, E., Kresse, G. B., Bode, W., Huber, R., and Engh, R. A. 1998. New enzyme lineages by subdomain shuffling. Proc. Natl. Acad. Sci. U.S.A. 95:9813–9818.

Ponting, C. P., Schultz, J., Copley, R. R., Andrade, M. A., and Bork, P. 2000. Evolution of domain families. Adv. Protein Chem. 54:185–244.

Caughey, B., Baron, G. S., Chesebro, B., and Jeffrey, M. 2009. Getting a grip on prions: Oligomers, amyloids, and pathological membrane interactions. Annu. Rev. Biochem. 78:177–204.

Cobb, N. J., and Surewicz, W. K. 2009. Prion diseases and their biochemical mechanisms. Biochemistry 48:2574–2585.

Soto, C. 2011. Prion diseases: The end of the controversy? Trends Biochem. Sci. 36:151–158.

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

Selkoe, D. J. 2003. Folding proteins in fatal ways. Nature 426:900–904.

Anfinsen, C. B. 1973. Principles that govern the folding of protein chains. Science 181:223–230.

Baldwin, R. L., and Rose, G. D. 1999. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem. Sci. 24:26–33.

Baldwin, R. L., and Rose, G. D. 1999. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem. Sci. 24:77–83.

Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L., and Baker, D. 2003. Design of a novel globular protein with atomic-level accuracy. Science 302:1364–1368.

Staley, J. P., and Kim, P. S. 1990. Role of a subdomain in the folding of bovine pancreatic trypsin inhibitor. Nature 344:685–688.

Tarrant, M. K., and Cole, P. A. 2009. The chemical biology of protein phosphorylation. Annu. Rev. Biochem. 78:797–825.

Krishna, R. G., and Wold, F. 1993. Post-translational modification of proteins. Adv. Enzymol. Relat. Areas. Mol. Biol. 67:265–298.

Aletta, J. M., Cimato, T. R., and Ettinger, M. J. 1998. Protein methylation: A signal event in post-translational modification. Trends Biochem. Sci. 23:89–91.

Tsien, R. Y. 1998. The green fluorescent protein. Annu. Rev. Biochem. 67:509–544.