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Volumn 36, Issue 4, 1999, Pages 436-446

Effects of core-packing on the structure, function, and mechanics of a four-helix-bundle protein ROP

Author keywords

Alpha helix; Coiled coil; Hydrophobic; Molecular dynamics; Protein structure; RNA binding; Rom; Structure function relationships

Indexed keywords

RNA BINDING PROTEIN;

EID: 0032808843     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990901)36:4<436::AID-PROT7>3.0.CO;2-L     Document Type: Article
Times cited : (14)

References (51)
  • 1
    • 0016606973 scopus 로고
    • Structural invariants in protein folding
    • Chothia C. Structural invariants in protein folding. Nature 1975; 254:304-308.
    • (1975) Nature , vol.254 , pp. 304-308
    • Chothia, C.1
  • 2
  • 4
    • 0030850226 scopus 로고    scopus 로고
    • Ideal architecture of residue packing and its observation in protein structures
    • Ragunathan G, Jernigan RL. Ideal architecture of residue packing and its observation in protein structures. Protein Sci 1997;6: 2072-2083.
    • (1997) Protein Sci , vol.6 , pp. 2072-2083
    • Ragunathan, G.1    Jernigan, R.L.2
  • 5
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill KA. Dominant forces in protein folding. Biochemistry 1990;29: 7133-7155.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 6
    • 0031779918 scopus 로고    scopus 로고
    • Design, structure and stability of a hyperthermophilic protein variant
    • Malakauskas SM, Mayo SL. Design, structure and stability of a hyperthermophilic protein variant. Nat Struct Biol 1998;5:470-475.
    • (1998) Nat Struct Biol , vol.5 , pp. 470-475
    • Malakauskas, S.M.1    Mayo, S.L.2
  • 7
    • 0030057864 scopus 로고    scopus 로고
    • What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties
    • Munson M, Balasubramanian S, Fleming KG, et al. What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties. Protein Sci 1996;5:1584-1593.
    • (1996) Protein Sci , vol.5 , pp. 1584-1593
    • Munson, M.1    Balasubramanian, S.2    Fleming, K.G.3
  • 8
    • 0029099960 scopus 로고
    • Engineering thermostability: Lessons from thermophilic proteins
    • Russell RJ, Taylor GL. Engineering thermostability: lessons from thermophilic proteins. Curr Opin Biotechnol 1995;6:360-374.
    • (1995) Curr Opin Biotechnol , vol.6 , pp. 360-374
    • Russell, R.J.1    Taylor, G.L.2
  • 9
    • 0028608066 scopus 로고
    • Redesigning the hydrophobic core of a four-helix-bundle protein
    • Munson M, O'Brien R, Sturtevant JM, Regan L. Redesigning the hydrophobic core of a four-helix-bundle protein. Protein Sci 1994; 3:2015-2022.
    • (1994) Protein Sci , vol.3 , pp. 2015-2022
    • Munson, M.1    O'Brien, R.2    Sturtevant, J.M.3    Regan, L.4
  • 10
    • 0027314187 scopus 로고
    • Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core
    • Ishikawa K, Nakamura H, Morikawa K, Kanaya S. Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core. Biochemistry 1993;32:6171-6178.
    • (1993) Biochemistry , vol.32 , pp. 6171-6178
    • Ishikawa, K.1    Nakamura, H.2    Morikawa, K.3    Kanaya, S.4
  • 11
    • 0023155210 scopus 로고
    • Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder JW, Richards FM. Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 1987;193:775-791.
    • (1987) J Mol Biol , vol.193 , pp. 775-791
    • Ponder, J.W.1    Richards, F.M.2
  • 12
    • 0025277191 scopus 로고
    • The classification and origins of protein folding patterns
    • Chothia C, Finkelstein AV. The classification and origins of protein folding patterns. Annu Rev Biochem 1990;59:1007-1039.
    • (1990) Annu Rev Biochem , vol.59 , pp. 1007-1039
    • Chothia, C.1    Finkelstein, A.V.2
  • 13
    • 0021118508 scopus 로고
    • Principles that determine the structure of proteins
    • Chothia C. Principles that determine the structure of proteins. Annu Rev Biochem 1984;53:537-572.
    • (1984) Annu Rev Biochem , vol.53 , pp. 537-572
