메뉴 건너뛰기




Volumn 8, Issue 6, 1999, Pages 1292-1304

Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures

Author keywords

BBA1; Energetics; Molecular dynamics simulation; Protein stability; Unfolding mechanism

Indexed keywords

SYNTHETIC PEPTIDE; ZINC FINGER PROTEIN;

EID: 0033022072     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.6.1292     Document Type: Article
Times cited : (50)

References (54)
  • 2
    • 0023675175 scopus 로고
    • Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulation
    • Anderson AG, Hermans J. 1988. Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulation. Proteins 3:262-265.
    • (1988) Proteins , vol.3 , pp. 262-265
    • Anderson, A.G.1    Hermans, J.2
  • 4
    • 3042524904 scopus 로고
    • A well behaved electrostatic potential base method using charge restraints for deriving atomic charges: The RESP model
    • Bayly CI, Cieplak P, Cornell WD, Kollman PA. 1993. A well behaved electrostatic potential base method using charge restraints for deriving atomic charges: The RESP model. J Phys Chem 97:10269-10280.
    • (1993) J Phys Chem , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 6
    • 0025279242 scopus 로고
    • Zinc finger domains: Hypotheses and current knowledge
    • Berg JM. 1990. Zinc finger domains: Hypotheses and current knowledge. Annu Rev Biophys Biophys Chem 19:405-421.
    • (1990) Annu Rev Biophys Biophys Chem , vol.19 , pp. 405-421
    • Berg, J.M.1
  • 7
    • 0029151245 scopus 로고
    • First-principles calculation of the folding free-energy of a 3-helix bundle protein
    • Boczko EM, Brooks CL III. 1995. First-principles calculation of the folding free-energy of a 3-helix bundle protein. Science 269:393-396.
    • (1995) Science , vol.269 , pp. 393-396
    • Boczko, E.M.1    Brooks C.L. III2
  • 9
    • 0028264860 scopus 로고
    • Molecular-dynamics simulation of protein denaturation - Solvation of the hydrophobic cores and secondary structure of barnase
    • Caflisch A, Karplus M. 1994. Molecular-dynamics simulation of protein denaturation - Solvation of the hydrophobic cores and secondary structure of barnase. Proc Natl Acad Sci USA 91:1746-1750.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 1746-1750
    • Caflisch, A.1    Karplus, M.2
  • 10
    • 0015914783 scopus 로고
    • Conformation of twisted β-pleated sheets in proteins
    • Chothia C. 1973. Conformation of twisted β-pleated sheets in proteins. J Mol Biol 75:295-302.
    • (1973) J Mol Biol , vol.75 , pp. 295-302
    • Chothia, C.1
  • 11
    • 0021095536 scopus 로고
    • Role of inter-chain interactions in the stabilization of the right-handed twist of β-sheets
    • Chou K-C, Nemethy G, Scheraga HA. 1983. Role of inter-chain interactions in the stabilization of the right-handed twist of β-sheets. J Mol Biol 68:389-407.
    • (1983) J Mol Biol , vol.68 , pp. 389-407
    • Chou, K.-C.1    Nemethy, G.2    Scheraga, H.A.3
  • 13
    • 0027219504 scopus 로고
    • Protein unfolding pathways explored through molecular dynamics simulations
    • Daggett V, Levitt M. 1993. Protein unfolding pathways explored through molecular dynamics simulations. J Mol Biol 232:600-619.
    • (1993) J Mol Biol , vol.232 , pp. 600-619
    • Daggett, V.1    Levitt, M.2
  • 14
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Fully automated sequence selection
    • Dahiyat BI, Mayo SL. 1997. De novo protein design: Fully automated sequence selection. Science 278:82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 15
    • 33846823909 scopus 로고
    • Particle mesh ewald - An N·log(n) method for ewald sums in large systems
    • Darden T, York D, Pedersen L. 1993. Particle Mesh Ewald - An N·log(n) method for Ewald sums in large systems. J Chem Phys 98:10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 16
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill KA. 1990. Dominant forces in protein folding. Biochemistry 29:7133-7155.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 18
    • 0027462173 scopus 로고
    • Principles of protein stability derived from protein engineering experiments
    • Fersht AR, Serrano L. 1993. Principles of protein stability derived from protein engineering experiments. Current Opinion in Structural Biology 3:75-83.
    • (1993) Current Opinion in Structural Biology , vol.3 , pp. 75-83
    • Fersht, A.R.1    Serrano, L.2
  • 19
    • 0023375317 scopus 로고
    • Metal-dependent folding of a single zinc finger from transcription factor IIIA
    • Frankel AD, Berg JM, Pabo CO. 1987. Metal-dependent folding of a single zinc finger from transcription factor IIIA. Proc Natl Acad Sci 84:4841.
    • (1987) Proc Natl Acad Sci , vol.84 , pp. 4841
    • Frankel, A.D.1    Berg, J.M.2    Pabo, C.O.3
