메뉴 건너뛰기




Volumn 110, Issue 2, 2016, Pages 348-361

Insights into Unfolded Proteins from the Intrinsic φ/ψ Propensities of the AAXAA Host-Guest Series

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; INTRINSICALLY DISORDERED PROTEIN; OLIGOPEPTIDE;

EID: 84955447535     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2015.12.008     Document Type: Article
Times cited : (12)

References (100)
  • 1
    • 84856414506 scopus 로고    scopus 로고
    • Residual structure in unfolded proteins
    • B.E. Bowler Residual structure in unfolded proteins Curr. Opin. Struct. Biol. 22 2012 4 13
    • (2012) Curr. Opin. Struct. Biol. , vol.22 , pp. 4-13
    • Bowler, B.E.1
  • 2
    • 84902160274 scopus 로고    scopus 로고
    • Intrinsically disordered proteins and intrinsically disordered protein regions
    • C.J. Oldfield, and A.K. Dunker Intrinsically disordered proteins and intrinsically disordered protein regions Annu. Rev. Biochem. 83 2014 553 584
    • (2014) Annu. Rev. Biochem. , vol.83 , pp. 553-584
    • Oldfield, C.J.1    Dunker, A.K.2
  • 3
    • 79951659192 scopus 로고    scopus 로고
    • Flexible nets of malleable guardians: Intrinsically disordered chaperones in neurodegenerative diseases
    • V.N. Uversky Flexible nets of malleable guardians: intrinsically disordered chaperones in neurodegenerative diseases Chem. Rev. 111 2011 1134 1166
    • (2011) Chem. Rev. , vol.111 , pp. 1134-1166
    • Uversky, V.N.1
  • 4
    • 84877896151 scopus 로고    scopus 로고
    • Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding
    • W.-L. Hsu, and C.J. Oldfield A.K. Dunker Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding Protein Sci. 22 2013 258 273
    • (2013) Protein Sci. , vol.22 , pp. 258-273
    • Hsu, W.-L.1    Oldfield, C.J.2    Dunker, A.K.3
  • 5
    • 40949117264 scopus 로고    scopus 로고
    • Flexible nets: Disorder and induced fit in the associations of p53 and 14-3-3 with their partners
    • C.J. Oldfield, and J. Meng A.K. Dunker Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners BMC Genomics 9 Suppl 1 2008 S1
    • (2008) BMC Genomics , vol.9 , pp. S1
    • Oldfield, C.J.1    Meng, J.2    Dunker, A.K.3
  • 6
    • 21744448828 scopus 로고    scopus 로고
    • Scaling behavior and structure of denatured proteins
    • F. Ding, R.K. Jha, and N.V. Dokholyan Scaling behavior and structure of denatured proteins Structure 13 2005 1047 1054
    • (2005) Structure , vol.13 , pp. 1047-1054
    • Ding, F.1    Jha, R.K.2    Dokholyan, N.V.3
  • 7
    • 0030320442 scopus 로고    scopus 로고
    • The concept of a random coil. Residual structure in peptides and denatured proteins
    • L.J. Smith, and K.M. Fiebig C.M. Dobson The concept of a random coil. Residual structure in peptides and denatured proteins Fold. Des. 1 1996 R95 R106
    • (1996) Fold. Des. , vol.1 , pp. R95-R106
    • Smith, L.J.1    Fiebig, K.M.2    Dobson, C.M.3
  • 8
    • 0014027356 scopus 로고
    • Proteins in 6-M guanidine hydrochloride. Demonstration of random coil behavior
    • C. Tanford, K. Kawahara, and S. Lapanje Proteins in 6-M guanidine hydrochloride. Demonstration of random coil behavior J. Biol. Chem. 241 1966 1921 1923
    • (1966) J. Biol. Chem. , vol.241 , pp. 1921-1923
    • Tanford, C.1    Kawahara, K.2    Lapanje, S.3
  • 9
    • 23744502246 scopus 로고    scopus 로고
    • Is there or isn't there? the case for (and against) residual structure in chemically denatured proteins
    • E.R. McCarney, J.E. Kohn, and K.W. Plaxco Is there or isn't there? The case for (and against) residual structure in chemically denatured proteins Crit. Rev. Biochem. Mol. Biol. 40 2005 181 189
    • (2005) Crit. Rev. Biochem. Mol. Biol. , vol.40 , pp. 181-189
    • McCarney, E.R.1    Kohn, J.E.2    Plaxco, K.W.3
  • 10
    • 34147162150 scopus 로고    scopus 로고
    • Further evidence for the absence of polyproline II stretch in the XAO peptide
    • J. Makowska, and S. Rodziewicz-Motowidlo H.A. Scheraga Further evidence for the absence of polyproline II stretch in the XAO peptide Biophys. J. 92 2007 2904 2917
    • (2007) Biophys. J. , vol.92 , pp. 2904-2917
    • Makowska, J.1    Rodziewicz-Motowidlo, S.2    Scheraga, H.A.3
  • 11
    • 0014349486 scopus 로고
    • Dimensions of protein random coils
    • W.G. Miller, and C.V. Goebel Dimensions of protein random coils Biochemistry 7 1968 3925 3935
