메뉴 건너뛰기




Volumn 71, Issue 4, 2008, Pages 1670-1685

Solvent-exposed residues located in the β-sheet modulate the stability of the tetramerization domain of p53-A structural and combinatorial approach

Author keywords

Combinatorial library; Hydrophobicity; NMR; Protein stability; Secondary structure propensity; Solvent exposed residues; Tetramerization domain of p53

Indexed keywords

GLYCINE; MUTANT PROTEIN; PROTEIN P53; SOLVENT; TETRAMER; THREONINE; TYROSINE;

EID: 44349183748     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21854     Document Type: Article
Times cited : (15)

References (66)
  • 1
    • 0032835617 scopus 로고    scopus 로고
    • De novo design and structural characterization of proteins and metalloproteins
    • DeGrado WF, Summa CM, Pavone V, Nastri F, Lombardi A. De novo design and structural characterization of proteins and metalloproteins. Annu Rev Biochem 1999;68:779-819.
    • (1999) Annu Rev Biochem , vol.68 , pp. 779-819
    • DeGrado, W.F.1    Summa, C.M.2    Pavone, V.3    Nastri, F.4    Lombardi, A.5
  • 3
    • 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
  • 4
    • 0024295240 scopus 로고
    • Contribution of hydrophobic interactions to protein stability
    • Kellis JT, Jr, Nyberg K, Sali D, Fersht AR. Contribution of hydrophobic interactions to protein stability. Nature 1988;333:784-786.
    • (1988) Nature , vol.333 , pp. 784-786
    • Kellis Jr, J.T.1    Nyberg, K.2    Sali, D.3    Fersht, A.R.4
  • 5
    • 0033006220 scopus 로고    scopus 로고
    • Tolerance of a protein to multiple polar-to-hydrophobic surface substitutions
    • Cordes MH, Sauer RT. Tolerance of a protein to multiple polar-to-hydrophobic surface substitutions. Protein Sci 1999;8:318-325.
    • (1999) Protein Sci , vol.8 , pp. 318-325
    • Cordes, M.H.1    Sauer, R.T.2
  • 6
    • 0036303785 scopus 로고    scopus 로고
    • The effects of ionic strength on protein stability: The cold shock protein family
    • Dominy BN, Perl D, Schmid FX, Brooks CL, III. The effects of ionic strength on protein stability: the cold shock protein family. J Mol Biol 2002;319:541-554.
    • (2002) J Mol Biol , vol.319 , pp. 541-554
    • Dominy, B.N.1    Perl, D.2    Schmid, F.X.3    Brooks III, C.L.4
  • 8
    • 29344472867 scopus 로고    scopus 로고
    • Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer
    • Lee CF, Makhatadze GI, Wong KB. Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer. Biochemistry 2005;44:16817-16825.
    • (2005) Biochemistry , vol.44 , pp. 16817-16825
    • Lee, C.F.1    Makhatadze, G.I.2    Wong, K.B.3
  • 9
    • 0033554840 scopus 로고    scopus 로고
    • Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface
    • Loladze W, Ibarra-Molero B, Sanchez-Ruiz JM, Makhatadze GI. Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface. Biochemistry 1999;38:16419-16423.
    • (1999) Biochemistry , vol.38 , pp. 16419-16423
    • Loladze, W.1    Ibarra-Molero, B.2    Sanchez-Ruiz, J.M.3    Makhatadze, G.I.4
  • 10
    • 0036307678 scopus 로고    scopus 로고
    • Electrostatics significantly affect the stability of designed homeodomain variants
    • Marshall SA, Morgan CS, Mayo SL. Electrostatics significantly affect the stability of designed homeodomain variants. J Mol Biol 2002;316:189-199.
    • (2002) J Mol Biol , vol.316 , pp. 189-199
    • Marshall, S.A.1    Morgan, C.S.2    Mayo, S.L.3
  • 11
    • 0034100848 scopus 로고    scopus 로고
    • Two exposed amino acid residues confer thermostability on a cold shock protein
    • Perl D, Mueller U, Heinemann U, Schmid FX. Two exposed amino acid residues confer thermostability on a cold shock protein. Nat Struct Biol 2000;7:380-383.
    • (2000) Nat Struct Biol , vol.7 , pp. 380-383
    • Perl, D.1    Mueller, U.2    Heinemann, U.3    Schmid, F.X.4
  • 14
    • 0035837241 scopus 로고    scopus 로고
    • The role of tetramerization in p53 function
    • Chene P. The role of tetramerization in p53 function. Oncogene 2001;20:2611-2617.
