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Volumn , Issue , 2012, Pages 131-158

Solvation and Electrostatics as Determinants of Local Structural Order in Unfolded Peptides and Proteins

Author keywords

Determining hydrogen exchange rates; ESM, backbone conformational preferences; Solvation and electrostatics, structural order

Indexed keywords


EID: 84888720145     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118183373.ch5     Document Type: Chapter
Times cited : (8)

References (160)
  • 1
    • 46149141431 scopus 로고
    • Seeding protein folding
    • Baldwin, R. L. (1986) Seeding protein folding, Trends Biochem Sci 11, 6-9.
    • (1986) Trends Biochem Sci , vol.11 , pp. 6-9
    • Baldwin, R.L.1
  • 2
    • 0030058302 scopus 로고    scopus 로고
    • Thermodynamic cycles as probes of structure in unfolded proteins
    • McGee, W. A., et al. (1996) Thermodynamic cycles as probes of structure in unfolded proteins, B iochemistry 35, 1995-2007.
    • (1996) B iochemistry , vol.35 , pp. 1995-2007
    • McGee, W.A.1
  • 3
    • 0025856806 scopus 로고
    • Denatured states of proteins
    • Dill, K. A. and Shortle, D. (1991) Denatured states of proteins, Annu Rev Biochem 60, 795-825.
    • (1991) Annu Rev Biochem , vol.60 , pp. 795-825
    • Dill, K.A.1    Shortle, D.2
  • 4
    • 0028297302 scopus 로고
    • Structural characterization of the FK506 binding protein unfolded in urea and guanidine hydrochloride
    • Logan, T. M., Theriault, Y., and Fesik, S. W. (1994) Structural characterization of the FK506 binding protein unfolded in urea and guanidine hydrochloride, J Mol Biol 236, 637-648.
    • (1994) J Mol Biol , vol.236 , pp. 637-648
    • Logan, T.M.1    Theriault, Y.2    Fesik, S.W.3
  • 5
    • 0028787226 scopus 로고
    • Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional NMR spectroscopy
    • Frank, M. K., Clore, G. M., and Gronenborn, A. M. (1995) Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional NMR spectroscopy, Protein Sci 4, 2605-2615.
    • (1995) Protein Sci , vol.4 , pp. 2605-2615
    • Frank, M.K.1    Clore, G.M.2    Gronenborn, A.M.3
  • 6
    • 0028806684 scopus 로고
    • A comparison of the pH, urea, and temperature - denatured states of barnase by heteronuclear NMR: Implications for the initiation of protein folding
    • Arcus, V. L., et al. (1995) A comparison of the pH, urea, and temperature - denatured states of barnase by heteronuclear NMR: Implications for the initiation of protein folding, J Mol Biol 254, 305-321.
    • (1995) J Mol Biol , vol.254 , pp. 305-321
    • Arcus, V.L.1
  • 7
    • 0030759665 scopus 로고    scopus 로고
    • Structural and dynamical properties of a denatured state. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea
    • Schwalbe, H., et al. (1997) Structural and dynamical properties of a denatured state. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea, Biochemistry 36, 8977-8991.
    • (1997) Biochemistry , vol.36 , pp. 8977-8991
    • Schwalbe, H.1
  • 8
    • 0032079638 scopus 로고    scopus 로고
    • Characterization of urea - denatured states of an immunoglobulin superfamily domain by heteronuclear NMR
    • Fong, S., et al. (1998) Characterization of urea - denatured states of an immunoglobulin superfamily domain by heteronuclear NMR, J Mol Biol 278, 417-429.
    • (1998) J Mol Biol , vol.278 , pp. 417-429
    • Fong, S.1
  • 9
    • 0033582680 scopus 로고    scopus 로고
    • Probing residual structure and backbone dynamics on the milli - to picosecond timescale in a urea - denatured fibronectin type III domain
    • Meekhof, A. E. and Freund, S. M. V. (1999) Probing residual structure and backbone dynamics on the milli - to picosecond timescale in a urea - denatured fibronectin type III domain, J Mol Biol 286, 579-592.
    • (1999) J Mol Biol , vol.286 , pp. 579-592
    • Meekhof, A.E.1    Freund, S.M.V.2
  • 10
    • 0034614051 scopus 로고    scopus 로고
    • NMR spectroscopic investigation of psi torsion angle distribution in unfolded ubiquitin from analysis of 3J(Calpha,Calpha) coupling constants and cross -correlated relaxation rates
    • Peti, W., et al. (2000) NMR spectroscopic investigation of psi torsion angle distribution in unfolded ubiquitin from analysis of 3J(Calpha,Calpha) coupling constants and cross -correlated relaxation rates, J Am Chem Soc 122, 12017-12018.
    • (2000) J Am Chem Soc , vol.122 , pp. 12017-12018
    • Peti, W.1
  • 11
    • 0035058986 scopus 로고    scopus 로고
    • Structural and dynamic characterization of an unfolded state of poplar Apo - plastocyanin formed under non - denaturing conditions
    • Bai, Y., et al. (2001) Structural and dynamic characterization of an unfolded state of poplar Apo - plastocyanin formed under non - denaturing conditions, Protein Sci 10, 1056-1066.
    • (2001) Protein Sci , vol.10 , pp. 1056-1066
    • Bai, Y.1
  • 12
    • 0037159208 scopus 로고    scopus 로고
    • Molecular hinges in proteins folding: The urea - denatured state of apomyoglobin
    • Schwarzinger, S., Wright, P. E., and Dyson, H. J. (2002) Molecular hinges in proteins folding: The urea - denatured state of apomyoglobin, Biochemistry 41, 12681-12686.
    • (2002) Biochemistry , vol.41 , pp. 12681-12686
    • Schwarzinger, S.1    Wright, P.E.2    Dyson, H.J.3
  • 13
    • 33646187492 scopus 로고    scopus 로고
    • Local structural preferences and dynamics restrictions in the urea - denatured state of SUMO - 1: NMR characterization
    • Kumar, A., et al. (2006) Local structural preferences and dynamics restrictions in the urea - denatured state of SUMO - 1: NMR characterization, Biophys J 90, 2498-2509.
    • (2006) Biophys J , vol.90 , pp. 2498-2509
    • Kumar, A.1
  • 14
    • 33947484491 scopus 로고
    • The configuration of random polypeptide chains. I. Experimental results
    • Brant, D. A. and Flory, P. J. (1965) The configuration of random polypeptide chains. I. Experimental results, J Am Chem Soc 87, 2788-2791.
    • (1965) J Am Chem Soc , vol.87 , pp. 2788-2791
    • Brant, D.A.1    Flory, P.J.2
  • 15
    • 0001502420 scopus 로고
    • The role of dipole interactions in determining polypeptide conformation
    • Brant, D. A. and Flory, P. J. (1965) The role of dipole interactions in determining polypeptide conformation, J Am Chem Soc 87, 663-664.
    • (1965) J Am Chem Soc , vol.87 , pp. 663-664
    • Brant, D.A.1    Flory, P.J.2
  • 17
    • 33847087323 scopus 로고
    • Solvent - dependent conformational distributions of some dipeptides
    • Madison, V. and Kopple, K. D. (1980) Solvent - dependent conformational distributions of some dipeptides, J Am Chem Soc 102, 4855-4863.
    • (1980) J Am Chem Soc , vol.102 , pp. 4855-4863
    • Madison, V.1    Kopple, K.D.2
  • 18
    • 0006279673 scopus 로고    scopus 로고
    • Solution - phase conformations of N - Acetyl - L - alanine N' -Methylamide from vibrational Raman optical activity
    • Deng, Z., et al. (1996) Solution - phase conformations of N - Acetyl - L - alanine N' -Methylamide from vibrational Raman optical activity, J Phys Chem B 100, 2025-2034.
    • (1996) J Phys Chem B , vol.100 , pp. 2025-2034
    • Deng, Z.1
  • 19
    • 0034647237 scopus 로고    scopus 로고
    • Do bridging water molecules dictate the structure of a model dipeptide in aqueous solution
    • Poon, C. - D. and Samulski, E. T. (2000) Do bridging water molecules dictate the structure of a model dipeptide in aqueous solution, J Am Chem Soc 122, 5642-5643.
