메뉴 건너뛰기




Volumn 7, Issue 12, 1998, Pages 2522-2532

Identification of kinetically hot residues in proteins

Author keywords

CheY; Chymotrypsin inhibitor; Conserved residues; Cytochrome c; Folding pathway; Hot residues; Thermal fluctuations; Vibrational dynamics

Indexed keywords

CHYMOTRYPSIN INHIBITOR; CYTOCHROME C;

EID: 0031672563     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560071205     Document Type: Article
Times cited : (114)

References (61)
  • 1
    • 0028024928 scopus 로고
    • Specific nucleus as the transition state for protein folding: Evidence from the lattice model
    • Abkevich VI, Gutin AM, Shakhnovich EI. 1994. Specific nucleus as the transition state for protein folding: Evidence from the lattice model. Biochemistry 33:10026-10036.
    • (1994) Biochemistry , vol.33 , pp. 10026-10036
    • Abkevich, V.I.1    Gutin, A.M.2    Shakhnovich, E.I.3
  • 2
    • 24244444170 scopus 로고
    • The absence of diffusion in certain random lattices
    • Anderson PW. 1958. The absence of diffusion in certain random lattices. Phys Rev 109:1492-1505.
    • (1958) Phys Rev , vol.109 , pp. 1492-1505
    • Anderson, P.W.1
  • 3
    • 35949039411 scopus 로고
    • Local moments and localized states (Nobel lectures in physics for 1977)
    • Anderson PW. 1978. Local moments and localized states (Nobel lectures in physics for 1977). Rev Mod Phys 50:191-201.
    • (1978) Rev Mod Phys , vol.50 , pp. 191-201
    • Anderson, P.W.1
  • 4
    • 0000134121 scopus 로고
    • Crystallization and X-ray structure determination of cytochrome c2 from Rhodobacter sphaeroides in three crystal forms
    • Axelrod HL, Feher G, Rees DC. 1994. Crystallization and X-ray structure determination of cytochrome c2 from Rhodobacter sphaeroides in three crystal forms. Acta Crystallog Sect D Biol Crystallog 50:596-602.
    • (1994) Acta Crystallog Sect D Biol Crystallog , vol.50 , pp. 596-602
    • Axelrod, H.L.1    Feher, G.2    Rees, D.C.3
  • 5
    • 0000496772 scopus 로고    scopus 로고
    • Vibrational dynamics of folded proteins: Significance of slow and fast modes in relation to function and stability
    • Bahar I, Atilgan AR, Demirel MC, Erman B. 1998a. Vibrational dynamics of folded proteins: Significance of slow and fast modes in relation to function and stability. Phys Rev Lett 80:2733-2736.
    • (1998) Phys Rev Lett , vol.80 , pp. 2733-2736
    • Bahar, I.1    Atilgan, A.R.2    Demirel, M.C.3    Erman, B.4
  • 6
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential
    • Bahar I, Atilgan AR, Erman B. 1997. Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential. Fold Design 2:173-181.
    • (1997) Fold Design , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 7
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • Bahar I. Jernigan RL. 1997. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 266:195-214.
    • (1997) J Mol Biol , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 8
    • 0032570266 scopus 로고    scopus 로고
    • Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model
    • Bahar I, Wallquist A, Covell D, Jernigan RL. 1998b. Correlation between native state hydrogen exchange and cooperative residue fluctuations from a simple model. Biochemistry 37:1067-1075.
    • (1998) Biochemistry , vol.37 , pp. 1067-1075
    • Bahar, I.1    Wallquist, A.2    Covell, D.3    Jernigan, R.L.4
  • 9
    • 0029643523 scopus 로고
    • Protein folding intermediates studied by native-state hydrogen exchange
    • Bai Y, Sosnick T, Mayne L, Englander SW. 1995. Protein folding intermediates studied by native-state hydrogen exchange. Science 26:192-197.
