메뉴 건너뛰기




Volumn 84, Issue 4, 2003, Pages 2207-2215

Molecular dynamics studies of caspase-3

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE 3; DIMER;

EID: 0037380948     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)75026-7     Document Type: Article
Times cited : (34)

References (64)
  • 4
    • 0034662749 scopus 로고    scopus 로고
    • A target within the target: Probing cruzain's P1' site to define structural determinants for the Chagas' disease protease
    • Brinen, L. S., E. Hansell, J. Cheng, W. R. Roush, J. H. McKerrow, and R. J. Fletterick. 2000. A target within the target: probing cruzain's P1' site to define structural determinants for the Chagas' disease protease. Struct. Fold. Des. 8:831-840.
    • (2000) Struct. Fold. Des. , vol.8 , pp. 831-840
    • Brinen, L.S.1    Hansell, E.2    Cheng, J.3    Roush, W.R.4    McKerrow, J.H.5    Fletterick, R.J.6
  • 5
    • 0030836641 scopus 로고    scopus 로고
    • The essential dynamics of Cu, Zn superoxide dismutase: Suggestion of intersubunit communication
    • Chillemi, G., M. Falconi, A. Amadei, G. Zimatore, A. Desideri, and A. Di Nola. 1997. The essential dynamics of Cu, Zn superoxide dismutase: suggestion of intersubunit communication. Biophys. J. 73:1007-1018.
    • (1997) Biophys. J. , vol.73 , pp. 1007-1018
    • Chillemi, G.1    Falconi, M.2    Amadei, A.3    Zimatore, G.4    Desideri, A.5    Di Nola, A.6
  • 6
    • 0030931876 scopus 로고    scopus 로고
    • Caspases: The executioners of apoptosis
    • Cohen, G. M. 1997. Caspases: the executioners of apoptosis. Biochem. J. 326:1-16.
    • (1997) Biochem. J. , vol.326 , pp. 1-16
    • Cohen, G.M.1
  • 7
    • 0032500552 scopus 로고    scopus 로고
    • Conversion of procaspase-3 to an autoactivating caspase by fusion to the caspase-2 prodomain
    • Colussi, P. A., N. L. Harvey, L. M. Shearwin-Whyatt, and S. Kumar. 1998. Conversion of procaspase-3 to an autoactivating caspase by fusion to the caspase-2 prodomain. J. Biol. Chem. 273:26566-26570.
    • (1998) J. Biol. Chem. , vol.273 , pp. 26566-26570
    • Colussi, P.A.1    Harvey, N.L.2    Shearwin-Whyatt, L.M.3    Kumar, S.4
  • 8
    • 0029902382 scopus 로고    scopus 로고
    • Structure of human procathepsin L reveals the molecular basis of inhibition by the prosegment
    • Coulombe, R., P. Grochulski, J. Sivaraman, R. Menard, J. S. Mort, and M. Cygler. 1996. Structure of human procathepsin L reveals the molecular basis of inhibition by the prosegment. EMBO J. 15:5492-5503.
    • (1996) EMBO J. , vol.15 , pp. 5492-5503
    • Coulombe, R.1    Grochulski, P.2    Sivaraman, J.3    Menard, R.4    Mort, J.S.5    Cygler, M.6
  • 9
    • 0029818017 scopus 로고    scopus 로고
    • The consistency of large concerted motions in proteins in molecular dynamics simulations
    • de Groot, B. L., D. M. van Aalten, A. Amadei, and H. J. Berendsen. 1996. The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophys. J. 71:1707-1713.
    • (1996) Biophys. J. , vol.71 , pp. 1707-1713
    • De Groot, B.L.1    Van Aalten, D.M.2    Amadei, A.3    Berendsen, H.J.4
  • 11
    • 0031888955 scopus 로고    scopus 로고
    • A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD
    • Enari, M., H. Sakahira, H. Yokoyama, K. Okawa, A. Iwamatsu, and S. Nagata. 1998. A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD. Nature. 391:43-50.
    • (1998) Nature , vol.391 , pp. 43-50
    • Enari, M.1    Sakahira, H.2    Yokoyama, H.3    Okawa, K.4    Iwamatsu, A.5    Nagata, S.6
  • 12
    • 0031736958 scopus 로고    scopus 로고
    • Three-dimensional structures of the cysteine proteases cathepsins K and S deduced by knowledge-based modelling and active site characteristics
    • Fengler, A., and W. Brandt. 1998. Three-dimensional structures of the cysteine proteases cathepsins K and S deduced by knowledge-based modelling and active site characteristics. Protein Eng. 11:1007-1013.
