메뉴 건너뛰기




Volumn 33, Issue 3, 1998, Pages 343-357

Kinetic steps for α-helix formation

Author keywords

helix; Folding; NEIMO; Polyalanine; Polyglutamine

Indexed keywords

ALANINE; GLYCINE; POLYAMINOACID; PROTEIN;

EID: 0032533396     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19981115)33:3<343::AID-PROT4>3.0.CO;2-B     Document Type: Article
Times cited : (45)

References (52)
  • 1
    • 0025876740 scopus 로고
    • Protein folding: Local structures, subunits, and assemblies
    • Jaenicke, R. Protein folding: Local structures, subunits, and assemblies. Biochemistry 30:3147-3161, 1991.
    • (1991) Biochemistry , vol.30 , pp. 3147-3161
    • Jaenicke, R.1
  • 2
    • 0023834933 scopus 로고
    • Surface amino acids as sites of temperature-sensitive folding mutations in the P22 tailspike protein
    • Yu, M.-H., King, J. Surface amino acids as sites of temperature-sensitive folding mutations in the P22 tailspike protein. J. Biol. Chem. 263:1424-1431, 1988.
    • (1988) J. Biol. Chem. , vol.263 , pp. 1424-1431
    • Yu, M.-H.1    King, J.2
  • 3
    • 0025850262 scopus 로고
    • Global suppression of protein folding defects and inclusion body formation
    • Mitraki, A., Fane, B., Haase-Pettingell, C., Sturtevant, J., King, J. Global suppression of protein folding defects and inclusion body formation. Science 253:54-58, 1991.
    • (1991) Science , vol.253 , pp. 54-58
    • Mitraki, A.1    Fane, B.2    Haase-Pettingell, C.3    Sturtevant, J.4    King, J.5
  • 4
    • 0026348316 scopus 로고
    • Inactive and temperature-sensitive folding mutants generated by tryptophan substitutions in the membrane-bound D-lactate dehydrogenase of Escherichia coli
    • Truong, H.-T., Pratt, E.A., Rule, G.S., Hsue, P.Y., Ho, C. Inactive and temperature-sensitive folding mutants generated by tryptophan substitutions in the membrane-bound D-lactate dehydrogenase of Escherichia coli. Biochemistry 30:10722-10729, 1991.
    • (1991) Biochemistry , vol.30 , pp. 10722-10729
    • Truong, H.-T.1    Pratt, E.A.2    Rule, G.S.3    Hsue, P.Y.4    Ho, C.5
  • 5
    • 3643063644 scopus 로고
    • Mutational effects on inclusion body formation
    • Himmel, M.E., Georgiou, G., (eds.). Washington, D.C.: American Chemical Society.
    • Wetzel, R., Chrunyk, B.A. Mutational effects on inclusion body formation. In: "Biocatalyst Design for Stability and Specificity." Himmel, M.E., Georgiou, G., (eds.). Washington, D.C.: American Chemical Society. 1993:116-125.
    • (1993) Biocatalyst Design for Stability and Specificity , pp. 116-125
    • Wetzel, R.1    Chrunyk, B.A.2
  • 7
    • 14744271625 scopus 로고
    • Protein aggregation in vitro and in vivo: A quantitative model of the kinetic competition between folding and aggregation
    • Kiefhaber, T., Rudolph, R., Kohler, H.-H., Buchner, J. Protein aggregation in vitro and in vivo: A quantitative model of the kinetic competition between folding and aggregation. Bio Technology 9:825-829, 1991.
    • (1991) Bio Technology , vol.9 , pp. 825-829
    • Kiefhaber, T.1    Rudolph, R.2    Kohler, H.-H.3    Buchner, J.4
  • 8
    • 0026751786 scopus 로고
    • The folding of hen lysozyme involves partially structured intermediates and multiple pathways
    • Radford, S.E., Dobson, C.M., Evans, P.A. The folding of hen lysozyme involves partially structured intermediates and multiple pathways. Nature 358:302-307, 1992.