    • (2000) J Am Chem Soc , vol.122 , pp. 5642-5643
    • Poon, C.-D.1    Samulski, E.T.2
  • 20
    • 0034315712 scopus 로고    scopus 로고
    • Structure determination of trialanine in water using polarization sensitive two - dimensional vibrational spectroscopy
    • Woutersen, S. and Hamm, P. (2000) Structure determination of trialanine in water using polarization sensitive two - dimensional vibrational spectroscopy, J Phys Chem B 104, 11316-11320.
    • (2000) J Phys Chem B , vol.104 , pp. 11316-11320
    • Woutersen, S.1    Hamm, P.2
  • 21
    • 0035802365 scopus 로고    scopus 로고
    • Dihedral angles of trialanine in D2O determined by combining FTIR and polarized visible Raman spectroscopy
    • Schweitzer - Stenner, R., et al. (2001) Dihedral angles of trialanine in D2O determined by combining FTIR and polarized visible Raman spectroscopy, J Am Chem Soc 123, 9628-9633.
    • (2001) J Am Chem Soc , vol.123 , pp. 9628-9633
    • Schweitzer-Stenner, R.1
  • 22
    • 0037021502 scopus 로고    scopus 로고
    • Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study
    • Eker, F., et al. (2002) Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study, J Am Chem Soc 124, 14330-14341.
    • (2002) J Am Chem Soc , vol.124 , pp. 14330-14341
    • Eker, F.1
  • 23
    • 0037047134 scopus 로고    scopus 로고
    • Polyproline II structure in a sequence of seven alanine residues
    • Shi, Z., et al. (2002) Polyproline II structure in a sequence of seven alanine residues, Proc Natl Acad Sci U S A 99, 9190-9195.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 9190-9195
    • Shi, Z.1
  • 24
    • 0038006081 scopus 로고    scopus 로고
    • The pentapeptide GGAGG has PII conformation
    • Ding, L., et al. (2003) The pentapeptide GGAGG has PII conformation, J Am Chem Soc 125, 8092-8093.
    • (2003) J Am Chem Soc , vol.125 , pp. 8092-8093
    • Ding, L.1
  • 25
    • 0037431356 scopus 로고    scopus 로고
    • Conformational analysis of alanine dipeptide from dipolar couplings in a water based liquid crystal
    • Weise, C. F. and Weisshaar, J. C. (2003) Conformational analysis of alanine dipeptide from dipolar couplings in a water based liquid crystal, J Phys Chem B 107, 3265-3277.
    • (2003) J Phys Chem B , vol.107 , pp. 3265-3277
    • Weise, C.F.1    Weisshaar, J.C.2
  • 26
    • 0038344087 scopus 로고    scopus 로고
    • Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy
    • Eker, F., Griebenow, K., and Schweitzer - Stenner, R. (2003) Stable conformations of tripeptides in aqueous solution studied by UV circular dichroism spectroscopy, J Am Chem Soc 125, 8178-8175.
    • (2003) J Am Chem Soc , vol.125 , pp. 8178-8175
    • Eker, F.1    Griebenow, K.2    Schweitzer-Stenner, R.3
  • 27
    • 1942489291 scopus 로고    scopus 로고
    • Vibrational Raman optical activity characterization of Poly(L - proline) II helix in alanine oligopeptides
    • McColl, I. H., et al. (2004) Vibrational Raman optical activity characterization of Poly(L - proline) II helix in alanine oligopeptides, J Am Chem Soc 126, 5076-5077.
    • (2004) J Am Chem Soc , vol.126 , pp. 5076-5077
    • McColl, I.H.1
  • 28
    • 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
  • 29
    • 3042750640 scopus 로고    scopus 로고
    • Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine - based (AXA) tripeptides in aqueous solution
    • Eker, F., et al. (2004) Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine - based (AXA) tripeptides in aqueous solution, P roc Natl Acad Sci U S A 101, 10054-10059.
    • (2004) P roc Natl Acad Sci U S A , vol.101 , pp. 10054-10059
    • Eker, F.1
  • 30
    • 1542310781 scopus 로고    scopus 로고
    • Tripeptides with ionizable side chains adopt a perturbed polyproline II structure in water
    • Eker, F., et al. (2004) Tripeptides with ionizable side chains adopt a perturbed polyproline II structure in water, Biochemistry 43, 613-621.
    • (2004) Biochemistry , vol.43 , pp. 613-621
    • Eker, F.1
  • 31
    • 1542347945 scopus 로고    scopus 로고
    • The conformation of tetraalanine in water determined by polarized Raman, FT - IR, and VCD spectroscopy
    • Schweitzer - Stenner, R., et al. (2004) The conformation of tetraalanine in water determined by polarized Raman, FT - IR, and VCD spectroscopy, J Am Chem Soc 126, 2768-2776.
    • (2004) J Am Chem Soc , vol.126 , pp. 2768-2776
    • Schweitzer-Stenner, R.1
  • 32
    • 7444255986 scopus 로고    scopus 로고
    • The polyproline II conformation in short alanine peptides is noncooperative
    • Chen, K., Liu, Z., and Kallenbach, N. R. (2004) The polyproline II conformation in short alanine peptides is noncooperative, Proc Natl Acad Sci U S A 101, 15352-15357.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 15352-15357
    • Chen, K.1    Liu, Z.2    Kallenbach, N.R.3
  • 33
    • 1242295205 scopus 로고    scopus 로고
    • Temperature and pressure effects on conformational equilibria of alanine dipeptide in aqueous solution
    • Takekiyo, T., et al. (2004) Temperature and pressure effects on conformational equilibria of alanine dipeptide in aqueous solution, Biopolymers 73, 283-290.
    • (2004) Biopolymers , vol.73 , pp. 283-290
    • Takekiyo, T.1
  • 34
    • 1542306742 scopus 로고    scopus 로고
    • Structure of the alanine dipeptide in condensed phases determined by 13C NMR
    • Mehta, M. A., et al. (2004) Structure of the alanine dipeptide in condensed phases determined by 13C NMR, J Phys Chem B 108, 2777-2780.
    • (2004) J Phys Chem B , vol.108 , pp. 2777-2780
    • Mehta, M.A.1
  • 35
    • 18144410941 scopus 로고    scopus 로고
    • Two - dimensional infrared spectroscopy of the alanine dipeptide in aqueous solution
    • Kim, Y. S., Wang, J., and Hochstrasser, R. H. (2005) Two - dimensional infrared spectroscopy of the alanine dipeptide in aqueous solution, J Phys Chem B 109, 7511-7521..
    • (2005) J Phys Chem B , vol.109
    • Kim, Y.S.1    Wang, J.2    Hochstrasser, R.H.3
  • 36
    • 22944442988 scopus 로고    scopus 로고
    • Neighbor effect on PPII conformation in alanine peptides
    • Chen, K., et al. (2005) Neighbor effect on PPII conformation in alanine peptides, J Am Chem Soc 127, 10146-10147.
    • (2005) J Am Chem Soc , vol.127 , pp. 10146-10147
    • Chen, K.1
  • 37
    • 31944437630 scopus 로고    scopus 로고
    • Intrinsic backbone preferences are fully present in blocked amino acids
    • Avbelj, F., et al. (2006) Intrinsic backbone preferences are fully present in blocked amino acids, Proc Natl Acad Sci U S A 103 (5), 1277-1277.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , Issue.5 , pp. 1277-1277
    • Avbelj, F.1
  • 38
    • 33644675820 scopus 로고    scopus 로고
    • Conformational analysis of XA and AX dipeptides in water by electronic circular dichroism and 1H NMR spectroscopy
    • Hagarman, A., et al. (2006) Conformational analysis of XA and AX dipeptides in water by electronic circular dichroism and 1H NMR spectroscopy, J Phys Chem B 110, 6979-6986.
    • (2006) J Phys Chem B , vol.110 , pp. 6979-6986
    • Hagarman, A.1
  • 39
    • 34249846749 scopus 로고    scopus 로고
    • The alanine - rich XAO peptide adopts a heterogeneous population, including turn - like and polyproline II conformations
    • Schweitzer - Stenner, R. and Measey, T. J. (2007) The alanine - rich XAO peptide adopts a heterogeneous population, including turn - like and polyproline II conformations, Proc Natl Acad Sci U S A 104, 6649-6654.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 6649-6654
    • Schweitzer-Stenner, R.1    Measey, T.J.2
  • 40
    • 33846783019 scopus 로고    scopus 로고
    • Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study
    • Graf, J., et al. (2007) Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study, J Am Chem Soc 129, 1179-1189.