  • 21
    • 0027499733 scopus 로고
    • Soluble proteins: Size, shape and function
    • Goodsell DS, Olson AJ. 1993. Soluble proteins: Size, shape and function. Trends Biochem Sci 18:65-68.
    • (1993) Trends Biochem Sci , vol.18 , pp. 65-68
    • Goodsell, D.S.1    Olson, A.J.2
  • 22
    • 0029011910 scopus 로고
    • Molecular dynamics simulations of isolated helices of myoglobin
    • Hirst JD, Brooks CL III. 1995. Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry 34:7614-7621.
    • (1995) Biochemistry , vol.34 , pp. 7614-7621
    • Hirst, J.D.1    Brooks C.L. III2
  • 23
    • 0023506457 scopus 로고
    • Folding and association of proteins
    • Jaenicke R. 1987. Folding and association of proteins. Prog Biophys Mol Biol 49:117-237.
    • (1987) Prog Biophys Mol Biol , vol.49 , pp. 117-237
    • Jaenicke, R.1
  • 25
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W. 1976. A solution for the best rotation to relate two sets of vectors. Acta Cryst A32:922-923.
    • (1976) Acta Cryst , vol.A32 , pp. 922-923
    • Kabsch, W.1
  • 26
    • 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 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 27
    • 0025345415 scopus 로고
    • Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding
    • Kim PS, Baldwin RL. 1982. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Ann Rev Biochem 59:631-660.
    • (1982) Ann Rev Biochem , vol.59 , pp. 631-660
    • Kim, P.S.1    Baldwin, R.L.2
  • 28
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biological phenomena
    • Kollman PA. 1993. Free energy calculations: Applications to chemical and biological phenomena. Chem Rev 93:2395-2417.
    • (1993) Chem Rev , vol.93 , pp. 2395-2417
    • Kollman, P.A.1
  • 29
    • 0002098417 scopus 로고    scopus 로고
    • The development/application of a "minimalist" organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data
    • van Gunsteren WF, ed. Dordrecht, The Netherlands: ESCOM
    • Kollman PA, Dixon RW, Cornell WD, Fox T, Chipot C, Pohorille A. 1997. The development/application of a "minimalist" organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data. In: van Gunsteren WF, ed. Computer simulations of biological systems. Dordrecht, The Netherlands: ESCOM.
    • (1997) Computer Simulations of Biological Systems
    • Kollman, P.A.1    Dixon, R.W.2    Cornell, W.D.3    Fox, T.4    Chipot, C.5    Pohorille, A.6
  • 31
    • 0031465967 scopus 로고    scopus 로고
    • "New view" of protein folding reconciled with the old through multiple unfolding simulations
    • Lazaridis T, Karplus M. 1997. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 278:1928-1931.
    • (1997) Science , vol.278 , pp. 1928-1931
    • Lazaridis, T.1    Karplus, M.2
  • 32
    • 84912079256 scopus 로고
    • Rapid approximation to molecular-surface area via the use of boolean logic and look-up tables
    • Le Grand SM, Merz KM. 1993. Rapid approximation to molecular-surface area via the use of boolean logic and look-up tables. J Comp Chem 14:349-352.
    • (1993) J Comp Chem , vol.14 , pp. 349-352
    • Le Grand, S.M.1    Merz, K.M.2
  • 33
    • 0029963345 scopus 로고    scopus 로고
    • Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
    • Li A, Daggett V. 1996. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Biol 257:412-429.
    • (1996) J Mol Biol , vol.257 , pp. 412-429
    • Li, A.1    Daggett, V.2
  • 34
    • 0027255479 scopus 로고
    • Structural and genetic analysis of protein stability
    • Matthews BW. 1993. Structural and genetic analysis of protein stability. Ann Rev Biochem 62:139-60.
    • (1993) Ann Rev Biochem , vol.62 , pp. 139-160
    • Matthews, B.W.1
  • 35
    • 0031058410 scopus 로고    scopus 로고
    • NMR structure of the 35-residue villin headpiece subdomain
    • McKnight CJ, Matsudaira PT, Kim PS. 1997. NMR structure of the 35-residue villin headpiece subdomain. Nat Struct Biol 4:180-184.
    • (1997) Nat Struct Biol , vol.4 , pp. 180-184
    • McKnight, C.J.1    Matsudaira, P.T.2    Kim, P.S.3
  • 36
    • 0015217634 scopus 로고
    • The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions
    • Nozaki Y, Tanford CH. 1971. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. J Biol Chem 246:2211-2217.
    • (1971) J Biol Chem , vol.246 , pp. 2211-2217
    • Nozaki, Y.1    Tanford, C.H.2
  • 37
    • 0025134134 scopus 로고
    • Spectroscopic studies of wild-type and mutant "zinc finger" peptides: Determinants of domain folding and structure
    • Parraga G, Horvath S, Hood L, Young ET, Klevit RE. 1990. Spectroscopic studies of wild-type and mutant "zinc finger" peptides: Determinants of domain folding and structure. Proc Natl Acad Sci USA 87:137-141.
