Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling

Apoptosis

Volumn 14, Issue 5, 2009, Pages 741-752

  Fang, Bin ^a   Fu, Guoxing ^a   Agniswamy, Johnson ^a   Harrison, Robert W ^a   Weber, Irene T ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

Author keywords

Apoptosis; Cysteine protease; Enzyme catalysis; Protein recognition

Indexed keywords

ACETIC ACID DERIVATIVE; ALDEHYDE; ASPARTIC ACID; CASPASE 3; PHENYLALANINE; PROLINE; THREONINE; TRYPTOPHAN; TYROSINE;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; HYDROPHOBICITY; MOLECULAR MECHANICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; BINDING SITES; CASPASE 3; CRYSTALLOGRAPHY, X-RAY; ENZYME INHIBITORS; HUMANS; HYDROGEN BONDING; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN BINDING; STATIC ELECTRICITY; SUBSTRATE SPECIFICITY; THERMODYNAMICS;

EID: 67349217364     PISSN: 13608185     EISSN: 1573675X     Source Type: Journal    
DOI: 10.1007/s10495-009-0333-y     Document Type: Article

References (45)

1. F Martinon N Holler C Richard J Tschopp 2000 Activation of a pro-apoptotic amplification loop through inhibition of NF-kappaB-dependent survival signals by caspase-mediated inactivation of RIP FEBS Lett 468 134 136 10.1016/S0014-5793(00)01212-6 (Pubitemid 30110782)
2. U Fischer RU Janicke K Schulze-Osthoff 2003 Many cuts to ruin: a comprehensive update of caspase substrates Cell Death Differ 10 76 100 10.1038/sj.cdd.4401160 (Pubitemid 36511834)
3. JC Timmer GS Salvesen 2007 Caspase substrates Cell Death Differ 14 66 72 10.1038/sj.cdd.4402059
4. A Hartmann JD Troadec S Hunot 2001 Caspase-8 is an effector in apoptotic death of dopaminergic neurons in Parkinson's disease, but pathway inhibition results in neuronal necrosis J Neurosci 21 2247 2255 (Pubitemid 32240523)
5. E Hermel J Gafni SS Propp 2004 Specific caspase interactions and amplification are involved in selective neuronal vulnerability in Huntington's disease Cell Death Differ 11 424 438 10.1038/sj.cdd.4401358 (Pubitemid 38489420)
6. S Tacconi R Perri E Balestrieri 2004 Increased caspase activation in peripheral blood mononuclear cells of patients with Alzheimer's disease Exp Neurol 190 254 262 10.1016/j.expneurol.2004.07.009 (Pubitemid 39335724)
7. SA Lakhani A Masud K Kuida 2006 Caspases 3 and 7: key mediators of mitochondrial events of apoptosis Science 311 847 851 10.1126/science.1115035 (Pubitemid 43228848)
8. X Volkmann M Cornberg H Wedemeyer 2006 Caspase activation is required for antiviral treatment response in chronic hepatitis C virus infection Hepatology 43 1311 1316 10.1002/hep.21186 (Pubitemid 43980110)
9. D Vucic HR Stennicke MT Pisabarro GS Salvesen VM Dixit 2000 ML-IAP, a novel inhibitor of apoptosis that is preferentially expressed in human melanomas Curr Biol 10 1359 1366 10.1016/S0960-9822(00)00781-8
10. T O'Brien D Lee 2004 Prospects for caspase inhibitors Mini Rev Med Chem 4 153 165 10.2174/1389557043487448 (Pubitemid 38854862)
11. BA Callus DL Vaux 2007 Caspase inhibitors: viral, cellular and chemical Cell Death Differ 14 73 78 10.1038/sj.cdd.4402034
12. NA Thornberry TA Rano EP Peterson 1997 A combinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis J Biol Chem 272 17907 17911 10.1074/jbc.272.29.17907 (Pubitemid 27306365)
13. IN Lavrik A Golks PH Krammer 2005 Caspases: pharmacological manipulation of cell death J Clin Invest 115 2665 2672 10.1172/JCI26252 (Pubitemid 41434390)
14. S Lien R Pastor D Sutherlin HB Lowman 2004 A substrate-phage approach for investigating caspase specificity Protein J 23 413 425 10.1023/B:JOPC. 0000039555.92058.51 (Pubitemid 40941073)
15. A Yoshimori J Sakai S Sunaga 2007 Structural and functional definition of the specificity of a novel caspase-3 inhibitor, Ac-DNLD-CHO BMC Pharmacol 7 8 10.1186/1471-2210-7-8 (Pubitemid 47163146)
16. A Schweizer C Briand MG Grutter 2003 Crystal structure of caspase-2, apical initiator of the intrinsic apoptotic pathway J Biol Chem 278 42441 42447 10.1074/jbc.M304895200 (Pubitemid 37310516)
17. B Fang PI Boross J Tozser IT Weber 2006 Structural and kinetic analysis of caspase-3 reveals role for s5 binding site in substrate recognition J Mol Biol 360 654 666 10.1016/j.jmb.2006.05.041 (Pubitemid 43975116)
18. C Backes J Kuentzer HP Lenhof N Comtesse E Meese 2005 GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences Nucleic Acids Res 33 W208 W213 10.1093/nar/gki433 (Pubitemid 44529910)
19. G Fu AA Chumanevich J Agniswamy B Fang RW Harrison IT Weber 2008 Structural basis for executioner caspase recognition of P5 position in substrates Apoptosis 13 1291 1302 10.1007/s10495-008-0259-9
