Molecular modeling of substrate-enzyme reactions for the cysteine protease papain

Shaw, 1990, Cysteinyl proteinases and their selective inactivation, Adv. Enzymol. Relat. Areas Mol. Biol., 63, 271 Duffy, 1992, The role of proteolytic enzymes in cancer invasion and metastasis, Clin. Exp. Metastasis, 10, 145, 10.1007/BF00132746 Berquin, 1994, Cysteine proteases and tumor progression, Perspect. Drug Design Discovery, 2, 371, 10.1007/BF02172031 Sloane, 1990, Cancer Metastasis Rev., 9, 333, 10.1007/BF00049523 Brocklehurst, 1987, Acyl group transfer-cysteine proteases, 140 Lowe, 1976, The cysteine proteases, Tetrahedron, 32, 291, 10.1016/0040-4020(76)80040-3 Lin, 1996 Musil, 1991, The refined 2.15 Å x-ray crystal structure of human liver cathepsin B: The structural basis for its specificity, EMBO J, 10, 2321, 10.1002/j.1460-2075.1991.tb07771.x Kamphuis, 1984, Structure of papain at 1.65 Å resolution, J. Mod. Biol., 179, 233, 10.1016/0022-2836(84)90467-4 Kamphuis, 1985, Thiol proteases: Comparative studies based on the high-resolution structures of papain and actinidin, and on amino acid sequence information for cathepsins B and H, and stem bromelain, J. Mol. Biol., 182, 317, 10.1016/0022-2836(85)90348-1 Huber, 1982, Precise structural information for transient enzyme-substrate complexes by a combined x-ray crystallographic-resonance Raman spectroscopic approach, Biochemistry, 21, 3109, 10.1021/bi00256a012 Carey, 1983, Molecular details of enzyme-substrate transients by resonance raman spectroscopy, Acc. Chem. Res., 16, 455, 10.1021/ar00096a005 Varughese, 1984, Directional preference for a catalytically important N ··· S contact seen in acyl-thiolproteases, J. Am. Chem. Soc., 106, 8252, 10.1021/ja00338a040 Carey, 1984, Rate-structure correlation for enzyme-substrates intermediates: Resonance Raman and kinetic studies on some N-benzoylglycine (dithioacyl) papains, J. Am. Chem. Soc., 106, 8258, 10.1021/ja00338a041 Storer, 1985, Comparison of the kinetics and mechanism of the papain-catalyzed hydrolysis of esters and thiono esters, Biochemistry, 24, 6808, 10.1021/bi00345a012 Tonge, 1989, Striking changes observed in key acylenzyme linkages by resonance raman experiments near 77 K, J. Am. Chem. Soc., 111, 1496, 10.1021/ja00186a055 Kim, 1993, Fine-tuned conformation of dithioacyl-papain intermediates: Insights from resonance raman spectroscopy, J. Am. Chem. Soc., 115, 6230, 10.1021/ja00067a042 Asboth, 1983, Transition-state at the oxyanion binding sites of serine and thiol proteinases: Hydrolysis of thiono and oxygen esters, Biochemistry, 22, 117, 10.1021/bi00270a017 Asboth, 1985, Mechanism of action of cysteine proteinases: Oxyanion binding site is not essential in the hydrolysis of specific substrates, Biochemistry, 24, 606, 10.1021/bi00324a010 Williams, 1988, The use of semiempirical energy partitioning in the study of through space (homoaromatic) interactions, Tetrahedron, 44, 7455, 10.1016/S0040-4020(01)86239-6 Sotomatsu, 1989, Correlation analysis of substituent effects on the acidity of benzoic acids by the AM1 method, J. Comput. Chem., 10, 94, 10.1002/jcc.540100109 Dewar, 1990, AM1 studies of E2 reactions. 1. Mechanism and leaving group effects, J. Am. Chem. Soc., 112, 2088, 10.1021/ja00162a008 Dewar, 1990, AM1 Studies of E2 reactions. 2. Regioselectivity, stereochemistry, kinetic isotope effects, and competition with SN2 reactions, J. Am. Chem. Soc., 112, 2095, 10.1021/ja00162a009 Merz, 1989, Mode of action of carbonic anhydrase, J. Am. Chem. Soc., 111, 5636, 10.1021/ja00197a021 Katagi, 1990, Theoretical studies on the alkaline hydrolysis of N-methylcarbamates, J. Comput. Chem., 11, 524, 10.1002/jcc.540110411 Bacaloglu, 1989, Interaction of nitroarenes with hydroxide ion. An AM1 molecular orbital treatment, J. Am. Chem. Soc., 111, 1041, 10.1021/ja00185a038 Duncan, 1992, Molecular orbital studies of the structure and reactivity of model substrate intermediates in the deacylation of the cysteine protease papain, J. Am. Chem. Soc., 114, 5784, 10.1021/ja00040a046 Dewar, 1985, AM1: A new general purpose quantum mechanical molecular model, J. Am. Chem. Soc., 107, 3902, 10.1021/ja00299a024 Schröder, 1991, A comparison of the AM1 and PM3 semiempirical models for evaluating model compounds relevant to catalysis by serine proteases, J. Am. Chem. Soc., 113, 8922, 10.1021/ja00023a046 Daggett, 1991, Catalytic pathway of serine proteases: Classical and quantum mechanical calculations, J. Am. Chem. Soc., 113, 8926, 10.1021/ja00023a047 Arad, 1990, A simulation of the sulfur attack in the catalytic pathway of papain using molecular mechanics and semiempirical quantum mechanics, J. Am. Chem. Soc., 112, 491, 10.1021/ja00158a004 Tsukada, 1985, Structure of α-chymotrypsin refined at 1.68 Å resolution, J. Mol. Biol., 184, 703, 10.1016/0022-2836(85)90314-6