    • (1995) Science , vol.26 , pp. 192-197
    • Bai, Y.1    Sosnick, T.2    Mayne, L.3    Englander, S.W.4
  • 10
    • 0028337124 scopus 로고
    • X-ray structure of the cytochrome c2 isolated from Paracoccus denitrificans refined to 1.7 Ångstroms resolution
    • Benning MM, Meyer TE, Holden HM. 1994. X-ray structure of the cytochrome c2 isolated from Paracoccus denitrificans refined to 1.7 Ångstroms resolution. Arch Biochem Biophys 310:460-466.
    • (1994) Arch Biochem Biophys , vol.310 , pp. 460-466
    • Benning, M.M.1    Meyer, T.E.2    Holden, H.M.3
  • 11
    • 0025007598 scopus 로고
    • High-resolution three-dimensional structure of horse heart cytochrome c
    • Bushnell GW, Louie GV, Brayer GD. 1990. High-resolution three-dimensional structure of horse heart cytochrome c. J Mol Biol 214:585-595.
    • (1990) J Mol Biol , vol.214 , pp. 585-595
    • Bushnell, G.W.1    Louie, G.V.2    Brayer, G.D.3
  • 12
    • 0029967474 scopus 로고    scopus 로고
    • Side chain packing of the N- and C-terminal helices plays a critical role in the kinetics of cytochrome c folding
    • Colón W, Elöve GA, Wakem LP, Sherman F, Roder H. 1996. Side chain packing of the N-and C-terminal helices plays a critical role in the kinetics of cytochrome c folding. Biochemistry 35:5538-5549.
    • (1996) Biochemistry , vol.35 , pp. 5538-5549
    • Colón, W.1    Elöve, G.A.2    Wakem, L.P.3    Sherman, F.4    Roder, H.5
  • 13
    • 0030473296 scopus 로고    scopus 로고
    • Kinetic intermediates in the formation of the cytochrome c molten globule
    • Colón W, Roder H. 1996, Kinetic intermediates in the formation of the cytochrome c molten globule. Nature Struct Biol 3:1019-1025.
    • (1996) Nature Struct Biol , vol.3 , pp. 1019-1025
    • Colón, W.1    Roder, H.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 AJ, 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 257:430-440.
    • (1996) J Mol Biol , vol.257 , pp. 430-440
    • Daggett, V.1    Li, A.J.2    Itzhaki, L.S.3    Otzen, D.E.4    Fersht, A.R.5
  • 15
    • 0343680823 scopus 로고
    • The nature of vibrational modes in disordered systems
    • Dean P, Bacon MD. 1963. The nature of vibrational modes in disordered systems. Proc Phys Soc 81:642-641.
    • (1963) Proc Phys Soc , vol.81 , pp. 642-1641
    • Dean, P.1    Bacon, M.D.2
  • 17
    • 0026781019 scopus 로고
    • Early steps in cytochrome c folding probed by time-resolved circular dichroism and fluorescence spectroscopy
    • Elöve GA, Chaffotte AF, Roder H, Goldberg ME. 1992. Early steps in cytochrome c folding probed by time-resolved circular dichroism and fluorescence spectroscopy. Biochemistry 31:6876-6883.
    • (1992) Biochemistry , vol.31 , pp. 6876-6883
    • Elöve, G.A.1    Chaffotte, A.F.2    Roder, H.3    Goldberg, M.E.4
  • 18
    • 0030612609 scopus 로고    scopus 로고
    • Hydrogen exchange: The modern legacy of Linderstrøm-Lang
    • Englander SW, Mayne L, Bai Y, Sosnick TR. 1997. Hydrogen exchange: The modern legacy of Linderstrøm-Lang. Protein Sci 6:1101-1109.
    • (1997) Protein Sci , vol.6 , pp. 1101-1109
    • Englander, S.W.1    Mayne, L.2    Bai, Y.3    Sosnick, T.R.4
  • 19
    • 0031043161 scopus 로고    scopus 로고
    • Nucleation mechanisms in protein folding
    • Fersht AR. 1997. Nucleation mechanisms in protein folding. Curr Opin Struct Biol 7:3-9.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 3-9
    • Fersht, A.R.1
  • 20
    • 0028037217 scopus 로고
    • Single versus parallel pathways of protein folding and fractional formation of structure in the transition state
    • Fersht AR, Itzhaki LS, ElMasry NF, Matthews JM. 1994. Single versus parallel pathways of protein folding and fractional formation of structure in the transition state. Proc Natl Acad Sci USA 91:10426-10429.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 10426-10429
    • Fersht, A.R.1    Itzhaki, L.S.2    ElMasry, N.F.3    Matthews, J.M.4
  • 21
    • 0345973041 scopus 로고    scopus 로고
    • Gaussian dynamics of folded proteins
    • Haliloglu T, Bahar I, Erman B. 1997. Gaussian dynamics of folded proteins. Phys Rev Lett 79:3090-3093.