    • (2001) Oncogene , vol.20 , pp. 2611-2617
    • Chene, P.1
  • 16
    • 0028952841 scopus 로고
    • Crystal structure of the tetramerization domain of the p53 tumor suppressor at 1.7 angstroms
    • Jeffrey PD, Gorina S, Pavletich NP. Crystal structure of the tetramerization domain of the p53 tumor suppressor at 1.7 angstroms. Science 1995;267:1498-1502.
    • (1995) Science , vol.267 , pp. 1498-1502
    • Jeffrey, P.D.1    Gorina, S.2    Pavletich, N.P.3
  • 17
    • 0032906377 scopus 로고    scopus 로고
    • Mechanism of folding and assembly of a small tetrameric protein domain from tumor suppressor p53
    • Mateu MG, Sánchez del Pino MM, Fersht AR. Mechanism of folding and assembly of a small tetrameric protein domain from tumor suppressor p53. Nat Struct Biol 1999;6:191-198.
    • (1999) Nat Struct Biol , vol.6 , pp. 191-198
    • Mateu, M.G.1    Sánchez del Pino, M.M.2    Fersht, A.R.3
  • 18
    • 0032525133 scopus 로고    scopus 로고
    • Nine hydrophobic side chains are key determinants of the thermodynamic stability and oligomerization status of tumour suppressor p53 tetramerization domain
    • Mateu MG, Fersht AR. Nine hydrophobic side chains are key determinants of the thermodynamic stability and oligomerization status of tumour suppressor p53 tetramerization domain. EMBO J 1998;17:2748-2758.
    • (1998) EMBO J , vol.17 , pp. 2748-2758
    • Mateu, M.G.1    Fersht, A.R.2
  • 19
    • 2342649511 scopus 로고    scopus 로고
    • Combinatorial approaches to protein stability and structure
    • Magliery TJ, Regan L. Combinatorial approaches to protein stability and structure. Eur J Biochem 2004;271:1595-1608.
    • (2004) Eur J Biochem , vol.271 , pp. 1595-1608
    • Magliery, T.J.1    Regan, L.2
  • 21
    • 0031951844 scopus 로고    scopus 로고
    • Crystallization and structure solution of p53 (residues 326-356) by molecular replacement using an NMR model as template
    • Mittl PR, Chene P, Grutter MG. Crystallization and structure solution of p53 (residues 326-356) by molecular replacement using an NMR model as template. Acta Crystallogr D Biol Crystallogr 1998;54:86-89.
    • (1998) Acta Crystallogr D Biol Crystallogr , vol.54 , pp. 86-89
    • Mittl, P.R.1    Chene, P.2    Grutter, M.G.3
  • 23
    • 7944235729 scopus 로고    scopus 로고
    • Design of bioactive and structurally well-defined peptides from conformationally restricted libraries
    • Pastor MT, Mora P, Ferrer-Montiel A, Perez-Paya E. Design of bioactive and structurally well-defined peptides from conformationally restricted libraries. Biopolymers 2004;76:357-365.
    • (2004) Biopolymers , vol.76 , pp. 357-365
    • Pastor, M.T.1    Mora, P.2    Ferrer-Montiel, A.3    Perez-Paya, E.4
  • 24
    • 0345827422 scopus 로고    scopus 로고
    • Combinatorial chemistry of beta-hairpins
    • Pastor MT, Perez-Paya E. Combinatorial chemistry of beta-hairpins. Mol Divers 2003;6:149-155.
    • (2003) Mol Divers , vol.6 , pp. 149-155
    • Pastor, M.T.1    Perez-Paya, E.2
  • 26
    • 0000478940 scopus 로고
    • General method for the rapid solid-phase synthesis of large number of peptides: Specificity of antigen-antibody interaction at the level of individual amino acids
    • Houghten RA. General method for the rapid solid-phase synthesis of large number of peptides: specificity of antigen-antibody interaction at the level of individual amino acids. Proc Natl Acad Sci USA 1985;82:5131-5135.
    • (1985) Proc Natl Acad Sci USA , vol.82 , pp. 5131-5135
    • Houghten, R.A.1
  • 27
    • 0025232814 scopus 로고
    • Solid phase peptide synthesis utilizing 9-fluorenylmethoxycarbonyl amino acids
    • Fields GB, Noble RL. Solid phase peptide synthesis utilizing 9-fluorenylmethoxycarbonyl amino acids. Int J Pept Protein Res 1990;35:161-214.
