메뉴 건너뛰기




Volumn 100, Issue 4, 2011, Pages 1083-1093

A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides

Author keywords

[No Author keywords available]

Indexed keywords


EID: 79951847345     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.12.3742     Document Type: Article
Times cited : (25)

References (50)
  • 1
    • 0027474991 scopus 로고
    • Left-handed polyproline II helices commonly occur in globular proteins
    • DOI 10.1006/jmbi.1993.1047
    • Adzhubei, A. A., and M. J. E. Sternberg. 1993. Left-handed polyproline II helices commonly occur in globular proteins. J. Mol. Biol. 229:472-493. (Pubitemid 23080393)
    • (1993) Journal of Molecular Biology , vol.229 , Issue.2 , pp. 472-493
    • Adzhubei, A.A.1    Sternberg, M.J.E.2
  • 2
    • 0014227144 scopus 로고
    • New chain conformations of poly (glutamic acid) and polylysine
    • Tiffany, M. L., and S. Krimm. 1968. New chain conformations of poly (glutamic acid) and polylysine. Biopolymers. 6:1379-1382.
    • (1968) Biopolymers , vol.6 , pp. 1379-1382
    • Tiffany, M.L.1    Krimm, S.2
  • 3
    • 0015888586 scopus 로고
    • Extended conformations of polypeptides and proteins in urea and guanidine hydrochloride
    • Tiffany, M. L., and S. Krimm. 1973. Extended conformations of polypeptides and proteins in urea and guanidine hydrochloride. Biopolymers. 12:575-587.
    • (1973) Biopolymers , vol.12 , pp. 575-587
    • Tiffany, M.L.1    Krimm, S.2
  • 5
    • 0036400325 scopus 로고    scopus 로고
    • Is polyproline II a major backbone conformation in unfolded proteins?
    • DOI 10.1016/S0065-3233(02)62008-X
    • Shi, Z., R. W. Woody, and N. R. Kallenbach. 2002. Is polyproline II a major backbone conformation in unfolded proteins? Adv. Protein Chem. 62:163-240. (Pubitemid 35204871)
    • (2002) Advances in Protein Chemistry , vol.62 , pp. 163-240
    • Shi, Z.1    Woody, R.W.2    Kallenbach, N.R.3
  • 6
    • 3242789489 scopus 로고    scopus 로고
    • Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings
    • Mohana-Borges, R., N. K. Goto, P. E. Wright. 2002. Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings. J. Mol. Biol. 340:1131-1142.
    • (2002) J. Mol. Biol. , vol.340 , pp. 1131-1142
    • Mohana-Borges, R.1    Goto, N.K.2    Wright, P.E.3
  • 7
    • 0036400324 scopus 로고    scopus 로고
    • Unfolded peptides and proteins studied with infrared absorption and vibrational CD spectra
    • Keiderling, T. A., and Q. Xu. 2002. Unfolded peptides and proteins studied with infrared absorption and vibrational CD spectra. Adv. Protein Chem. 62:91-162.
    • (2002) Adv. Protein Chem. , vol.62 , pp. 91-162
    • Keiderling, T.A.1    Xu, Q.2
  • 8
    • 0036399145 scopus 로고    scopus 로고
    • Unfolded proteins studied by Raman optical activity
    • DOI 10.1016/S0065-3233(02)62005-4
    • Barron, L. D., E. W. Blanch, and L. Hecht. 2002. Unfolded proteins studied by Raman optical activity. Adv. Protein Chem. 62:51-90. (Pubitemid 35204868)
    • (2002) Advances in Protein Chemistry , vol.62 , pp. 51-90
    • Barron, L.D.1    Blanch, E.W.2    Hecht, L.3
  • 10
    • 33846783019 scopus 로고    scopus 로고
    • Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study
    • DOI 10.1021/ja0660406
    • Graf, J., P. H. Nguyen, H. Schwalbe. 2007. Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study. J. Am. Chem. Soc. 129:1179-1189. (Pubitemid 46208587)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.5 , pp. 1179-1189
    • Graf, J.1    Nguyen, P.H.2    Stock, G.3    Schwalbe, H.4
  • 11
    • 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
  • 12
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensedphase quantum mechanical calculations
    • Duan, Y., C. Wu, P. Kollman. 2003. A point-charge force field for molecular mechanics simulations of proteins based on condensedphase quantum mechanical calculations. J. Comput. Chem. 24:1999-2012.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Kollman, P.3
  • 13
    • 0037407208 scopus 로고    scopus 로고
    • Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of Sem-5 indicate cooperative conformational coupling