    • (1968) Biochemistry , vol.7 , pp. 3925-3935
    • Miller, W.G.1    Goebel, C.V.2
  • 12
    • 4344716256 scopus 로고    scopus 로고
    • Random-coil behavior and the dimensions of chemically unfolded proteins
    • J.E. Kohn, and I.S. Millett K.W. Plaxco Random-coil behavior and the dimensions of chemically unfolded proteins Proc. Natl. Acad. Sci. USA 101 2004 12491 12496
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 12491-12496
    • Kohn, J.E.1    Millett, I.S.2    Plaxco, K.W.3
  • 13
    • 4344704080 scopus 로고    scopus 로고
    • Reassessing random-coil statistics in unfolded proteins
    • N.C. Fitzkee, and G.D. Rose Reassessing random-coil statistics in unfolded proteins Proc. Natl. Acad. Sci. USA 101 2004 12497 12502
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 12497-12502
    • Fitzkee, N.C.1    Rose, G.D.2
  • 14
    • 23944453852 scopus 로고    scopus 로고
    • Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins
    • H.T. Tran, X. Wang, and R.V. Pappu Reconciling observations of sequence-specific conformational propensities with the generic polymeric behavior of denatured proteins Biochemistry 44 2005 11369 11380
    • (2005) Biochemistry , vol.44 , pp. 11369-11380
    • Tran, H.T.1    Wang, X.2    Pappu, R.V.3
  • 15
    • 84873379826 scopus 로고    scopus 로고
    • Temperature and urea have opposing impacts on polyproline II conformational bias
    • W.A. Elam, and T.P. Schrank V.J. Hilser Temperature and urea have opposing impacts on polyproline II conformational bias Biochemistry 52 2013 949 958
    • (2013) Biochemistry , vol.52 , pp. 949-958
    • Elam, W.A.1    Schrank, T.P.2    Hilser, V.J.3
  • 16
    • 84863091846 scopus 로고    scopus 로고
    • Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides
    • K.-I. Oh, and Y.-S. Jung M. Cho Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides J. Biomol. NMR 53 2012 25 41
    • (2012) J. Biomol. NMR , vol.53 , pp. 25-41
    • Oh, K.-I.1    Jung, Y.-S.2    Cho, M.3
  • 17
    • 84857783671 scopus 로고    scopus 로고
    • A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins
    • K.-I. Oh, and K.-K. Lee M. Cho A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins Proteins 80 2012 977 990
    • (2012) Proteins , vol.80 , pp. 977-990
    • Oh, K.-I.1    Lee, K.-K.2    Cho, M.3
  • 18
    • 0014227144 scopus 로고
    • New chain conformations of poly(glutamic acid) and polylysine
    • M.L. Tiffany, and S. Krimm New chain conformations of poly(glutamic acid) and polylysine Biopolymers 6 1968 1379 1382
    • (1968) Biopolymers , vol.6 , pp. 1379-1382
    • Tiffany, M.L.1    Krimm, S.2
  • 19
    • 17644422781 scopus 로고    scopus 로고
    • Urea promotes polyproline II helix formation: Implications for protein denatured states
    • S.J. Whittington, and B.W. Chellgren T.P. Creamer Urea promotes polyproline II helix formation: implications for protein denatured states Biochemistry 44 2005 6269 6275
    • (2005) Biochemistry , vol.44 , pp. 6269-6275
    • Whittington, S.J.1    Chellgren, B.W.2    Creamer, T.P.3
  • 20
    • 1842500992 scopus 로고    scopus 로고
    • Polyproline II helix is the preferred conformation for unfolded polyalanine in water
    • M. Mezei, and P.J. Fleming G.D. Rose Polyproline II helix is the preferred conformation for unfolded polyalanine in water Proteins 55 2004 502 507
    • (2004) Proteins , vol.55 , pp. 502-507
    • Mezei, M.1    Fleming, P.J.2    Rose, G.D.3
  • 21
    • 29144433298 scopus 로고    scopus 로고
    • Polyproline II propensities from GGXGG peptides reveal an anticorrelation with β-sheet scales
    • Z. Shi, and K. Chen N.R. Kallenbach Polyproline II propensities from GGXGG peptides reveal an anticorrelation with β-sheet scales Proc. Natl. Acad. Sci. USA 102 2005 17964 17968
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 17964-17968
    • Shi, Z.1    Chen, K.2    Kallenbach, N.R.3
  • 22
    • 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
    • J. Makowska, and S. Rodziewicz-Motowidło H.A. Scheraga 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 2006 1744 1749
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 1744-1749
    • Makowska, J.1    Rodziewicz-Motowidło, S.2    Scheraga, H.A.3
  • 23
    • 84862835564 scopus 로고    scopus 로고
