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Volumn 57, Issue 4, 2004, Pages 645-650

Modeling loop reorganization free energies of acetylcholinesterase: A comparison of explicit and implicit solvent models

Author keywords

Atomic solvation potential; Dielectric screening; Generalized Born; Hydration; Molecular dynamics; Poisson equation

Indexed keywords

ACETYLCHOLINESTERASE; SOLVENT;

EID: 10344234690     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20294     Document Type: Article
Times cited : (16)

References (29)
  • 2
  • 3
    • 0014578420 scopus 로고
    • Affinity and phosphorylation constants of a series of O,O-dialkyl malaoxons and paraoxons with acetylcholinesterase
    • Chiu YC, Main AR, Dauterman WC. Affinity and phosphorylation constants of a series of O,O-dialkyl malaoxons and paraoxons with acetylcholinesterase. Biochem Pharmacol 1969;18:2171-2177.
    • (1969) Biochem Pharmacol , vol.18 , pp. 2171-2177
    • Chiu, Y.C.1    Main, A.R.2    Dauterman, W.C.3
  • 4
    • 0015789712 scopus 로고
    • Recording spectrophotometric method for determination of dissociation and phosphorylation constants for the inhibition of acetylcholinesterase by organophosphates in the presence of substrate
    • Hart GJ, O'Brien RD. Recording spectrophotometric method for determination of dissociation and phosphorylation constants for the inhibition of acetylcholinesterase by organophosphates in the presence of substrate. Biochem 1973;12:2940-2945.
    • (1973) Biochem , vol.12 , pp. 2940-2945
    • Hart, G.J.1    O'Brien, R.D.2
  • 5
    • 0021240282 scopus 로고
    • Kinetics for the inhibition of acetylcholinesterase from the electric eel by some organophosphates and carbamates
    • Forsberg A, Puu G. Kinetics for the inhibition of acetylcholinesterase from the electric eel by some organophosphates and carbamates. Eur J Biochem 1984;140:153-156.
    • (1984) Eur J Biochem , vol.140 , pp. 153-156
    • Forsberg, A.1    Puu, G.2
  • 6
    • 0027217179 scopus 로고    scopus 로고
    • Dissection of the human acetylcholinesterase active center determinants of substrate specificity. Identification of residues constituting the anionic site, the hydrophobic site, and the acyl pocket
    • Ordentlich A, Barak D, Kronman C, Flashner Y, Leitner M, Segall Y, Ariel N, Cohen S, Velan B, Shafferman A. Dissection of the human acetylcholinesterase active center determinants of substrate specificity. Identification of residues constituting the anionic site, the hydrophobic site, and the acyl pocket. J Biol Chem 1996;268:17083-17095.
    • (1996) J Biol Chem , vol.268 , pp. 17083-17095
    • Ordentlich, A.1    Barak, D.2    Kronman, C.3    Flashner, Y.4    Leitner, M.5    Segall, Y.6    Ariel, N.7    Cohen, S.8    Velan, B.9    Shafferman, A.10
  • 7
    • 0027373839 scopus 로고
    • Engineering resistance to 'aging' of phosphylated human acetylcholinesterase. Role of hydrogen bond network in the active center
    • Ordentlich A, Kronman C, Barak D, Stein D, Ariel N, Marcus D, Velan B, Shafferman A. Engineering resistance to 'aging' of phosphylated human acetylcholinesterase. Role of hydrogen bond network in the active center. FEBS Lett 1993;334:215-220.
    • (1993) FEBS Lett , vol.334 , pp. 215-220
    • Ordentlich, A.1    Kronman, C.2    Barak, D.3    Stein, D.4    Ariel, N.5    Marcus, D.6    Velan, B.7    Shafferman, A.8
  • 8
    • 0032031405 scopus 로고    scopus 로고
    • Electrostatic contributions to protein-protein binding affinities: Application to Rap/Raf interaction
    • Muegge I, Schweins T, Warshel A. Electrostatic contributions to protein-protein binding affinities: application to Rap/Raf interaction. Proteins 1998;30:407-423.
    • (1998) Proteins , vol.30 , pp. 407-423
    • Muegge, I.1    Schweins, T.2    Warshel, A.3
  • 9
    • 0342321950 scopus 로고    scopus 로고
    • Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease
    • Sham YY, Chu ZT, Tao H, Warshel A. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins 2000;39:393-407.
    • (2000) Proteins , vol.39 , pp. 393-407
    • Sham, Y.Y.1    Chu, Z.T.2    Tao, H.3    Warshel, A.4
  • 10
    • 0021476470 scopus 로고
    • Calculations of electrostatic interactions in biological systems and in solutions
    • Warshel A, Russel ST. Calculations of electrostatic interactions in biological systems and in solutions. Q Rev Biophys 1984;17:283-421.
    • (1984) Q Rev Biophys , vol.17 , pp. 283-421
    • Warshel, A.1    Russel, S.T.2
  • 11
    • 0034816706 scopus 로고    scopus 로고
