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Volumn 105, Issue 9, 2008, Pages 3321-3326

Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model

Author keywords

turns; Hydrogen bonding; Protein folding; Unfolded state

Indexed keywords

CYCLOPROPANE; NITROUS OXIDE; SOLVENT; OLIGOPEPTIDE; PEPTIDE; POLYALANINE; UNCLASSIFIED DRUG;

EID: 42149084432     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0712240105     Document Type: Article
Times cited : (34)

References (60)
  • 1
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 2
    • 0035022941 scopus 로고    scopus 로고
    • Intrinsically disordered protein
    • Dunker AK, et al. (2001) Intrinsically disordered protein. J Mol Graphics Model 19:26-59.
    • (2001) J Mol Graphics Model , vol.19 , pp. 26-59
    • Dunker, A.K.1
  • 3
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman HM, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 5
    • 0014364651 scopus 로고
    • Protein denaturation
    • Tanford C (1968) Protein denaturation. Adv Protein Chem 23:121-282.
    • (1968) Adv Protein Chem , vol.23 , pp. 121-282
    • Tanford, C.1
  • 6
    • 4344704080 scopus 로고    scopus 로고
    • Reassessing random-coil statistics in unfolded proteins
    • Fitzkee NC, Rose GD (2004) Reassessing random-coil statistics in unfolded proteins. Proc Natl Acad Sci USA 101:12497-12502.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 12497-12502
    • Fitzkee, N.C.1    Rose, G.D.2
  • 7
    • 84888644486 scopus 로고    scopus 로고
    • eds Kiefhaber T, Buchner J Wiley-VCH, Weinheim
    • Fleming PJ, Rose GD (2005) in Protein Folding Handbook, eds Kiefhaber T, Buchner J (Wiley-VCH, Weinheim), Vol 2, pp 710-736.
    • (2005) Protein Folding Handbook , vol.2 , pp. 710-736
    • Fleming, P.J.1    Rose, G.D.2
  • 8
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein structure
    • Richards FM (1977) Areas, volumes, packing, and protein structure. Annu Rev Biophys Bioeng 6:151-176.
    • (1977) Annu Rev Biophys Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 9
    • 27244437952 scopus 로고    scopus 로고
    • Predicting the energetics of osmolyte-induced protein folding/unfolding
    • Auton M, Bolen DW (2005) Predicting the energetics of osmolyte-induced protein folding/unfolding. Proc Natl Acad Sci USA 102:15065-15068.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 15065-15068
    • Auton, M.1    Bolen, D.W.2
  • 10
    • 34848916114 scopus 로고    scopus 로고
    • Anatomy of energetic changes accompanying urea-induced protein denaturation
    • Auton M, Holthauzen LM, Bolen DW (2007) Anatomy of energetic changes accompanying urea-induced protein denaturation. Proc Natl Acad Sci USA 104:15317-15322.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 15317-15322
    • Auton, M.1    Holthauzen, L.M.2    Bolen, D.W.3
  • 11
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee B, Richards FM (1971) The interpretation of protein structures: Estimation of static accessibility. J Mol Biol 55:379-400.
    • (1971) J Mol Biol , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 12
    • 0025374190 scopus 로고
    • Hydrophobicity of amino acid subgroups in proteins
    • Lesser GJ, Rose GD (1990) Hydrophobicity of amino acid subgroups in proteins. Proteins Struct Funct Genet 8:6-13.
    • (1990) Proteins Struct Funct Genet , vol.8 , pp. 6-13
    • Lesser, G.J.1    Rose, G.D.2
  • 14
    • 0029620316 scopus 로고
    • Modeling unfolded states of peptides and proteins
    • Creamer TP, Srinivasan R, Rose GD (1995) Modeling unfolded states of peptides and proteins. Biochemistry 34:16245-16250.
    • (1995) Biochemistry , vol.34 , pp. 16245-16250
    • Creamer, T.P.1    Srinivasan, R.2    Rose, G.D.3
  • 15
    • 0030933329 scopus 로고    scopus 로고
    • Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility
    • Creamer TP, Srinivasan R, Rose GD (1997) Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility. Biochemistry 36:2832-2835.
    • (1997) Biochemistry , vol.36 , pp. 2832-2835
    • Creamer, T.P.1    Srinivasan, R.2    Rose, G.D.3
  • 16
    • 0038311869 scopus 로고    scopus 로고
    • Protein stability in mixed solvents: A balance of contact interaction and excluded volume
    • Schellman JA (2003) Protein stability in mixed solvents: A balance of contact interaction and excluded volume. Biophys J 85:108-125.
    • (2003) Biophys J , vol.85 , pp. 108-125
    • Schellman, J.A.1
  • 17
    • 0037424614 scopus 로고    scopus 로고
    • Computational simulation of the statistical properties of unfolded proteins