    • A propensity scale for type II polyproline helices (PPII): Aromatic amino acids in proline-rich sequences strongly disfavor PPII due to proline-aromatic interactions
    • A.M. Brown, and N.J. Zondlo A propensity scale for type II polyproline helices (PPII): aromatic amino acids in proline-rich sequences strongly disfavor PPII due to proline-aromatic interactions Biochemistry 51 2012 5041 5051
    • (2012) Biochemistry , vol.51 , pp. 5041-5051
    • Brown, A.M.1    Zondlo, N.J.2
  • 24
    • 22144480962 scopus 로고    scopus 로고
    • Single peptide bonds exhibit poly(pro)II ("random coil") circular dichroism spectra
    • I. Gokce, and R.W. Woody J.H. Lakey Single peptide bonds exhibit poly(pro)II ("random coil") circular dichroism spectra J. Am. Chem. Soc. 127 2005 9700 9701
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 9700-9701
    • Gokce, I.1    Woody, R.W.2    Lakey, J.H.3
  • 25
    • 84878259928 scopus 로고    scopus 로고
    • Polyproline-II helix in proteins: Structure and function
    • A.A. Adzhubei, M.J.E. Sternberg, and A.A. Makarov Polyproline-II helix in proteins: structure and function J. Mol. Biol. 425 2013 2100 2132
    • (2013) J. Mol. Biol. , vol.425 , pp. 2100-2132
    • Adzhubei, A.A.1    Sternberg, M.J.E.2    Makarov, A.A.3
  • 26
    • 33646908786 scopus 로고    scopus 로고
    • Conformation of the backbone in unfolded proteins
    • Z. Shi, and K. Chen N.R. Kallenbach Conformation of the backbone in unfolded proteins Chem. Rev. 106 2006 1877 1897
    • (2006) Chem. Rev. , vol.106 , pp. 1877-1897
    • Shi, Z.1    Chen, K.2    Kallenbach, N.R.3
  • 27
    • 0036400325 scopus 로고    scopus 로고
    • Is polyproline II a major backbone conformation in unfolded proteins?
    • Z. Shi, R.W. Woody, and N.R. Kallenbach Is polyproline II a major backbone conformation in unfolded proteins? Adv. Protein Chem. 62 2002 163 240
    • (2002) Adv. Protein Chem. , vol.62 , pp. 163-240
    • Shi, Z.1    Woody, R.W.2    Kallenbach, N.R.3
  • 28
    • 0037047134 scopus 로고    scopus 로고
    • Polyproline II structure in a sequence of seven alanine residues
    • Z. Shi, and C.A. Olson N.R. Kallenbach Polyproline II structure in a sequence of seven alanine residues Proc. Natl. Acad. Sci. USA 99 2002 9190 9195
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 9190-9195
    • Shi, Z.1    Olson, C.A.2    Kallenbach, N.R.3
  • 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
    • F. Eker, and K. Griebenow R. Schweitzer-Stenner Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution Proc. Natl. Acad. Sci. USA 101 2004 10054 10059
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 10054-10059
    • Eker, F.1    Griebenow, K.2    Schweitzer-Stenner, R.3
  • 30
    • 1542310781 scopus 로고    scopus 로고
    • Tripeptides with ionizable side chains adopt a perturbed polyproline II structure in water
    • F. Eker, and K. Griebenow R. Schweitzer-Stenner Tripeptides with ionizable side chains adopt a perturbed polyproline II structure in water Biochemistry 43 2004 613 621
    • (2004) Biochemistry , vol.43 , pp. 613-621
    • Eker, F.1    Griebenow, K.2    Schweitzer-Stenner, R.3
  • 31
    • 0035919635 scopus 로고    scopus 로고
    • Persistence of native-like topology in a denatured protein in 8 M urea
    • D. Shortle, and M.S. Ackerman Persistence of native-like topology in a denatured protein in 8 M urea Science 293 2001 487 489
    • (2001) Science , vol.293 , pp. 487-489
    • Shortle, D.1    Ackerman, M.S.2
  • 32
    • 0036389787 scopus 로고    scopus 로고
    • Mapping long-range contacts in a highly unfolded protein
    • M.A. Lietzow, and M. Jamin P.E. Wright Mapping long-range contacts in a highly unfolded protein J. Mol. Biol. 322 2002 655 662
    • (2002) J. Mol. Biol. , vol.322 , pp. 655-662
    • Lietzow, M.A.1    Jamin, M.2    Wright, P.E.3
  • 33
    • 15244342213 scopus 로고    scopus 로고
    • Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies
    • S. Kristjansdottir, and K. Lindorff-Larsen F.M. Poulsen Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies J. Mol. Biol. 347 2005 1053 1062
    • (2005) J. Mol. Biol. , vol.347 , pp. 1053-1062
    • Kristjansdottir, S.1    Lindorff-Larsen, K.2    Poulsen, F.M.3
  • 34
    • 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
