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Structural and kinetic analysis of caspase-3 reveals role for s5 binding site in substrate recognition.

Fang B, Boross PI, Tozser J, Weber IT
J Mol Biol 360 654-66 (2006)
Related entries: 2h5i, 2h65

Cited: 41 times
EuropePMC logo PMID: 16781734

Abstract

The molecular basis for the substrate specificity of human caspase-3 has been investigated using peptide analog inhibitors and substrates that vary at the P2, P3, and P5 positions. Crystal structures were determined of caspase-3 complexes with the substrate analogs at resolutions of 1.7 A to 2.3 A. Differences in the interactions of caspase-3 with the analogs are consistent with the Ki values of 1.3 nM, 6.5 nM, and 12.4 nM for Ac-DEVD-Cho, Ac-VDVAD-Cho and Ac-DMQD-Cho, respectively, and relative kcat/Km values of 100%, 37% and 17% for the corresponding peptide substrates. The bound peptide analogs show very similar interactions for the main-chain atoms and the conserved P1 Asp and P4 Asp, while interactions vary for P2 and P3. P2 lies in a hydrophobic S2 groove, consistent with the weaker inhibition of Ac-DMQD-Cho with polar P2 Gln. S3 is a surface hydrophilic site with favorable polar interactions with P3 Glu in Ac-DEVD-Cho. Ac-DMQD-Cho and Ac-VDVAD-Cho have hydrophobic P3 residues that are not optimal in the polar S3 site, consistent with their weaker inhibition. A hydrophobic S5 site was identified for caspase-3, where the side-chains of Phe250 and Phe252 interact with P5 Val of Ac-VDVAD-Cho, and enclose the substrate-binding site by conformational change. The kinetic importance of hydrophobic P5 residues was confirmed by more efficient hydrolysis of caspase-3 substrates Ac-VDVAD-pNA and Ac-LDVAD-pNA compared with Ac-DVAD-pNA. In contrast, caspase-7 showed less efficient hydrolysis of the substrates with P5 Val or Leu compared with Ac-DVAD-pNA. Caspase-3 and caspase-2 share similar hydrophobic S5 sites, while caspases 1, 7, 8 and 9 do not have structurally equivalent hydrophobic residues; these caspases are likely to differ in their selectivity for the P5 position of substrates. The distinct selectivity for P5 will help define the particular substrates and signaling pathways associated with each caspase.

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  1. Small Molecule Active Site Directed Tools for Studying Human Caspases. Poreba M, Szalek A, Kasperkiewicz P, Rut W, Salvesen GS, Drag M. Chem Rev 115 12546-12629 (2015)

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  2. Application of the Movable Type Free Energy Method to the Caspase-Inhibitor BindingAffinity Study. Xue S, Liu H, Zheng Z. Int J Mol Sci 20 E4850 (2019)
  3. Protocol for iterative optimization of modified peptides bound to protein targets. Ochoa R, Cossio P, Fox T. J Comput Aided Mol Des 36 825-835 (2022)


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  1. Caspase substrates and cellular remodeling. Crawford ED, Wells JA. Annu Rev Biochem 80 1055-1087 (2011)