    • (1997) Phys Rev Lett , vol.79 , pp. 3090-3093
    • Haliloglu, T.1    Bahar, I.2    Erman, B.3
  • 22
    • 0028290005 scopus 로고
    • Parser for protein folding units
    • Holm L, Sander C. 1994. Parser for protein folding units. Proteins 19:256-268.
    • (1994) Proteins , vol.19 , pp. 256-268
    • Holm, L.1    Sander, C.2
  • 23
    • 0028868995 scopus 로고
    • The structure of the transition state for folding of chymotrypsin inhibitor 2 analyzed by protein engineering methods: Evidence for a nucleation condensation mechanism for protein folding
    • Itzhaki LS, Otzen DE, Fersht AR. 1995. The structure of the transition state for folding of chymotrypsin inhibitor 2 analyzed by protein engineering methods: Evidence for a nucleation condensation mechanism for protein folding. J Mol Biol 254:260-288.
    • (1995) J Mol Biol , vol.254 , pp. 260-288
    • Itzhaki, L.S.1    Otzen, D.E.2    Fersht, A.R.3
  • 24
    • 0027382315 scopus 로고
    • Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: A critical test of the protein engineering method of analysis
    • Jackson SE, ElMasry N, Fersht AR. 1993. Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: A critical test of the protein engineering method of analysis. Biochemistry 32:11270-11278.
    • (1993) Biochemistry , vol.32 , pp. 11270-11278
    • Jackson, S.E.1    Elmasry, N.2    Fersht, A.R.3
  • 25
    • 0026009213 scopus 로고
    • Stable submolecular folding units in non-compact form of cytochrome c
    • Jeng MF, Englander SW. 1991. Stable submolecular folding units in non-compact form of cytochrome c. J Mol Biol 221:1045-1061.
    • (1991) J Mol Biol , vol.221 , pp. 1045-1061
    • Jeng, M.F.1    Englander, S.W.2
  • 26
  • 27
    • 0027400842 scopus 로고
    • Molten globule of cytochrome c studied by small angle X-ray scattering
    • Kataoka M, Hagihara Y, Mihara K, Goto Y. 1993. Molten globule of cytochrome c studied by small angle X-ray scattering. J Mol Biol 229:591-596.
    • (1993) J Mol Biol , vol.229 , pp. 591-596
    • Kataoka, M.1    Hagihara, Y.2    Mihara, K.3    Goto, Y.4
  • 28
    • 0025345415 scopus 로고
    • Intermediates in the folding reactions of small proteins
    • Kim PS, Baldwin RL. 1990. Intermediates in the folding reactions of small proteins. Annu Rev Biochem 59:631-660.
    • (1990) Annu Rev Biochem , vol.59 , pp. 631-660
    • Kim, P.S.1    Baldwin, R.L.2
  • 29
    • 0028988453 scopus 로고
    • Stability of α-helices in a molten globule state of cytochrome c by hydrogen/deuterium exchange and two-dimensional NMR spectroscopy
    • Kuroda Y, Endo A, Nagayama K, Wada A. 1995. Stability of α-helices in a molten globule state of cytochrome c by hydrogen/deuterium exchange and two-dimensional NMR spectroscopy. J Mol Biol 247:682-688.
    • (1995) J Mol Biol , vol.247 , pp. 682-688
    • Kuroda, Y.1    Endo, A.2    Nagayama, K.3    Wada, A.4
  • 30
    • 0029963345 scopus 로고    scopus 로고
    • Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
    • Li AJ, 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.J.1    Daggett, V.2
  • 31
    • 0030334834 scopus 로고    scopus 로고
    • Structure of the transition state for the folding of the 129-amino acid protein CheY resembles that of the smaller protein CI2
    • López-Hernández I, Serrano L. 1996. Structure of the transition state for the folding of the 129-amino acid protein CheY resembles that of the smaller protein CI2. Fold Design 2:43-55.