    • V.L. Arcus, and S. Vuilleumier A.R. Fersht 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 1995 305 321
    • (1995) J. Mol. Biol. , vol.254 , pp. 305-321
    • Arcus, V.L.1    Vuilleumier, S.2    Fersht, A.R.3
  • 35
    • 0034620507 scopus 로고    scopus 로고
    • Structure and dynamics of an acid-denatured protein G mutant
    • N. Sari, and P. Alexander J. Orban Structure and dynamics of an acid-denatured protein G mutant Biochemistry 39 2000 965 977
    • (2000) Biochemistry , vol.39 , pp. 965-977
    • Sari, N.1    Alexander, P.2    Orban, J.3
  • 36
    • 50449111518 scopus 로고    scopus 로고
    • The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins
    • D.A.C. Beck, and D.O.V. Alonso V. Daggett The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins Proc. Natl. Acad. Sci. USA 105 2008 12259 12264
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 12259-12264
    • Beck, D.A.C.1    Alonso, D.O.V.2    Daggett, V.3
  • 37
    • 0024293204 scopus 로고
    • Conformation of peptide fragments of proteins in aqueous solution: Implications for initiation of protein folding
    • P.E. Wright, H.J. Dyson, and R.A. Lerner Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding Biochemistry 27 1988 7167 7175
    • (1988) Biochemistry , vol.27 , pp. 7167-7175
    • Wright, P.E.1    Dyson, H.J.2    Lerner, R.A.3
  • 38
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm
    • P.E. Wright, and H.J. Dyson Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm J. Mol. Biol. 293 1999 321 331
    • (1999) J. Mol. Biol. , vol.293 , pp. 321-331
    • Wright, P.E.1    Dyson, H.J.2
  • 39
    • 84926068561 scopus 로고    scopus 로고
    • Functional roles of transiently and intrinsically disordered regions within proteins
    • V.N. Uversky Functional roles of transiently and intrinsically disordered regions within proteins FEBS J. 282 2015 1182 1189
    • (2015) FEBS J. , vol.282 , pp. 1182-1189
    • Uversky, V.N.1
  • 40
    • 80055012207 scopus 로고    scopus 로고
    • Expanding the proteome: Disordered and alternatively folded proteins
    • H.J. Dyson Expanding the proteome: disordered and alternatively folded proteins Q. Rev. Biophys. 44 2011 467 518
    • (2011) Q. Rev. Biophys. , vol.44 , pp. 467-518
    • Dyson, H.J.1
  • 41
    • 0348047627 scopus 로고    scopus 로고
    • Proteomic signatures: Amino acid and oligopeptide compositions differentiate among phyla
    • I. Pe'er, and C.E. Felder J.S. Beckmann Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla Proteins 54 2004 20 40
    • (2004) Proteins , vol.54 , pp. 20-40
    • Pe'Er, I.1    Felder, C.E.2    Beckmann, J.S.3
  • 42
    • 40549104431 scopus 로고    scopus 로고
    • Conformational properties of a peptide model for unfolded α-helices
    • A.M. Firestine, and V.M. Chellgren T.P. Creamer Conformational properties of a peptide model for unfolded α-helices Biochemistry 47 2008 3216 3224
    • (2008) Biochemistry , vol.47 , pp. 3216-3224
    • Firestine, A.M.1    Chellgren, V.M.2    Creamer, T.P.3
  • 43
    • 84879549760 scopus 로고    scopus 로고
    • Chemical shift prediction for denatured proteins
    • J.H. Prestegard, and S.C. Sahu C. Gruta Chemical shift prediction for denatured proteins J. Biomol. NMR 55 2013 201 209
    • (2013) J. Biomol. NMR , vol.55 , pp. 201-209
    • Prestegard, J.H.1    Sahu, S.C.2    Gruta, C.3
  • 44
    • 3342918929 scopus 로고    scopus 로고
    • Methods for molecular dynamics simulations of protein folding/unfolding in solution
    • D.A.C. Beck, and V. Daggett Methods for molecular dynamics simulations of protein folding/unfolding in solution Methods 34 2004 112 120
    • (2004) Methods , vol.34 , pp. 112-120
    • Beck, D.A.C.1    Daggett, V.2
  • 46
    • 0029633167 scopus 로고
    • Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
    • M. Levitt, and M. Hirshberg V. Daggett Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution Comput. Phys. Commun. 91 1995 215 231
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 215-231
    • Levitt, M.1    Hirshberg, M.2    Daggett, V.3
  • 47
    • 12144275299 scopus 로고    scopus 로고
    • Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides
    • D.A.C. Beck, R.S. Armen, and V. Daggett Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides Biochemistry 44 2005 609 616
    • (2005) Biochemistry , vol.44 , pp. 609-616