    • Goldenberg DP (2003) Computational simulation of the statistical properties of unfolded proteins. J Mol Biol 326:1615-1633.
    • (2003) J Mol Biol , vol.326 , pp. 1615-1633
    • Goldenberg, D.P.1
  • 18
    • 28044472257 scopus 로고    scopus 로고
    • Building native protein conformation from highly approximate backbone torsion angles
    • Gong H, Fleming PJ, Rose GD (2005) Building native protein conformation from highly approximate backbone torsion angles. Proc Natl Acad Sci USA 102:16227-16232.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 16227-16232
    • Gong, H.1    Fleming, P.J.2    Rose, G.D.3
  • 19
    • 34547572386 scopus 로고    scopus 로고
    • Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly
    • Gong H, Shen Y, Rose GD (2007) Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly. Protein Sci 16:1515-1521.
    • (2007) Protein Sci , vol.16 , pp. 1515-1521
    • Gong, H.1    Shen, Y.2    Rose, G.D.3
  • 20
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • Wang G, Dunbrack RL, Jr (2003) PISCES: A protein sequence culling server. Bioinformatics 19:1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr, R.L.2
  • 21
    • 13944275960 scopus 로고    scopus 로고
    • The Protein Coil Library: A structural database of nonhelix, nonstrand fragments derived from the PDB
    • Fitzkee NC, Fleming PJ, Rose GD (2005) The Protein Coil Library: A structural database of nonhelix, nonstrand fragments derived from the PDB. Proteins 58:852-854.
    • (2005) Proteins , vol.58 , pp. 852-854
    • Fitzkee, N.C.1    Fleming, P.J.2    Rose, G.D.3
  • 22
    • 0028790273 scopus 로고
    • Comparison between the phi distribution of the amino acids in the protein database and NMR data indicates that amino acids have various phi propensities in the random coil conformation
    • Serrano L (1995) Comparison between the phi distribution of the amino acids in the protein database and NMR data indicates that amino acids have various phi propensities in the random coil conformation. J Mol Biol 254:322-333.
    • (1995) J Mol Biol , vol.254 , pp. 322-333
    • Serrano, L.1
  • 23
    • 0029978353 scopus 로고    scopus 로고
    • Analysis of main chain torsion angles in proteins: Prediction of NMR coupling constants for native and random coil conformations
    • Smith LJ, et al. (1996) Analysis of main chain torsion angles in proteins: Prediction of NMR coupling constants for native and random coil conformations. J Mol Biol 255:494-506.
    • (1996) J Mol Biol , vol.255 , pp. 494-506
    • Smith, L.J.1
  • 24
    • 26844480393 scopus 로고    scopus 로고
    • Sterics and solvation winnow accessible conformational space for unfolded proteins
    • Fitzkee NC, Rose GD (2005) Sterics and solvation winnow accessible conformational space for unfolded proteins. J Mol Biol 353:873-887.
    • (2005) J Mol Biol , vol.353 , pp. 873-887
    • Fitzkee, N.C.1    Rose, G.D.2
  • 25
    • 0033730431 scopus 로고    scopus 로고
    • The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding
    • Pappu RV, Srinivasan R, Rose GD (2000) The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding. Proc Natl Acad Sci USA 97:12565-12570.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 12565-12570
    • Pappu, R.V.1    Srinivasan, R.2    Rose, G.D.3
  • 26
    • 1342268081 scopus 로고    scopus 로고
    • Steric restrictions in protein folding: An alpha-helix cannot be followed by a contiguous beta-strand
    • Fitzkee NC, Rose GD (2004) Steric restrictions in protein folding: An alpha-helix cannot be followed by a contiguous beta-strand. Protein Sci 13:633-639.
    • (2004) Protein Sci , vol.13 , pp. 633-639
    • Fitzkee, N.C.1    Rose, G.D.2
  • 28
    • 4344716256 scopus 로고    scopus 로고
    • Random-coil behavior and the dimensions of chemically unfolded proteins
    • Kohn JE, et al. (2004) Random-coil behavior and the dimensions of chemically unfolded proteins. Proc Natl Acad Sci USA 101:12491-12496.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 12491-12496
    • Kohn, J.E.1
  • 30
    • 0025849701 scopus 로고
    • Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water
    • Scholtz JM, et al. (1991) Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water. Proc Natl Acad Sci USA 88:2854-2858.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 2854-2858
    • Scholtz, J.M.1
  • 31
    • 13444279887 scopus 로고    scopus 로고
    • Enthalpy of helix-coil transition: Missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues
    • Richardson JM, Lopez MM, Makhatadze GI (2005) Enthalpy of helix-coil transition: missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues. Proc Natl Acad Sci USA 102:1413-1418.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 1413-1418
    • Richardson, J.M.1    Lopez, M.M.2    Makhatadze, G.I.3
  • 33
    • 34250869055 scopus 로고    scopus 로고
    • Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism
    • O'Brien EP, Dima RI, Brooks B, Thirumalai D (2007) Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism. J Am Chem Soc 129:7346-7353.
    • (2007) J Am Chem Soc , vol.129 , pp. 7346-7353
    • O'Brien, E.P.1    Dima, R.I.2    Brooks, B.3    Thirumalai, D.4
  • 34
    • 34548270876 scopus 로고    scopus 로고
    • Urea-amide preferential interactions in water: Quantitative comparison of model compound data with biopolymer results using water accessible surface areas
    • Cannon JG, Anderson CF, Record MT, Jr (2007) Urea-amide preferential interactions in water: quantitative comparison of model compound data with biopolymer results using water accessible surface areas. J Phys Chem B 111:9675-9685.
    • (2007) J Phys Chem B , vol.111 , pp. 9675-9685
    • Cannon, J.G.1    Anderson, C.F.2    Record Jr, M.T.3
  • 35
    • 33746882148 scopus 로고    scopus 로고
    • Metrics that differentiate the origins of osmolyte effects on protein stability: A test of the surface tension proposal
    • Auton M, Ferreon AC, Bolen DW (2006) Metrics that differentiate the origins of osmolyte effects on protein stability: A test of the surface tension proposal. J Mol Biol 361:983-992.
    • (2006) J Mol Biol , vol.361 , pp. 983-992
    • Auton, M.1    Ferreon, A.C.2    Bolen, D.W.3
  • 36
    • 0032483027 scopus 로고    scopus 로고
    • Osmolyte-driven contraction of a random coil protein
    • Qu Y, Bolen CL, Bolen DW (1998) Osmolyte-driven contraction of a random coil protein. Proc Natl Acad Sci USA 95:9268-9273.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 9268-9273
    • Qu, Y.1    Bolen, C.L.2    Bolen, D.W.3
  • 37
    • 33749365298 scopus 로고    scopus 로고
    • A molecular mechanism for osmolyte-induced protein stability
    • Street TO, Bolen DW, Rose GD (2006) A molecular mechanism for osmolyte-induced protein stability. Proc Natl Acad Sci USA 103:13997-14002.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 13997-14002
    • Street, T.O.1    Bolen, D.W.2    Rose, G.D.3
  • 38
    • 33746823043 scopus 로고    scopus 로고
    • Coil-globule transition in the denatured state of a small protein
    • Sherman E, Haran G (2006) Coil-globule transition in the denatured state of a small protein. Proc Natl Acad Sci USA 103:11539-11543.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 11539-11543
    • Sherman, E.1    Haran, G.2
  • 39
    • 0031692650 scopus 로고    scopus 로고
    • Left-handed polyproline II helix formation is (very) locally driven
    • Creamer TP (1998) Left-handed polyproline II helix formation is (very) locally driven. Proteins 33:218-226.
    • (1998) Proteins , vol.33 , pp. 218-226
    • Creamer, T.P.1
  • 41
    • 0034718590 scopus 로고    scopus 로고
    • Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities
    • Avbelj F, Luo P, Baldwin RL (2000) Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities. Proc Natl Acad Sci USA 97:10786-10791.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10786-10791
    • Avbelj, F.1    Luo, P.2    Baldwin, R.L.3
  • 42
    • 1842500992 scopus 로고    scopus 로고
    • Polyproline II helix is the preferred conformation for unfolded polyalanine in water
    • Mezei M, Fleming PJ, Srinivasan R, Rose GD (2004) Polyproline II helix is the preferred conformation for unfolded polyalanine in water. Proteins 55:502-507.
    • (2004) Proteins , vol.55 , pp. 502-507
    • Mezei, M.1    Fleming, P.J.2    Srinivasan, R.3    Rose, G.D.4
  • 43
    • 0032570873 scopus 로고    scopus 로고
    • Forcing thermodynamically unfolded proteins to fold
    • Baskakov I, Bolen DW (1998) Forcing thermodynamically unfolded proteins to fold. J Biol Chem 273:4831-4834.
    • (1998) J Biol Chem , vol.273 , pp. 4831-4834
    • Baskakov, I.1    Bolen, D.W.2
  • 45
    • 9344251691 scopus 로고    scopus 로고
    • Solvent dependence of PII conformation in model alanine peptides
    • Liu Z, et al. (2004) Solvent dependence of PII conformation in model alanine peptides. J Am Chem Soc 126:15141-15150.
    • (2004) J Am Chem Soc , vol.126 , pp. 15141-15150
    • Liu, Z.1
  • 46
    • 23844465902 scopus 로고    scopus 로고
    • Unusual compactness of a polyproline type II structure