    • (1996) Fold Design , vol.2 , pp. 43-55
    • López-Hernández, I.1    Serrano, L.2
  • 32
    • 0028926855 scopus 로고
    • A native tertiary interaction stabilizes the A state of cytochrome c
    • Marmorino JL, Pielak GJ. 1995. A native tertiary interaction stabilizes the A state of cytochrome c. Biochemistry 34:3140-3143.
    • (1995) Biochemistry , vol.34 , pp. 3140-3143
    • Marmorino, J.L.1    Pielak, G.J.2
  • 33
    • 0023652256 scopus 로고
    • Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds
    • McPhalen CA, James MNG. 1987. Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds. Biochemistry 26:261-269.
    • (1987) Biochemistry , vol.26 , pp. 261-269
    • McPhalen, C.A.1    James, M.N.G.2
  • 34
    • 0029112231 scopus 로고
    • Refined crystal structure of ferrocytochrome C2 from Rhodopseudomonas viridis at 1.6 Å resolution
    • Miki K, Sogabe S. 1995. Refined crystal structure of ferrocytochrome C2 from Rhodopseudomonas viridis at 1.6 Å resolution. J Mol Biol 252:235-247.
    • (1995) J Mol Biol , vol.252 , pp. 235-247
    • Miki, K.1    Sogabe, S.2
  • 35
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa S, Jernigan RL. 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256:623-644.
    • (1996) J Mol Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 36
    • 0028176281 scopus 로고
    • Kinetic characterization of the chemotactic protein from E. coli CheY. Kinetic analysis of the inverse hydrophobic effect
    • Muñoz V, Lopez E, Serrano L. 1994. Kinetic characterization of the chemotactic protein from E. coli CheY. Kinetic analysis of the inverse hydrophobic effect. Biochemistry 33:5858-5866.
    • (1994) Biochemistry , vol.33 , pp. 5858-5866
    • Muñoz, V.1    Lopez, E.2    Serrano, L.3
  • 37
  • 39
    • 0027948175 scopus 로고
    • Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding
    • Otzen DE, Itzhaki LS, ElMasry NF, Jackson S, Fersht, AR. 1994. Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. Proc Natl Acad Sci USA 91:10422-10425.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 10422-10425
    • Otzen, D.E.1    Itzhaki, L.S.2    ElMasry, N.F.3    Jackson, S.4    Fersht, A.R.5
  • 41
    • 0032496419 scopus 로고    scopus 로고
    • Protein folds, and protein evolution: Common folding nucleus in different subfamilies of C-type cytochromes?
    • Ptitsyn O. 1998. Protein folds, and protein evolution: Common folding nucleus in different subfamilies of C-type cytochromes? J Mol Biol 278:655-666.
    • (1998) J Mol Biol , vol.278 , pp. 655-666
    • Ptitsyn, O.1
  • 42
    • 0029124248 scopus 로고
    • Molten globule and protein folding
    • Ptitsyn OB. 1995. Molten globule and protein folding. Adv Protein Chem 47:83-229.
    • (1995) Adv Protein Chem , vol.47 , pp. 83-229
    • Ptitsyn, O.B.1
  • 43
    • 0029886627 scopus 로고    scopus 로고
    • How molten is the molten globule?
    • Ptitsyn OB. 1996. How molten is the molten globule? Nature Struct Biol 3:488-490.
    • (1996) Nature Struct Biol , vol.3 , pp. 488-490
    • Ptitsyn, O.B.1
  • 44
    • 0016671420 scopus 로고
    • A model of myoglobin self-organization
    • Ptitsyn OB, Rashin AA. 1975. A model of myoglobin self-organization. Biophys Chem 3:1-20.