    • DOI 10.1110/ps.0238003
    • Ferreon, J. C., and V. J. Hilser. 2003. Ligand-induced changes in dynamics in the RTloop of the C-terminal SH3 domain of Sem-5 indicate cooperative conformational coupling. Protein Sci. 12:982-996. (Pubitemid 36505433)
    • (2003) Protein Science , vol.12 , Issue.5 , pp. 982-996
    • Ferreon, J.C.1    Hilser, V.J.2
  • 16
    • 1142274316 scopus 로고    scopus 로고
    • Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study
    • Vila, J. A., H. A. Baldoni, H. A. Scheraga. 2004. Polyproline II helix conformation in a proline-rich environment: a theoretical study. Biophys. J. 86:731-742. (Pubitemid 38209521)
    • (2004) Biophysical Journal , vol.86 , Issue.2 , pp. 731-742
    • Vila, J.A.1    Baldoni, H.A.2    Ripoll, D.R.3    Ghosh, A.4    Scheraga, H.A.5
  • 21
  • 22
    • 58749097266 scopus 로고    scopus 로고
    • Characterizing aqueous solution conformations of a peptide backbone using Raman optical activity computations
    • Mukhopadhyay, P., G. Zuber, and D. N. Beratan. 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
  • 23
    • 0030475459 scopus 로고    scopus 로고
    • Structural requirements and thermodynamics of the interaction of proline peptides with profilin
    • DOI 10.1021/bi961498d
    • Petrella, E. C., L. M. Machesky, T. D. Pollard. 1996. Structural requirements and thermodynamics of the interaction of proline peptides with profilin. Biochemistry. 35:16535-16543. (Pubitemid 27020495)
    • (1996) Biochemistry , vol.35 , Issue.51 , pp. 16535-16543
    • Petrella, E.C.1    Machesky, L.M.2    Kaiser, D.A.3    Pollard, T.D.4
  • 26
    • 2442522724 scopus 로고    scopus 로고
    • Short Sequences of Non-Proline Residues Can Adopt the Polyproline II Helical Conformation
    • DOI 10.1021/bi049922v
    • Chellgren, B. W., and T. P. Creamer. 2004. Short sequences of nonproline residues can adopt the polyproline II helical conformation. Biochemistry. 43:5864-5869. (Pubitemid 38623619)
    • (2004) Biochemistry , vol.43 , Issue.19 , pp. 5864-5869
    • Chellgren, B.W.1    Creamer, T.P.2
  • 27
    • 8844242458 scopus 로고    scopus 로고
    • 2O on polyproline II helical structure
    • DOI 10.1021/ja045425q
    • Chellgren, B. W., and T. P. Creamer. 2004. Effects of H2O and D2O on polyproline II helical structure. J. Am. Chem. Soc. 126:14734-14735. (Pubitemid 39532150)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.45 , pp. 14734-14735
    • Chellgren, B.W.1    Creamer, T.P.2
  • 28
    • 17644422781 scopus 로고    scopus 로고
    • Urea promotes polyproline II helix formation: Implications for protein denatured states
    • DOI 10.1021/bi050124u
    • Whittington, S. J., B. W. Chellgren, T. P. Creamer. 2005. Urea promotes polyproline II helix formation: implications for protein denatured states. Biochemistry. 44:6269-6275. (Pubitemid 40570720)
    • (2005) Biochemistry , vol.44 , Issue.16 , pp. 6269-6275
    • Whittington, S.J.1    Chellgren, B.W.2    Hermann, V.M.3    Creamer, T.P.4
  • 29
    • 33746376976 scopus 로고    scopus 로고
    • Evidence for Polyproline II Helical Structure in Short Polyglutamine Tracts
    • DOI 10.1016/j.jmb.2006.06.044, PII S0022283606007728
    • Chellgren, B. W., A. F. Miller, and T. P. Creamer. 2006. Evidence for polyproline II helical structure in short polyglutamine tracts. J. Mol. Biol. 361:362-371. (Pubitemid 44109704)
    • (2006) Journal of Molecular Biology , vol.361 , Issue.2 , pp. 362-371
    • Chellgren, B.W.1    Miller, A.-F.2    Creamer, T.P.3
  • 30
    • 0028222235 scopus 로고
    • Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
    • Chakrabartty, A., T. Kortemme, and R. L. Baldwin. 1994. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 3:843-852. (Pubitemid 24139910)
    • (1994) Protein Science , vol.3 , Issue.5 , pp. 843-852
    • Chakrabartty, A.1    Kortemme, T.2    Baldwin, R.L.3
  • 31
    • 0025260032 scopus 로고
    • Side chain contributions to the stability of alpha-helical structure in peptides
