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Volumn 86, Issue 1 I, 2004, Pages 23-30

On Hydrophobicity and Conformational Specificity in Proteins

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN; MONOMER;

EID: 0347949638     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74080-1     Document Type: Article
Times cited : (26)

References (53)
  • 1
    • 0035964177 scopus 로고    scopus 로고
    • Polar residues in the core of Escherichia coli thioredoxin are important for fold specificity
    • Bolon, D. N., and S. L. Mayo. 2001. Polar residues in the core of Escherichia coli thioredoxin are important for fold specificity. Biochemistry. 40:10047-10053.
    • (2001) Biochemistry , vol.40 , pp. 10047-10053
    • Bolon, D.N.1    Mayo, S.L.2
  • 2
    • 0030782481 scopus 로고    scopus 로고
    • How are model protein structures distributed in sequence space?
    • Bornberg-Bauer, E. 1997. How are model protein structures distributed in sequence space? Biochemistry. 73:2393-2403.
    • (1997) Biochemistry , vol.73 , pp. 2393-2403
    • Bornberg-Bauer, E.1
  • 3
    • 13044269058 scopus 로고    scopus 로고
    • Modeling evolutionary landscapes: Mutational stability, topology and superfunnels in sequence space
    • Bornberg-Bauer, E. and H. S. Chan. 1999. Modeling evolutionary landscapes: mutational stability, topology and superfunnels in sequence space. Proc. Natl. Acad. Sci. USA. 96:10689-10694.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 10689-10694
    • Bornberg-Bauer, E.1    Chan, H.S.2
  • 4
    • 0023449962 scopus 로고
    • Spin-glasses and the statistical-mechanics of protein folding
    • Bryngelson, J. D., and P. G. Wolynes. 1987. Spin-glasses and the statistical-mechanics of protein folding. Proc. Natl Natl. Acad. Sci. USA. 84:7524-7528.
    • (1987) Proc. Natl. Natl. Acad. Sci. USA , vol.84 , pp. 7524-7528
    • Bryngelson, J.D.1    Wolynes, P.G.2
  • 5
    • 0034284366 scopus 로고    scopus 로고
    • Modeling protein density of states: Additive hydrophobic effects are insufficient for calorimetric two-state cooperativity
    • Chan, H. S. 2000. Modeling protein density of states: additive hydrophobic effects are insufficient for calorimetric two-state cooperativity. Prot. Struct. Funct. Gen. 40:543-571.
    • (2000) Prot. Struct. Funct. Gen. , vol.40 , pp. 543-571
    • Chan, H.S.1
  • 6
    • 0002134029 scopus 로고    scopus 로고
    • Computational methods for protein folding: Scaling a hierarchy of complexities
    • T. Jiang, Y. Xu, and M. Q. Zhang, editors. MIT Press, Cambridge, MA
    • Chan, H. S., H. Kaya, and S. Shimizu. 2002. Computational methods for protein folding: scaling a hierarchy of complexities. In Current Topics in Computational Molecular Biology. T. Jiang, Y. Xu, and M. Q. Zhang, editors. MIT Press, Cambridge, MA. 403-447.
    • (2002) Current Topics in Computational Molecular Biology , pp. 403-447
    • Chan, H.S.1    Kaya, H.2    Shimizu, S.3
  • 7
    • 0013527261 scopus 로고    scopus 로고
    • Perspectives on protein evolution from simple exact models
    • Chan, H. S., and E. Bornberg-Bauer. 2002. Perspectives on protein evolution from simple exact models. Appl. Bioinformatics. 1:121-144.
    • (2002) Appl. Bioinformatics , vol.1 , pp. 121-144
    • Chan, H.S.1    Bornberg-Bauer, E.2
  • 8
    • 0016606973 scopus 로고
    • Structural invariants in protein folding
    • Chothia, C. 1975. Structural invariants in protein folding. Nature. 254:304-308.
