메뉴 건너뛰기




Volumn 31, Issue 3, 2007, Pages 186-195

Why does β-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies

Author keywords

Drug design; Free energy; Homolgy modeling; MM PBSA; Steered MD

Indexed keywords

DRUG DESIGN; HOMOLGY MODELING; MM-PBSA; STEERED MD;

EID: 34248513174     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2007.03.007     Document Type: Article
Times cited : (9)

References (57)
  • 1
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
    • Bayly C.I., Cieplak P., Cornell W.D., and Kollman P.A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 97 (1993) 10269-10280
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 2
    • 0035815635 scopus 로고    scopus 로고
    • Post-translational processing of beta-secretase (beta-amyloid-converting enzyme) and its ectodomain shedding. The pro- and transmembrane/cytosolic domains affect its cellular activity and amyloid-beta production
    • Benjannet S., Elagoz A., Wickham L., Mamarbachi M., Munzer J.S., Basak A., Lazure C., Cromlish J.A., Sisodia S., Checler F., Chretien M., and Seidah N.G. Post-translational processing of beta-secretase (beta-amyloid-converting enzyme) and its ectodomain shedding. The pro- and transmembrane/cytosolic domains affect its cellular activity and amyloid-beta production. J. Biol. Chem. 276 (2001) 10879-10887
    • (2001) J. Biol. Chem. , vol.276 , pp. 10879-10887
    • Benjannet, S.1    Elagoz, A.2    Wickham, L.3    Mamarbachi, M.4    Munzer, J.S.5    Basak, A.6    Lazure, C.7    Cromlish, J.A.8    Sisodia, S.9    Checler, F.10    Chretien, M.11    Seidah, N.G.12
  • 4
    • 0029633168 scopus 로고
    • GROMACS: a message-passing parallel molecular dynamics implementation
    • Berendsen H.J.C., van der Spoel D., and van Drunen R. GROMACS: a message-passing parallel molecular dynamics implementation. Comp. Phys. Commun. 91 (1995) 43-56
    • (1995) Comp. Phys. Commun. , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    van der Spoel, D.2    van Drunen, R.3
  • 6
    • 34248530580 scopus 로고    scopus 로고
    • Case, D.A., Darden, T.A., Cheatham, T.E., Simmerling, C.L., Wang, J., Duke, R.E., Luo, R., Merz, K.M., Pearlman, D.A., Crowley, M., Walker, R.C., Zhang, W., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Wong, K.F., Paesani, F., Wu, X., Brozell, S., Tsui, V., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Beroza, P., Mathews, D.H., Schafmeister, C., Ross, W.S., Kollman, P.A., 2006. AMBER 9, University of California, San Francisco.
  • 7
    • 0033405041 scopus 로고    scopus 로고
    • Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7
    • Chong L.T., Duan Y., Wang L., Massova I., and Kollman P.A. Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 14330-14335
    • (1999) Proc. Natl. Acad. Sci. U. S. A. , vol.96 , pp. 14330-14335
    • Chong, L.T.1    Duan, Y.2    Wang, L.3    Massova, I.4    Kollman, P.A.5
  • 8
    • 0036079733 scopus 로고    scopus 로고
    • Prediction of the tertiary structure of the beta-secretase zymogen
    • Chou K.C., and Howe W.J. Prediction of the tertiary structure of the beta-secretase zymogen. Biochem. Biophys. Res. Commun. 292 (2002) 702-708
    • (2002) Biochem. Biophys. Res. Commun. , vol.292 , pp. 702-708
    • Chou, K.C.1    Howe, W.J.2
  • 9
    • 0027180507 scopus 로고
    • Verification of protein structures: patterns of nonbonded atomic interactions
    • Colovos C., and Yeates T.O. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 2 (1993) 1511-1519
    • (1993) Protein Sci. , vol.2 , pp. 1511-1519
    • Colovos, C.1    Yeates, T.O.2
  • 11
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald: An N log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 12
    • 0034633995 scopus 로고    scopus 로고
    • Proteolytic activation of recombinant pro-memapsin 2 (pro-beta-secretase) studied with new fluorogenic substrates
    • Ermolieff J., Loy J.A., Koelsch G., and Tang J. Proteolytic activation of recombinant pro-memapsin 2 (pro-beta-secretase) studied with new fluorogenic substrates. Biochemistry 39 (2000) 12450-12456
    • (2000) Biochemistry , vol.39 , pp. 12450-12456
    • Ermolieff, J.1    Loy, J.A.2    Koelsch, G.3    Tang, J.4
  • 14
    • 0029062769 scopus 로고
    • Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces
    • Evans E., Ritchie K., and Merkel R. Sensitive force technique to probe molecular adhesion and structural linkages at biological interfaces. Biophys. J. 68 (1995) 2580-2587
    • (1995) Biophys. J. , vol.68 , pp. 2580-2587
    • Evans, E.1    Ritchie, K.2    Merkel, R.3
  • 16
    • 0036263257 scopus 로고    scopus 로고
    • Beta-secretase as a therapeutic target for inhibitor drugs
    • Ghosh A.K., Hong L., and Tang J. Beta-secretase as a therapeutic target for inhibitor drugs. Curr. Med. Chem. 9 (2002) 1135-1144
    • (2002) Curr. Med. Chem. , vol.9 , pp. 1135-1144
    • Ghosh, A.K.1    Hong, L.2    Tang, J.3
  • 17
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S., and Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U. S. A. 89 (1992) 10915-10919
    • (1992) Proc. Natl. Acad. Sci. U. S. A. , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 22
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B., and Nicholls A. Classical electrostatics in biology and chemistry. Science 268 (1995) 1144-1149
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 24
    • 0026005186 scopus 로고
    • Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism
    • Hyland L.J., Tomaszek Jr. T.A., and Meek T.D. Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism. Biochemistry 30 (1991) 8454-8463
    • (1991) Biochemistry , vol.30 , pp. 8454-8463
    • Hyland, L.J.1    Tomaszek Jr., T.A.2    Meek, T.D.3
  • 25
    • 0026325601 scopus 로고
    • Kinetic studies of human immunodeficiency virus type 1 protease and its active-site hydrogen bond mutant A28S
    • Ido E., Han H.P., Kezdy F.J., and Tang J. Kinetic studies of human immunodeficiency virus type 1 protease and its active-site hydrogen bond mutant A28S. J. Biol. Chem. 266 (1991) 24359-24366
    • (1991) J. Biol. Chem. , vol.266 , pp. 24359-24366
    • Ido, E.1    Han, H.P.2    Kezdy, F.J.3    Tang, J.4
  • 27
    • 0000243829 scopus 로고
    • PROCHECK-a program to check the stereochemical quality of protein structures
    • Laskowski R.A., MacArthur M.W., Moss D.S., and Thomton J.M. PROCHECK-a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thomton, J.M.4
  • 29
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Luthy R., Bowie J.U., and Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 356 (1992) 83-85
    • (1992) Nature , vol.356 , pp. 83-85
    • Luthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 30
    • 0033568644 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies
    • Massova I., and Kollman P.A. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 121 (1999) 8133-8143
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 32
    • 0022522422 scopus 로고
    • Calculation of electrostatic interactions in proteins
    • Matthew J.B., and Gurd F.R. Calculation of electrostatic interactions in proteins. Methods Enzymol. 130 (1986) 413-436
    • (1986) Methods Enzymol. , vol.130 , pp. 413-436
    • Matthew, J.B.1    Gurd, F.R.2
  • 34
    • 0037083363 scopus 로고    scopus 로고
    • Essential domain motions in barnase revealed by MD simulations
    • Nolde S.B., Arseniev A.S., Orekhov V.Y., and Billeter M. Essential domain motions in barnase revealed by MD simulations. Proteins 46 (2002) 250-258
    • (2002) Proteins , vol.46 , pp. 250-258
    • Nolde, S.B.1    Arseniev, A.S.2    Orekhov, V.Y.3    Billeter, M.4
  • 36
    • 0033609449 scopus 로고    scopus 로고
    • Cleavage of Alzheimer's amyloid precursor protein by alpha-secretase occurs at the surface of neuronal cells
    • Parvathy S., Hussain I., Karran E.H., Turner A.J., and Hooper N.M. Cleavage of Alzheimer's amyloid precursor protein by alpha-secretase occurs at the surface of neuronal cells. Biochemistry 38 (1999) 9728-9734
    • (1999) Biochemistry , vol.38 , pp. 9728-9734
    • Parvathy, S.1    Hussain, I.2    Karran, E.H.3    Turner, A.J.4    Hooper, N.M.5
  • 37
    • 0033988141 scopus 로고    scopus 로고
    • Four companies announce discovery of beta-secretase gene
    • Phimister B. Four companies announce discovery of beta-secretase gene. Nat. Biotechnol. 18 (2000) 16
    • (2000) Nat. Biotechnol. , vol.18 , pp. 16
    • Phimister, B.1
  • 38
    • 0036008530 scopus 로고    scopus 로고
    • Role of water molecules in the structure and function of aspartic proteinases