    • Beck, D.A.C.1    Armen, R.S.2    Daggett, V.3
  • 48
    • 0037138672 scopus 로고    scopus 로고
    • The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea
    • Q. Zou, and B.J. Bennion K.P. Murphy The molecular mechanism of stabilization of proteins by TMAO and its ability to counteract the effects of urea J. Am. Chem. Soc. 124 2002 1192 1202
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 1192-1202
    • Zou, Q.1    Bennion, B.J.2    Murphy, K.P.3
  • 49
    • 0000125216 scopus 로고    scopus 로고
    • Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
    • M. Levitt, and M. Hirshberg V. Daggett Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution J. Phys. Chem. B 101 1997 5051 5061
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5051-5061
    • Levitt, M.1    Hirshberg, M.2    Daggett, V.3
  • 50
    • 0009979659 scopus 로고
    • Precise representation of volume properties of water at one atmosphere
    • G.S. Kell Precise representation of volume properties of water at one atmosphere J. Chem. Eng. Data 12 1967 66 69
    • (1967) J. Chem. Eng. Data , vol.12 , pp. 66-69
    • Kell, G.S.1
  • 51
    • 0033794319 scopus 로고    scopus 로고
    • Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView
    • S. Schwarzinger, and G.J.A. Kroon H.J. Dyson Random coil chemical shifts in acidic 8 M urea: implementation of random coil shift data in NMRView J. Biomol. NMR 18 2000 43 48
    • (2000) J. Biomol. NMR , vol.18 , pp. 43-48
    • Schwarzinger, S.1    Kroon, G.J.A.2    Dyson, H.J.3
  • 52
    • 33846783019 scopus 로고    scopus 로고
    • Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study
    • J. Graf, and P.H. Nguyen H. Schwalbe Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study J. Am. Chem. Soc. 129 2007 1179 1189
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 1179-1189
    • Graf, J.1    Nguyen, P.H.2    Schwalbe, H.3
  • 53
    • 80051673221 scopus 로고    scopus 로고
    • SHIFTX2: Significantly improved protein chemical shift prediction
    • B. Han, and Y. Liu D.S. Wishart SHIFTX2: significantly improved protein chemical shift prediction J. Biomol. NMR 50 2011 43 57
    • (2011) J. Biomol. NMR , vol.50 , pp. 43-57
    • Han, B.1    Liu, Y.2    Wishart, D.S.3
  • 54
    • 0345517099 scopus 로고    scopus 로고
    • 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles
    • 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles J. Biomol. NMR 14 1999 1 12
    • (1999) J. Biomol. NMR , vol.14 , pp. 1-12
    • Schmidt, J.M.1    Blümel, M.2    Rüterjans, H.3
  • 55
    • 0037438967 scopus 로고    scopus 로고
    • A microscopic view of peptide and protein solvation
    • D.A.C. Beck, D.O.V. Alonso, and V. Daggett A microscopic view of peptide and protein solvation Biophys. Chem. 100 2003 221 237
    • (2003) Biophys. Chem. , vol.100 , pp. 221-237
    • Beck, D.A.C.1    Alonso, D.O.V.2    Daggett, V.3
  • 56
    • 0038370011 scopus 로고    scopus 로고
    • The molecular basis for the chemical denaturation of proteins by urea
    • B.J. Bennion, and V. Daggett The molecular basis for the chemical denaturation of proteins by urea Proc. Natl. Acad. Sci. USA 100 2003 5142 5147
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 5142-5147
    • Bennion, B.J.1    Daggett, V.2
  • 57
    • 35748930873 scopus 로고    scopus 로고
    • Simulations of macromolecules in protective and denaturing osmolytes: Properties of mixed solvent systems and their effects on water and protein structure and dynamics
    • D.A.C. Beck, and B.J. Bennion V. Daggett Simulations of macromolecules in protective and denaturing osmolytes: properties of mixed solvent systems and their effects on water and protein structure and dynamics Methods Enzymol. 428 2007 373 396
    • (2007) Methods Enzymol. , vol.428 , pp. 373-396
    • Beck, D.A.C.1    Bennion, B.J.2    Daggett, V.3
  • 58
    • 0142179047 scopus 로고    scopus 로고
    • Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the α-helix
    • B.K. Ho, A. Thomas, and R. Brasseur Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the α-helix Protein Sci. 12 2003 2508 2522
    • (2003) Protein Sci. , vol.12 , pp. 2508-2522
    • Ho, B.K.1    Thomas, A.2    Brasseur, R.3
  • 60
    • 0033731782 scopus 로고    scopus 로고
    • Are denatured proteins ever random coils?
