메뉴 건너뛰기




Volumn 15, Issue 4, 2010, Pages 2730-2748

MMPBSA decomposition of the binding energy throughout a molecular dynamics simulation of amyloid-beta (Aß10-35) aggregation

Author keywords

Alzheimer's disease; Amyloid beta (A ) peptides; Binding free energy calculations; Dimerization; Kepler scientific workflow; Replica exchange molecular dynamics (REMD)

Indexed keywords

AMYLOID BETA PROTEIN; AMYLOID BETA PROTEIN (10 35); AMYLOID BETA-PROTEIN (10-35); PEPTIDE FRAGMENT;

EID: 77951841239     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules15042730     Document Type: Article
Times cited : (33)

References (40)
  • 1
    • 0347717736 scopus 로고    scopus 로고
    • Modulation of β-amyloid metabolism by non-steroidal anti-inflammatory drugs in neuronal cell cultures
    • Gasparini, L.; Rusconi, L.; Huaxi, X.; Del Soldato, P.; Ongini, E. Modulation β-Amyloid metabolism by non-steroidal antiinflammatory drugs in neuronal cell cultures. J. Neurochem. 2004, 88, 337?348. (Pubitemid 38084550)
    • (2004) Journal of Neurochemistry , vol.88 , Issue.2 , pp. 337-348
    • Gasparini, L.1    Rusconi, L.2    Xu, H.3    Del Soldato, P.4    Ongini, E.5
  • 3
    • 0033927533 scopus 로고    scopus 로고
    • Cyclo-oxygenase-2 inhibitors. Rationale and therapeutic potential for Alzheimer's disease
    • McGeer, P.L. Cyclooxygenase-2 inhibitors rationales and therapeutic potential for Alzheimer's disease. Drugs Aging 2000, 17, 1-11. (Pubitemid 30459477)
    • (2000) Drugs and Aging , vol.17 , Issue.1 , pp. 1-11
    • McGeer, P.L.1
  • 4
    • 39649124929 scopus 로고    scopus 로고
    • Designing peptide inhibitors for oligomerization and toxicity of Alzheimer's β-amyloid peptide
    • DOI 10.1021/bi701415b
    • Austen, B.M.; Paleologou, K.E.; Ali, S.A.E.A.; Qureshi, M.M.; Allsop, D.; El-Agnaf, O.M.A. Designing Peptide Inhibitors for Oligomerization and Toxicity of Alzheimer's β-Amyloid Peptide. Biochem. 2008, 47, 1984-1992. (Pubitemid 351287124)
    • (2008) Biochemistry , vol.47 , Issue.7 , pp. 1984-1992
    • Austen, B.M.1    Paleologou, K.E.2    Ali, S.A.E.3    Qureshi, M.M.4    Allsop, D.5    El-Agnaf, O.M.A.6
  • 5
    • 0036820768 scopus 로고    scopus 로고
    • Structure-based QSAR study on differential inhibition of human prostaglandin endoperoxide H synthase-2 (COX-2) by nonsteroidal anti-inflammatory drugs
    • DOI 10.1023/A:1022488507391
    • Pouplana, R.; Lozano, J.J.; Pérez, C.; Ruiz, J. Structure-based QSAR study on differential inhibition of human Prostaglandin Endoperoxide H Synthase-2 (COX-2) by nonsteroidal antiinflammatory drugs. J. Comput.-Aided Mol. Des. 2002, 16, 683?710. (Pubitemid 36336180)
    • (2002) Journal of Computer-Aided Molecular Design , vol.16 , Issue.10 , pp. 683-709
    • Pouplana, R.1    Lozano, J.J.2    Perez, C.3    Ruiz, J.4
  • 6
    • 0042389543 scopus 로고    scopus 로고
    • QSAR study of dual cyclooxygenase and 5-lipoxygenase inhibitors 2,6-di-tert-butylphenol derivatives
    • DOI 10.1016/S0968-0896(03)00449-8
    • Ruiz, J.; Pérez, C.; Pouplana, R. QSAR Study of dual Cyclooxygenase and 5-Lipoxygenase inhibitors 2,6 diterbutylphenol derivatives. Bioorg. Med. Chem. 2003, 11, 4207?4216. (Pubitemid 37013571)
    • (2003) Bioorganic and Medicinal Chemistry , vol.11 , Issue.19 , pp. 4207-4216
    • Ruiz, J.1    Perez, C.2    Pouplana, R.3
  • 7
    • 0034924557 scopus 로고    scopus 로고
    • Cyclooxygenase and alzheimeŕs disease: Implications for preventive initiatives to slow the progression of clinical dementia
    • Pasinetti, G.M. Cyclooxygenase and Alzheimeŕs disease: implications for preventive initiatives to slow the progression of clinical dementia. Arch. Geront. Geriat. 2001, 33, 13-28.
    • (2001) Arch. Geront. Geriat. , vol.33 , pp. 13-28
    • Pasinetti, G.M.1
  • 8
    • 0242668337 scopus 로고    scopus 로고
    • Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis
    • DOI 10.1126/science.1079469