    • (2007) J Am Chem Soc , vol.129 , pp. 1179-1189
    • Graf, J.1
  • 41
    • 35648983933 scopus 로고    scopus 로고
    • Dipeptide structure determination by vibrational circular dichroism combined with the quantum chemistry calculations
    • Lee, K. - K., et al. (2007) Dipeptide structure determination by vibrational circular dichroism combined with the quantum chemistry calculations, Chemphyschem 8, 2218-2226.
    • (2007) Chemphyschem , vol.8 , pp. 2218-2226
    • Lee, K.K.1
  • 42
    • 58749097266 scopus 로고    scopus 로고
    • Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations
    • Mukhopadhyay, P., Zuber, G., and Beratan, D. N. (2008) Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations, Biophys J 95, 5574-5586.
    • (2008) Biophys J , vol.95 , pp. 5574-5586
    • Mukhopadhyay, P.1    Zuber, G.2    Beratan, D.N.3
  • 43
    • 41549100710 scopus 로고    scopus 로고
    • Determination of conformational preferences of dipeptides using vibrational spectroscopy
    • Grdadolnik, J., Grdadolnik, S. G., and Avbelj, F. (2008) Determination of conformational preferences of dipeptides using vibrational spectroscopy, J Phys Chem B 112, 2712-2718.
    • (2008) J Phys Chem B , vol.112 , pp. 2712-2718
    • Grdadolnik, J.1    Grdadolnik, S.G.2    Avbelj, F.3
  • 44
    • 65249128090 scopus 로고    scopus 로고
    • Distribution of conformations sampled by the central amino acid residue in tripeptides inferred from amide I band profiles and NMR scalar coupling constants
    • Schweitzer - Stenner, R. (2009) Distribution of conformations sampled by the central amino acid residue in tripeptides inferred from amide I band profiles and NMR scalar coupling constants, J Phys Chem B 113, 2922-2932.
    • (2009) J Phys Chem B , vol.113 , pp. 2922-2932
    • Schweitzer-Stenner, R.1
  • 45
    • 74949106813 scopus 로고    scopus 로고
    • Intrinsic propensities of amino acid residues in GXG peptides inferred from amide I' band profiles and NMR scalar coupling constants
    • Hagarman, A., et al. (2010) Intrinsic propensities of amino acid residues in GXG peptides inferred from amide I' band profiles and NMR scalar coupling constants, J Am Chem Soc 132, 540-551.
    • (2010) J Am Chem Soc , vol.132 , pp. 540-551
    • Hagarman, A.1
  • 46
    • 33846496735 scopus 로고    scopus 로고
    • Electrostatic screening and backbone preferences of amino acid residues in urea - denatured ubiquitin
    • Avbelj, F. and Grdadolnik, S. G. (2007) Electrostatic screening and backbone preferences of amino acid residues in urea - denatured ubiquitin, Protein Sci 16, 273-284.
    • (2007) Protein Sci , vol.16 , pp. 273-284
    • Avbelj, F.1    Grdadolnik, S.G.2
  • 47
    • 0000084729 scopus 로고
    • Sequence - corrected 15 - N random coil chemical shifts
    • Braun, D., Wider, G., and Wuthrich, K. (1994) Sequence - corrected 15 - N random coil chemical shifts, J Am Chem Soc 116, 8466-8469.
    • (1994) J Am Chem Soc , vol.116 , pp. 8466-8469
    • Braun, D.1    Wider, G.2    Wuthrich, K.3
  • 48
    • 0029181728 scopus 로고
    • 1H 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigation of nearest - neighbor effects
    • Wishart, D. S., et al. (1995) 1H 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigation of nearest - neighbor effects, J Biomol NMR 5, 67-81.
    • (1995) J Biomol NMR , vol.5 , pp. 67-81
    • Wishart, D.S.1
  • 49
    • 0030726550 scopus 로고    scopus 로고
    • NMR analysis of main - chain conformational preferences in an unfolded fibronectin - binding Protein
    • Penkett, C. J., et al. (1997) NMR analysis of main - chain conformational preferences in an unfolded fibronectin - binding Protein, J Mol Biol 274, 152-159.
    • (1997) J Mol Biol , vol.274 , pp. 152-159
    • Penkett, C.J.1
  • 50
    • 0032545189 scopus 로고    scopus 로고
    • Modulation of intrinsic phi,psi propensities in the coil regions of protein structures: NMR analysis and dissection of beta - hairpin peptide
    • Griffiths - Jones, S. R., et al. (1998) Modulation of intrinsic phi,psi propensities in the coil regions of protein structures: NMR analysis and dissection of beta - hairpin peptide, J Mol Biol 284, 1597-1609.
    • (1998) J Mol Biol , vol.284 , pp. 1597-1609
    • Griffiths-Jones, S.R.1
  • 51
    • 0035119625 scopus 로고    scopus 로고
    • Chemical shifts in denatured proteins: Resonance assignment for denatured ubiquitin and comparisons with other denatured proteins
    • Peti, W., et al. (2001) Chemical shifts in denatured proteins: Resonance assignment for denatured ubiquitin and comparisons with other denatured proteins, J Biomol NMR 19, 153-165.
    • (2001) J Biomol NMR , vol.19 , pp. 153-165
    • Peti, W.1
  • 52
    • 0034836367 scopus 로고    scopus 로고
    • Sequence - dependent correction of random coil NMR chemical shifts
    • Schwarzinger, S., et al. (2001) Sequence - dependent correction of random coil NMR chemical shifts, J Am Chem Soc 123, 2970-2978.
    • (2001) J Am Chem Soc , vol.123 , pp. 2970-2978
    • Schwarzinger, S.1
  • 53
    • 3342969223 scopus 로고    scopus 로고
    • Origin of the neighboring residue effect on peptide backbone conformation
    • Avbelj, F. and Baldwin, R. L. (2004) Origin of the neighboring residue effect on peptide backbone conformation, Proc Natl Acad Sci U S A 101, 10967-10972.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 10967-10972
    • Avbelj, F.1    Baldwin, R.L.2
  • 54
    • 0031027137 scopus 로고    scopus 로고
    • Characterization of the backbone dynamics of folded and denatured states of an SH3 domain
    • Farrow, N. A., et al. (1997) Characterization of the backbone dynamics of folded and denatured states of an SH3 domain, Biochemistry 36, 2390-2402.
    • (1997) Biochemistry , vol.36 , pp. 2390-2402
    • Farrow, N.A.1
  • 55
    • 0037340833 scopus 로고    scopus 로고
    • Observation of residual dipolar couplings in short peptides
    • Ohnishi, S. and Shortle, D. (2003) Observation of residual dipolar couplings in short peptides, Proteins 50, 546-551.
    • (2003) Proteins , vol.50 , pp. 546-551
    • Ohnishi, S.1    Shortle, D.2
  • 56
    • 3242789489 scopus 로고    scopus 로고
    • Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings
    • Mohana - Borges, R., et al. (2004) Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings, J Mol Biol 340, 1131-1142.
    • (2004) J Mol Biol , vol.340 , pp. 1131-1142
    • Mohana-Borges, R.1
  • 57
    • 33746592145 scopus 로고    scopus 로고
    • Motional properties of unfolded ubiquitin: A model for a random coil protein
    • Wirmer, J., Peti, W., and Schwalbe, H. (2006) Motional properties of unfolded ubiquitin: A model for a random coil protein, J Biomol NMR 35, 175-186.
    • (2006) J Biomol NMR , vol.35 , pp. 175-186
    • Wirmer, J.1    Peti, W.2    Schwalbe, H.3
  • 58
    • 0026672305 scopus 로고
    • NMR determination of residual structure in a urea - denatured protein, the 434 - repressor
    • Neri, D., et al. (1992) NMR determination of residual structure in a urea - denatured protein, the 434 - repressor, Science 257, 1559-1563.
    • (1992) Science , vol.257 , pp. 1559-1563
    • Neri, D.1
  • 59
    • 0028805413 scopus 로고
    • Extensive nonrandom structure in reduced and unfolded bovine pancreatic trypsin inhibitor
    • Pan, H., et al. (1995) Extensive nonrandom structure in reduced and unfolded bovine pancreatic trypsin inhibitor, Biochemistry 34, 13974-13981.