    • R.L. Baldwin, and B.H. Zimm Are denatured proteins ever random coils? Proc. Natl. Acad. Sci. USA 97 2000 12391 12392
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 12391-12392
    • Baldwin, R.L.1    Zimm, B.H.2
  • 61
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • J.S. Richardson The anatomy and taxonomy of protein structure Adv. Protein Chem. 34 1981 167 339
    • (1981) Adv. Protein Chem. , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 62
    • 4444221565 scopus 로고    scopus 로고
    • UCSF Chimera - A visualization system for exploratory research and analysis
    • E.F. Pettersen, and T.D. Goddard T.E. Ferrin UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 1605 1612
    • (2004) J. Comput. Chem. , vol.25 , pp. 1605-1612
    • Pettersen, E.F.1    Goddard, T.D.2    Ferrin, T.E.3
  • 63
    • 0032168569 scopus 로고    scopus 로고
    • Catalytic triads and their relatives
    • G. Dodson, and A. Wlodawer Catalytic triads and their relatives Trends Biochem. Sci. 23 1998 347 352
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 347-352
    • Dodson, G.1    Wlodawer, A.2
  • 64
    • 27144523783 scopus 로고    scopus 로고
    • The catalytic triad of serine peptidases
    • L. Polgár The catalytic triad of serine peptidases Cell. Mol. Life Sci. 62 2005 2161 2172
    • (2005) Cell. Mol. Life Sci. , vol.62 , pp. 2161-2172
    • Polgár, L.1
  • 65
    • 56749154097 scopus 로고    scopus 로고
    • Unconventional serine proteases: Variations on the catalytic Ser/His/Asp triad configuration
    • Ö.D. Ekici, M. Paetzel, and R.E. Dalbey Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration Protein Sci. 17 2008 2023 2037
    • (2008) Protein Sci. , vol.17 , pp. 2023-2037
    • Ekici, Ö.D.1    Paetzel, M.2    Dalbey, R.E.3
  • 66
    • 0028175780 scopus 로고
    • A thermodynamic scale for the β-sheet forming tendencies of the amino acids
    • C.K. Smith, J.M. Withka, and L. Regan A thermodynamic scale for the β-sheet forming tendencies of the amino acids Biochemistry 33 1994 5510 5517
    • (1994) Biochemistry , vol.33 , pp. 5510-5517
    • Smith, C.K.1    Withka, J.M.2    Regan, L.3
  • 67
    • 0028176595 scopus 로고
    • Measurement of the β-sheet-forming propensities of amino acids
    • D.L. Minor Jr., and P.S. Kim Measurement of the β-sheet-forming propensities of amino acids Nature 367 1994 660 663
    • (1994) Nature , vol.367 , pp. 660-663
    • Minor, D.L.1    Kim, P.S.2
  • 68
    • 0027411181 scopus 로고
    • Thermodynamic β-sheet propensities measured using a zinc-finger host peptide
    • C.A. Kim, and J.M. Berg Thermodynamic β-sheet propensities measured using a zinc-finger host peptide Nature 362 1993 267 270
    • (1993) Nature , vol.362 , pp. 267-270
    • Kim, C.A.1    Berg, J.M.2
  • 69
    • 0015967881 scopus 로고
    • Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins
    • P.Y. Chou, and G.D. Fasman Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins Biochemistry 13 1974 211 222
    • (1974) Biochemistry , vol.13 , pp. 211-222
    • Chou, P.Y.1    Fasman, G.D.2
  • 70
    • 0029588554 scopus 로고
    • High helical propensity of the peptide fragments derived from β-lactoglobulin, a predominantly β-sheet protein
    • D. Hamada, and Y. Kuroda Y. Goto High helical propensity of the peptide fragments derived from β-lactoglobulin, a predominantly β-sheet protein J. Mol. Biol. 254 1995 737 746
    • (1995) J. Mol. Biol. , vol.254 , pp. 737-746
    • Hamada, D.1    Kuroda, Y.2    Goto, Y.3
  • 71
    • 0031580203 scopus 로고    scopus 로고
    • The equilibrium intermediate of β-lactoglobulin with non-native α-helical structure
    • D. Hamada, and Y. Goto The equilibrium intermediate of β-lactoglobulin with non-native α-helical structure J. Mol. Biol. 269 1997 479 487
    • (1997) J. Mol. Biol. , vol.269 , pp. 479-487
    • Hamada, D.1    Goto, Y.2
  • 72
    • 0029740071 scopus 로고    scopus 로고
    • Non-native α-helical intermediate in the refolding of β-lactoglobulin, a predominantly β-sheet protein
    • D. Hamada, S. Segawa, and Y. Goto Non-native α-helical intermediate in the refolding of β-lactoglobulin, a predominantly β-sheet protein Nat. Struct. Biol. 3 1996 868 873
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 868-873
    • Hamada, D.1    Segawa, S.2    Goto, Y.3
  • 73
    • 0028040301 scopus 로고
    • Equilibrium folding studies of cellular retinoic acid binding protein, a predominantly β-sheet protein
    • Z.P. Liu, J. Rizo, and L.M. Gierasch Equilibrium folding studies of cellular retinoic acid binding protein, a predominantly β-sheet protein Biochemistry 33 1994 134 142
    • (1994) Biochemistry , vol.33 , pp. 134-142
    • Liu, Z.P.1    Rizo, J.2    Gierasch, L.M.3
  • 74
    • 79952805688 scopus 로고    scopus 로고
    • The denatured state dictates the topology of two proteins with almost identical sequence but different native structure and function
    • A. Morrone, and M.E. McCully C. Travaglini-Allocatelli The denatured state dictates the topology of two proteins with almost identical sequence but different native structure and function J. Biol. Chem. 286 2011 3863 3872
    • (2011) J. Biol. Chem. , vol.286 , pp. 3863-3872
    • Morrone, A.1    McCully, M.E.2    Travaglini-Allocatelli, C.3
  • 75
    • 0032509152 scopus 로고    scopus 로고
    • High populations of non-native structures in the denatured state are compatible with the formation of the native folded state
    • F.J. Blanco, L. Serrano, and J.D. Forman-Kay High populations of non-native structures in the denatured state are compatible with the formation of the native folded state J. Mol. Biol. 284 1998 1153 1164
    • (1998) J. Mol. Biol. , vol.284 , pp. 1153-1164
    • Blanco, F.J.1    Serrano, L.2    Forman-Kay, J.D.3
  • 76
    • 0031808074 scopus 로고    scopus 로고
    • A helix propensity scale based on experimental studies of peptides and proteins
    • C.N. Pace, and J.M. Scholtz A helix propensity scale based on experimental studies of peptides and proteins Biophys. J. 75 1998 422 427
    • (1998) Biophys. J. , vol.75 , pp. 422-427
    • Pace, C.N.1    Scholtz, J.M.2
  • 77
    • 84906850422 scopus 로고    scopus 로고
    • A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein
    • A.B. Mantsyzov, and A.S. Maltsev A. Bax A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein Protein Sci. 23 2014 1275 1290
    • (2014) Protein Sci. , vol.23 , pp. 1275-1290
    • Mantsyzov, A.B.1    Maltsev, A.S.2    Bax, A.3
  • 78
    • 84874072440 scopus 로고    scopus 로고
    • The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development
    • F. Jiang, W. Han, and Y.-D. Wu The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development Phys. Chem. Chem. Phys. 15 2013 3413 3428
    • (2013) Phys. Chem. Chem. Phys. , vol.15 , pp. 3413-3428
    • Jiang, F.1    Han, W.2    Wu, Y.-D.3
  • 79
    • 46749127364 scopus 로고    scopus 로고
    • Are current molecular dynamics force fields too helical?
