Chapter 10

Where to Start

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Neurath, H. 1989. Proteolytic processing and physiological regulation. Trends Biochem. Sci. 14:268–271.

Bode, W., and Huber, R. 1992. Natural protein proteinase inhibitors and their interaction with proteinases. Eur. J. Biochem. 204: 433–451.

Aspartate Transcarbamoylase and Allosteric Interactions

Changeux, J.-P. 2012. Allostery and the Monod-Wyman-Changeux Model After 50 Years. Annu. Rev. Biophys. 41:103–133.

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Newell, J. O., Markby, D. W., and Schachman, H. K. 1989. Cooperative binding of the bisubstrate analog N-(phosphonacetyl)-L-aspartate to aspartate transcarbamoylase and the heterotropic effects of ATP and CTP. J. Biol. Chem. 264:2476–2481.

Stevens, R. C., Gouaux, J. E., and Lipscomb, W. N. 1990. Structural consequences of effector binding to the T state of aspartate carbamoyl-transferase: Crystal structures of the unligated and ATP- and CTP-complexed enzymes at 2.6-Å resolution. Biochemistry 29:7691–7701.

Gouaux, J. E., and Lipscomb, W. N. 1990. Crystal structures of phosphonoacetamide ligated T and phosphonoacetamide and malonate ligated R states of aspartate carbamoyltransferase at 2.8-Å resolution and neutral pH. Biochemistry 29:389–402.

Labedan, B., Boyen, A., Baetens, M., Charlier, D., Chen, P., Cunin, R., Durbeco, V., Glansdorff, N., Herve, G., Legrain, C., et al. 1999. The evolutionary history of carbamoyltransferases: A complex set of paralogous genes was already present in the last universal common ancestor. J. Mol. Evol. 49:461–473.

Covalent Modification

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Guarente, L. 2011. The logic linking protein acetylation and metabolism. Cell Metab. 14:151–153.

Guan, K-L., and Xiong, Y. 2011. Regulation of intermediary metabolism by protein acetylation. Trends Biochem. Sci. 36:108–116.

Johnson, L. N., and Barford, D. 1993. The effects of phosphorylation on the structure and function of proteins. Annu. Rev. Biophys. Biomol. Struct. 22:199–232.

Barford, D., Das, A. K., and Egloff, M. P. 1998. The structure and mechanism of protein phosphatases: Insights into catalysis and regulation. Annu. Rev. Biophys. Biomol. Struct. 27:133–164.

Protein Kinase A

Taylor, S. S., Ilouz, R., Zhang, P., and Kornev, A. P. 2012. Assembly of allosteric macromolecular switches: Lessons from PKA. Nature Rev. Mol. Cell Biol. 13:646–658.

Zhang, P., Smith-Nguyen, E. V., Keshwani, M. M., Deal, M. S., Kornev, A. P., and Taylor, S. S. 2012. Structure and allostery of the PKA RIIb tetrameric holoenzyme. Science 334:712–716.

Taylor, S. S., and Kornev, A. P. 2011. Protein kinases: evolution of dynamic regulatory proteins. Trends Biochem. Sci. 36:65–77.

Pearlman, S. M., Serber, Z., and Ferrell Jr., J. E. 2011. A mechanism for the evolution of phosphorylation sites. Cell 147:934–946.

Knighton, D. R., Zheng, J. H., TenEyck, L., Xuong, N. H., Taylor, S. S., and Sowadski, J. M. 1991. Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science 253:414–420.

Zymogen Activation

Artenstein, A. W., and Opal, S. M. 2011. Proprotein convertases in health and disease. New Engl. J. Med. 65:2507–2518.

Neurath, H. 1986. The versatility of proteolytic enzymes. J. Cell. Biochem. 32:35–49.

Bode, W., and Huber, R. 1986. Crystal structure of pancreatic serine endopeptidases. In Molecular and Cellular Basis of Digestion (pp. 213–234), edited by P. Desnuelle, H. Sjostrom, and O. Noren. Elsevier.

James, M. N. 1991. Refined structure of porcine pepsinogen at 1.8 Å resolution. J. Mol. Biol. 219:671–692.

Protease Inhibitors

Gooptu, B., and Lomas, D. A. 2009. Conformational Pathology of the Serpins: Themes, Variations, and Therapeutic Strategies. Annu. Rev. Biochem. 78:147–167.

Carrell, R., and Travis, J. 1985. α1-Antitrypsin and the serpins: Variation and countervariation. Trends Biochem. Sci. 10:20–24.

Carp, H., Miller, F., Hoidal, J. R., and Janoff, A. 1982. Potential mechanism of emphysema: α1-Proteinase inhibitor recovered from lungs of cigarette smokers contains oxidized methionine and has decreased elastase inhibitory capacity. Proc. Natl. Acad. Sci. U.S.A. 79:2041–2045.

B10

Owen, M. C., Brennan, S. O., Lewis, J. H., and Carrell, R. W. 1983. Mutation of antitrypsin to antithrombin. New Engl. J. Med. 309: 694–698.

Travis, J., and Salvesen, G. S. 1983. Human plasma proteinase inhibitors. Annu. Rev. Biochem. 52:655–709.

Clotting Cascade

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Furie, B., and Furie, B. C. 2008. Mechanisms of thrombus formation. New Engl. J. Med. 359:938–949.

Orfeo, T., Brufatto, N., Nesheim, M. E., Xu, H., Butenas, S., and Mann, K. G. 2004. The factor V activation paradox. J. Biol. Chem. 279:19580–19591.

Mann, K. G. 2003. Thrombin formation. Chest 124:4S–10S.

Rose, T., and Di Cera, E. 2002. Three-dimensional modeling of thrombin–-fibrinogen interaction. J. Biol. Chem. 277:18875–18880.

Krem, M. M., and Di Cera, E. 2002. Evolution of cascades from embryonic development to blood coagulation. Trends Biochem. Sci. 27:67–74.

Fuentes-Prior, P., Iwanaga, Y., Huber, R., Pagila, R., Rumennik, G., Seto, M., Morser, J., Light, D. R., and Bode, W. 2000. Structural basis for the anticoagulant activity of the thrombin–thrombomodulin complex. Nature 404:518–525.

Lawn, R. M., and Vehar, G. A. 1986. The molecular genetics of hemophilia. Sci. Am. 254(3):48–65.