    • (1995) Biochemistry , vol.34 , pp. 13974-13981
    • Pan, H.1
  • 60
    • 18244364614 scopus 로고    scopus 로고
    • Long - range interactions within a non - native protein
    • Klein - Seetharaman, J. K., et al. (2002) Long - range interactions within a non - native protein, Science 295, 1719-1722.
    • (2002) Science , vol.295 , pp. 1719-1722
    • Klein-Seetharaman, J.K.1
  • 61
    • 0028950079 scopus 로고
    • Urea unfolding of peptide helices as a model for interpreting protein unfolding
    • Scholtz, J. M., et al. (1995) Urea unfolding of peptide helices as a model for interpreting protein unfolding, Proc Natl Acad Sci U S A 92, 185-189.
    • (1995) Proc Natl Acad Sci U S A , vol.92 , pp. 185-189
    • Scholtz, J.M.1
  • 62
    • 0028820703 scopus 로고
    • Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein folding
    • Myers, J. K., Pace, C. N., and Scholtz, J. M. (1995) Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein folding, Protein Sci 4, 2138-2148.
    • (1995) Protein Sci , vol.4 , pp. 2138-2148
    • Myers, J.K.1    Pace, C.N.2    Scholtz, J.M.3
  • 63
    • 0032080534 scopus 로고    scopus 로고
    • Urea effects on protein stability: Hydrogen bonding and the hydrophobic effect
    • Zou, Q., Habermann - Rottinghous, S. M., and Murphy, K. P. (1998) Urea effects on protein stability: Hydrogen bonding and the hydrophobic effect, Proteins 31, 107-115..
    • (1998) Proteins , vol.31 , pp. 107-115
    • Zou, Q.1    Habermann-Rottinghous, S.M.2    Murphy, K.P.3
  • 64
    • 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
  • 65
    • 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, L. J., 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
  • 66
    • 0000749460 scopus 로고    scopus 로고
    • Toward a description of the conformations of denatured states of proteins. Comparison of a random coil model with NMR measurements
    • Fiebig, K. M., et al. (1996) Toward a description of the conformations of denatured states of proteins. Comparison of a random coil model with NMR measurements, J Phys Chem 100, 2661-2666.
    • (1996) J Phys Chem , vol.100 , pp. 2661-2666
    • Fiebig, K.M.1
  • 67
    • 0037610743 scopus 로고    scopus 로고
    • Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi
    • Avbelj, F. and Baldwin, R. L. (2003) Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi, Proc Natl Acad Sci U S A 100, 5742-5747.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 5742-5747
    • Avbelj, F.1    Baldwin, R.L.2
  • 68
    • 0024836024 scopus 로고
    • A comparison of the CHARMM, AMBER and ECCEP potentials for peptides. II. phi - psi maps for N - Acetyl alanine N' - methyl amide: Comparisons, contrasts and simple experimental tests
    • Roterman, I. K., et al. (1989) A comparison of the CHARMM, AMBER and ECCEP potentials for peptides. II. phi - psi maps for N - Acetyl alanine N' - methyl amide: Comparisons, contrasts and simple experimental tests, J Biomol Struct Dyn 7, 421-453.
    • (1989) J Biomol Struct Dyn , vol.7 , pp. 421-453
    • Roterman, I.K.1
  • 69
    • 0027996432 scopus 로고
    • A quantum mechanical investigation of the conformational energetics of the alanine and glycine dipeptides in the gas phase and in aqueous solution
    • Gould, I. R., Cornell, W. D., and Hillier, I. H. (1994) A quantum mechanical investigation of the conformational energetics of the alanine and glycine dipeptides in the gas phase and in aqueous solution, J Am Chem Soc 116, 9250-9256.
    • (1994) J Am Chem Soc , vol.116 , pp. 9250-9256
    • Gould, I.R.1    Cornell, W.D.2    Hillier, I.H.3
  • 70
    • 0028372251 scopus 로고
    • Stabilization of helices in glycine and alanine dipeptides in a reaction field model of solvent
    • Shang, H. S. and Head - Gordon, T. (1994) Stabilization of helices in glycine and alanine dipeptides in a reaction field model of solvent, J Am Chem Soc 116, 1528-1532.
    • (1994) J Am Chem Soc , vol.116 , pp. 1528-1532
    • Shang, H.S.1    Head-Gordon, T.2
  • 71
    • 0037441479 scopus 로고    scopus 로고
    • Comparison of a QM/MM force filed and molecular mechanics force fields in simulations of alanine and glycine dipeptides (Ace -Ala - Nme and Ace - Gly - Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
    • Hu, H., Elstner, M., and Hermans, J. (2003) Comparison of a QM/MM force filed and molecular mechanics force fields in simulations of alanine and glycine dipeptides (Ace -Ala - Nme and Ace - Gly - Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution, Proteins 50, 451-463.
    • (2003) Proteins , vol.50 , pp. 451-463
    • Hu, H.1    Elstner, M.2    Hermans, J.3
  • 72
    • 4043082766 scopus 로고    scopus 로고
    • Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model
    • Hudaky, I., Hudaky, P., and Perczel, A. (2004) Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model, J Comput Chem 25, 1522-1531.
    • (2004) J Comput Chem , vol.25 , pp. 1522-1531
    • Hudaky, I.1    Hudaky, P.2    Perczel, A.3
  • 73
    • 5544301524 scopus 로고    scopus 로고
    • Solvations effects on alanine dipeptide: A MP2/cc -pVTZ//MP2/6-31G study of (Phi,Psi) energy maps and conformers in the gas phase, ether, and water
    • Wang, Z. - X. and Duan, Y. (2004) Solvations effects on alanine dipeptide: A MP2/cc -pVTZ//MP2/6 - 31G study of (Phi,Psi) energy maps and conformers in the gas phase, ether, and water, J Comput Chem 25, 1699-1716.
    • (2004) J Comput Chem , vol.25 , pp. 1699-1716
    • Wang, Z.X.1    Duan, Y.2
  • 74
    • 70350391878 scopus 로고    scopus 로고
    • Are current semiempirical methods better than force fields? A study from the thermodynamics perspective
    • Seabra, G. D. M., Walker, R. C., and Roitberg, A. E. (2009) Are current semiempirical methods better than force fields? A study from the thermodynamics perspective, J Phys Chem A 113, 11938-11948.
    • (2009) J Phys Chem A , vol.113 , pp. 11938-11948
    • Seabra, G.D.M.1    Walker, R.C.2    Roitberg, A.E.3
  • 75
    • 0028960071 scopus 로고
    • Role of electrostatic screening in determining protein main chain conformational preferences
    • Avbelj, F. and Moult, J. (1995) Role of electrostatic screening in determining protein main chain conformational preferences, Biochemistry 34, 755-764.
    • (1995) Biochemistry , vol.34 , pp. 755-764
    • Avbelj, F.1    Moult, J.2
  • 76
    • 0032511138 scopus 로고    scopus 로고
    • Role of main - chain electrostatics, hydrophobic effect, and side - chain conformational entropy in determining the secondary structure of proteins
    • Avbelj, F. and Fele, L. (1998) Role of main - chain electrostatics, hydrophobic effect, and side - chain conformational entropy in determining the secondary structure of proteins, J Mol Biol 279, 665-684.
    • (1998) J Mol Biol , vol.279 , pp. 665-684
    • Avbelj, F.1    Fele, L.2
  • 77
    • 0034725551 scopus 로고    scopus 로고
    • Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins
    • Avbelj, F. (2000) Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins, J Mol Biol 300, 1337-1361.
    • (2000) J Mol Biol , vol.300 , pp. 1337-1361
    • Avbelj, F.1
  • 78
    • 0028883794 scopus 로고
    • The conformation of folding initiation sites in proteins determined by computer simulation
    • Avbelj, F. and Moult, J. (1995) The conformation of folding initiation sites in proteins determined by computer simulation, Proteins Struct Funct Genet 23, 129-141.
    • (1995) Proteins Struct Funct Genet , vol.23 , pp. 129-141
    • Avbelj, F.1    Moult, J.2
  • 79
    • 0032053525 scopus 로고    scopus 로고
    • Prediction of the three dimensional structure of proteins using the electrostatic screening model and hierarchic condensation
    • Avbelj, F. and Fele, L. (1998) Prediction of the three dimensional structure of proteins using the electrostatic screening model and hierarchic condensation, Proteins Struct Funct Genet 31, 74-96.