    • Calculations of free energy contributions to protein-RNA complex stabilization
    • Olson MA. Calculations of free energy contributions to protein-RNA complex stabilization. Biophys J 2001;81:1841-1853.
    • (2001) Biophys J , vol.81 , pp. 1841-1853
    • Olson, M.A.1
  • 12
    • 0032993447 scopus 로고    scopus 로고
    • Polymer principles and protein folding
    • Dill KA. Polymer principles and protein folding. Protein Sci 1999;8:1166-1180.
    • (1999) Protein Sci , vol.8 , pp. 1166-1180
    • Dill, K.A.1
  • 13
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
    • Vorobjev YN, Almagro JC, Hermans J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins 1998;32:399-413.
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 15
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks BR, Janezic D, Karplus M. Harmonic analysis of large systems. I. Methodology. J Comp Chem 1995;16:1522-1542.
    • (1995) J Comp Chem , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janezic, D.2    Karplus, M.3
  • 16
    • 84986469420 scopus 로고
    • Harmonic analysis of large systems. II. Comparison of different protein models
    • Janezic D, Brooks BR. Harmonic analysis of large systems. II. Comparison of different protein models. J Comp Chem 1995;16:1543-1553.
    • (1995) J Comp Chem , vol.16 , pp. 1543-1553
    • Janezic, D.1    Brooks, B.R.2
  • 17
    • 84986473952 scopus 로고
    • Harmonic analysis of large systems. III. Comparison with molecular dynamics
    • Janezic D, Venable RM, Brooks BR. Harmonic analysis of large systems. III. Comparison with molecular dynamics. J Comp Chem 1995;16:1554-1566.
    • (1995) J Comp Chem , vol.16 , pp. 1554-1566
    • Janezic, D.1    Venable, R.M.2    Brooks, B.R.3
  • 18
    • 4644360675 scopus 로고    scopus 로고
    • Conformational energy landscape of the acyl pocket loop in acetylcholinesterase: A Monte Carlo-generalized Born model study
    • In press
    • Carlacci L, Millard CB, Olson MA. Conformational energy landscape of the acyl pocket loop in acetylcholinesterase: A Monte Carlo-generalized Born model study. Biophys Chem 2004, In press.
    • (2004) Biophys Chem
    • Carlacci, L.1    Millard, C.B.2    Olson, M.A.3
  • 19
    • 0344736689 scopus 로고    scopus 로고
    • Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase
    • Strajbl M, Shurki A, Warshel A. Converting conformational changes to electrostatic energy in molecular motors: the energetics of ATP synthase. Proc Natl Acad Sci USA 2003;25:14834-14839.
    • (2003) Proc Natl Acad Sci USA , vol.25 , pp. 14834-14839
    • Strajbl, M.1    Shurki, A.2    Warshel, A.3
  • 23
    • 4043171970 scopus 로고    scopus 로고
    • The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
    • Qiu D, Shenkin PS, Hollinger FP, Still WC. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J Phys Chem A 1997;101:3005-3014.
    • (1997) J Phys Chem A , vol.101 , pp. 3005-3014
    • Qiu, D.1    Shenkin, P.S.2    Hollinger, F.P.3    Still, W.C.4
  • 24
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenber D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199-203.
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenber, D.1    McLachlan, A.D.2
  • 25
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly ML. Analytical molecular surface calculation. J Appl Cryst 1983;16:548-558.
    • (1983) J Appl Cryst , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 26
    • 0028180523 scopus 로고
    • Application of scaled particle theory to model the hydrophobic effect: Implications for molecular association and protein stability
    • Jackson RM, Sternberg MJE. Application of scaled particle theory to model the hydrophobic effect: implications for molecular association and protein stability. Protein Eng 1994;7:371-383.
    • (1994) Protein Eng , vol.7 , pp. 371-383
    • Jackson, R.M.1    Sternberg, M.J.E.2
  • 27
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformation analysis
    • Gilson MK, Hongi B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformation analysis. Proteins 1988;4:7-18.
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Hongi, B.2
  • 29
    • 0035501755 scopus 로고    scopus 로고
    • Protein molecular dynamics with the generalized Born/ACE solvent model
    • Calimet N, Schaefer M, Simonson T. Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins. 2001;45:144-158.
    • (2001) Proteins , vol.45 , pp. 144-158
    • Calimet, N.1    Schaefer, M.2    Simonson, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.