    • (1992) Nature , vol.358 , pp. 302-307
    • Radford, S.E.1    Dobson, C.M.2    Evans, P.A.3
  • 9
    • 0026781019 scopus 로고
    • Early steps in cytochrome c folding probed by time-resolved circular dichroism and fluorescence spectroscopy
    • Elöve, G.A., Chaffotte, A.F., Roder, H., Goldberg, M.E. Early steps in cytochrome c folding probed by time-resolved circular dichroism and fluorescence spectroscopy. Biochemistry 31:6876-6883, 1992.
    • (1992) Biochemistry , vol.31 , pp. 6876-6883
    • Elöve, G.A.1    Chaffotte, A.F.2    Roder, H.3    Goldberg, M.E.4
  • 11
    • 0029973119 scopus 로고    scopus 로고
    • Direct observation of fast protein folding: The initial collapse of apomyoglobin
    • Ballew, R.M., Sabelko, J., Gruebele, M. Direct observation of fast protein folding: The initial collapse of apomyoglobin. Proc. Natl. Acad. Sci. USA 93:5759-5764, 1996.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 5759-5764
    • Ballew, R.M.1    Sabelko, J.2    Gruebele, M.3
  • 12
    • 0030963424 scopus 로고    scopus 로고
    • Fast events in protein folding: Relaxation dynamics of secondary and teriary structure in native apomyoglobin
    • Gilmanshin, R., Williams, S., Callender, R.H., Woodruff, W.H., Dyer, R.B. Fast events in protein folding: Relaxation dynamics of secondary and teriary structure in native apomyoglobin. Proc. Natl. Acad. Sci. USA 94:3709-3713, 1997.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 3709-3713
    • Gilmanshin, R.1    Williams, S.2    Callender, R.H.3    Woodruff, W.H.4    Dyer, R.B.5
  • 13
    • 0030154861 scopus 로고    scopus 로고
    • Cytochrome-c folding triggered by electron-transfer
    • Mines, G.A., Pascher, T., Lee, S.C. Cytochrome-c folding triggered by electron-transfer. Chemistry and Biology 3:491-497, 1996.
    • (1996) Chemistry and Biology , vol.3 , pp. 491-497
    • Mines, G.A.1    Pascher, T.2    Lee, S.C.3
  • 14
    • 0030584652 scopus 로고    scopus 로고
    • Protein folding triggered by electron-transfer
    • Pascher, T., Chesick, J.P., Winkler, J.R., Gray, H.B. Protein folding triggered by electron-transfer. Science 271:1558-1560, 1996.
    • (1996) Science , vol.271 , pp. 1558-1560
    • Pascher, T.1    Chesick, J.P.2    Winkler, J.R.3    Gray, H.B.4
  • 15
    • 0009525454 scopus 로고    scopus 로고
    • Optical triggers of Protein-folding-Response
    • Winkler, J.R., Gray, H.B. Optical triggers of Protein-folding-Response. Science 274:629, 1996.
    • (1996) Science , vol.274 , pp. 629
    • Winkler, J.R.1    Gray, H.B.2
  • 18
    • 0001172389 scopus 로고    scopus 로고
    • Synthesis and photolysis properties of a photolabile linker based on 3-methoxybenzoin
    • Rock, R.S., Chan, S.I. Synthesis and photolysis properties of a photolabile linker based on 3-methoxybenzoin. J. Org. Chem. 61:1526-1529, 1996.
    • (1996) J. Org. Chem. , vol.61 , pp. 1526-1529
    • Rock, R.S.1    Chan, S.I.2
  • 19
    • 0021757436 scopus 로고
    • A new force field for molecular mechanical simulation of nucleic acids and proteins
    • Weiner, S.J., Kollman, P.A., Case, D.A., et al. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:765-784, 1984.
    • (1984) J. Am. Chem. Soc. , vol.106 , pp. 765-784
    • Weiner, S.J.1    Kollman, P.A.2    Case, D.A.3
  • 20
    • 0003864349 scopus 로고    scopus 로고
    • Constant temperature constrained molecular dynamics: The Newton-Euler inverse mass operator method
    • Vaidehi, N., Jain, A., Goddard, W.A., III. Constant temperature constrained molecular dynamics: the Newton-Euler inverse mass operator method. J. Phys. Chem. 100:10508-10517, 1996.