    • (1998) Proteins Struct Funct Genet , vol.31 , pp. 74-96
    • Avbelj, F.1    Fele, L.2
  • 80
    • 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., and Baldwin, R. L. (2000) Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities, Proc Natl Acad Sci U S A 97, 10786-10791.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 10786-10791
    • Avbelj, F.1    Luo, P.2    Baldwin, R.L.3
  • 81
    • 0037022289 scopus 로고    scopus 로고
    • Role of backbone solvation in determining thermodynamic beta - propensities of the amino acids
    • Avbelj, F. and Baldwin, R. L. (2002) Role of backbone solvation in determining thermodynamic beta - propensities of the amino acids, Proc Natl Acad Sci U S A 99, 1309-1313.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 1309-1313
    • Avbelj, F.1    Baldwin, R.L.2
  • 82
    • 10644250720 scopus 로고    scopus 로고
    • Protein chemical shifts arising from alpha - helices and beta - sheets depend on solvent exposure
    • Avbelj, F., Kocjan, D., and Baldwin, R. L. (2004) Protein chemical shifts arising from alpha - helices and beta - sheets depend on solvent exposure, Proc Natl Acad Sci U S A 101, 17394.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 17394
    • Avbelj, F.1    Kocjan, D.2    Baldwin, R.L.3
  • 83
    • 0021476470 scopus 로고
    • Calculation of electrostatic interactions in biological systems and in solutions
    • Warshel, A. and Russell, S. T. (1984) Calculation of electrostatic interactions in biological systems and in solutions, Q Rev Biophys 17, 283-422.
    • (1984) Q Rev Biophys , vol.17 , pp. 283-422
    • Warshel, A.1    Russell, S.T.2
  • 84
    • 0000503513 scopus 로고
    • Evaluation of the dipeptide approximation in peptide modeling by ab initio geometry optimization of oligopeptides
    • Schafer, L., et al. (1993) Evaluation of the dipeptide approximation in peptide modeling by ab initio geometry optimization of oligopeptides, J Am Chem Soc 115, 272-280.
    • (1993) J Am Chem Soc , vol.115 , pp. 272-280
    • Schafer, L.1
  • 85
    • 0030745939 scopus 로고    scopus 로고
    • Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields
    • Beachy, M. D., et al. (1997) Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields, J Am Chem Soc 119, 5908-5920.
    • (1997) J Am Chem Soc , vol.119 , pp. 5908-5920
    • Beachy, M.D.1
  • 86
    • 0037018526 scopus 로고    scopus 로고
    • Conformational study of the alanine dipeptide at the MP2 and DFT levels
    • Vargas, R., et al. (2002) Conformational study of the alanine dipeptide at the MP2 and DFT levels, J Phys Chem A 106, 3213-3218.
    • (2002) J Phys Chem A , vol.106 , pp. 3213-3218
    • Vargas, R.1
  • 87
    • 0037495961 scopus 로고    scopus 로고
    • Peptide models. XXXIII. Extrapolation of low - level Hartree -Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory
    • Perczel, A., et al. (2003) Peptide models. XXXIII. Extrapolation of low - level Hartree -Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory, J Comput Chem 24, 1026-1042.
    • (2003) J Comput Chem , vol.24 , pp. 1026-1042
    • Perczel, A.1
  • 88
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas - phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • Mackerell, A. D., Feig, M., and Brooks, C. L. III (2004) Extending the treatment of backbone energetics in protein force fields: Limitations of gas - phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations, J Comput Chem 25, 1400-1415.
    • (2004) J Comput Chem , vol.25 , pp. 1400-1415
    • Mackerell, A.D.1    Feig, M.2    Brooks III, C.L.3
  • 89
    • 3142735758 scopus 로고    scopus 로고
    • Assessing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions
    • Improta, R. and Barone, V. (2004) Assessing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions, J Comput Chem 25, 1333-1341.
    • (2004) J Comput Chem , vol.25 , pp. 1333-1341
    • Improta, R.1    Barone, V.2
  • 91
    • 11744256643 scopus 로고
    • Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
    • Tomasi, J. and Persico, M. (1994) Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent, Chem Rev 94, 2027-2094.
    • (1994) Chem Rev , vol.94 , pp. 2027-2094
    • Tomasi, J.1    Persico, M.2
  • 92
    • 32844457567 scopus 로고
    • Accurate calculations of hydration free energies using macroscopic solvent models
    • Sitkoff, D., Sharp, K. A., and Honig, B. (1994) Accurate calculations of hydration free energies using macroscopic solvent models, J Phys Chem 98, 1978-1988.
    • (1994) J Phys Chem , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 93
    • 0031187388 scopus 로고    scopus 로고
    • Langevin dipoles model for ab initio calculations of chemical processes in solution: Parameterization and application to hydration free energies of neutral and ionic solutes and conformational analysis in aqueous solution
    • Florian, J. and Warshel, A. (1997) Langevin dipoles model for ab initio calculations of chemical processes in solution: Parameterization and application to hydration free energies of neutral and ionic solutes and conformational analysis in aqueous solution, J Phys Chem B 101, 5583-5595.
    • (1997) J Phys Chem B , vol.101 , pp. 5583-5595
    • Florian, J.1    Warshel, A.2
  • 94
    • 0019883174 scopus 로고
    • Affinities of amino acid side chain for solvent water
    • Wolfenden, R., et al. (1981) Affinities of amino acid side chain for solvent water, Biochemistry 20, 849-855.
    • (1981) Biochemistry , vol.20 , pp. 849-855
    • Wolfenden, R.1
  • 95
    • 0000484499 scopus 로고
    • Hydrophobic parameters of amino acid side chains from partitioning of N - acetyl - amino - acid amides
    • Fauchere, J. - L. and Pliska, V. (1983) Hydrophobic parameters of amino acid side chains from partitioning of N - acetyl - amino - acid amides, Eur J Med Chem - Chim Ther 18, 369-375.
    • (1983) Eur J Med Chem - Chim Ther , vol.18 , pp. 369-375
    • Fauchere, J.-L.1    Pliska, V.2
  • 96
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg, D. and McLachlan, A. D. (1986) Solvation energy in protein folding and binding, Nature 319, 199-203.
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 97
    • 0026723852 scopus 로고
    • Use of a potential of mean force to analyze free energy contributions in protein folding
    • Avbelj, F. (1992) Use of a potential of mean force to analyze free energy contributions in protein folding, Biochemistry 31, 6290-6297.
    • (1992) Biochemistry , vol.31 , pp. 6290-6297
    • Avbelj, F.1
  • 99
    • 0000333671 scopus 로고
    • On the theory of helix - coil transition in polypeptides
    • Lifson, S. and Roig, A. (1961) On the theory of helix - coil transition in polypeptides, J Chem Phys 34, 1963-1974.
    • (1961) J Chem Phys , vol.34 , pp. 1963-1974
    • Lifson, S.1    Roig, A.2
  • 100
    • 0015967881 scopus 로고
    • Conformational parameters for amino acid in helical, beta - sheet, and random coil regions calculated from proteins
    • Chou, P. Y. and Fasman, G. D. (1974) Conformational parameters for amino acid in helical, beta - sheet, and random coil regions calculated from proteins, Biochemistry 13, 211-222.
    • (1974) Biochemistry , vol.13 , pp. 211-222
    • Chou, P.Y.1    Fasman, G.D.2
  • 101
    • 0029147823 scopus 로고
    • Intrinsic phi,psi propensities if amino acids, derived from the coil regions of known structures
    • Swindellls, M. B., MacArthur, M. W., and Thornton, J. M. (1995) Intrinsic phi,psi propensities if amino acids, derived from the coil regions of known structures, Nat Struct Biol 2, 596-603.
    • (1995) Nat Struct Biol , vol.2 , pp. 596-603
    • Swindellls, M.B.1    MacArthur, M.W.2    Thornton, J.M.3
  • 102
    • 0031808074 scopus 로고    scopus 로고
    • A helix propensity scale based on experimental studies of peptides and proteins
    • Pace, C. N. and Scholtz, J. M. (1998) A helix propensity scale based on experimental studies of peptides and proteins, Biophys J 75, 422-427.