    • Chothia, C.1
  • 14
    • 0000920828 scopus 로고
    • The packing of alpha-helices: Simple coiled-coils
    • Crick FHC. The packing of alpha-helices: simple coiled-coils. Acta Crystallogr 1953;6:689-697.
    • (1953) Acta Crystallogr , vol.6 , pp. 689-697
    • Crick, F.H.C.1
  • 15
    • 0027934571 scopus 로고
    • Crystal structure of an isoleucine-zipper trimer
    • Harbury PB, Kim PS, Alber T. Crystal structure of an isoleucine-zipper trimer. Nature 1994;371:80-83.
    • (1994) Nature , vol.371 , pp. 80-83
    • Harbury, P.B.1    Kim, P.S.2    Alber, T.3
  • 16
    • 0027756896 scopus 로고
    • A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants
    • Harbury PB, Zhang T, Kim PS, Alber T. A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 1993;262:1401-1407.
    • (1993) Science , vol.262 , pp. 1401-1407
    • Harbury, P.B.1    Zhang, T.2    Kim, P.S.3    Alber, T.4
  • 17
    • 0025759275 scopus 로고
    • The protein folding problem: The native fold determines packing, but does packing determine the native fold?
    • Behe MJ, Lattman EE, Rose GD. The protein folding problem: the native fold determines packing, but does packing determine the native fold? Proc Natl Acad Sci USA 1991;88:4195-4199.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 4195-4199
    • Behe, M.J.1    Lattman, E.E.2    Rose, G.D.3
  • 18
    • 0032563127 scopus 로고    scopus 로고
    • A general rule for the relationship between hydrophobic effect and conformational stability of a protein: Stability and structure of a series of hydrophobic mutants of human lysozyme
    • Takano K, Yamagat Y, Yutani K. A general rule for the relationship between hydrophobic effect and conformational stability of a protein: stability and structure of a series of hydrophobic mutants of human lysozyme. J Mol Biol 1998:280:749-761.
    • (1998) J Mol Biol , vol.280 , pp. 749-761
    • Takano, K.1    Yamagat, Y.2    Yutani, K.3
  • 19
    • 0027535130 scopus 로고
    • Structural study of mutants of Escherichia coli ribonuclease HI with enhanced thermostability
    • Ishikawa K, Kimura S, Kanaya S, Morikawa K, Nakamura H. Structural study of mutants of Escherichia coli ribonuclease HI with enhanced thermostability. Protein Eng 1993;6:85-91.
    • (1993) Protein Eng , vol.6 , pp. 85-91
    • Ishikawa, K.1    Kimura, S.2    Kanaya, S.3    Morikawa, K.4    Nakamura, H.5
  • 20
    • 0027384577 scopus 로고
    • Effect of cavity creating mutations in the hydrophobic core of chymotrypsin inhibitor 2
    • Jackson SE, Moracci M, elMasry N, Johnson CM, Fersht AR. Effect of cavity creating mutations in the hydrophobic core of chymotrypsin inhibitor 2. Biochemistry 1993;32:11259-11269.
    • (1993) Biochemistry , vol.32 , pp. 11259-11269
    • Jackson, S.E.1    Moracci, M.2    ElMasry, N.3    Johnson, C.M.4    Fersht, A.R.5
  • 21
    • 0029980972 scopus 로고    scopus 로고
    • Active barnase variants with completely random hydrophobic cores
    • Axe DD, Foster NW, Fersht AR. Active barnase variants with completely random hydrophobic cores. Proc Natl Acad Sci USA 1996;93:5590-5594.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 5590-5594
    • Axe, D.D.1    Foster, N.W.2    Fersht, A.R.3
  • 22
    • 0029958604 scopus 로고
    • A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme
    • Gassner NC, Baase WA, Matthews BW. A test of the "jigsaw puzzle" model for protein folding by multiple methionine substitutions within the core of T4 lysozyme. Proc Natl Acad Sci USA 1993;93:12155-12158.
    • (1993) Proc Natl Acad Sci USA , vol.93 , pp. 12155-12158
    • Gassner, N.C.1    Baase, W.A.2    Matthews, B.W.3
  • 23
    • 0024507791 scopus 로고
    • Alternative packing arrangements in the hydrophobic core of λ repressor
    • Lim WA, Sauer RT. Alternative packing arrangements in the hydrophobic core of λ repressor. Nature 1989;339:31-36.
    • (1989) Nature , vol.339 , pp. 31-36
    • Lim, W.A.1    Sauer, R.T.2
  • 24
    • 0032560505 scopus 로고    scopus 로고
    • Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins
    • Závodszky P, Kardos J, Svingor A, Petsko GA. Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins. Proc Natl Acad Sci USA 1998;95:7406-7411.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 7406-7411
    • Závodszky, P.1    Kardos, J.2    Svingor, A.3    Petsko, G.A.4
  • 25
    • 0030987610 scopus 로고    scopus 로고
    • Probing the role of packing specificity in protein design
    • Dahiyat BI, Mayo SL. Probing the role of packing specificity in protein design. Proc Natl Acad Sci USA 1997;94:10172-10177.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 10172-10177
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 26
    • 0030762021 scopus 로고    scopus 로고
    • Coupling backbone flexibility and amino acid sequence selection in protein design
    • Su A, Mayo SL. Coupling backbone flexibility and amino acid sequence selection in protein design. Protein Sci 1997;6:1701-1707.
    • (1997) Protein Sci , vol.6 , pp. 1701-1707
    • Su, A.1    Mayo, S.L.2
  • 27
    • 0029920337 scopus 로고    scopus 로고
    • Protein design automation
    • Dahiyat BI, Mayo SL. Protein design automation. Protein Sci 1996;5:895-903.
    • (1996) Protein Sci , vol.5 , pp. 895-903
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 28
    • 0029091449 scopus 로고
    • Repacking protein cores with backbone freedom: Structure prediction for coiled coils
    • Harbury PB, Tidor B, Kim PS. Repacking protein cores with backbone freedom: structure prediction for coiled coils. Proc Natl Acad Sci USA 1995;92:8408-8412.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 8408-8412
    • Harbury, P.B.1    Tidor, B.2    Kim, P.S.3
  • 29
    • 0028048679 scopus 로고
    • Core-packing constraints hydrophobicity and protein design
    • Baldwin EP, Matthews BW. Core-packing constraints hydrophobicity and protein design. Curr Opin Biotechnol 1994;5:396-402.
    • (1994) Curr Opin Biotechnol , vol.5 , pp. 396-402
    • Baldwin, E.P.1    Matthews, B.W.2
  • 30
    • 0027716138 scopus 로고
    • The role of backbone flexibility in the accomodation of variants that repack the core of T4 lysozyme
    • Baldwin EP, Hajiseyedjavadi O, Baase WA, Matthews BW. The role of backbone flexibility in the accomodation of variants that repack the core of T4 lysozyme. Science 1993;262:1715-1717.
    • (1993) Science , vol.262 , pp. 1715-1717
    • Baldwin, E.P.1    Hajiseyedjavadi, O.2    Baase, W.A.3    Matthews, B.W.4
  • 31
    • 0031018393 scopus 로고    scopus 로고
    • De novo design of native proteins: Characterization of proteins intended to fold into antiparallel, Rop-like, four-helix bundles
    • Betz SF, Liebman PA, DeGrado WF. De novo design of native proteins: characterization of proteins intended to fold into antiparallel, Rop-like, four-helix bundles. Biochemistry 1997:36:2450-2458.
    • (1997) Biochemistry , vol.36 , pp. 2450-2458
    • Betz, S.F.1    Liebman, P.A.2    DeGrado, W.F.3
  • 32
    • 0029899119 scopus 로고    scopus 로고
    • Controlling topology and native-like behavior of de novo designed peptides: Design and characterization of antiparallel four-stranded coiled coils
    • Betz SF, DeGrado WF. Controlling topology and native-like behavior of de novo designed peptides: Design and characterization of antiparallel four-stranded coiled coils. Biochemistry 1996;35:6955-6962.
    • (1996) Biochemistry , vol.35 , pp. 6955-6962
    • Betz, S.F.1    DeGrado, W.F.2
  • 33
    • 0028873824 scopus 로고
    • Dissecting RNA-protein interactions: RNA-RNA recognition by Rop
    • Predki PF, Nayak LM, Gottlieb MBC, Regan L. Dissecting RNA-protein interactions: RNA-RNA recognition by Rop. Cell 1995;80: 41-50.
    • (1995) Cell , vol.80 , pp. 41-50
    • Predki, P.F.1    Nayak, L.M.2    Gottlieb, M.B.C.3    Regan, L.4
  • 35
    • 0021645946 scopus 로고
    • Control of ColEl1 plamid replication: Enhancement of binding of RNA I to the primer transcript by the ROM protein