    • (1975) Nature , vol.254 , pp. 304-308
    • Chothia, C.1
  • 9
    • 0017187836 scopus 로고
    • The nature of the accessible and buried surfaces in proteins
    • Chothia, C. 1976. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105:1-14.
    • (1976) J. Mol. Biol. , vol.105 , pp. 1-14
    • Chothia, C.1
  • 12
    • 0037154157 scopus 로고    scopus 로고
    • Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes
    • Cui, Y., W. H. Wong, E. Bornberg-Bauer, and H. S. Chan. 2002. Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes. Proc. Natl. Acad. Sci. USA. 99:809-814.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 809-814
    • Cui, Y.1    Wong, W.H.2    Bornberg-Bauer, E.3    Chan, H.S.4
  • 13
    • 0031558762 scopus 로고    scopus 로고
    • De novo protein design: Towards fully automated sequence selection
    • Dahiyat, B. I., C. A. Sarisky, and S. L. Mayo. 1997. De novo protein design: towards fully automated sequence selection. J. Mol. Biol. 273:789-796.
    • (1997) J. Mol. Biol. , vol.273 , pp. 789-796
    • Dahiyat, B.I.1    Sarisky, C.A.2    Mayo, S.L.3
  • 14
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill, K. A. 1990. Dominant forces in protein folding. Biochemistry. 29:7133-7155.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 15
    • 0026567907 scopus 로고
    • Response of a protein-structure to cavity-creating mutations and its relation to the hydrophobic effect
    • Eriksson, A. E., W. A. Baase, X. J. Zhang, D. W. Heinz, M. Blaber, E. P. Baldwin, and B. W. Matthews. 1992. Response of a protein-structure to cavity-creating mutations and its relation to the hydrophobic effect. Science. 255:178-183.
    • (1992) Science , vol.255 , pp. 178-183
    • Eriksson, A.E.1    Baase, W.A.2    Zhang, X.J.3    Heinz, D.W.4    Blaber, M.5    Baldwin, E.P.6    Matthews, B.W.7
  • 16
    • 0020972782 scopus 로고
    • Theoretical studies of protein folding
    • Gõ, N. 1983. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12:183-210.
    • (1983) Annu. Rev. Biophys. Bioeng. , vol.12 , pp. 183-210
    • Gõ, N.1
  • 18
    • 0028204490 scopus 로고
    • Do salt bridges stabilize proteins? A continuum electrostatic analysis
    • Hendsch, Z. S., and B. Tidor. 1994. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Prot. Sci. 3:211-226.
    • (1994) Prot. Sci. , vol.3 , pp. 211-226
    • Hendsch, Z.S.1    Tidor, B.2
  • 19
    • 0000773431 scopus 로고
    • Studies of an off-lattice model for protein folding: Sequence dependence and improved sampling at finite temperature
    • Irbäck, A., and F. Potthast. 1995. Studies of an off-lattice model for protein folding: sequence dependence and improved sampling at finite temperature. J. Chem. Phys. 103:10298-10305.
    • (1995) J. Chem. Phys. , vol.103 , pp. 10298-10305
    • Irbäck, A.1    Potthast, F.2
  • 20
    • 0033103164 scopus 로고    scopus 로고
    • Design of sequences with good folding properties in coarse-grained protein models
    • Irbäck, A., C. Peterson, F. Potthast, and E. Sandelin. 1999. Design of sequences with good folding properties in coarse-grained protein models. Struct. Fold. Des. 7:347-360.
    • (1999) Struct. Fold. Des. , vol.7 , pp. 347-360
    • Irbäck, A.1    Peterson, C.2    Potthast, F.3    Sandelin, E.4
  • 21
    • 0033738980 scopus 로고    scopus 로고
    • On hydrophobicity correlations in protein chains
    • Irbäck, A., and E. Sandelin. 2000. On hydrophobicity correlations in protein chains. Biophys. J. 79:2252-2258.