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  1. Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity. Demon D, Van Damme P, Vanden Berghe T, Deceuninck A, Van Durme J, Verspurten J, Helsens K, Impens F, Wejda M, Schymkowitz J, Rousseau F, Madder A, Vandekerckhove J, Declercq W, Gevaert K, Vandenabeele P. Mol Cell Proteomics 8 2700-2714 (2009)
  2. Three distinct neuroprotective functions of myricetin against glutamate-induced neuronal cell death: involvement of direct inhibition of caspase-3. Shimmyo Y, Kihara T, Akaike A, Niidome T, Sugimoto H. J Neurosci Res 86 1836-1845 (2008)
  3. Plasticity of S2-S4 specificity pockets of executioner caspase-7 revealed by structural and kinetic analysis. Agniswamy J, Fang B, Weber IT. FEBS J 274 4752-4765 (2007)
  4. Degradomics reveals that cleavage specificity profiles of caspase-2 and effector caspases are alike. Wejda M, Impens F, Takahashi N, Van Damme P, Gevaert K, Vandenabeele P. J Biol Chem 287 33983-33995 (2012)
  5. Design, synthesis and evaluation of 1,2-benzisothiazol-3-one derivatives as potent caspase-3 inhibitors. Liu D, Tian Z, Yan Z, Wu L, Ma Y, Wang Q, Liu W, Zhou H, Yang C. Bioorg Med Chem 21 2960-2967 (2013)
  6. Structural basis for executioner caspase recognition of P5 position in substrates. Fu G, Chumanevich AA, Agniswamy J, Fang B, Harrison RW, Weber IT. Apoptosis 13 1291-1302 (2008)
  7. Structural and Functional Diversity of Nairovirus-Encoded Nucleoproteins. Wang W, Liu X, Wang X, Dong H, Ma C, Wang J, Liu B, Mao Y, Wang Y, Li T, Yang C, Guo Y. J Virol 89 11740-11749 (2015)
  8. Conformational similarity in the activation of caspase-3 and -7 revealed by the unliganded and inhibited structures of caspase-7. Agniswamy J, Fang B, Weber IT. Apoptosis 14 1135-1144 (2009)
  9. Structural and enzymatic insights into caspase-2 protein substrate recognition and catalysis. Tang Y, Wells JA, Arkin MR. J Biol Chem 286 34147-34154 (2011)
  10. Ursolic Acid, a Natural Nutraceutical Agent, Targets Caspase3 and Alleviates Inflammation-Associated Downstream Signal Transduction. Ma X, Zhang Y, Wang Z, Shen Y, Zhang M, Nie Q, Hou Y, Bai G. Mol Nutr Food Res 61 (2017)
  11. Glyceraldehyde-3-phosphate, a glycolytic intermediate, plays a key role in controlling cell fate via inhibition of caspase activity. Jang M, Kang HJ, Lee SY, Chung SJ, Kang S, Chi SW, Cho S, Lee SC, Lee CK, Park BC, Bae KH, Park SG. Mol Cells 28 559-563 (2009)
  12. Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling. Fang B, Fu G, Agniswamy J, Harrison RW, Weber IT. Apoptosis 14 741-752 (2009)
  13. DIDS (4,4'-Diisothiocyanatostilbene-2,2'-disulfonate) directly inhibits caspase activity in HeLa cell lysates. Benítez-Rangel E, López-Méndez MC, García L, Guerrero-Hernández A. Cell Death Discov 1 15037 (2015)
  14. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces. Haider K, Wickstrom L, Ramsey S, Gilson MK, Kurtzman T. J Phys Chem B 120 8743-8756 (2016)
  15. Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories. Haider K, Cruz A, Ramsey S, Gilson MK, Kurtzman T. J Chem Theory Comput 14 418-425 (2018)
  16. A new technique for real-time analysis of caspase-3 dependent neuronal cell death. Golbs A, Heck N, Luhmann HJ. J Neurosci Methods 161 234-243 (2007)
  17. Phage display and structural studies reveal plasticity in substrate specificity of caspase-3a from zebrafish. Tucker MB, MacKenzie SH, Maciag JJ, Dirscherl Ackerman H, Swartz P, Yoder JA, Hamilton PT, Clay Clark A. Protein Sci 25 2076-2088 (2016)
  18. Letter MerCASBA: an updated and refined database of caspase substrates. Fridman A, Pak I, Butts BD, Hoek M, Nicholson DW, Mehmet H. Apoptosis 18 369-371 (2013)
  19. Secretory lysosomes of mouse mast cells store and exocytose active caspase-3 in a strictly granzyme B dependent manner. Zorn CN, Pardo J, Martin P, Kuhny M, Simon MM, Huber M. Eur J Immunol 43 3209-3218 (2013)
  20. Ursolic acid reduces hepatocellular apoptosis and alleviates alcohol-induced liver injury via irreversible inhibition of CASP3 in vivo. Ma XY, Zhang M, Fang G, Cheng CJ, Wang MK, Han YM, Hou XT, Hao EW, Hou YY, Bai G. Acta Pharmacol Sin 42 1101-1110 (2021)