    • (1998) Protein Eng. , vol.11 , pp. 1007-1013
    • Fengler, A.1    Brandt, W.2
  • 14
    • 0033181018 scopus 로고    scopus 로고
    • Conformational dynamics of cytochrome c: Correlation to hydrogen exchange
    • Garcia, A. E., and G. Hummer. 1999. Conformational dynamics of cytochrome c: correlation to hydrogen exchange. Proteins. 36:175-191.
    • (1999) Proteins , vol.36 , pp. 175-191
    • Garcia, A.E.1    Hummer, G.2
  • 15
    • 0030841381 scopus 로고    scopus 로고
    • Structural determinants of specificity in the cysteine protease cruzain
    • Gillmor, S. A., C. S. Craik, and R. J. Fletterick. 1997. Structural determinants of specificity in the cysteine protease cruzain. Protein Sci. 6:1603-1611.
    • (1997) Protein Sci. , vol.6 , pp. 1603-1611
    • Gillmor, S.A.1    Craik, C.S.2    Fletterick, R.J.3
  • 16
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
    • Gilson, M. K., and B. Honig. 1988. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins. 4:7-18.
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 17
    • 0032518496 scopus 로고    scopus 로고
    • Crystal structure of porcine cathepsin H determined at 2.1 Å resolution: Location of the mini-chain C-terminal carboxyl group defines cathepsin H aminopeptidase function
    • Guncar, G., M. Podobnik, J. Pungercar, B. Strukelj, V. Turk, and D. Turk. 1998. Crystal structure of porcine cathepsin H determined at 2.1 Å resolution: location of the mini-chain C-terminal carboxyl group defines cathepsin H aminopeptidase function. Structure. 6:51-61.
    • (1998) Structure , vol.6 , pp. 51-61
    • Guncar, G.1    Podobnik, M.2    Pungercar, J.3    Strukelj, B.4    Turk, V.5    Turk, D.6
  • 18
    • 0039547996 scopus 로고    scopus 로고
    • Crystal structure of MHC class H-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S
    • Guncar, G., G. Pungercic, I. Klemencic, V. Turk, and D. Turk. 1999. Crystal structure of MHC class H-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S. EMBO J. 18:793-803.
    • (1999) EMBO J. , vol.18 , pp. 793-803
    • Guncar, G.1    Pungercic, G.2    Klemencic, I.3    Turk, V.4    Turk, D.5
  • 19
    • 0035831022 scopus 로고    scopus 로고
    • Structural basis of caspase inhibition by XIAP: Differential roles of the linker versus the BIR domain
    • Huang, Y., Y. C. Park, R. L. Rich, D. Segal, D. G. Myszka, and H. Wu. 2001. Structural basis of caspase inhibition by XIAP: differential roles of the linker versus the BIR domain. Cell. 104:781-790.
    • (2001) Cell , vol.104 , pp. 781-790
    • Huang, Y.1    Park, Y.C.2    Rich, R.L.3    Segal, D.4    Myszka, D.G.5    Wu, H.6
  • 20
    • 0038080491 scopus 로고    scopus 로고
    • Optimal charge-shaping functions for the particle-particle-particle-mesh (P3M) method for computing electrostatic interactions in molecular simulations
    • Hunenberger, P. 2000. Optimal charge-shaping functions for the particle-particle-particle-mesh (P3M) method for computing electrostatic interactions in molecular simulations. J. Chem. Phys. 113:10464-10476.
    • (2000) J. Chem. Phys. , vol.113 , pp. 10464-10476
    • Hunenberger, P.1
  • 21
    • 0028968184 scopus 로고
    • Crystal structures of recombinant rat cathepsin B and a cathepsin B- inhibitor complex. Implications for structure-based inhibitor design
    • Jia, Z., S. Hasnain, T. Hirama, X. Lee, J. S. Mort, R. To, and C. P. Huber. 1995. Crystal structures of recombinant rat cathepsin B and a cathepsin B- inhibitor complex. Implications for structure-based inhibitor design. J. Biol. Chem. 270:5527-5533.