    • Prasad B.V., and Suguna K. Role of water molecules in the structure and function of aspartic proteinases. Acta. Crystallogr. D Biol. Crystallogr. 58 (2002) 250-259
    • (2002) Acta. Crystallogr. D Biol. Crystallogr. , vol.58 , pp. 250-259
    • Prasad, B.V.1    Suguna, K.2
  • 39
    • 0036467174 scopus 로고    scopus 로고
    • Dynamic and structural analysis of isotropically distributed molecular ensembles
    • Prompers J.J., and Bruschweiler R. Dynamic and structural analysis of isotropically distributed molecular ensembles. Proteins 46 (2002) 177-189
    • (2002) Proteins , vol.46 , pp. 177-189
    • Prompers, J.J.1    Bruschweiler, R.2
  • 41
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: an efficient way to compute molecular surfaces
    • Sanner M.F., Olson A.J., and Spehner J.C. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38 (1996) 305-320
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 42
    • 0033600274 scopus 로고    scopus 로고
    • Translating cell biology into therapeutic advances in Alzheimer's disease
    • Selkoe D.J. Translating cell biology into therapeutic advances in Alzheimer's disease. Nature 399 (1999) A23-A31
    • (1999) Nature , vol.399
    • Selkoe, D.J.1
  • 43
    • 0034701238 scopus 로고    scopus 로고
    • The origins of Alzheimer disease: a is for amyloid
    • Selkoe D.J. The origins of Alzheimer disease: a is for amyloid. JAMA 283 (2000) 1615-1617
    • (2000) JAMA , vol.283 , pp. 1615-1617
    • Selkoe, D.J.1
  • 45
    • 0025768248 scopus 로고
    • Refined structure of porcine pepsinogen at 1.8 Å resolution
    • Sielecki A.R., Fujinaga M., Read R.J., and James M.N. Refined structure of porcine pepsinogen at 1.8 Å resolution. J. Mol. Biol. 219 (1991) 671-692
    • (1991) J. Mol. Biol. , vol.219 , pp. 671-692
    • Sielecki, A.R.1    Fujinaga, M.2    Read, R.J.3    James, M.N.4
  • 46
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff D., Sharp K.A., and Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98 (1994) 1978-1988
    • (1994) J. Phys. Chem. , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 47
    • 0032560959 scopus 로고    scopus 로고
    • Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices
    • Srinivasan J., Cheatham T.E., Cieplak P., Kollman P.A., and Case D.A. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices. J. Am. Chem. Soc. 120 (1998) 9401-9409
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 50
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids. Res. 22 (1994) 4673-4680
    • (1994) Nucleic Acids. Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 51
    • 0346216028 scopus 로고    scopus 로고
    • Principal components of the protein dynamical transition
    • Tournier A.L., and Smith J.C. Principal components of the protein dynamical transition. Phys. Rev. Lett. 91 (2003) 208106
    • (2003) Phys. Rev. Lett. , vol.91 , pp. 208106
    • Tournier, A.L.1    Smith, J.C.2
  • 54
    • 34248591561 scopus 로고    scopus 로고
    • Van der Spoel, D., van Buuren, A.R., Apol, E., Meulenhoff, P.J., Tieleman, D.P., Sijbers, A.L., Hess, B., Feenstra, K.A., Lindahl, E., van Drunen, R., Berendsen, H.J.C., 2002. Gromacs User Manual, Version 3.1. Nijenborgh, AG Groningen, The Netherlands. Internet: www.gromacs.org.
  • 55
    • 0030256107 scopus 로고    scopus 로고
    • Molecular dynamics simulations of peptides from BPTI: a closer look at amide-aromatic interactions
    • Van der Spoel D., van Buuren A.R., Tieleman D.P., and Berendsen H.J. Molecular dynamics simulations of peptides from BPTI: a closer look at amide-aromatic interactions. J. Biomol. NMR 8 (1996) 229-238
    • (1996) J. Biomol. NMR , vol.8 , pp. 229-238
    • Van der Spoel, D.1    van Buuren, A.R.2    Tieleman, D.P.3    Berendsen, H.J.4
  • 57
    • 0041691306 scopus 로고    scopus 로고
    • How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations
    • Xu Y., Shen J., Luo X., Silman I., Sussman J.L., Chen K., and Jiang H. How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations. J. Am. Chem. Soc. 125 (2003) 11340-11349
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 11340-11349
    • Xu, Y.1    Shen, J.2    Luo, X.3    Silman, I.4    Sussman, J.L.5    Chen, K.6    Jiang, H.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.