    • R.B. Best, N.-V. Buchete, and G. Hummer Are current molecular dynamics force fields too helical? Biophys. J. 95 2008 L07 L09
    • (2008) Biophys. J. , vol.95 , pp. L07-L09
    • Best, R.B.1    Buchete, N.-V.2    Hummer, G.3
  • 80
    • 84878243253 scopus 로고    scopus 로고
    • Experimental and computational studies of polyproline II propensity
    • R. Schweitzer-Stenner, John Wiley & Sons Hoboken, NJ
    • W.A. Elam, T.P. Schrank, and V.J. Hilser Experimental and computational studies of polyproline II propensity R. Schweitzer-Stenner, Protein and Peptide Folding, Misfolding, and Non-folding 2012 John Wiley & Sons Hoboken, NJ 159 185
    • (2012) Protein and Peptide Folding, Misfolding, and Non-folding , pp. 159-185
    • Elam, W.A.1    Schrank, T.P.2    Hilser, V.J.3
  • 81
    • 0345862082 scopus 로고    scopus 로고
    • Characterization of non-α helical conformations in Ala peptides
    • A.E. García Characterization of non-α helical conformations in Ala peptides Polymer (Guildf.) 45 2004 669 676
    • (2004) Polymer (Guildf.) , vol.45 , pp. 669-676
    • García, A.E.1
  • 82
    • 0041319047 scopus 로고    scopus 로고
    • Host-guest scale of left-handed polyproline II helix formation
    • A.L. Rucker, and C.T. Pager T.P. Creamer Host-guest scale of left-handed polyproline II helix formation Proteins 53 2003 68 75
    • (2003) Proteins , vol.53 , pp. 68-75
    • Rucker, A.L.1    Pager, C.T.2    Creamer, T.P.3
  • 83
    • 14644390842 scopus 로고    scopus 로고
    • A survey of left-handed helices in protein structures
    • M. Novotny, and G.J. Kleywegt A survey of left-handed helices in protein structures J. Mol. Biol. 347 2005 231 241
    • (2005) J. Mol. Biol. , vol.347 , pp. 231-241
    • Novotny, M.1    Kleywegt, G.J.2
  • 84
    • 70350493975 scopus 로고    scopus 로고
    • Mirrors in the PDB: Left-handed α-turns guide design with D-amino acids
    • S. Annavarapu, and V. Nanda Mirrors in the PDB: left-handed α-turns guide design with D-amino acids BMC Struct. Biol. 9 2009 61
    • (2009) BMC Struct. Biol. , vol.9 , pp. 61
    • Annavarapu, S.1    Nanda, V.2
  • 85
    • 84928957480 scopus 로고    scopus 로고
    • Nature versus design: The conformational propensities of D-amino acids and the importance of side chain chirality
    • C.-L. Towse, and G. Hopping V. Daggett Nature versus design: the conformational propensities of D-amino acids and the importance of side chain chirality Protein Eng. Des. Sel. 27 2014 447 455
    • (2014) Protein Eng. Des. Sel. , vol.27 , pp. 447-455
    • Towse, C.-L.1    Hopping, G.2    Daggett, V.3
  • 86
    • 84904437918 scopus 로고    scopus 로고
    • Designed α-sheet peptides inhibit amyloid formation by targeting toxic oligomers
    • G. Hopping, and J. Kellock V. Daggett Designed α-sheet peptides inhibit amyloid formation by targeting toxic oligomers eLife 3 2014 e01681
    • (2014) ELife , vol.3 , pp. e01681
    • Hopping, G.1    Kellock, J.2    Daggett, V.3
  • 87
    • 0242353212 scopus 로고    scopus 로고
    • Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway
    • J. Sivaraman, and Y. Li M. Cygler Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway J. Biol. Chem. 278 2003 43682 43690
    • (2003) J. Biol. Chem. , vol.278 , pp. 43682-43690
    • Sivaraman, J.1    Li, Y.2    Cygler, M.3
  • 88
    • 26444534036 scopus 로고    scopus 로고
    • Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases
    • R.S. Armen, and B.M. Bernard V. Daggett Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases Proc. Natl. Acad. Sci. USA 102 2005 13433 13438
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 13433-13438
    • Armen, R.S.1    Bernard, B.M.2    Daggett, V.3
  • 89
    • 33749857843 scopus 로고    scopus 로고
    • α-sheet: The toxic conformer in amyloid diseases?