    • (1996) J. Phys. Chem. , vol.100 , pp. 10508-10517
    • Vaidehi, N.1    Jain, A.2    Goddard III, W.A.3
  • 21
    • 0028222235 scopus 로고
    • Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
    • Chakrabartty, A., Kortemme, T., Baldwin, R.L. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 3:843-852, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 843-852
    • Chakrabartty, A.1    Kortemme, T.2    Baldwin, R.L.3
  • 22
    • 0342546152 scopus 로고
    • Étude, par Spectroscopie infra-rouge, de la Conformation de quelques Composés peptidiques modèles
    • Avignon, M., Huong, P.V., Lascombe, J. Étude, par Spectroscopie infra-rouge, de la Conformation de quelques Composés peptidiques modèles. Biopolymers 8:69-89, 1969.
    • (1969) Biopolymers , vol.8 , pp. 69-89
    • Avignon, M.1    Huong, P.V.2    Lascombe, J.3
  • 23
    • 0014467163 scopus 로고
    • Conformational studies of peptide systems: The rotational states of the NH-CH fragment of alanine dipeptides by nuclear magnetic resonance
    • Bystrov, V.F., Portnova, S.L., Tsetlin, V.I., Ivanov, V.T., Ovchinnikov, Yu, A. Conformational studies of peptide systems: The rotational states of the NH-CH fragment of alanine dipeptides by nuclear magnetic resonance. Tetrahedron 25:493-515, 1969.
    • (1969) Tetrahedron , vol.25 , pp. 493-515
    • Bystrov, V.F.1    Portnova, S.L.2    Tsetlin, V.I.3    Ivanov, V.T.4    Ovchinnikov, Yu.A.5
  • 24
    • 0017411710 scopus 로고    scopus 로고
    • The Protein Data Bank: A computer based archival file for macromolecular structures
    • Bernstein, F.C., Koetzle, T.F., Williams, G.J.B, et al. The Protein Data Bank: A computer based archival file for macromolecular structures. J. Mol. Biol. 122:535-542, 1997.
    • (1997) J. Mol. Biol. , vol.122 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.B.3
  • 25
    • 0028952952 scopus 로고
    • Folding simulations of alanine-based peptides with lysine residues
    • Sung, S.-S. Folding simulations of alanine-based peptides with lysine residues. Biophys. J. 68:826-834, 1995.
    • (1995) Biophys. J. , vol.68 , pp. 826-834
    • Sung, S.-S.1
  • 26
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26:283-291, 1993.
    • (1993) J. Appl. Cryst. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 27
    • 0025690309 scopus 로고
    • Situations of gamma-turns in proteins: Their relation to alpha-helices, beta-sheets and ligand binding sites
    • Milner-White, J.E. Situations of gamma-turns in proteins: Their relation to alpha-helices, beta-sheets and ligand binding sites. J. Mol. Biol. 216:385-397, 1990.
    • (1990) J. Mol. Biol. , vol.216 , pp. 385-397
    • Milner-White, J.E.1
  • 28
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W., Saunder, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Saunder, C.2
  • 29
    • 0028200975 scopus 로고
    • Helix folding simulations with various initial conformations
    • Sung, S.-S. Helix folding simulations with various initial conformations. Biophys. J. 66:1796-1803, 1994.
    • (1994) Biophys. J. , vol.66 , pp. 1796-1803
    • Sung, S.-S.1
  • 30
    • 0029011910 scopus 로고
    • Molecular dynamics simulations of isolated helices of myoglobin
    • Hirst, J.D., Brooks, C.L., III. Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry 34:7614-7621, 1995.