  21. Autoantibody against caspase-3, an executioner of apoptosis, in patients with systemic sclerosis. Okazaki S, Ogawa F, Iwata Y, Hara T, Muroi E, Komura K, Takenaka M, Shimizu K, Hasegawa M, Fujimoto M, Sato S. Rheumatol Int 30 871-878 (2010)
  22. Synthesis, enzymatic evaluation, and docking studies of fluorogenic caspase 8 tetrapeptide substrates. Reszka P, Schulz R, Methling K, Lalk M, Bednarski PJ. ChemMedChem 5 103-117 (2010)
  23. Development of a protease activity assay using heat-sensitive Tus-GFP fusion protein substrates. Askin SP, Morin I, Schaeffer PM. Anal Biochem 415 126-133 (2011)
  24. Human caspase-3 inhibition by Z-tLeu-Asp-H: tLeu(P2) counterbalances Asp(P4) and Glu(P3) specific inhibitor truncation. Colantonio P, Leboffe L, Bolli A, Marino M, Ascenzi P, Luisi G. Biochem Biophys Res Commun 377 757-762 (2008)
  25. Designing caspase-3 sensors for imaging of apoptosis in living cells. Chen N, Huang Y, Yang L, Liu R, Yang JJ. Chemistry 15 9311-9314 (2009)
  26. Structure-Based Design and Biological Evaluation of Novel Caspase-2 Inhibitors Based on the Peptide AcVDVAD-CHO and the Caspase-2-Mediated Tau Cleavage Sequence YKPVD314. Bresinsky M, Strasser JM, Vallaster B, Liu P, McCue WM, Fuller J, Hubmann A, Singh G, Nelson KM, Cuellar ME, Wilmot CM, Finzel BC, Ashe KH, Walters MA, Pockes S. ACS Pharmacol Transl Sci 5 20-40 (2022)
  27. Ac-tLeu-Asp-H is the minimal and highly effective human caspase-3 inhibitor: biological and in silico studies. Ferrucci A, Leboffe L, Agamennone M, Di Pizio A, Fiocchetti M, Marino M, Ascenzi P, Luisi G. Amino Acids 47 153-162 (2015)
  28. Biochemical characterization of a Caspase-3 far-red fluorescent probe for non-invasive optical imaging of neuronal apoptosis. Jolivel V, Arthaud S, Botia B, Portal C, Delest B, Clavé G, Leprince J, Romieu A, Renard PY, Touzani O, Ligeret H, Noack P, Massonneau M, Fournier A, Vaudry H, Vaudry D. J Mol Neurosci 54 451-462 (2014)
  29. Comparison of S-nitrosoglutathione- and staurosporine-induced apoptosis in human neural cells. Sodja C, Ribecco-Lutkiewicz M, Haukenfrers J, Merchant F, Costain WJ, Bani-Yaghoub M. Can J Physiol Pharmacol 92 1001-1011 (2014)
  30. Endogenous Hydrogen Sulfide Persulfidates Caspase-3 at Cysteine 163 to Inhibit Doxorubicin-Induced Cardiomyocyte Apoptosis. Ye X, Li Y, Lv B, Qiu B, Zhang S, Peng H, Kong W, Tang C, Huang Y, Du J, Jin H. Oxid Med Cell Longev 2022 6153772 (2022)
  31. PE-only/PE_PGRS proteins of Mycobacterium tuberculosis contain a conserved tetra-peptide sequence DEVS/DXXS that is a potential caspase-3 cleavage motif. Bachhawat N. J Biosci 43 597-604 (2018)
  32. Compressed images for affinity prediction-2 (CIFAP-2): an improved machine learning methodology on protein-ligand interactions based on a study on caspase 3 inhibitors. Erdas O, Andac CA, Gurkan-Alp AS, Alpaslan FN, Buyukbingol E. J Enzyme Inhib Med Chem 30 809-815 (2015)
  33. Design, synthesis, and in vitro evaluation of aza-peptide aldehydes and ketones as novel and selective protease inhibitors. Corrigan TS, Lotti Diaz LM, Border SE, Ratigan SC, Kasper KQ, Sojka D, Fajtova P, Caffrey CR, Salvesen GS, McElroy CA, Hadad CM, Doğan Ekici Ö. J Enzyme Inhib Med Chem 35 1387-1402 (2020)
  34. Genuine selective caspase-2 inhibition with new irreversible small peptidomimetics. Bosc E, Anastasie J, Soualmia F, Coric P, Kim JY, Wang LQ, Lacin G, Zhao K, Patel R, Duplus E, Tixador P, Sproul AA, Brugg B, Reboud-Ravaux M, Troy CM, Shelanski ML, Bouaziz S, Karin M, El Amri C, Jacotot ED. Cell Death Dis 13 959 (2022)
  35. Inhibitor-3 inhibits Protein Phosphatase 1 via a metal binding dynamic protein-protein interaction. Srivastava G, Choy MS, Bolik-Coulon N, Page R, Peti W. Nat Commun 14 1798 (2023)
  36. TNF-α-Mediated Endothelial Cell Apoptosis Is Rescued by Hydrogen Sulfide. Diaz Sanchez L, Sanchez-Aranguren L, Wang K, Spickett CM, Griffiths HR, Dias IHK. Antioxidants (Basel) 12 734 (2023)


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