    • Zagrovic B, et al. (2005) Unusual compactness of a polyproline type II structure. Proc Natl Acad Sci USA 102:11698-11703.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 11698-11703
    • Zagrovic, B.1
  • 47
    • 33750934185 scopus 로고    scopus 로고
    • Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions
    • Crick SL, Jayaraman M, Frieden C, Wetzel R, Pappu RV (2006) Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions. Proc Natl Acad Sci USA 103:16764-16769.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 16764-16769
    • Crick, S.L.1    Jayaraman, M.2    Frieden, C.3    Wetzel, R.4    Pappu, R.V.5
  • 48
    • 32444434361 scopus 로고    scopus 로고
    • Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins
    • Makowska J, et al. (2006) Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. Proc Natl Acad Sci USA 103:1744-1749.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 1744-1749
    • Makowska, J.1
  • 49
    • 34249846749 scopus 로고    scopus 로고
    • The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations
    • Schweitzer-Stenner R, Measey TJ (2007) The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations. Proc Natl Acad Sci USA 104:6649-6654.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 6649-6654
    • Schweitzer-Stenner, R.1    Measey, T.J.2
  • 50
    • 84910374907 scopus 로고
    • Solvent effect on conformational stability in the Ala dipeptide: Full free energy simulations
    • Beveridge DL, Ravishanker G, Mezei M, Gedulin B (1986) Solvent effect on conformational stability in the Ala dipeptide: Full free energy simulations. J Biomol Struct Dyn 3:237-252.
    • (1986) J Biomol Struct Dyn , vol.3 , pp. 237-252
    • Beveridge, D.L.1    Ravishanker, G.2    Mezei, M.3    Gedulin, B.4
  • 51
    • 0043073519 scopus 로고
    • The γ-turn: Ab initio calculations on proline and N-acetylproline amide
    • Sapse A-M, Mallah-Levy L, Daniels SB, Erickson BW (1987) The γ-turn: Ab initio calculations on proline and N-acetylproline amide. J Am Chem Soc 109:3526-3529.
    • (1987) J Am Chem Soc , vol.109 , pp. 3526-3529
    • Sapse, A.-M.1    Mallah-Levy, L.2    Daniels, S.B.3    Erickson, B.W.4
  • 52
    • 0025690309 scopus 로고
    • Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites
    • Milner-White EJ (1990) Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites. J Mol Biol 216:386-397.
    • (1990) J Mol Biol , vol.216 , pp. 386-397
    • Milner-White, E.J.1
  • 53
    • 17644422781 scopus 로고    scopus 로고
    • Urea promotes polyproline II helix formation: Implications for protein denatured states
    • Whittington SJ, Chellgren BW, Hermann VM, Creamer TP (2005) Urea promotes polyproline II helix formation: implications for protein denatured states. Biochemistry 44:6269-6275.
    • (2005) Biochemistry , vol.44 , pp. 6269-6275
    • Whittington, S.J.1    Chellgren, B.W.2    Hermann, V.M.3    Creamer, T.P.4
  • 54
    • 33646908786 scopus 로고    scopus 로고
    • Conformation of the backbone in unfolded proteins
    • Shi Z, Chen K, Liu Z, Kallenbach NR (2006) Conformation of the backbone in unfolded proteins. Chem Rev 106:1877-1897.
    • (2006) Chem Rev , vol.106 , pp. 1877-1897
    • Shi, Z.1    Chen, K.2    Liu, Z.3    Kallenbach, N.R.4
  • 56
    • 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
  • 57
    • 0030059690 scopus 로고    scopus 로고
    • The molten globule state of alpha-lactalbumin
    • Kuwajima K (1996) The molten globule state of alpha-lactalbumin. FASEB J 10:102-109.
    • (1996) FASEB J , vol.10 , pp. 102-109
    • Kuwajima, K.1
  • 58
    • 22244449669 scopus 로고    scopus 로고
    • Do all backbone polar groups in proteins form hydrogen bonds?
    • Fleming PJ, Rose GD (2005) Do all backbone polar groups in proteins form hydrogen bonds? Protein Sci 14:1911-1917.
    • (2005) Protein Sci , vol.14 , pp. 1911-1917
    • Fleming, P.J.1    Rose, G.D.2
  • 59
    • 0036606453 scopus 로고    scopus 로고
    • Ab initio prediction of protein structure using LINUS
    • Srinivasan R, Rose GD (2002) Ab initio prediction of protein structure using LINUS. Proteins 47:489-495.
    • (2002) Proteins , vol.47 , pp. 489-495
    • Srinivasan, R.1    Rose, G.D.2
  • 60
    • 0033405203 scopus 로고    scopus 로고
    • A physical basis for protein secondary structure
    • Srinivasan R, Rose GD (1999) A physical basis for protein secondary structure. Proc Natl Acad Sci USA 96:14258-14263.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 14258-14263
    • Srinivasan, R.1    Rose, G.D.2


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