    • (1990) Int J Pept Protein Res , vol.35 , pp. 161-214
    • Fields, G.B.1    Noble, R.L.2
  • 28
    • 0030047220 scopus 로고    scopus 로고
    • Functionalized protein-like structures from conformationally defined synthetic combinatorial libraries
    • Perez-Paya E, Houghten RA, Blondelle SE. Functionalized protein-like structures from conformationally defined synthetic combinatorial libraries. J Biol Chem 1996;271:4120-4126.
    • (1996) J Biol Chem , vol.271 , pp. 4120-4126
    • Perez-Paya, E.1    Houghten, R.A.2    Blondelle, S.E.3
  • 29
    • 0026633609 scopus 로고
    • Singular value decomposition: Application to analysis of experimental data
    • Henry ER, Hofrichter J. Singular value decomposition: application to analysis of experimental data. Methods Enzymol 1992;210:129-192.
    • (1992) Methods Enzymol , vol.210 , pp. 129-192
    • Henry, E.R.1    Hofrichter, J.2
  • 31
    • 0026608073 scopus 로고
    • Environment affects amino acid preference for secondary structure
    • Zhong L, Johnson WC, Jr. Environment affects amino acid preference for secondary structure. Proc Natl Acad Sci USA. 1992;89:4462-4465.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 4462-4465
    • Zhong, L.1    Johnson Jr., W.C.2
  • 32
    • 0028174643 scopus 로고
    • Quantitative determination of helical propensities from trifluoroethanol titration curves
    • Jasanoff A, Fersht AR. Quantitative determination of helical propensities from trifluoroethanol titration curves. Biochemistry 1994;33:2129-2135.
    • (1994) Biochemistry , vol.33 , pp. 2129-2135
    • Jasanoff, A.1    Fersht, A.R.2
  • 33
    • 0028890190 scopus 로고
    • Induced conformational states of amphipathic peptides in aqueous/lipid environments
    • Blondelle SE, Ostresh JM, Floughten RA, Perez-Paya E. Induced conformational states of amphipathic peptides in aqueous/lipid environments. Biophys J 1995;68:351-359.
    • (1995) Biophys J , vol.68 , pp. 351-359
    • Blondelle, S.E.1    Ostresh, J.M.2    Floughten, R.A.3    Perez-Paya, E.4
  • 34
    • 0029000171 scopus 로고
    • Thermodynamic analysis of the structural stability of the tetrameric oligomerization domain of p53 tumor suppressor
    • Johnson CR, Morin PE, Arrowsmith CH, Freire E. Thermodynamic analysis of the structural stability of the tetrameric oligomerization domain of p53 tumor suppressor. Biochemistry 1995;34:5309-5316.
    • (1995) Biochemistry , vol.34 , pp. 5309-5316
    • Johnson, C.R.1    Morin, P.E.2    Arrowsmith, C.H.3    Freire, E.4
  • 35
    • 0027733616 scopus 로고
    • Use of fast protein size-exclusion liquid chromatography to study the unfolding of proteins which denature through the molten globule
    • Uversky VN. Use of fast protein size-exclusion liquid chromatography to study the unfolding of proteins which denature through the molten globule. Biochemistry 1993;32:13288-13298.
    • (1993) Biochemistry , vol.32 , pp. 13288-13298
    • Uversky, V.N.1
  • 37
    • 0002498995 scopus 로고
    • Computer-aided interpretation of analytical sedimentation data for proteins
    • Harding SE, Rowe AJ, Horton JC, editors, Cambridge, UK: The Royal Society of Chemistry;
    • Laue T, Shaw BD, Ridgeway TM, Pelletier SL. Computer-aided interpretation of analytical sedimentation data for proteins. In: Harding SE, Rowe AJ, Horton JC, editors. Analytical Ultracentrifugation in Biochemistry and Polymer Science. Cambridge, UK: The Royal Society of Chemistry; 1992. pp 90-125.
    • (1992) Analytical Ultracentrifugation in Biochemistry and Polymer Science , pp. 90-125
    • Laue, T.1    Shaw, B.D.2    Ridgeway, T.M.3    Pelletier, S.L.4
  • 39
    • 44349088526 scopus 로고    scopus 로고
    • Goddard TD, Kneller DG. SPARKY 3. San Francisco: University of California; 2005.
    • Goddard TD, Kneller DG. SPARKY 3. San Francisco: University of California; 2005.
  • 41
    • 0021719074 scopus 로고
    • Synthesis of a model protein of defined secondary and quaternary structure. Effect of chain length on the stabilization and formation of two-stranded alpha-helical coiled-coils
    • Lau SY, Taneja AK, Hodges RS. Synthesis of a model protein of defined secondary and quaternary structure. Effect of chain length on the stabilization and formation of two-stranded alpha-helical coiled-coils. J Biol Chem 1984;259:13253-13261.