    • Tomizawa J-I, Som T. Control of ColEl1 plamid replication: enhancement of binding of RNA I to the primer transcript by the ROM protein. Cell 1984;38:871-878.
    • (1984) Cell , vol.38 , pp. 871-878
    • Tomizawa, J.-I.1    Som, T.2
  • 36
    • 0011230535 scopus 로고
    • Control of ColE1 DNA replication: The rop gene product negatively effects transcription from the replication primer promoter
    • Cesarini G, Muesing MA, Polisky B. Control of ColE1 DNA replication: the rop gene product negatively effects transcription from the replication primer promoter. Proc Natl Acad Sci USA 1982;79:6313-6317.
    • (1982) Proc Natl Acad Sci USA , vol.79 , pp. 6313-6317
    • Cesarini, G.1    Muesing, M.A.2    Polisky, B.3
  • 39
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • Pullman B, editor. Dordrecht: D. Reidel Publishing Company
    • Berendsen HJC, Postma JPM, Van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular forces. Dordrecht: D. Reidel Publishing Company; 1981. p 331-342.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gunsteren, W.F.3    Hermans, J.4
  • 41
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes. J Comp Phys 1977;23:327-341.
    • (1977) J Comp Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 42
    • 0023645282 scopus 로고
    • Structure of the ColE1 Rop protein at 1.7 Å resolution
    • Banner DW, Kokkinidis M, Tsernoglou D. Structure of the ColE1 Rop protein at 1.7 Å resolution. J Mol Biol 1987;196:657-675.
    • (1987) J Mol Biol , vol.196 , pp. 657-675
    • Banner, D.W.1    Kokkinidis, M.2    Tsernoglou, D.3
  • 43
    • 0024997234 scopus 로고
    • Proton nuclear magnetic resonance assignments and secondary structure determination of the ColE1 rop (rom) protein
    • Eberle W, Klaus W, Cesareni G, Sander C, Roch P. Proton nuclear magnetic resonance assignments and secondary structure determination of the ColE1 rop (rom) protein. Biochemistry 1990;29: 7402-7407.
    • (1990) Biochemistry , vol.29 , pp. 7402-7407
    • Eberle, W.1    Klaus, W.2    Cesareni, G.3    Sander, C.4    Roch, P.5
  • 45
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 46
    • 0001592034 scopus 로고    scopus 로고
    • Free energy calculations in globular proteins: Methods to reduce errors
    • Di Nola A, Brünger AT. Free energy calculations in globular proteins: methods to reduce errors. J Comp Chem 1998;19:1229-1240.
    • (1998) J Comp Chem , vol.19 , pp. 1229-1240
    • Di Nola, A.1    Brünger, A.T.2
  • 47
    • 0029957901 scopus 로고    scopus 로고
    • Heptad breaks in α-helical coiled-coils: Stutters and stammers
    • Brown JH, Cohen C, Parry DAD. Heptad breaks in α-helical coiled-coils: stutters and stammers. Proteins 1996;26:134-145.
    • (1996) Proteins , vol.26 , pp. 134-145
    • Brown, J.H.1    Cohen, C.2    Parry, D.A.D.3
  • 48
    • 0032901423 scopus 로고    scopus 로고
    • Mechanics and dynamics of B1 domain of protein G: Role of packing and surface hydrophobic residues
    • Ceruso MA, Amadei A, Di Nola A. Mechanics and dynamics of B1 domain of protein G: role of packing and surface hydrophobic residues. Protein Sci 1999;8:147-160.
    • (1999) Protein Sci , vol.8 , pp. 147-160
    • Ceruso, M.A.1    Amadei, A.2    Di Nola, A.3
  • 49
    • 0029147823 scopus 로고
    • Intrinsic Φ Ψ propensities of amino acids, derived from the coil regions of known structures
    • Swindells MB, MacArthur MW, Thornton JM. Intrinsic Φ Ψ propensities of amino acids, derived from the coil regions of known structures. Nat Struct Biol 1995;2:596-603.
    • (1995) Nat Struct Biol , vol.2 , pp. 596-603
    • Swindells, M.B.1    Macarthur, M.W.2    Thornton, J.M.3
  • 50
    • 0027532105 scopus 로고
    • Pitch diversity in a-helical coiled coils
    • Seo J, Cohen C. Pitch diversity in a-helical coiled coils. Proteins 1993;15:223-234.
    • (1993) Proteins , vol.15 , pp. 223-234
    • Seo, J.1    Cohen, C.2


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