    • (1998) Biophys J , vol.75 , pp. 422-427
    • Pace, C.N.1    Scholtz, J.M.2
  • 103
    • 0025113815 scopus 로고
    • Helix - coil stability constants for the naturally occurring amino acids in water. XXIV. Half - cysteine parameters from random Poly(Hydroxybutylglutamine - co - S - Methylthio - l - Cysteine)
    • Wojcik, J., Altmann, K. - H., and Scheraga, H. A. (1990) Helix - coil stability constants for the naturally occurring amino acids in water. XXIV. Half - cysteine parameters from random Poly(Hydroxybutylglutamine - co - S - Methylthio - l - Cysteine), B iopolymers 30, 121-134.
    • (1990) B iopolymers , vol.30 , pp. 121-134
    • Wojcik, J.1    Altmann, K.-H.2    Scheraga, H.A.3
  • 104
    • 0028142385 scopus 로고
    • Helix - forming tendencies of amino acids in short (Hydroxybutyl) - L - glutamine peptides: An evaluation of the contradictory results from host - guest studies and short alanine - based peptides
    • Padmanabham, S., et al. (1994) Helix - forming tendencies of amino acids in short (Hydroxybutyl) - L - glutamine peptides: An evaluation of the contradictory results from host - guest studies and short alanine - based peptides, Biochemistry 33, 8604-8609.
    • (1994) Biochemistry , vol.33 , pp. 8604-8609
    • Padmanabham, S.1
  • 105
    • 0027411181 scopus 로고
    • Thermodynamic beta - sheet propensities measured using a zinc finger host peptide
    • Kim, C. A. and Berg, J. M. (1993) Thermodynamic beta - sheet propensities measured using a zinc finger host peptide, Nature 362, 267-270.
    • (1993) Nature , vol.362 , pp. 267-270
    • Kim, C.A.1    Berg, J.M.2
  • 106
    • 0027998757 scopus 로고
    • Context is a major determinant of beta - sheet propensity
    • Minor, D. L. and Kim, P. S. (1994) Context is a major determinant of beta - sheet propensity, Nature 371, 264-267.
    • (1994) Nature , vol.371 , pp. 264-267
    • Minor, D.L.1    Kim, P.S.2
  • 107
    • 0028175780 scopus 로고
    • A thermodynamic scale for the beta -sheet forming tendencies of the amino acids
    • Smith, C. K., Withka, J. M., and Regan, L. (1994) A thermodynamic scale for the beta -sheet forming tendencies of the amino acids, Biochemistry 33, 5510-5517.
    • (1994) Biochemistry , vol.33 , pp. 5510-5517
    • Smith, C.K.1    Withka, J.M.2    Regan, L.3
  • 108
    • 0028176595 scopus 로고
    • Measurement of the beta - sheet - forming propensities of amino acids
    • Minor, D. L. and Kim, P. S. (1994) Measurement of the beta - sheet - forming propensities of amino acids, Nature 367, 660-663.
    • (1994) Nature , vol.367 , pp. 660-663
    • Minor, D.L.1    Kim, P.S.2
  • 109
    • 0025222978 scopus 로고
    • A thermodynamics scale for the helix - forming tendencies of the commonly occurring amino acids
    • O ' Neal, K. T. and DeGrado, W. F. (1990) A thermodynamics scale for the helix - forming tendencies of the commonly occurring amino acids, Science 250, 646-651.
    • (1990) Science , vol.250 , pp. 646-651
    • O' Neal, K.T.1    DeGrado, W.F.2
  • 110
    • 0025804130 scopus 로고
    • Large differences in the helix propensities of alanine and glycine
    • Chakrabartty, A., Shellman, J. A., and Baldwin, R. L. (1991) Large differences in the helix propensities of alanine and glycine, Nature 351, 586-588.
    • (1991) Nature , vol.351 , pp. 586-588
    • Chakrabartty, A.1    Shellman, J.A.2    Baldwin, R.L.3
  • 111
    • 0025260032 scopus 로고
    • Side chain contribution to the stability of alpha - helical structure in proteins
    • Lyu, P. C., et al. (1990) Side chain contribution to the stability of alpha - helical structure in proteins, Science 250, 669-673.
    • (1990) Science , vol.250 , pp. 669-673
    • Lyu, P.C.1
  • 112
    • 0024997237 scopus 로고
    • Effect of central - residue replacement on the helical stability of a monomeric peptide
    • Merutka, G., et al. (1990) Effect of central - residue replacement on the helical stability of a monomeric peptide, Biochemistry 29, 7511-7515.
    • (1990) Biochemistry , vol.29 , pp. 7511-7515
    • Merutka, G.1
  • 113
    • 0025849701 scopus 로고
    • Calorimetric determination of the enthalpy change for the alpha - helix to coil transition of an alanine peptide in water
    • Scholtz, J. M., 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 U S A 88, 2854-2858.
    • (1991) Proc Natl Acad Sci U S A , vol.88 , pp. 2854-2858
    • Scholtz, J.M.1
  • 114
    • 0026209013 scopus 로고
    • The helical s constant for alanine in water derived from template - nucleated helices
    • Kemp, D. S., Boyd, J. G., and Muendel, C. C. (1991) The helical s constant for alanine in water derived from template - nucleated helices, Nature 352, 451-454.
    • (1991) Nature , vol.352 , pp. 451-454
    • Kemp, D.S.1    Boyd, J.G.2    Muendel, C.C.3
  • 115
    • 0028222235 scopus 로고
    • Helix propensities of the amino acids measured in alanine - based peptides without helix - stabilizing side - chain interactions
    • Chakrabartty, A., Kortemme, T., and Baldwin, R. L. (1994) Helix propensities of the amino acids measured in alanine - based peptides without helix - stabilizing side - chain interactions, P rotein Sci 3, 843-852.
    • (1994) P rotein Sci , vol.3 , pp. 843-852
    • Chakrabartty, A.1    Kortemme, T.2    Baldwin, R.L.3
  • 116
    • 29144433298 scopus 로고    scopus 로고
    • Polyproline II propensities from GGXGG peptides reveal anticorrelation with beta - sheet scales
    • Shi, Z., et al. (2005) Polyproline II propensities from GGXGG peptides reveal anticorrelation with beta - sheet scales, Proc Natl Acad Sci U S A 102, 17964-17968.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 17964-17968
    • Shi, Z.1
  • 117
    • 70349085815 scopus 로고    scopus 로고
    • Context - independent, temperature - dependent helical propensities for amino acid residues
    • Moreau, R. J., et al. (2009) Context - independent, temperature - dependent helical propensities for amino acid residues, J Am Chem Soc 131, 13107-13116.
    • (2009) J Am Chem Soc , vol.131 , pp. 13107-13116
    • Moreau, R.J.1
  • 118
    • 11644317783 scopus 로고    scopus 로고
    • Theoretical study of aqueous N - Acetyl - L - alanine N' -Methylamide: Structure and Raman VCD, and ROA spectra
    • Han, W. - G., et al. (1998) Theoretical study of aqueous N - Acetyl - L - alanine N' -Methylamide: Structure and Raman VCD, and ROA spectra, J Phys Chem B 102, 2587-2602.
    • (1998) J Phys Chem B , vol.102 , pp. 2587-2602
    • Han, W.-G.1
  • 119
    • 0037044485 scopus 로고    scopus 로고
    • Peptide conformational heterogeneity revealed from nonlinear vibrational spectroscopy and molecular - dynamics simulations
    • Woutersen, S., et al. (2002) Peptide conformational heterogeneity revealed from nonlinear vibrational spectroscopy and molecular - dynamics simulations, J Chem Phys 117, 6833-6840.
    • (2002) J Chem Phys , vol.117 , pp. 6833-6840
    • Woutersen, S.1
  • 120
    • 0034700155 scopus 로고    scopus 로고
    • Physical reasons for the unusual alpha - helix stabilization afforded by charged or neutral polar residues in alanine - rich peptides
    • Vila, J. A., Ripoll, D. R., and Scheraga, H. A. (2000) Physical reasons for the unusual alpha - helix stabilization afforded by charged or neutral polar residues in alanine - rich peptides, P roc Natl Acad Sci U S A 97, 13075-13079.