    • (1984) J Biol Chem , vol.259 , pp. 13253-13261
    • Lau, S.Y.1    Taneja, A.K.2    Hodges, R.S.3
  • 42
    • 0029058159 scopus 로고
    • An analysis of side chain interactions and pair correlations within antiparallel β-sheets: The differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs
    • Wouters MA, Curmi PM. An analysis of side chain interactions and pair correlations within antiparallel β-sheets: the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs. Proteins 1995;22:119-131.
    • (1995) Proteins , vol.22 , pp. 119-131
    • Wouters, M.A.1    Curmi, P.M.2
  • 43
    • 0025906146 scopus 로고
    • Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area
    • Livingstone JR, Spolar RS, Record MT, Jr. Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry 1991;30:4237-4244.
    • (1991) Biochemistry , vol.30 , pp. 4237-4244
    • Livingstone, J.R.1    Spolar, R.S.2    Record Jr., M.T.3
  • 44
    • 0030722137 scopus 로고    scopus 로고
    • Hydrophobic side-chain size is a determinant of the three-dimensional structure of the p53 oligomerization domain
    • McCoy M, Stavridi ES, Waterman JL, Wieczorek AM, Opella SJ, Halazonetis TD. Hydrophobic side-chain size is a determinant of the three-dimensional structure of the p53 oligomerization domain. EMBO J 1997;16:6230-6236.
    • (1997) EMBO J , vol.16 , pp. 6230-6236
    • McCoy, M.1    Stavridi, E.S.2    Waterman, J.L.3    Wieczorek, A.M.4    Opella, S.J.5    Halazonetis, T.D.6
  • 45
    • 0034786608 scopus 로고    scopus 로고
    • Hydrogen exchange of the tetramerization domain of the human tumour suppressor p53 probed by denaturants and temperature
    • Neira JL, Mateu MG. Hydrogen exchange of the tetramerization domain of the human tumour suppressor p53 probed by denaturants and temperature. Eur J Biochem 2001;268:4868-4877.
    • (2001) Eur J Biochem , vol.268 , pp. 4868-4877
    • Neira, J.L.1    Mateu, M.G.2
  • 47
    • 0031558782 scopus 로고    scopus 로고
    • In vitro structure-function analysis of the β-strand 326-333 of human p53
    • Chene P, Mittl P, Grutter M. In vitro structure-function analysis of the β-strand 326-333 of human p53. J Mol Biol 1997;273:873-881.
    • (1997) J Mol Biol , vol.273 , pp. 873-881
    • Chene, P.1    Mittl, P.2    Grutter, M.3
  • 49
    • 0034685612 scopus 로고    scopus 로고
    • Stabilization of GroEL minichaperones by core and surface mutations
    • Wang Q, Buckle AM, Fersht AR. Stabilization of GroEL minichaperones by core and surface mutations. J Mol Biol 2000;298:917-926.
    • (2000) J Mol Biol , vol.298 , pp. 917-926
    • Wang, Q.1    Buckle, A.M.2    Fersht, A.R.3
  • 50
    • 0028568650 scopus 로고
    • Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: Comparison with experimental scales
    • Muñoz V, Serrano L. Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales. Proteins 1994;20:301-311.
    • (1994) Proteins , vol.20 , pp. 301-311
    • Muñoz, V.1    Serrano, L.2
  • 51
    • 0018093765 scopus 로고
    • Conformational preferences of amino acids in globular proteins
    • Levitt M. Conformational preferences of amino acids in globular proteins. Biochemistry 1978;17:4277-4285.
    • (1978) Biochemistry , vol.17 , pp. 4277-4285
    • Levitt, M.1
  • 52
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235:983-1002.
    • (1994) J Mol Biol , vol.235 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 53
    • 0029900846 scopus 로고    scopus 로고
    • The magnitude of the backbone conformational entropy change in protein folding
    • D'Aquino JA, Gomez J, Hilser VJ, Lee KH, Amzel LM, Freire E. The magnitude of the backbone conformational entropy change in protein folding. Proteins 1996;25:143-156.
    • (1996) Proteins , vol.25 , pp. 143-156
    • D'Aquino, J.A.1    Gomez, J.2    Hilser, V.J.3    Lee, K.H.4    Amzel, L.M.5    Freire, E.6
  • 54
    • 0027991081 scopus 로고
    • Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation
    • Lee KH, Xie D, Freire E, Amzel LM. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins 1994;20:68-84.