    • Kayed, R.; Head, E.; Thompson, J.L.; McIntire, T.M; Milton, S.; Cotman, C.W.; Glabe, C.G. Common Structure of Soluble Amyloid Oligomers Implies Common Mechanism of Pathogenesis. Science 2003, 300, 486-489. (Pubitemid 36444329)
    • (2003) Science , vol.300 , Issue.5618 , pp. 486-489
    • Kayed, R.1    Head, E.2    Thompson, J.L.3    McIntire, T.M.4    Milton, S.C.5    Cotman, C.W.6    Glabel, C.G.7
  • 10
    • 0034649352 scopus 로고    scopus 로고
    • Amyloid fibril formation by A-β(16-22), a seven-residue fragment of the Alzheimer's beta-amyloid peptide, and structural characterization by solid state NMR
    • Balbach, J.J.; Ishii, Y.; Antzutkin, O.N.; Leapman, R.D.; Rizzo, N.W.; Dyda, F.; Reed, J.; Tycko, R. Amyloid fibril formation by A-β(16-22), a seven-residue fragment of the Alzheimer's beta-amyloid peptide, and structural characterization by solid state NMR. Biochemistry 2000, 39, 13748-13759.
    • (2000) Biochemistry , vol.39 , pp. 13748-13759
    • Balbach, J.J.1    Ishii, Y.2    Antzutkin, O.N.3    Leapman, R.D.4    Rizzo, N.W.5    Dyda, F.6    Reed, J.7    Tycko, R.8
  • 14
    • 0035812658 scopus 로고    scopus 로고
    • Identification and characterization of key kinetic intermediates in amyloid β-protein fibrillogenesis
    • Kirkitadze, M.D.; Condron, M.M.; Teplow, D.B. Identification and characterization of key kinetic intermediates in amyloid β-protein fibrillogenesis. J. Mol. Biol. 2001, 312, 1103-1119.
    • (2001) J. Mol. Biol. , vol.312 , pp. 1103-1119
    • Kirkitadze, M.D.1    Condron, M.M.2    Teplow, D.B.3
  • 15
    • 0025838381 scopus 로고
    • Ph dependent structural transitions of Alzheimer's amyloid peptides
    • Fraser, P.E.; Nguyen, J.T.; Surewiez, W.K.; Kirschner, D.A. Ph dependent structural transitions of Alzheimer's amyloid peptides. Biophys. J. 1991, 60, 1190-1201.
    • (1991) Biophys. J. , vol.60 , pp. 1190-1201
    • Fraser, P.E.1    Nguyen, J.T.2    Surewiez, W.K.3    Kirschner, D.A.4
  • 18
    • 61949475048 scopus 로고    scopus 로고
    • Influence of preformed asp23-lys28 salt bridge on the conformational fluctuations of monomers and dimers of Aβ peptides with implications for Rates of Fibril Formation
    • Reddy, G.; Straub, J.E.; Thirumalai D. Influence of Preformed Asp23-Lys28 salt bridge on the conformational fluctuations of Monomers and Dimers of Aβ peptides with implications for Rates of Fibril Formation. J. Phys. Chem. 2009, 113, 1162-1172.
    • (2009) J. Phys. Chem. , vol.113 , pp. 1162-1172
    • Reddy, G.1    Straub, J.E.2    Thirumalai, D.3
  • 22
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N logN method for ewald sums in large systems
    • Darden T.; York, D.; Pedersen, L. Particle mesh Ewald: an N logN method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 23
    • 33644768461 scopus 로고    scopus 로고
    • Amyloid β-peptide oligomerization in silico: Dimer and trimer
    • DOI 10.1021/jp055568e
    • Jang, S.; Shin, S. Amyloid β-peptide oligomerizationin silico: dimer and trimer. J. Phys. Chem. B 2006, 110, 1955-1958. (Pubitemid 43342893)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.5 , pp. 1955-1958
    • Jang, S.1    Shin, S.2
  • 25
    • 11844255790 scopus 로고    scopus 로고
    • 10-35- protein: Assessing the propensity for peptide dimerization
    • DOI 10.1016/j.jmb.2004.11.022, PII S0022283604014615
    • Tarus, B.; Straub, J.; Thirumalai, D. Probing the initial stage of aggregation of the Aβ10-35 protein: Assesssing the propensity for peptide dimerization. J. Mol. Biol. 2005, 345, 1141-1158. (Pubitemid 40092230)
    • (2005) Journal of Molecular Biology , vol.345 , Issue.5 , pp. 1141-1156
    • Tarus, B.1    Straub, J.E.2    Thirumalai, D.3
  • 26
    • 45949099262 scopus 로고    scopus 로고
    • Computational study on the structural diversity of amyloid beta peptide (Aβ10-35) Oligomers
    • Jang. S.; Shin, S.J. Computational Study on the Structural Diversity of Amyloid Beta Peptide (Aβ10-35) Oligomers. Phys. Chem. B 2008, 112, 3479?3483.
    • (2008) Phys. Chem. B , vol.112 , pp. 3479-3483
    • Jang., S.1    Shin, S.J.2
  • 27