    • (2000) P roc Natl Acad Sci U S A , vol.97 , pp. 13075-13079
    • Vila, J.A.1    Ripoll, D.R.2    Scheraga, H.A.3
  • 121
    • 0035845493 scopus 로고    scopus 로고
    • Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C' position of the C - capping box of alpha - helices
    • Thomas, S. T., Loladze, V. V., and Makhatadze, G. I. (2001) Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C' position of the C - capping box of alpha - helices, Proc Natl Acad Sci U S A 98, 10670-10675.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 10670-10675
    • Thomas, S.T.1    Loladze, V.V.2    Makhatadze, G.I.3
  • 122
    • 0037022332 scopus 로고    scopus 로고
    • The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metal - binding to induce helix formation
    • Lopez, M. M., et al. (2002) The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metal - binding to induce helix formation, Proc Natl Acad Sci U S A 99, 1298-1302.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 1298-1302
    • Lopez, M.M.1
  • 123
    • 0026050172 scopus 로고
    • Conformational equilibria of valine studied by dynamics simulation
    • Yun, R. H. and Hermans, J. (1991) Conformational equilibria of valine studied by dynamics simulation, Protein Eng 4, 761-766.
    • (1991) Protein Eng , vol.4 , pp. 761-766
    • Yun, R.H.1    Hermans, J.2
  • 124
    • 0026748637 scopus 로고
    • Differential helix propensity of small apolar side chains studied by molecular dynamics simulations
    • Hermans, J., Anderson, A. G., and Yun, R. H. (1992) Differential helix propensity of small apolar side chains studied by molecular dynamics simulations, Biochemistry 31, 5646-5653.
    • (1992) Biochemistry , vol.31 , pp. 5646-5653
    • Hermans, J.1    Anderson, A.G.2    Yun, R.H.3
  • 125
    • 1542366657 scopus 로고    scopus 로고
    • Role of solvent in determining conformational preferences of alanine dipeptide in water
    • Drozdov, A. N., Grossfield, A., and Pappu, R. V. (2004) Role of solvent in determining conformational preferences of alanine dipeptide in water, J Am Chem Soc 126, 2574-2581.
    • (2004) J Am Chem Soc , vol.126 , pp. 2574-2581
    • Drozdov, A.N.1    Grossfield, A.2    Pappu, R.V.3
  • 126
    • 0025764258 scopus 로고
    • Straight - chain non - polar amino acids are good helix - formers in water
    • Padmanabhan, S. and Baldwin, R. L. (1991) Straight - chain non - polar amino acids are good helix - formers in water, J Mol Biol 219, 135-137.
    • (1991) J Mol Biol , vol.219 , pp. 135-137
    • Padmanabhan, S.1    Baldwin, R.L.2
  • 127
    • 0026665778 scopus 로고
    • Side - chain entropy opposes alpha - helix formation but rationalizes experimentally determined helix - forming propensities
    • Creamer, T. P. and Rose, G. D. (1992) Side - chain entropy opposes alpha - helix formation but rationalizes experimentally determined helix - forming propensities, Proc Natl Acad Sci U S A 89, 5937-5941.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 5937-5941
    • Creamer, T.P.1    Rose, G.D.2
  • 128
    • 0028178865 scopus 로고
    • Alpha - helix - forming propensities in peptides and proteins
    • Creamer, T. C. and Rose, G. D. (1994) Alpha - helix - forming propensities in peptides and proteins, Proteins Struct Funct Genet 19, 85-97.
    • (1994) Proteins Struct Funct Genet , vol.19 , pp. 85-97
    • Creamer, T.C.1    Rose, G.D.2
  • 129
    • 0033529861 scopus 로고    scopus 로고
    • Intrinsic beta - sheet propensities result from van der Waals interactions between side chains and the local backbone
    • Street, A. G. and Mayo, S. L. (1999) Intrinsic beta - sheet propensities result from van der Waals interactions between side chains and the local backbone, Proc Natl Acad Sci U S A 96, 9074-9076.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 9074-9076
    • Street, A.G.1    Mayo, S.L.2
  • 130
    • 0027236794 scopus 로고
    • Structural basis of amino acid alpha - helix propensity
    • Blaber, M., Zhang, X., and Matthews, B. W. (1993) Structural basis of amino acid alpha - helix propensity, S cience 260, 1637-1640.
    • (1993) S cience , vol.260 , pp. 1637-1640
    • Blaber, M.1    Zhang, X.2    Matthews, B.W.3
  • 131
    • 0028178528 scopus 로고
    • Determination of alpha - helix propensity within the context of a folded protein
    • Blaber, M., et al. (1994) Determination of alpha - helix propensity within the context of a folded protein, J Mol Biol 235, 600-624.
    • (1994) J Mol Biol , vol.235 , pp. 600-624
    • Blaber, M.1
  • 132
    • 0029077857 scopus 로고
    • Interactions between hydrophobic side chains within alpha - helices
    • Creamer, T. P. and Rose, G. D. (1995) Interactions between hydrophobic side chains within alpha - helices, P rotein Sci 4, 1305-1314.
    • (1995) P rotein Sci , vol.4 , pp. 1305-1314
    • Creamer, T.P.1    Rose, G.D.2
  • 133
    • 0028882032 scopus 로고
    • Measuring the strength of side - chain hydrogen bonds in peptide helices: The Gln Asp (i,i + 4) interaction
    • Huyghues - Despointes, B. M. P., Klinger, T. M., and Baldwin, R. L. (1995) Measuring the strength of side - chain hydrogen bonds in peptide helices: The Gln Asp (i,i + 4) interaction, B iochemistry 34, 13267-13271.
    • (1995) B iochemistry , vol.34 , pp. 13267-13271
    • Huyghues-Despointes, B.M.P.1    Klinger, T.M.2    Baldwin, R.L.3
  • 134
    • 0344962370 scopus 로고    scopus 로고
    • Validation of an all - atom protein force field: From dipeptides to larger proteins
    • Gnanakaran, S. and Garcia, A. E. (2003) Validation of an all - atom protein force field: From dipeptides to larger proteins, J Phys Chem B 107, 12555-12557.
    • (2003) J Phys Chem B , vol.107 , pp. 12555-12557
    • Gnanakaran, S.1    Garcia, A.E.2
  • 135
    • 40849105036 scopus 로고    scopus 로고
    • Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: Comparisons with IR and vibrational circular dichroism spectra
    • Kwac, K., et al. (2008) Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: Comparisons with IR and vibrational circular dichroism spectra, J Chem Phys 128, 105106 - 1-105106 - 13.
    • (2008) J Chem Phys , vol.128 , pp. 1051061-10510613
    • Kwac, K.1
  • 136
    • 0025281956 scopus 로고
    • Local interactions in peptides: H - H and 13C - H coupling constants for the conformational analysis of N - acetyl - N' - methylamides of aliphatic amino acids
    • Fermandjian, S., et al. (1990) Local interactions in peptides: H - H and 13C - H coupling constants for the conformational analysis of N - acetyl - N' - methylamides of aliphatic amino acids, Int J Pept Protein Res 35, 473-480.
    • (1990) Int J Pept Protein Res , vol.35 , pp. 473-480
    • Fermandjian, S.1
  • 137
    • 0033604845 scopus 로고    scopus 로고
    • Effects of core mutations on the folding of a beta - sheet protein: Implications for backbone organization in the I - state
    • Lorch, M., et al. (1999) Effects of core mutations on the folding of a beta - sheet protein: Implications for backbone organization in the I - state, Biochemistry 38, 1377-1385.
    • (1999) Biochemistry , vol.38 , pp. 1377-1385
    • Lorch, M.1
  • 138
    • 0034724160 scopus 로고    scopus 로고
    • Effects of mutants on the thermodynamics of a protein folding reactions: Implications for the mechanism of formation of the intermediate and transition states
    • Lorch, M., et al. (2000) Effects of mutants on the thermodynamics of a protein folding reactions: Implications for the mechanism of formation of the intermediate and transition states, Biochemistry 39, 3480-3485.
    • (2000) Biochemistry , vol.39 , pp. 3480-3485
    • Lorch, M.1
  • 139
    • 0035957221 scopus 로고    scopus 로고
    • NMR structural and dynamic characterization of the acid - unfolded state of apomyoglobin provides insight into the early events in protein folding
    • Yao, J., et al. (2001) NMR structural and dynamic characterization of the acid - unfolded state of apomyoglobin provides insight into the early events in protein folding, Biochemistry 40, 3561-3571.
    • (2001) Biochemistry , vol.40 , pp. 3561-3571
    • Yao, J.1
  • 140
    • 0022412192 scopus 로고
    • Hydrophobicity of amino acid residues in globular proteins
    • Rose, G. D., et al. (1985) Hydrophobicity of amino acid residues in globular proteins, Science 229, 834-838.
