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Volumn 109, Issue 44, 2012, Pages 17851-17856

Multimolecule test-tube simulations of protein unfolding and aggregation

Author keywords

Protein dynamics; Protein folding

Indexed keywords

ENGRAILED HOMEODOMAIN PROTEIN; HOMEODOMAIN PROTEIN; UNCLASSIFIED DRUG;

EID: 84868120948     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1201809109     Document Type: Article
Times cited : (13)

References (25)
  • 1
    • 0034610360 scopus 로고    scopus 로고
    • Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
    • Mayor U, Johnson CM, Daggett V, Fersht AR (2000) Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc Natl Acad Sci USA 97(25):13518-13522.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.25 , pp. 13518-13522
    • Mayor, U.1    Johnson, C.M.2    Daggett, V.3    Fersht, A.R.4
  • 2
    • 0345255608 scopus 로고    scopus 로고
    • Unifying features in protein-folding mechanisms
    • Gianni S, et al. (2003) Unifying features in protein-folding mechanisms. Proc Natl Acad Sci USA 100(23):13286-13291.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.23 , pp. 13286-13291
    • Gianni, S.1
  • 3
    • 0142185492 scopus 로고    scopus 로고
    • The denatured state of Engrailed Homeodomain under denaturing and native conditions
    • Mayor U, Grossmann JG, Foster NW, Freund SM, Fersht AR (2003) The denatured state of Engrailed Homeodomain under denaturing and native conditions. J Mol Biol 333 (5):977-991.
    • (2003) J Mol Biol , vol.333 , Issue.5 , pp. 977-991
    • Mayor, U.1    Grossmann, J.G.2    Foster, N.W.3    Freund, S.M.4    Fersht, A.R.5
  • 4
    • 0037456298 scopus 로고    scopus 로고
    • The complete folding pathway of a protein from nanoseconds to microseconds
    • Mayor U, et al. (2003) The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421(6925):863-867.
    • (2003) Nature , vol.421 , Issue.6925 , pp. 863-867
    • Mayor, U.1
  • 5
    • 27144532135 scopus 로고    scopus 로고
    • Solution structure of a protein denatured state and folding intermediate
    • Religa TL, Markson JS, Mayor U, Freund SM, Fersht AR (2005) Solution structure of a protein denatured state and folding intermediate. Nature 437(7061):1053-1056.
    • (2005) Nature , vol.437 , Issue.7061 , pp. 1053-1056
    • Religa, T.L.1    Markson, J.S.2    Mayor, U.3    Freund, S.M.4    Fersht, A.R.5
  • 6
    • 46849113841 scopus 로고    scopus 로고
    • Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain
    • McCully ME, Beck DAC, Daggett V (2008) Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain. Biochemistry 47 (27):7079-7089.
    • (2008) Biochemistry , vol.47 , Issue.27 , pp. 7079-7089
    • McCully, M.E.1    Beck, D.A.C.2    Daggett, V.3
  • 7
    • 77956567928 scopus 로고    scopus 로고
    • Refolding the engrailed homeodomain: Structural basis for the accumulation of a folding intermediate
    • McCully ME, Beck DAC, Fersht AR, Daggett V (2010) Refolding the engrailed homeodomain: Structural basis for the accumulation of a folding intermediate. Biophys J 99 (5):1628-1636.
    • (2010) Biophys J , vol.99 , Issue.5 , pp. 1628-1636
    • McCully, M.E.1    Beck, D.A.C.2    Fersht, A.R.3    Daggett, V.4
  • 8
    • 0014481598 scopus 로고
    • Measurement of protein concentration by quantitative electron microscopy
    • Silverman L, Glick D (1969) Measurement of protein concentration by quantitative electron microscopy. J Cell Biol 40(3):773-778.
    • (1969) J Cell Biol , vol.40 , Issue.3 , pp. 773-778
    • Silverman, L.1    Glick, D.2
  • 9
    • 3843135179 scopus 로고    scopus 로고
    • Diffusing and colliding: The atomic level folding/unfolding pathway of a small helical protein
    • DeMarco ML, Alonso DOV, Daggett V (2004) Diffusing and colliding: The atomic level folding/unfolding pathway of a small helical protein. J Mol Biol 341(4):1109-1124.
    • (2004) J Mol Biol , vol.341 , Issue.4 , pp. 1109-1124
    • Demarco, M.L.1    Alonso, D.O.V.2    Daggett, V.3
  • 10
    • 0033516512 scopus 로고    scopus 로고
    • Analysis methods for comparison of multiple molecular dynamics trajectories: Applications to protein unfolding pathways and denatured ensembles
