General

Kornberg, A. 1989. Never a dull enzyme. Annu. Rev. Biochem. 58:1–30. An especially illuminating essay for young scientists.

Kornberg, A. 1990. Why purify enzymes? Methods Enzymol. 182:1–5.

Kornberg, A. 1996. Chemistry: The lingua franca of the medical and biological sciences. Chem. Biol. 3:3–5. This and the two articles above provide inspiration from one of the great biochemists of the past century.

Nelson, D.L., and M.M. Cox. 2013. Lehninger Principles of Biochemistry, 6th ed. New York: W. H. Freeman. See Chapters 3 through 6 for more detailed background on enzyme kinetics.

von Hippel, P.H. 2007. From “simple” DNA-protein interactions to the macromolecular machines of gene expression. Annu. Rev. Biophys. Biomol. Struct. 36:79–105.

Protein-Ligand Interactions

Jayaram, B., and T. Jain. 2004. The role of water in protein-DNA recognition. Annu. Rev. Biophys. Biomol. Struct. 33:343–361.

Kalodimos, C.G., N. Biris, A.M.J.J. Bonvin, M.M. Levandoski, M. Guennuegues, R. Boelens, and R. Kaptein. 2004. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305:386–389.

Lohman, T.M., and D.P. Mascotti. 1992. Thermodynamics of ligand–nucleic acid interactions. Methods Enzymol. 212:400–424.

Raghunathan, S., A.G. Kozlov, T.M. Lohman, and G. Waksman. 2000. Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nat. Struct. Biol. 7:648–652.

Enzymes: The Reaction Catalysts of Biological Systems

Arabshahi, A., and P.A. Frey. 1999. Standard free energy for the hydrolysis of adenylylated T4 DNA ligase and the apparent pK_a of lysine 159. J. Biol. Chem. 274:8586–8588.

Ellenberger, T., and A.E. Tomkinson. 2008. Eukaryotic DNA ligases: Structural and functional insights. Annu. Rev. Biochem. 77:313–338. A complete summary of many details gleaned from structural analysis.

Lehman, I.R. 1974. DNA ligase: Structure, mechanism, and function. Science 186:790–797.

Liu, P., A. Burdzy, and L.C. Sowers. 2004. DNA ligases ensure fidelity by interrogating minor groove contacts. Nucleic Acids Res. 32:4503–4511.

Motor Proteins

Lohman, T.M., and K.P. Bjornson. 1996. Mechanisms of helicase-catalyzed DNA unwinding. Annu. Rev. Biochem. 65:169–214.

Lohman, T.M., E.J. Tomko, and C.G. Wu. 2008. Nonhexameric DNA helicases and translocases: Mechanisms and regulation. Nat. Rev. Mol. Cell Biol. 9:391–401.

Pyle, A.M. 2008. Translocation and unwinding mechanisms of RNA and DNA helicases. Annu. Rev. Biophys. 37:317–336.

Singleton, M.R., M.S. Dillingham, and D.B. Wigley. 2007. Structure and mechanism of helicases and nucleic acid translocases. Annu. Rev. Biochem. 76:23–50.

Regulation of Protein Function

Bialik, S., and A. Kimchi. 2006. The death-associated protein kinases: Structure, function, and beyond. Annu. Rev. Biochem. 75:189–210.

Elphick, L.M., S.E. Lee, V. Gouverneur, and D.J. Mann. 2007. Using chemical genetics and ATP analogues to dissect protein kinase function. ACS Chem. Biol. 2:299–314.

Gelato, K.A., and W. Fischle. 2008. Role of histone modifications in defining chromatin structure and function. Biol. Chem. 389:353–363.

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

Millar, C.B., and M. Grunstein. 2006. Genome-wide patterns of histone modifications in yeast. Nat. Rev. Mol. Cell Biol. 7:657–666.

Moorhead, G.B.G., L. Trinkle-Mulcahy, and A. Ulke-Lemee. 2007. Emerging roles of nuclear protein phosphatases. Nat. Rev. Mol. Cell Biol. 8:234–244.

Shahbazian, M.D., and M. Grunstein. 2007. Functions of site-specific histone acetylation and deacetylation. Annu. Rev. Biochem. 76:75–100.

Tonks, N.K. 2006. Protein tyrosine phosphatases: From genes, to function, to disease. Nat. Rev. Mol. Cell Biol. 7:833–846.

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