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • DOI 10.1021/ar000033j
    • Kollman, P.A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D.A.; Cheatham III, T.E. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33, 889-897. (Pubitemid 32056774)
    • (2000) Accounts of Chemical Research , vol.33 , Issue.12 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5    Chong, L.6    Lee, M.7    Lee, T.8    Duan, Y.9    Wang, W.10    Donini, O.11
  • 29
    • 0347602124 scopus 로고    scopus 로고
    • Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex ras-raf.
    • Gohlke, H.; Case, D.A. Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf. J. Comput. Chem. 2004, 25, 238-250.
    • (2004) J. Comput. Chem. , vol.25 , pp. 238-250
    • Gohlke, H.1    Case, D.A.2
  • 30
    • 84961980685 scopus 로고    scopus 로고
    • Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
    • Kuhn, B.; Kollman, P.A. Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models. J. Med. Chem. 2000, 43, 3786-3791.
    • (2000) J. Med. Chem. , vol.43 , pp. 3786-3791
    • Kuhn, B.1    Kollman, P.A.2
  • 32
    • 32844457567 scopus 로고
    • Accurate calculations of hydration free energies using macroscopic solvents
    • Sitkoff, D.; Sharp, K.; Honing, B. Accurate calculations of hydration free energies using macroscopic solvents. J. Phys. Chem. 1994, 98, 1978-1988.
    • (1994) J. Phys. Chem. , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.2    Honing, B.3
  • 33
    • 0001351515 scopus 로고
    • Estimation of absolute and relative entropies of macromolecules using the covariance matrix
    • Schlitter, J. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem. Phys. Lett. 1993, 215, 617-621.
    • (1993) Chem. Phys. Lett. , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 34
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
    • DOI 10.1021/ja003834q
    • Wang, J.; Morin, P.; Wang, W.; Kollman, P.A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J. Am. Chem. Soc. 2001, 123, 5221-5230. (Pubitemid 32910665)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.22 , pp. 5221-5230
    • Wang, J.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 35
    • 59849095562 scopus 로고    scopus 로고
    • Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations
    • Liang, S.; Li, L.; Hsu, W.L.; Pilcher, M.N.; Uversky, V.; Zhou, Y.; Dunker, A.K.; Meroueh, S.O. Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. Biochemistry 2009, 48, 399-414
    • (2009) Biochemistry , vol.48 , pp. 399-414
    • Liang, S.1    Li, L.2    Hsu, W.L.3    Pilcher, M.N.4    Uversky, V.5    Zhou, Y.6    Dunker, A.K.7    Meroueh, S.O.8
  • 36
    • 2642574503 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing: Vienna, Austria, accessed on 13 April 2010, R-Development-Core-Team.
    • R-Development-Core-Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2007; http://www.R-project.org, accessed on 13 April 2010.
    • (2007) A Language and Environment for Statistical Computing
  • 37
    • 59849095285 scopus 로고    scopus 로고
    • Workflows and e-Science: An overview of workflow system features and capabilities
    • Deelman, E.; Gannon, D., Shields, M. and Taylor, I. Workflows and e-Science: An overview of workflow system features and capabilities. Future Gener. Comp. Sys. 2009, 25, 528-540.
    • (2009) Future Gener. Comp. Sys. , vol.25 , pp. 528-540
    • Deelman, E.1    Gannon, D.2    Shields, M.3    Taylor, I.4
  • 40
    • 0035133048 scopus 로고    scopus 로고
    • Simulation study of the structure and dynamics of the Alzheimer's amyloid peptide congener in solution
    • Massi, F.; Peng, J.; Lee, J.P.; and Straub, J. Simulation study of the structure and dynamics of the Alzheimer's amyloid peptide congener in solution. Biophys. J. 2001, 80, 31-44. (Pubitemid 32108161)
    • (2001) Biophysical Journal , vol.80 , Issue.1 , pp. 31-44
    • Massi, F.1    Peng, J.W.2    Lee, J.P.3    Straub, J.E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.