    • Kazmirski SL, Li A, Daggett V (1999) Analysis methods for comparison of multiple molecular dynamics trajectories: Applications to protein unfolding pathways and denatured ensembles. J Mol Biol 290(1):283-304.
    • (1999) J Mol Biol , vol.290 , Issue.1 , pp. 283-304
    • Kazmirski, S.L.1    Li, A.2    Daggett, V.3
  • 11
    • 77951685093 scopus 로고    scopus 로고
    • A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding
    • Toofanny RD, Jonsson AL, Daggett V (2010) A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding. Biophys J 98(11):2671-2681.
    • (2010) Biophys J , vol.98 , Issue.11 , pp. 2671-2681
    • Toofanny, R.D.1    Jonsson, A.L.2    Daggett, V.3
  • 12
    • 36549027538 scopus 로고    scopus 로고
    • A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations
    • Beck DAC, Daggett V (2007) A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Biophys J 93(10): 3382-3391.
    • (2007) Biophys J , vol.93 , Issue.10 , pp. 3382-3391
    • Beck, D.A.C.1    Daggett, V.2
  • 13
    • 0028143603 scopus 로고
    • Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2
    • Li A, Daggett V (1994) Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Proc Natl Acad Sci USA 91(22): 10430-10434.
    • (1994) Proc Natl Acad Sci USA , vol.91 , Issue.22 , pp. 10430-10434
    • Li, A.1    Daggett, V.2
  • 14
    • 0029981188 scopus 로고    scopus 로고
    • Structure of the transition state for folding of a protein derived from experiment and simulation
    • Daggett V, Li A, Itzhaki LS, Otzen DE, Fersht AR (1996) Structure of the transition state for folding of a protein derived from experiment and simulation. J Mol Biol 257(2): 430-440.
    • (1996) J Mol Biol , vol.257 , Issue.2 , pp. 430-440
    • Daggett, V.1    Li, A.2    Itzhaki, L.S.3    Otzen, D.E.4    Fersht, A.R.5
  • 16
    • 0029633167 scopus 로고
    • Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt M, Hirshberg M, Sharon R, Daggett V (1995) Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comput Phys Commun 91:215-231.
    • (1995) Comput Phys Commun , vol.91 , pp. 215-231
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Daggett, V.4
  • 18
    • 0036968512 scopus 로고    scopus 로고
    • Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
    • Day R, Bennion BJ, Ham S, Daggett V (2002) Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J Mol Biol 322(1): 189-203.
    • (2002) J Mol Biol , vol.322 , Issue.1 , pp. 189-203
    • Day, R.1    Bennion, B.J.2    Ham, S.3    Daggett, V.4
  • 19
    • 0000125216 scopus 로고    scopus 로고
    • Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt M, Hirshberg M, Sharon R, Laidig KE, Daggett V (1997) Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution. J Phys Chem B 101:5051-5061.
    • (1997) J Phys Chem B , vol.101 , pp. 5051-5061
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Laidig, K.E.4    Daggett, V.5
  • 20
    • 0009979659 scopus 로고
    • Precise representation of volume properties of water at one atmosphere
    • Kell GS (1967) Precise representation of volume properties of water at one atmosphere. J Chem Eng Data 12:66-69.
    • (1967) J Chem Eng Data , vol.12 , pp. 66-69
    • Kell, G.S.1
  • 22
    • 12144275299 scopus 로고    scopus 로고
    • Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides
    • Beck DAC, Armen RS, Daggett V (2005) Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. Biochemistry 44(2):609-616.
    • (2005) Biochemistry , vol.44 , Issue.2 , pp. 609-616
    • Beck, D.A.C.1    Armen, R.S.2    Daggett, V.3
  • 23
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22(12):2577-2637.
    • (1983) Biopolymers , vol.22 , Issue.12 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 25
    • 41149169500 scopus 로고    scopus 로고
    • Comparison of multiple crystal structures with NMR data for engrailed homeodomain
    • Religa TL (2008) Comparison of multiple crystal structures with NMR data for engrailed homeodomain. J Biomol NMR 40(3):189-202.
    • (2008) J Biomol NMR , vol.40 , Issue.3 , pp. 189-202
    • Religa, T.L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.