    • (1975) Biophys Chem , vol.3 , pp. 1-20
    • Ptitsyn, O.B.1    Rashin, A.A.2
  • 45
    • 0023705432 scopus 로고
    • Structural characterization of folding intermediates in cytochrome c by H-exchange labeling and proton NMR
    • Roder H, Elöve GA, Englander SW. 1988. Structural characterization of folding intermediates in cytochrome c by H-exchange labeling and proton NMR. Nature 335:700-704.
    • (1988) Nature , vol.335 , pp. 700-704
    • Roder, H.1    Elöve, G.A.2    Englander, S.W.3
  • 46
    • 0344252790 scopus 로고
    • A theory of the linear viscoelastic properties of dilute solutions of coiling polymers
    • Rouse PE. 1953. A theory of the linear viscoelastic properties of dilute solutions of coiling polymers. J Chem Phys 21:1272-1280.
    • (1953) J Chem Phys , vol.21 , pp. 1272-1280
    • Rouse, P.E.1
  • 47
  • 48
    • 0026030641 scopus 로고
    • Database of homology derived protein structures and the structural meaning of sequence alignment
    • Sander C, Schneider R. 1991. Database of homology derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-68.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 49
    • 0043077149 scopus 로고    scopus 로고
    • Dynamics of disordered structures: Effect of nonlinearity on the localization
    • Sayar M, Demirel MC, Atilgan AR. 1997. Dynamics of disordered structures: Effect of nonlinearity on the localization. J Sound Vib 205:372-379.
    • (1997) J Sound Vib , vol.205 , pp. 372-379
    • Sayar, M.1    Demirel, M.C.2    Atilgan, A.R.3
  • 50
    • 0001340839 scopus 로고
    • Kinetics of unfolding and refolding of single-domain proteins
    • Creighton TE, ed. New York: W.H. Freeman and Company
    • Schmid FX 1992. Kinetics of unfolding and refolding of single-domain proteins. In: Creighton TE, ed. Protein folding. New York: W.H. Freeman and Company, pp 197-241.
    • (1992) Protein Folding , pp. 197-241
    • Schmid, F.X.1
  • 51
    • 0030768045 scopus 로고    scopus 로고
    • A residue-specific NMR view of the non-cooperative unfolding of a molten globule
    • Schulman BA, Kim PS, Dobson CM, Redfield C. 1997. A residue-specific NMR view of the non-cooperative unfolding of a molten globule. Nature Struct Biol 4:630-634.
    • (1997) Nature Struct Biol , vol.4 , pp. 630-634
    • Schulman, B.A.1    Kim, P.S.2    Dobson, C.M.3    Redfield, C.4
  • 52
    • 0029670994 scopus 로고    scopus 로고
    • Conserved residues and the mechanism of protein folding
    • Shakhnovich E, Abkevich V, Ptitsyn O. 1996. Conserved residues and the mechanism of protein folding. Nature 379:96-98.
    • (1996) Nature , vol.379 , pp. 96-98
    • Shakhnovich, E.1    Abkevich, V.2    Ptitsyn, O.3
  • 54
    • 0029940033 scopus 로고    scopus 로고
    • Molecular collapse: The rate-limiting step in two-state cytochrome c folding
    • Sosnick TR, Mayne L, Englander SW. 1996. Molecular collapse: The rate-limiting step in two-state cytochrome c folding. Proteins 24:413-426.
    • (1996) Proteins , vol.24 , pp. 413-426
    • Sosnick, T.R.1    Mayne, L.2    Englander, S.W.3
  • 58
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion MM. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77:1905-1908.
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 59
    • 0025741662 scopus 로고
    • Crystal structure of E. coli Che-Y refined at 1.7 Ångstrom resolution
    • Volz K, Matsumura P. 1991. Crystal structure of E. coli Che-Y refined at 1.7 Ångstrom resolution. J Biol Chem 266:15511-15519.
    • (1991) J Biol Chem , vol.266 , pp. 15511-15519
    • Volz, K.1    Matsumura, P.2
  • 61
    • 0031022024 scopus 로고    scopus 로고
    • Two-state models of protein folding kinetics
    • Zwanzig R. 1997. Two-state models of protein folding kinetics. Proc Natl Acad Sci USA 94:148-150.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 148-150
    • Zwanzig, R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.