    • (1995) Biochemistry , vol.34 , pp. 7614-7621
    • Hirst, J.D.1    Brooks III, C.L.2
  • 31
    • 0026205054 scopus 로고
    • A Molecular dynamics simulation of polyalanine: An analysis of equilibrium motions and helix-coil transitions
    • Daggett, V., Kollman, P.A., Kuntz, I.D. A Molecular dynamics simulation of polyalanine: An analysis of equilibrium motions and helix-coil transitions. Biopolymers 31:1115-1134, 1991.
    • (1991) Biopolymers , vol.31 , pp. 1115-1134
    • Daggett, V.1    Kollman, P.A.2    Kuntz, I.D.3
  • 32
    • 0030006074 scopus 로고    scopus 로고
    • Molecular dynamics simulations of synthetic peptide folding
    • Sung, S.-S., Wu, X.-W. Molecular dynamics simulations of synthetic peptide folding. Proteins 25:202-214, 1996.
    • (1996) Proteins , vol.25 , pp. 202-214
    • Sung, S.-S.1    Wu, X.-W.2
  • 34
    • 0026552361 scopus 로고
    • Folding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence
    • Heinz, D.W., Baase, W.A., Matthew, B.W. Folding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence. Proc. Natl. Acad. Sci. USA 89:3751-3755, 1992.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 3751-3755
    • Heinz, D.W.1    Baase, W.A.2    Matthew, B.W.3
  • 36
  • 37
    • 0344557043 scopus 로고
    • Molecular dynamics and Monte Carlo simulations favor the alpha-helical form for alanine-based peptides in water
    • Tirado-Rives, J., Maxwell, D.S., Jorgensen, W.L. Molecular dynamics and Monte Carlo simulations favor the alpha-helical form for alanine-based peptides in water. J. Am. Chem. Soc. 115:11590-11593, 1993.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 11590-11593
    • Tirado-Rives, J.1    Maxwell, D.S.2    Jorgensen, W.L.3
  • 38
    • 0028831115 scopus 로고
    • 10-helical conformation of alanine-based peptides in aqueous solutions: An electron spin resonance investigation
    • 10-helical conformation of alanine-based peptides in aqueous solutions: An electron spin resonance investigation. J. Am. Chem. Soc. 117:10555-10562, 1995.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 10555-10562
    • Smythe, M.L.1    Nakaie, C.R.2    Marshall, G.R.3
  • 39
    • 0025904730 scopus 로고
    • Defining solution conformations of small linear peptides
    • Dyson, H.J., Wright, P.E. Defining solution conformations of small linear peptides. Annu. Rev. Biophys. Biophys. Chem. 20:519-538, 1991.
    • (1991) Annu. Rev. Biophys. Biophys. Chem. , vol.20 , pp. 519-538
    • Dyson, H.J.1    Wright, P.E.2
  • 40
    • 84988053694 scopus 로고
    • An all atom force-field for simulations of proteins and nucleic acids
    • Weiner, S.J., Kollman, P.A., Nguyen, D.T., Case, D.A. 1986. An all atom force-field for simulations of proteins and nucleic acids. J. Comp. Chem. 7:230-252.
    • (1986) J. Comp. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 41
    • 84860960789 scopus 로고
    • Constrained dynamics of flexible molecules
    • van Gunsteren, W.F. Constrained dynamics of flexible molecules. Mol. Phys. 40:1015-1019, 1980.
    • (1980) Mol. Phys. , vol.40 , pp. 1015-1019
    • Van Gunsteren, W.F.1
  • 42
    • 0030789351 scopus 로고    scopus 로고
    • Temperature jump study of the Helix-coil kinetics of an alaninr peptide interpreted using a kinetic zipper model
    • Thompson, P.A., Eaton, W.A., Hofrichter, J. Temperature jump study of the Helix-coil kinetics of an alaninr peptide interpreted using a kinetic zipper model. Biochemistry 36:9200-9210, 1997.
    • (1997) Biochemistry , vol.36 , pp. 9200-9210
    • Thompson, P.A.1    Eaton, W.A.2    Hofrichter, J.3
  • 43
    • 0030046906 scopus 로고    scopus 로고
    • Fast events in protein folding: Helix melting and formation in a small peptide
    • Williams, S., Causgrove, T.P., Gilmanshin, R., et al. Fast events in protein folding: Helix melting and formation in a small peptide. Biochemistry 35:691-697, 1996.