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 137-141
    • Parraga, G.1    Horvath, S.2    Hood, L.3    Young, E.T.4    Klevit, R.E.5
  • 38
    • 0025773296 scopus 로고
    • Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 Å
    • Pavletich NP, Pabo CO. 1991. Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 Å. Science 252:809-817.
    • (1991) Science , vol.252 , pp. 809-817
    • Pavletich, N.P.1    Pabo, C.O.2
  • 40
    • 0024290488 scopus 로고
    • Helix signals in proteins
    • Presta LG, Rose GD. 1988. Helix signals in proteins. Science 240:1632-1641.
    • (1988) Science , vol.240 , pp. 1632-1641
    • Presta, L.G.1    Rose, G.D.2
  • 41
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson JS. 1981. The anatomy and taxonomy of protein structure. Adv Protein Chem 34:167-339.
    • (1981) Adv Protein Chem , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 42
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of alpha helices
    • Richardson JS, Richardson DC. 1988. Amino acid preferences for specific locations at the ends of alpha helices. Science 240:1648-1652.
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 43
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert J-P, Ciccotti G, Berendsen HJC. 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
  • 44
    • 0030220763 scopus 로고    scopus 로고
    • Engineering enzymes for stability
    • Shaw A, Bott R. 1996. Engineering enzymes for stability. Curr Opin Struct Biol 6:546-550.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 546-550
    • Shaw, A.1    Bott, R.2
  • 45
    • 0021844602 scopus 로고
    • Beta-hairpin families in globular proteins
    • Sibanda BL, Thornton JM. 1985. Beta-hairpin families in globular proteins. Nature 316:170-174.
    • (1985) Nature , vol.316 , pp. 170-174
    • Sibanda, B.L.1    Thornton, J.M.2
  • 46
    • 48549111326 scopus 로고
    • Why are enzymes so big?
    • Srere PA. 1984. Why are enzymes so big? Trends Biochem Sci 9:387-390.
    • (1984) Trends Biochem Sci , vol.9 , pp. 387-390
    • Srere, P.A.1
  • 47
    • 0030593029 scopus 로고    scopus 로고
    • Design of a monomeric 23-residue polypeptide with defined tertiary structure
    • Struthers MD, Cheng RP, Imperiali B. 1996a. Design of a monomeric 23-residue polypeptide with defined tertiary structure. Science 271:342-345.
    • (1996) Science , vol.271 , pp. 342-345
    • Struthers, M.D.1    Cheng, R.P.2    Imperiali, B.3
  • 48
    • 0030567375 scopus 로고    scopus 로고
    • Economy in protein design -evolution of a metal-independent β-β-α motif based on the zinc finger domains
    • Struthers MD, Cheng RP, Imperiali B. 1996b. Economy in protein design -Evolution of a metal-independent β-β-α motif based on the zinc finger domains. JACS 118:3073-3081.
    • (1996) JACS , vol.118 , pp. 3073-3081
    • Struthers, M.D.1    Cheng, R.P.2    Imperiali, B.3
  • 49
    • 0002543810 scopus 로고    scopus 로고
    • Design and NMR analyses of compact, independently folded BBA motifs
    • Struthers MD, Ottesen JJ, Imperiali B. 1998. Design and NMR analyses of compact, independently folded BBA motifs. Folding Design 3:95-103.
    • (1998) Folding Design , vol.3 , pp. 95-103
    • Struthers, M.D.1    Ottesen, J.J.2    Imperiali, B.3
  • 50
    • 0027316216 scopus 로고
    • Molecular-dynamics simulations of the unfolding of apomyoglobin in water
    • Tirado-Rives J, Jorgensen WL. 1993. Molecular-dynamics simulations of the unfolding of apomyoglobin in water. Biochemistry 32:4175-4184.
    • (1993) Biochemistry , vol.32 , pp. 4175-4184
    • Tirado-Rives, J.1    Jorgensen, W.L.2
  • 51
    • 0025767212 scopus 로고
    • Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides
    • Tobias DJ, Brooks CL III. 1991. Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. Biochemistry 30:6059-6070.
    • (1991) Biochemistry , vol.30 , pp. 6059-6070
    • Tobias, D.J.1    Brooks C.L. III2
  • 52
    • 0002531265 scopus 로고
    • Methods for calculation of free energies and binding constants: Successes and problems
    • van Gunsteren WF, Weiner PK, eds. Leiden: ESCOM
    • van Gunsteren WF. 1989. Methods for calculation of free energies and binding constants: Successes and problems. In: van Gunsteren WF, Weiner PK, eds. Computer simulations of biomolecular systems. Leiden: ESCOM, pp 27-59.
    • (1989) Computer Simulations of Biomolecular Systems , pp. 27-59
    • Gunsteren, W.F.1
  • 54
    • 0030134514 scopus 로고    scopus 로고
    • Chaos in biomolecular dynamics
    • Zhou HB, Wang L. 1996. Chaos in biomolecular dynamics. J Phys Chem 100:8101-8105.
    • (1996) J Phys Chem , vol.100 , pp. 8101-8105
    • Zhou, H.B.1    Wang, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.