    • (1985) Science , vol.229 , pp. 834-838
    • Rose, G.D.1
  • 141
    • 33846513125 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte, J. and Doolittle, R. F. (1992) A simple method for displaying the hydropathic character of a protein, J Mol Biol 12, 345-364.
    • (1992) J Mol Biol , vol.12 , pp. 345-364
    • Kyte, J.1    Doolittle, R.F.2
  • 142
    • 33644846737 scopus 로고    scopus 로고
    • Folding and amyloid - fibril formation for a series of human stefins ' chimeras: Any correlation?
    • Kenig, M., et al. (2006) Folding and amyloid - fibril formation for a series of human stefins ' chimeras: Any correlation? Proteins 62, 918-927.
    • (2006) Proteins , vol.62 , pp. 918-927
    • Kenig, M.1
  • 143
    • 0026597879 scopus 로고
    • The chemical shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy
    • Wishart, D. S., Sykes, B. D., and Richards, F. M. (1992) The chemical shift index: A fast and simple method for the assignment of protein secondary structure through NMR spectroscopy, Biochemistry 31, 1647-1651.
    • (1992) Biochemistry , vol.31 , pp. 1647-1651
    • Wishart, D.S.1    Sykes, B.D.2    Richards, F.M.3
  • 144
    • 0347610773 scopus 로고
    • Empirical correlation between protein backbone conformation and C - alpha and C - beta 13C nuclear magnetic resonance chemical shifts
    • Spera, S. and Bax, A. (1991) Empirical correlation between protein backbone conformation and C - alpha and C - beta 13C nuclear magnetic resonance chemical shifts, J Am Chem Soc 113, 5490-5492.
    • (1991) J Am Chem Soc , vol.113 , pp. 5490-5492
    • Spera, S.1    Bax, A.2
  • 145
    • 0000865993 scopus 로고
    • A new analysis of proton chemical shifts in proteins
    • Osapay, K. and Case, D. A. (1991) A new analysis of proton chemical shifts in proteins, J Am Chem Soc 113, 9436-9444.
    • (1991) J Am Chem Soc , vol.113 , pp. 9436-9444
    • Osapay, K.1    Case, D.A.2
  • 146
    • 0027308278 scopus 로고
    • Secondary and tertiary structural effects on proteins NMR chemical shifts: An ab initio approach
    • Dios, A. C. D., Pearson, J. G., and Oldfield, E. (1993) Secondary and tertiary structural effects on proteins NMR chemical shifts: An ab initio approach, Science 260, 1491-1496.
    • (1993) Science , vol.260 , pp. 1491-1496
    • Dios, A.C.D.1    Pearson, J.G.2    Oldfield, E.3
  • 147
    • 44949269218 scopus 로고
    • Empirical comparison of models for chemical -shift calculation in proteins
    • Williamson, M. P. and Asakura, T. (1993) Empirical comparison of models for chemical -shift calculation in proteins, J Magn Reson B 101, 63-71.
    • (1993) J Magn Reson B , vol.101 , pp. 63-71
    • Williamson, M.P.1    Asakura, T.2
  • 148
    • 0028394633 scopus 로고
    • Analysis of proton chemical shifts in regular secondary structure of proteins
    • Osapay, K. and Case, D. A. (1994) Analysis of proton chemical shifts in regular secondary structure of proteins, J Biomol NMR 4, 215-230.
    • (1994) J Biomol NMR , vol.4 , pp. 215-230
    • Osapay, K.1    Case, D.A.2
  • 149
    • 0000635348 scopus 로고
    • The relationship between amide proton chemical shifts and secondary structure in proteins
    • Asakura, T., et al. (1995) The relationship between amide proton chemical shifts and secondary structure in proteins, J Biomol NMR 6, 227-236.
    • (1995) J Biomol NMR , vol.6 , pp. 227-236
    • Asakura, T.1
  • 150
    • 0031576676 scopus 로고    scopus 로고
    • Density functional calculations of proton chemical shifts in model peptides
    • Sitkoff, D. and Case, D. A. (1997) Density functional calculations of proton chemical shifts in model peptides, J Am Chem Soc 119, 12262-12273.
    • (1997) J Am Chem Soc , vol.119 , pp. 12262-12273
    • Sitkoff, D.1    Case, D.A.2
  • 151
    • 0347358202 scopus 로고    scopus 로고
    • Theories of chemical shift anisotropies in proteins and nucleic acids
    • Sitkoff, D. and Case, D. A. (1998) Theories of chemical shift anisotropies in proteins and nucleic acids, Prog Nucl Magn Reson Spectrosc 32, 165-190.
    • (1998) Prog Nucl Magn Reson Spectrosc , vol.32 , pp. 165-190
    • Sitkoff, D.1    Case, D.A.2
  • 152
    • 0032454094 scopus 로고    scopus 로고
    • Protein chemical shift analysis: A practical guide
    • Wishart, D. S. and Nip, A. M. (1998) Protein chemical shift analysis: A practical guide, Biochem Cell Biol 76, 153-163.
    • (1998) Biochem Cell Biol , vol.76 , pp. 153-163
    • Wishart, D.S.1    Nip, A.M.2
  • 153
    • 0034923356 scopus 로고    scopus 로고
    • Use of chemical shifts in macromolecular structure determination
    • Wishart, D. S. and Case, D. A. (2001) Use of chemical shifts in macromolecular structure determination, Methods Enzymol 338, 3-34.
    • (2001) Methods Enzymol , vol.338 , pp. 3-34
    • Wishart, D.S.1    Case, D.A.2
  • 154
    • 0027250665 scopus 로고
    • Primary structure effects on peptide group hydrogen exchange
    • Bai, Y., et al. (1993) Primary structure effects on peptide group hydrogen exchange, Proteins 17, 75-86.
    • (1993) Proteins , vol.17 , pp. 75-86
    • Bai, Y.1
  • 155
    • 0028226386 scopus 로고
    • Hydrogen bond strength and beta - sheet propensities: The role of a side chain blocking effect
    • Bai, Y. and Englander, S. W. (1994) Hydrogen bond strength and beta - sheet propensities: The role of a side chain blocking effect, Proteins 18, 262-266.
    • (1994) Proteins , vol.18 , pp. 262-266
    • Bai, Y.1    Englander, S.W.2
  • 156
    • 0014958362 scopus 로고
    • Determination of an acidity scale for peptide hydrogens from nuclear magnetic resonance kinetic studies
    • Sheinblatt, M. (1970) Determination of an acidity scale for peptide hydrogens from nuclear magnetic resonance kinetic studies, J Am Chem Soc 92, 2505-2509.
    • (1970) J Am Chem Soc , vol.92 , pp. 2505-2509
    • Sheinblatt, M.1
  • 157
    • 33947090634 scopus 로고
    • Substituent effects on amide hydrogen exchange rates in aqueous solution
    • Molday, R. S. and Kallen, R. G. (1972) Substituent effects on amide hydrogen exchange rates in aqueous solution, J Am Chem Soc 94, 6739-6745.
    • (1972) J Am Chem Soc , vol.94 , pp. 6739-6745
    • Molday, R.S.1    Kallen, R.G.2
  • 158
    • 0032557227 scopus 로고    scopus 로고
    • pKa shift effects on backbone amide base - catalyzed hydrogen exchange rates in peptides
    • Fogolari, F., et al. (1998) pKa shift effects on backbone amide base - catalyzed hydrogen exchange rates in peptides, J Am Chem Soc 120, 3735-3738.
    • (1998) J Am Chem Soc , vol.120 , pp. 3735-3738
    • Fogolari, F.1
  • 159
    • 62549159643 scopus 로고    scopus 로고
    • Origin of the change in solvation enthalpy of the peptide group when neighboring peptide groups are added
    • Avbelj, F. and Baldwin, R. L. (2009) Origin of the change in solvation enthalpy of the peptide group when neighboring peptide groups are added, Proc Natl Acad Sci U S A 106, 3137-3141.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 3137-3141
    • Avbelj, F.1    Baldwin, R.L.2
  • 160
    • 0020997912 scopus 로고
    • Dictionary of protein structure: Pattern recognition of hydrogen - bonded and geometrical features
    • Kabsch, W. and Sander, C. (1983) Dictionary of protein structure: Pattern recognition of hydrogen - bonded and geometrical features, Biopolymers 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2


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