20. HR Stennicke M Renatus M Meldal GS Salvesen 2000 Internally quenched fluorescent peptide substrates disclose the subsite preferences of human caspases 1, 3, 6, 7 and 8 Biochem J 350 Pt 2 563 568 10.1042/0264-6021:3500563
21. J Maibaum DH Rich 1988 Inhibition of porcine pepsin by two substrate analogues containing statine. The effect of histidine at the P2 subsite on the inhibition of aspartic proteinases J Med Chem 31 625 629 10.1021/jm00398a022 (Pubitemid 18070582)
22. M Donepudi A Mac Sweeney C Briand MG Grutter 2003 Insights into the regulatory mechanism for caspase-8 activation Mol Cell 11 543 549 10.1016/S1097-2765(03)00059-5 (Pubitemid 36297058)
23. ZM Otwinowski W Minor 1997 Processing of X-ray diffraction data in oscillation mode Meth Enzymol 276 307 326 10.1016/S0076-6879(97)76066-X (Pubitemid 27085611)
24. J Navaza 1994 AMoRe: an automated package for molecular replacemnet Acta Crystallogr D Biol Crystallogr 50 157 163
25. AT Brunger PD Adams GM Clore 1998 Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr D Biol Crystallogr 54 Pt 5 905 921 10.1107/S0907444998003254 (Pubitemid 28443603)
26. TA Jones JY Zou SW Cowan M Kjeldgaard 1991 Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr A 47 Pt 2 110 119 10.1107/S0108767390010224
27. RM Esnouf 1997 An extensively modified version of MolScript that includes greatly enhanced coloring capabilities J Mol Graph Model 15 132-134 112 133 (Pubitemid 27484260)
28. RM Esnouf 1999 Further additions to MolScript version 1.4, including reading and contouring of electron-density maps Acta Crystallogr D Biol Crystallogr 55 Pt 4 938 940 10.1107/S0907444998017363 (Pubitemid 29194558)
29. RW Harrison 1993 Stiffness and energy conservation in the molecular dynamics: an improved integrator J Comput Chem 14 1112 1122 10.1002/jcc. 540140912
30. P Emsley K Cowtan 2004 Coot: model-building tools for molecular graphics Acta Crystallogr D Biol Crystallogr 60 2126 2132 10.1107/S0907444904019158 (Pubitemid 41742764)
31. P Bagossi J Tozser IT Weber RW Harrison 1999 Modification of parameters of the charge equilibrium scheme to achieve better correlation with experimental dipole moments J Mol Model 5 143 152 10.1007/s008940050114
32. RWA Harrison 1999 Self-assembling neural network for modeling polymers J Math Chem 26 125 137 10.1023/A:1019181811090
33. RA Sayle EJ Milner-White 1995 RASMOL: biomolecular graphics for all Trends Biochem Sci 20 374 10.1016/S0968-0004(00)89080-5
34. RV Talanian C Quinlan S Trautz 1997 Substrate specificities of caspase family proteases J Biol Chem 272 9677 9682 10.1074/jbc.272.15.9677 (Pubitemid 27171628)
35. M Garcia-Calvo EP Peterson B Leiting R Ruel DW Nicholson NA Thornberry 1998 Inhibition of human caspases by peptide-based and macromolecular inhibitors J Biol Chem 273 32608 32613 10.1074/jbc.273.49.32608 (Pubitemid 28557641)
36. DW Nicholson A Ali NA Thornberry 1995 Identification and inhibition of the ICE/CED-3 protease necessary for mammalian apoptosis Nature 376 37 43 10.1038/376037a0
37. L Qiu QX Chen Q Wang H Huang KK Song 2005 Irreversibly inhibitory kinetics of 3, 5-dihydroxyphenyl decanoate on mushroom (Agaricus bisporus) tyrosinase Bioorg Med Chem 13 6206 6211 10.1016/j.bmc.2005.06.034 (Pubitemid 41400143)
38. R Ganesan PR Mittl S Jelakovic MG Grutter 2006 Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis J Mol Biol 359 1378 1388 10.1016/j.jmb.2006.04.051 (Pubitemid 43922445)
39. J Agniswamy B Fang IT Weber 2007 Plasticity of S2-S4 specificity pockets of executioner caspase-7 revealed by structural and kinetic analysis FEBS J 274 4752 4765 10.1111/j.1742-4658.2007.05994.x (Pubitemid 47353120)
40. D Lee SA Long JL Adams 2000 Potent and selective nonpeptide inhibitors of caspases 3 and 7 inhibit apoptosis and maintain cell functionality J Biol Chem 275 16007 16014 10.1074/jbc.275.21.16007 (Pubitemid 30366906)
41. H Blanchard M Donepudi M Tschopp L Kodandapani JC Wu MG Grutter 2000 Caspase-8 specificity probed at subsite S(4): crystal structure of the caspase-8-Z-DEVD-cho complex J Mol Biol 302 9 16 10.1006/jmbi.2000.4041
42. SJ Riedl M Renatus R Schwarzenbacher 2001 Structural basis for the inhibition of caspase-3 by XIAP Cell 104 791 800 10.1016/S0092-8674(01)00274-4 (Pubitemid 32241028)
43. PJ Pockros ER Schiff ML Shiffman 2007 Oral IDN-6556, an antiapoptotic caspase inhibitor, may lower aminotransferase activity in patients with chronic hepatitis C Hepatology 46 324 329 10.1002/hep.21664 (Pubitemid 47344766)
44. T Irene 2008 Weber BFaJA. Caspases: structure-guided design of drugs to control cell death Mini Rev Med Chem 8 1154 1162 10.2174/138955708785909899
45. ES Baskin-Bey K Washburn S Feng 2007 Clinical trial of the pan-caspase inhibitor, IDN-6556, in human liver preservation injury Am J Transplant 7 218 225 10.1111/j.1600-6143.2006.01595.x