    • (2000) Biophys. J. , vol.79 , pp. 2252-2258
    • Irbäck, A.1    Sandelin, E.2
  • 22
    • 0036345270 scopus 로고    scopus 로고
    • Enumerating designing sequences in the HP model
    • Irbäck, A., and C. Troein. 2002. Enumerating designing sequences in the HP model. J. Biol. Phys. 28:1-15.
    • (2002) J. Biol. Phys. , vol.28 , pp. 1-15
    • Irbäck, A.1    Troein, C.2
  • 23
    • 0017154517 scopus 로고
    • Surface area of globular proteins
    • Janin, J. 1976. Surface area of globular proteins. J. Mol. Biol. 105:13-14.
    • (1976) J. Mol. Biol. , vol.105 , pp. 13-14
    • Janin, J.1
  • 24
    • 0034142250 scopus 로고    scopus 로고
    • Buried polar interactions and conformational stability in the simian immunodeficiency virus (SIV) gp41 core
    • Ji, H., C. Bracken, and M. Lu. 2000. Buried polar interactions and conformational stability in the simian immunodeficiency virus (SIV) gp41 core. Biochemistry. 4:676-685.
    • (2000) Biochemistry , vol.4 , pp. 676-685
    • Ji, H.1    Bracken, C.2    Lu, M.3
  • 27
    • 0034284060 scopus 로고    scopus 로고
    • Polymer principles of protein calorimetric two-state cooperativity
    • Kaya, H., and H. S. Chan. 2000a. Polymer principles of protein calorimetric two-state cooperativity. Prot. Struct. Funct. Gen. 40:637-661.
    • (2000) Prot. Struct. Funct. Gen. , vol.40 , pp. 637-661
    • Kaya, H.1    Chan, H.S.2
  • 28
    • 0034310589 scopus 로고    scopus 로고
    • Energetic components of cooperative protein folding
    • Kaya, H., and H. S. Chan. 2000b. Energetic components of cooperative protein folding. Phys. Rev. Lett. 85:4823-4826.
    • (2000) Phys. Rev. Lett. , vol.85 , pp. 4823-4826
    • Kaya, H.1    Chan, H.S.2
  • 29
    • 0033550206 scopus 로고    scopus 로고
    • De novo protein design. I. In search of stability and specificity
    • Koehl, P., and M. Levitt. 1999. De novo protein design. I. In search of stability and specificity. J. Mol. Biol. 293:1161-1181.
    • (1999) J. Mol. Biol. , vol.293 , pp. 1161-1181
    • Koehl, P.1    Levitt, M.2
  • 30
    • 0024750637 scopus 로고
    • A lattice statistical model for the conformational and sequence spaces of proteins
    • Lau, K. F., and K. A. Dill. 1989. A lattice statistical model for the conformational and sequence spaces of proteins. Macromolecules. 22:3986-3997.
    • (1989) Macromolecules , vol.22 , pp. 3986-3997
    • Lau, K.F.1    Dill, K.A.2
  • 31
    • 0029772552 scopus 로고    scopus 로고
    • Emergence of preferred structures in a simple model of protein folding
    • Li, H., R. Helling, C. Tang, and N. Wingreen. 1996. Emergence of preferred structures in a simple model of protein folding. Science. 273:666-669.
    • (1996) Science , vol.273 , pp. 666-669
    • Li, H.1    Helling, R.2    Tang, C.3    Wingreen, N.4
  • 32
    • 84912079256 scopus 로고
    • Rapid approximation to molecular-surface area via the use of Boolean logic and look-up tables
    • Legrand, S. M., and K. M. Merz. 1993. Rapid approximation to molecular-surface area via the use of Boolean logic and look-up tables. J. Comput. Chem. 14:349-352.
    • (1993) J. Comput. Chem. , vol.14 , pp. 349-352
    • Legrand, S.M.1    Merz, K.M.2
  • 33
    • 0036297743 scopus 로고    scopus 로고
    • Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior
    • Loladze, V. V., D. N. Ermolenko, and G. I. Makhatadze. 2002. Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior. J. Mol. Biol. 320:343-357.