    • (1994) Proteins , vol.20 , pp. 68-84
    • Lee, K.H.1    Xie, D.2    Freire, E.3    Amzel, L.M.4
  • 55
    • 0027166270 scopus 로고
    • Empirical scale of side-chain conformational entropy in protein folding
    • Pickett SD, Sternberg MJ. Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 1993;231:825-839.
    • (1993) J Mol Biol , vol.231 , pp. 825-839
    • Pickett, S.D.1    Sternberg, M.J.2
  • 56
    • 0029070109 scopus 로고
    • Conserved structural features on protein surfaces: Small exterior hydrophobic clusters
    • Tisi LC, Evans PA. Conserved structural features on protein surfaces: small exterior hydrophobic clusters. J Mol Biol 1995;249:251-258.
    • (1995) J Mol Biol , vol.249 , pp. 251-258
    • Tisi, L.C.1    Evans, P.A.2
  • 57
    • 0032510765 scopus 로고    scopus 로고
    • Stability effects of increasing the hydrophobicity of solvent-exposed side chains in staphylococcal nuclease
    • Schwehm JM, Kristyanne ES, Biggers CC, Stites WE. Stability effects of increasing the hydrophobicity of solvent-exposed side chains in staphylococcal nuclease. Biochemistry 1998;37:6939-6948.
    • (1998) Biochemistry , vol.37 , pp. 6939-6948
    • Schwehm, J.M.1    Kristyanne, E.S.2    Biggers, C.C.3    Stites, W.E.4
  • 58
    • 0034657321 scopus 로고    scopus 로고
    • A polar, solvent-exposed residue can be essential for native protein structure
    • Hill RB, DeGrado WF. A polar, solvent-exposed residue can be essential for native protein structure. Struct Fold Des 2000;8:471-479.
    • (2000) Struct Fold Des , vol.8 , pp. 471-479
    • Hill, R.B.1    DeGrado, W.F.2
  • 59
    • 2542509342 scopus 로고    scopus 로고
    • Cellular characterisation of p53 mutants with a single missense mutation in the beta-strand 326-333 and correlation of their cellular activities with in vitro properties
    • Chene P, Bechter E. Cellular characterisation of p53 mutants with a single missense mutation in the beta-strand 326-333 and correlation of their cellular activities with in vitro properties. J Mol Biol 1999;288:891-897.
    • (1999) J Mol Biol , vol.288 , pp. 891-897
    • Chene, P.1    Bechter, E.2
  • 60
    • 0030850228 scopus 로고    scopus 로고
    • Evaluating the energetics of empty cavities and internal mutations in proteins
    • Rashin AA, Rashin BH, Rashin A, Abagyan R. Evaluating the energetics of empty cavities and internal mutations in proteins. Protein Sci 1997;6:2143-2158.
    • (1997) Protein Sci , vol.6 , pp. 2143-2158
    • Rashin, A.A.1    Rashin, B.H.2    Rashin, A.3    Abagyan, R.4
  • 61
    • 0036266942 scopus 로고    scopus 로고
    • Conformational strain in the hydrophobic core and its implications for protein folding and design
    • Ventura S, Vega MC, Lacroix E, Angrand I, Spagnolo L, Serrano L. Conformational strain in the hydrophobic core and its implications for protein folding and design. Nat Struct Biol 2002;9:485-493.
    • (2002) Nat Struct Biol , vol.9 , pp. 485-493
    • Ventura, S.1    Vega, M.C.2    Lacroix, E.3    Angrand, I.4    Spagnolo, L.5    Serrano, L.6
  • 62
    • 0029927321 scopus 로고    scopus 로고
    • A recipe for designing water-soluble, β-sheet-forming peptides
    • Mayo KH, Ilyina E, Park H. A recipe for designing water-soluble, β-sheet-forming peptides. Protein Sci 1996;5:1301-1315.
    • (1996) Protein Sci , vol.5 , pp. 1301-1315
    • Mayo, K.H.1    Ilyina, E.2    Park, H.3
  • 63
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:379-400.
    • (1971) J Mol Biol , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 64
    • 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 1991;253:54-58.
    • (1991) Science , vol.253 , pp. 54-58
    • Mitraki, A.1    Fane, B.2    Haase-Pettingell, C.3    Sturtevant, J.4    King, J.5
  • 66
    • 2542599277 scopus 로고    scopus 로고
    • Phi-value analysis and the nature of protein-folding transition states
    • Fersht AR, Sato S. Phi-value analysis and the nature of protein-folding transition states. Proc Natl Acad Sci USA 2004;101:7976-7981.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7976-7981
    • Fersht, A.R.1    Sato, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.