The realization of structure based molecular design is linked to our ability to accurately estimate or predict protein stabilities or binding affinities from structural considerations. This task essentially reduces to the ability of predicting the Gibbs energy that accounts for the stability of a protein or the binding affinity of a complex from a detailed knowledge of their structure. Recently, it has been realized that the thermodynamic parameters (deltaCp, deltaH, deltaS) that define the Gibbs energy of protein stabilization or binding can be parametrized in structural terms. This empirical approach appears to be promising and to have predictive potential, provided that the structural parametrization is extended and refined. The main goal of this proposal is precisely to extend and refine the existing structural parametrization of the thermodynamic parameters deltaCp, deltaH, and deltaS using systems in which the effects of specific contributions have a higher impact and are therefore easier to identify and candidate. These systems include folding/unfolding of specific mutants of low molecular weight proteins, and the binding of different peptides to specific protein binding sites. The thermodynamic parameters for those events will be measured directly by high sensitivity calorimetric techniques. In our studies, we will consider specific mutants of a 33 amino acid peptide corresponding to the coiled coil (leucine zipper) region of GCN4, and the binding of specific inhibitors to aspartic proteases. The protease systems include endothiapepsin for which the structure of several inhibitor complexes is known at high resolution and the human immunodeficiency virus (HIV) protease for which high resolution structural information is also available. Besides providing information of general significance and applicability, the systems chosen are of intrinsic importance and medical relevance.

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National Institute of General Medical Sciences (NIGMS)
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Maynard, Ernest L; Berg, Jeremy M (2007) Quantitative analysis of peroxisomal targeting signal type-1 binding to wild-type and pathogenic mutants of Pex5p supports an affinity threshold for peroxisomal protein targeting. J Mol Biol 368:1259-66
Amzel, L Mario; Siebert, Xavier; Armstrong, Anthony et al. (2005) Thermodynamic calculations in biological systems. Biophys Chem 117:239-54
Siebert, Xavier; Amzel, L Mario (2004) Loss of translational entropy in molecular associations. Proteins 54:104-15
Gatto Jr, Gregory J; Maynard, Ernest L; Guerrerio, Anthony L et al. (2003) Correlating structure and affinity for PEX5:PTS1 complexes. Biochemistry 42:1660-6
Kang, Lin-Woo; Gabelli, Sandra B; Bianchet, Mario A et al. (2003) Structure of a coenzyme A pyrophosphatase from Deinococcus radiodurans: a member of the Nudix family. J Bacteriol 185:4110-8
Ahmed, Hafiz; Bianchet, Mario A; Amzel, L Mario et al. (2002) Novel carbohydrate specificity of the 16-kDa galectin from Caenorhabditis elegans: binding to blood group precursor oligosaccharides (type 1, type 2, Talpha, and Tbeta) and gangliosides. Glycobiology 12:451-61
Nezami, Azin; Luque, Irene; Kimura, Tooru et al. (2002) Identification and characterization of allophenylnorstatine-based inhibitors of plasmepsin II, an antimalarial target. Biochemistry 41:2273-80
Luque, Irene; Leavitt, Stephanie A; Freire, Ernesto (2002) The linkage between protein folding and functional cooperativity: two sides of the same coin? Annu Rev Biophys Biomol Struct 31:235-56
Velazquez-Campoy, A; Kiso, Y; Freire, E (2001) The binding energetics of first- and second-generation HIV-1 protease inhibitors: implications for drug design. Arch Biochem Biophys 390:169-75
Velazquez-Campoy, A; Todd, M J; Vega, S et al. (2001) Catalytic efficiency and vitality of HIV-1 proteases from African viral subtypes. Proc Natl Acad Sci U S A 98:6062-7

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