    • (2002) J. Mol. Biol. , vol.320 , pp. 343-357
    • Loladze, V.V.1    Ermolenko, D.N.2    Makhatadze, G.I.3
  • 34
    • 0029008590 scopus 로고
    • A buried polar interaction imparts structural uniqueness in a designed Heterodimeric coiled-coil
    • Lumb, K. J., and P. S. Kim. 1995. A buried polar interaction imparts structural uniqueness in a designed Heterodimeric coiled-coil. Biochemistry. 34:8642-8648.
    • (1995) Biochemistry , vol.34 , pp. 8642-8648
    • Lumb, K.J.1    Kim, P.S.2
  • 35
    • 0031779918 scopus 로고    scopus 로고
    • Design, structure and stability of a hyperthermophilic protein variant
    • Malakauskas, S. M., and S. L. Mayo. 1998. Design, structure and stability of a hyperthermophilic protein variant. Nat. Struct. Biol. 5:470-475.
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 470-475
    • Malakauskas, S.M.1    Mayo, S.L.2
  • 36
    • 0035910266 scopus 로고    scopus 로고
    • Achieving stability and conformational specificity in designed proteins via binary patterning
    • Marshall, S. A., and S. L. Mayo. 2001. Achieving stability and conformational specificity in designed proteins via binary patterning. J. Mol. Biol. 305:619-631.
    • (2001) J. Mol. Biol. , vol.305 , pp. 619-631
    • Marshall, S.A.1    Mayo, S.L.2
  • 37
    • 0023741058 scopus 로고
    • Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of ILE-3
    • Matsumura, M., W. J. Becktel, and B. W. Matthews. 1988. Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of ILE-3. Nature. 334:406-410.
    • (1988) Nature , vol.334 , pp. 406-410
    • Matsumura, M.1    Becktel, W.J.2    Matthews, B.W.3
  • 38
    • 0023645203 scopus 로고
    • Interior and surface of monomeric proteins
    • Miller, S., J. Janin, A. M. Lesk, and C. Chothia. 1987. Interior and surface of monomeric proteins. J. Mol. Biol. 196:641-656.
    • (1987) J. Mol. Biol. , vol.196 , pp. 641-656
    • Miller, S.1    Janin, J.2    Lesk, A.M.3    Chothia, C.4
  • 39
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A. G., S. E. Brenner, T. Hubbard, and C. Chothia. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 41
    • 0026571898 scopus 로고
    • Mechanism of specificity in the Fos-Jun oncoprotein heterodimer
    • O'Shea, E. K., R. Rutkowski, and P. S. Kim. 1992. Mechanism of specificity in the Fos-Jun oncoprotein heterodimer. Cell. 68:699-708.
    • (1992) Cell , vol.68 , pp. 699-708
    • O'Shea, E.K.1    Rutkowski, R.2    Kim, P.S.3
  • 42
    • 0030059689 scopus 로고    scopus 로고
    • Forces contributing to the conformational stability of proteins
    • Pace, C. N., B. A. Shirley, M. McNutt, and K. Gaijwala. 1996. Forces contributing to the conformational stability of proteins. FASEB J. 10:75-83.
    • (1996) FASEB J. , vol.10 , pp. 75-83
    • Pace, C.N.1    Shirley, B.A.2    McNutt, M.3    Gaijwala, K.4
  • 43
    • 85021467943 scopus 로고
    • Structure and function of haemoglobin II. Some relations between polypeptide chain configuration and amino acid sequence
    • Perutz, M. F., J. C. Kendrew, and H. C. Watson. 1965. Structure and function of haemoglobin II. Some relations between polypeptide chain configuration and amino acid sequence. J. Mol. Biol. 13:669-678.