    • V. Daggett α-sheet: The toxic conformer in amyloid diseases? Acc. Chem. Res. 39 2006 594 602
    • (2006) Acc. Chem. Res. , vol.39 , pp. 594-602
    • Daggett, V.1
  • 90
    • 4143067019 scopus 로고    scopus 로고
    • Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease
    • R.S. Armen, and M.L. DeMarco V. Daggett Pauling and Corey's α-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease Proc. Natl. Acad. Sci. USA 101 2004 11622 11627
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 11622-11627
    • Armen, R.S.1    DeMarco, M.L.2    Daggett, V.3
  • 91
    • 84897083667 scopus 로고    scopus 로고
    • Sequence complexity of amyloidogenic regions in intrinsically disordered human proteins
    • S. Das, and U. Pal N.C. Maiti Sequence complexity of amyloidogenic regions in intrinsically disordered human proteins PLoS One 9 2014 e89781
    • (2014) PLoS One , vol.9 , pp. e89781
    • Das, S.1    Pal, U.2    Maiti, N.C.3
  • 92
    • 84876041730 scopus 로고    scopus 로고
    • Breaking the amyloidogenicity code: Methods to predict amyloids from amino acid sequence
    • A.B. Ahmed, and A.V. Kajava Breaking the amyloidogenicity code: methods to predict amyloids from amino acid sequence FEBS Lett. 587 2013 1089 1095
    • (2013) FEBS Lett. , vol.587 , pp. 1089-1095
    • Ahmed, A.B.1    Kajava, A.V.2
  • 94
    • 84884241538 scopus 로고    scopus 로고
    • Conformational propensities of intrinsically disordered proteins from NMR chemical shifts
    • J. Kragelj, and V. Ozenne M.R. Jensen Conformational propensities of intrinsically disordered proteins from NMR chemical shifts ChemPhysChem 14 2013 3034 3045
    • (2013) ChemPhysChem , vol.14 , pp. 3034-3045
    • Kragelj, J.1    Ozenne, V.2    Jensen, M.R.3
  • 95
    • 0014966180 scopus 로고
    • IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains
    • O. Hoffman-Ostenhof, and W.E. Cohn W.J. Whelan IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains J. Mol. Biol. 52 1970 1 17
    • (1970) J. Mol. Biol. , vol.52 , pp. 1-17
    • Hoffman-Ostenhof, O.1    Cohn, W.E.2    Whelan, W.J.3
  • 96
    • 77956567928 scopus 로고    scopus 로고
    • Refolding the engrailed homeodomain: Structural basis for the accumulation of a folding intermediate
    • M.E. McCully, and D.A.C. Beck V. Daggett Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate Biophys. J. 99 2010 1628 1636
    • (2010) Biophys. J. , vol.99 , pp. 1628-1636
    • McCully, M.E.1    Beck, D.A.C.2    Daggett, V.3
  • 97
    • 0036968512 scopus 로고    scopus 로고
    • Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
    • R. Day, and B.J. Bennion V. Daggett Increasing temperature accelerates protein unfolding without changing the pathway of unfolding J. Mol. Biol. 322 2002 189 203
    • (2002) J. Mol. Biol. , vol.322 , pp. 189-203
    • Day, R.1    Bennion, B.J.2    Daggett, V.3
  • 98
    • 0242610902 scopus 로고    scopus 로고
    • All-atom simulations of protein folding and unfolding
    • R. Day, and V. Daggett All-atom simulations of protein folding and unfolding Adv. Protein Chem. 66 2003 373 403
    • (2003) Adv. Protein Chem. , vol.66 , pp. 373-403
    • Day, R.1    Daggett, V.2
  • 99
    • 0034610360 scopus 로고    scopus 로고
    • Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
    • U. Mayor, and C.M. Johnson A.R. Fersht Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation Proc. Natl. Acad. Sci. USA 97 2000 13518 13522
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 13518-13522
    • Mayor, U.1    Johnson, C.M.2    Fersht, A.R.3
  • 100
    • 84926305827 scopus 로고    scopus 로고
    • Integrative, dynamic structural biology at atomic resolution - It's about time
    • H. van den Bedem, and J.S. Fraser Integrative, dynamic structural biology at atomic resolution - it's about time Nat. Methods 12 2015 307 318
    • (2015) Nat. Methods , vol.12 , pp. 307-318
    • Van Den Bedem, H.1    Fraser, J.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.