    • (1996) Biochemistry , vol.35 , pp. 691-697
    • Williams, S.1    Causgrove, T.P.2    Gilmanshin, R.3
  • 44
    • 0001623168 scopus 로고    scopus 로고
    • Helix-coil kinetics: Folding time scales for helical peptides from a sequential kinetic model
    • Brooks, C.L. Helix-coil kinetics: Folding time scales for helical peptides from a sequential kinetic model. J. Phys. Chem. 100:2546-2549, 1996.
    • (1996) J. Phys. Chem. , vol.100 , pp. 2546-2549
    • Brooks, C.L.1
  • 45
    • 3643144954 scopus 로고    scopus 로고
    • Molecular Simulations, Incorporated, San Diego, CA. (MSC version 3.30)
    • POLYGRAF/BIOGRAF. Molecular Simulations, Incorporated, San Diego, CA. (MSC version 3.30).
    • POLYGRAF/BIOGRAF.
  • 46
    • 0000040038 scopus 로고
    • A fast recursive algorithm for molecular dynamics simulations
    • The NEIMO-Hoover alogithm was incorporated into POLYGRAF by N. Vaidehi
    • Jain, A., Vaidehi, N., Rodriguez, G. A fast recursive algorithm for molecular dynamics simulations. J Comp Phys 106:258-268. 1993. The NEIMO-Hoover alogithm was incorporated into POLYGRAF by N. Vaidehi.
    • (1993) J Comp Phys , vol.106 , pp. 258-268
    • Jain, A.1    Vaidehi, N.2    Rodriguez, G.3
  • 47
    • 0028063256 scopus 로고
    • Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics
    • Mathiowetz, A.M., Jain, A., Karasawa, N., Goddard, W.A. Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins 20:227-247, 1994.
    • (1994) Proteins , vol.20 , pp. 227-247
    • Mathiowetz, A.M.1    Jain, A.2    Karasawa, N.3    Goddard, W.A.4
  • 48
    • 33751391161 scopus 로고
    • Helix-coil theories: A comparative study for finite length polypeptides
    • Qian, H., Schellman, J.A. Helix-coil theories: A comparative study for finite length polypeptides. J. Phys. Chem. 96:3987-3994, 1992.
    • (1992) J. Phys. Chem. , vol.96 , pp. 3987-3994
    • Qian, H.1    Schellman, J.A.2
  • 49
    • 34250173942 scopus 로고
    • Conformational equilibria of polypeptides and proteins: The helix-coil transition
    • San Francisco: W.H. Freeman and Co.
    • Cantor, C.R., Schimmel, P.R. Conformational equilibria of polypeptides and proteins: The helix-coil transition. In: "Biophysical Chemistry: The Behavior of Biological Macromolecules." vol. III. San Francisco: W.H. Freeman and Co., 1980:1063-1066.
    • (1980) Biophysical Chemistry: The Behavior of Biological Macromolecules , vol.3 , pp. 1063-1066
    • Cantor, C.R.1    Schimmel, P.R.2
  • 51
    • 0030458565 scopus 로고    scopus 로고
    • A leucine-rich repeat variant with a novel repetitive protein structural motif
    • Peters, J.W., Stowell, M.H.B., Rees, B.C. A leucine-rich repeat variant with a novel repetitive protein structural motif. Nat. Struct. Biol. 3:991-994, 1996.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 991-994
    • Peters, J.W.1    Stowell, M.H.B.2    Rees, B.C.3
  • 52
    • 0000432701 scopus 로고
    • Crystal structure of holoenzyme refined at 1.9 Å resolution: Trigonal-Bipyramidal geometry of the cation binding site
    • Lebioda, L., Stec, B. Crystal structure of holoenzyme refined at 1.9 Å resolution: Trigonal-Bipyramidal geometry of the cation binding site. J. Am. Chem. Soc. 111:8511-8513, 1989.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 8511-8513
    • Lebioda, L.1    Stec, B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.