    • (1965) J. Mol. Biol. , vol.13 , pp. 669-678
    • Perutz, M.F.1    Kendrew, J.C.2    Watson, H.C.3
  • 45
    • 33845280446 scopus 로고
    • Comparing the polarities of the amino acids-side-chain distribution coefficients between the vapor-phase, cyclohexane, 1-octanol, and neutral aqueous-solution
    • Radzicka, A., and R. Wolfenden. 1988. Comparing the polarities of the amino acids-side-chain distribution coefficients between the vapor-phase, cyclohexane, 1-octanol, and neutral aqueous-solution. Biochemistry. 27:1664-1670.
    • (1988) Biochemistry , vol.27 , pp. 1664-1670
    • Radzicka, A.1    Wolfenden, R.2
  • 46
    • 0028081403 scopus 로고
    • Structural features can be unconserved in proteins with similar folds - An analysis of side-chain to side-chain contacts secondary structure and accessibility
    • Russell, R. B., and G. J. Barton. 1994. Structural features can be unconserved in proteins with similar folds - an analysis of side-chain to side-chain contacts secondary structure and accessibility. J. Mol. Biol. 244:332-350.
    • (1994) J. Mol. Biol. , vol.244 , pp. 332-350
    • Russell, R.B.1    Barton, G.J.2
  • 47
    • 0028958462 scopus 로고
    • Conservation of salt bridges in protein families
    • Schueler, O., and H. Margalit. 1995. Conservation of salt bridges in protein families. J. Mol. Biol. 248:125-135.
    • (1995) J. Mol. Biol. , vol.248 , pp. 125-135
    • Schueler, O.1    Margalit, H.2
  • 48
    • 0036643497 scopus 로고    scopus 로고
    • Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins
    • Shimizu, S., and H. S. Chan. 2002. Anti-cooperativity and cooperativity in hydrophobic interactions: three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins. Prot. Struct. Funct. Gen. 48:15-30.
    • (2002) Prot. Struct. Funct. Gen. , vol.48 , pp. 15-30
    • Shimizu, S.1    Chan, H.S.2
  • 49
    • 0015866154 scopus 로고
    • Environment and exposure to solvent of protein atoms. Lysozyme and insulin
    • Shrake, A., and J. A. Rupley. 1973. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. 79:351-371.
    • (1973) J. Mol. Biol. , vol.79 , pp. 351-371
    • Shrake, A.1    Rupley, J.A.2
  • 50
    • 0035901483 scopus 로고    scopus 로고
    • Contribution of polar groups in the interior of a protein to the conformational stability
    • Takano, K., Y. Yamagata, and K. Yutani. 2001. Contribution of polar groups in the interior of a protein to the conformational stability. Biochemistry. 40:4853-4858.
    • (2001) Biochemistry , vol.40 , pp. 4853-4858
    • Takano, K.1    Yamagata, Y.2    Yutani, K.3
  • 51
    • 0017294711 scopus 로고
    • Accessible area, packing volumes and interaction surfaces of globular proteins
    • Teller, D. C. 1976. Accessible area, packing volumes and interaction surfaces of globular proteins. Nature. 260:729-731.
    • (1976) Nature , vol.260 , pp. 729-731
    • Teller, D.C.1
  • 52
    • 0029564595 scopus 로고
    • Are buried salt bridges important for protein stability and conformational specificity?
    • Waldburger, C. D., J. F. Schildbach, and R. T. Sauer. 1995. Are buried salt bridges important for protein stability and conformational specificity? Nat. Struct. Biol. 2:122-128.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 122-128
    • Waldburger, C.D.1    Schildbach, J.F.2    Sauer, R.T.3
  • 53
    • 0027080909 scopus 로고
    • Atomic solvation parameters applied to mlcular dynamics of proteins in solution
    • Wesson, L., and D. Eisenberg. 1992. Atomic solvation parameters applied to mlcular dynamics of proteins in solution. Protein Sci. 1:227-235.
    • (1992) Protein Sci. , vol.1 , pp. 227-235
    • Wesson, L.1    Eisenberg, D.2


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