    • (1995) J. Biol. Chem. , vol.270 , pp. 5527-5533
    • Jia, Z.1    Hasnain, S.2    Hirama, T.3    Lee, X.4    Mort, J.S.5    To, R.6    Huber, C.P.7
  • 22
    • 0031011721 scopus 로고    scopus 로고
    • Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 Å resolution
    • Johnston, S. C., C. N. Larsen, W. J. Cook, K. D. Wilkinson, and C. P. Hill. 1997. Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 Å resolution. EMBO J. 16:3787-3796.
    • (1997) EMBO J. , vol.16 , pp. 3787-3796
    • Johnston, S.C.1    Larsen, C.N.2    Cook, W.J.3    Wilkinson, K.D.4    Hill, C.P.5
  • 23
    • 0033565867 scopus 로고    scopus 로고
    • Structural basis for the specificity of ubiquitin C-terminal hydrolases
    • Johnston, S. C., S. M. Riddle, R. E. Cohen, and C. P. Hill. 1999. Structural basis for the specificity of ubiquitin C-terminal hydrolases. EMBO J. 18:3877-3887.
    • (1999) EMBO J. , vol.18 , pp. 3877-3887
    • Johnston, S.C.1    Riddle, S.M.2    Cohen, R.E.3    Hill, C.P.4
  • 25
  • 26
    • 0033773114 scopus 로고    scopus 로고
    • Apoptosis in cancer: Cause and cure
    • Kaufmann, S. H., and G. J. Gores. 2000. Apoptosis in cancer: cause and cure. Bioessays. 22:1007-1017.
    • (2000) Bioessays , vol.22 , pp. 1007-1017
    • Kaufmann, S.H.1    Gores, G.J.2
  • 27
    • 0028102478 scopus 로고
    • Cleavage of poly(ADP-ribose) polymerase by a proteinase with properties like ICE
    • Lazebnik, Y. A., S. H. Kaufmann, S. Desnoyers, G. G. Poirier, and W. C. Eamshaw. 1994. Cleavage of poly(ADP-ribose) polymerase by a proteinase with properties like ICE. Nature. 371:346-347.
    • (1994) Nature , vol.371 , pp. 346-347
    • Lazebnik, Y.A.1    Kaufmann, S.H.2    Desnoyers, S.3    Poirier, G.G.4    Eamshaw, W.C.5
  • 30
    • 0035789518 scopus 로고    scopus 로고
    • Gromacs 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., B. Hess, and D. van der Spoel. 2001. Gromacs 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Mod. 7:306-317.
    • (2001) J. Mol. Mod. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van der Spoel, D.3
  • 31
    • 0030916417 scopus 로고    scopus 로고
    • DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis
    • Liu, X., H. Zou, C. Slaughter, and X. Wang. 1997. DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis. Cell. 89:175-184.
    • (1997) Cell , vol.89 , pp. 175-184
    • Liu, X.1    Zou, H.2    Slaughter, C.3    Wang, X.4
  • 33
    • 12044253640 scopus 로고
    • The refined 2.15 Å X-ray crystal structure of human liver cathepsin B: The structural basis for its specificity
    • Musil, D., D. Zucic, D. Turk, R. A. Engh, I. Mayr, R. Huber, T. Popovic, V. Turk, T. Towatari, N. Katunuma, et al. 1991. The refined 2.15 Å X-ray crystal structure of human liver cathepsin B: the structural basis for its specificity. EMBO J. 10:2321-2330.
    • (1991) EMBO J. , vol.10 , pp. 2321-2330
    • Musil, D.1    Zucic, D.2    Turk, D.3    Engh, R.A.4    Mayr, I.5    Huber, R.6    Popovic, T.7    Turk, V.8    Towatari, T.9    Katunuma, N.10
  • 37
    • 0036306459 scopus 로고    scopus 로고
    • Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease
    • Piana, S., P. Carloni, and M. Parrinello. 2002. Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. J. Mol. Biol. 319:567-83.
    • (2002) J. Mol. Biol. , vol.319 , pp. 567-583
    • Piana, S.1    Carloni, P.2    Parrinello, M.3
  • 38
    • 0344142396 scopus 로고    scopus 로고
    • Emerging roles of caspase-3 in apoptosis
    • Porter, A. G., and R. U. Janicke. 1999. Emerging roles of caspase-3 in apoptosis. Cell Death Differ. 6:99-104.
    • (1999) Cell Death Differ. , vol.6 , pp. 99-104
    • Porter, A.G.1    Janicke, R.U.2
  • 39
    • 0033955055 scopus 로고    scopus 로고
    • Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase
    • Radkiewicz, J., and C. Brooks. 2000. Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase. J. Am. Chem. Soc. 122:225-231.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 225-231
    • Radkiewicz, J.1    Brooks, C.2
  • 44
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 45
    • 0030702084 scopus 로고    scopus 로고
    • Caspases: Intracellular signaling by proteolysis
    • Salvesen, G. S., and V. M. Dixit. 1997. Caspases: intracellular signaling by proteolysis. Cell. 91:443-446.
    • (1997) Cell , vol.91 , pp. 443-446
    • Salvesen, G.S.1    Dixit, V.M.2
  • 46
    • 0034018813 scopus 로고    scopus 로고
    • Apoptosis in Alzheimer's disease - An update
    • Shimohama, S. 2000. Apoptosis in Alzheimer's disease - an update. Apoptosis. 5:9-16.
    • (2000) Apoptosis , vol.5 , pp. 9-16
    • Shimohama, S.1
  • 47
    • 0030881603 scopus 로고    scopus 로고
    • Biochemical characteristics of caspases-3, -6, -7, and -8
    • Stennicke, H. R., and G. S. Salvesen. 1997. Biochemical characteristics of caspases-3, -6, -7, and -8. J. Biol. Chem. 272:25719-25723.
    • (1997) J. Biol. Chem. , vol.272 , pp. 25719-25723
    • Stennicke, H.R.1    Salvesen, G.S.2
  • 50
    • 0034618635 scopus 로고    scopus 로고
    • Caspases as targets for anti-inflammatory and anti-apoptotic drug discovery
    • Talanian, R. V., K. D. Brady, and V. L. Cryns. 2000. Caspases as targets for anti-inflammatory and anti-apoptotic drug discovery. J. Med. Chem. 43:3351-3371.
    • (2000) J. Med. Chem. , vol.43 , pp. 3351-3371
    • Talanian, R.V.1    Brady, K.D.2    Cryns, V.L.3
  • 53
    • 0028908350 scopus 로고
    • Crystal structure of cathepsin B inhibited with CA030 at 2.0-A resolution: A basis for the design of specific epoxysuccinyl inhibitors
    • Turk, D., M. Podobnik, T. Popovic, N. Katunuma, W. Bode, R. Huber, and V. Turk. 1995. Crystal structure of cathepsin B inhibited with CA030 at 2.0-A resolution: a basis for the design of specific epoxysuccinyl inhibitors. Biochemistry. 34:4791-4797.
    • (1995) Biochemistry , vol.34 , pp. 4791-4797
    • Turk, D.1    Podobnik, M.2    Popovic, T.3    Katunuma, N.4    Bode, W.5    Huber, R.6    Turk, V.7
  • 60
    • 0035932465 scopus 로고    scopus 로고
    • Covalent inhibition revealed by the crystal structure of the caspase- 8/p35 complex
    • Xu, G., M. Cirilli, Y. Huang, R. L. Rich, D. G. Myszka, and H. Wu. 2001. Covalent inhibition revealed by the crystal structure of the caspase- 8/p35 complex. Nature. 410:494-497.
    • (2001) Nature , vol.410 , pp. 494-497
    • Xu, G.1    Cirilli, M.2    Huang, Y.3    Rich, R.L.4    Myszka, D.G.5    Wu, H.6
  • 61
    • 0034007762 scopus 로고    scopus 로고
    • Substrate specificity of bovine cathepsin B and its inhibition by CA074, based on crystal structure refinement of the complex
    • Yamamoto, A., K. Tomoo, T. Hara, M. Murata, K. Kitamura, and T. Ishida. 2000. Substrate specificity of bovine cathepsin B and its inhibition by CA074, based on crystal structure refinement of the complex. J. Biochem. (Tokyo). 127:635-643.
    • (2000) J. Biochem. (Tokyo) , vol.127 , pp. 635-643
    • Yamamoto, A.1    Tomoo, K.2    Hara, T.3    Murata, M.4    Kitamura, K.5    Ishida, T.6
  • 63
    • 0031615875 scopus 로고    scopus 로고
    • Autoproteolytic activation of pro-caspases by oligomerization
    • Yang, X., H. Y. Chang, and D. Baltimore. 1998. Autoproteolytic activation of pro-caspases by oligomerization. Mol. Cell. 1:319-325.
    • (1998) Mol. Cell , vol.1 , pp. 319-325
    • Yang, X.1    Chang, H.Y.2    Baltimore, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.