    • Lyu, P. C., M. I. Liff, N. R. Kallenbach. 1990. Side chain contributions to the stability of α-helical structure in peptides. Science. 250:669-673. (Pubitemid 120034286)
    • (1990) Science , vol.250 , Issue.4981 , pp. 669-673
    • Lyu, P.C.1    Liff, M.I.2    Marky, L.A.3    Kallenbach, N.R.4
  • 32
    • 0028175780 scopus 로고
    • A thermodynamic scale for the β-sheet forming tendencies of the amino acids
    • Smith, C. K., J. M. Withka, and L. Regan. 1994. A thermodynamic scale for the β-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
  • 33
    • 0027998757 scopus 로고
    • Context is a major determinant of β-sheet propensity
    • DOI 10.1038/371264a0
    • Minor, Jr., D. L., and P. S. Kim. 1994. Context is a major determinant of β-sheet propensity. Nature. 371:264-267. (Pubitemid 24293028)
    • (1994) Nature , vol.371 , Issue.6494 , pp. 264-267
    • Minor Jr., D.L.1    Kim, P.S.2
  • 34
    • 0025890946 scopus 로고
    • Influence of proline residues on protein conformation
    • MacArthur, M. W., and J. M. Thornton. 1991. Influence of proline residues on protein conformation. J. Mol. Biol. 218:397-412. (Pubitemid 121003355)
    • (1991) Journal of Molecular Biology , vol.218 , Issue.2 , pp. 397-412
    • MacArthur, M.W.1    Thornton, J.M.2
  • 35
    • 73949141579 scopus 로고    scopus 로고
    • Conformations and free energy landscapes of polyproline peptides
    • Moradi, M., V. Babin, C. Sagui. 2009. Conformations and free energy landscapes of polyproline peptides. Proc. Natl. Acad. Sci. USA. 106:20746-20751.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 20746-20751
    • Moradi, M.1    Babin, V.2    Sagui, C.3
  • 36
    • 77957744536 scopus 로고    scopus 로고
    • A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers
    • Moradi, M., V. Babin, C. Sagui. 2010. A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers. J. Chem. Phys. 133:125104.
    • (2010) J. Chem. Phys. , vol.133 , pp. 125104
    • Moradi, M.1    Babin, V.2    Sagui, C.3
  • 37
    • 77957747138 scopus 로고    scopus 로고
    • Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation
    • Moradi, M., J.-G. Lee, C. Sagui. 2010. Free energy and structure of polyproline peptides: an ab initio and classical molecular dynamics investigation. Int. J. Quantum Chem. 110:2865-2879.
    • (2010) Int. J. Quantum. Chem. , vol.110 , pp. 2865-2879
    • Moradi, M.1    Lee, J.-G.2    Sagui, C.3
  • 38
    • 0031692650 scopus 로고    scopus 로고
    • Left-handed polyproline II helix formation is (very) locally driven
    • DOI 10.1002/(SICI)1097-0134(19981101)33:2<218::AID-PROT6>3.0.CO;2-E
    • Creamer, T. P. 1998. Left-handed polyproline II helix formation is (very) locally driven. Proteins. 33:218-226. (Pubitemid 28457974)
    • (1998) Proteins: Structure, Function and Genetics , vol.33 , Issue.2 , pp. 218-226
    • Creamer, T.P.1
  • 39
    • 0001678182 scopus 로고
    • The measure of association in a 2 × 2 table
    • Edwards, A. W. F 1963. The measure of association in a 2 × 2 table. J. R. Stat. Soc. [Ser A]. 126:109-114.
    • (1963) J. R. Stat. Soc. [Ser A] , vol.126 , pp. 109-114
    • Edwards, A.W.F.1
  • 40
    • 41849093720 scopus 로고    scopus 로고
    • Adaptively biased molecular dynamics for free energy calculations
    • Babin, V., C. Roland, and C. Sagui. 2008. Adaptively biased molecular dynamics for free energy calculations. J. Chem. Phys. 128:134101.
    • (2008) J. Chem. Phys. , vol.128 , pp. 134101
    • Babin, V.1    Roland, C.2    Sagui, C.3
  • 42
    • 20644449471 scopus 로고    scopus 로고
    • Modification of the generalized Born model suitable for macromolecules
    • Onufriev, A., D. Bashford, and D. A. Case. 2000. Modification of the generalized Born model suitable for macromolecules. J. Phys. Chem. B. 104:3712-3720.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 3712-3720
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 43
    • 1842479952 scopus 로고    scopus 로고
    • Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
    • DOI 10.1002/prot.20033
    • Onufriev, A., D. Bashford, and D. A. Case. 2004. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins. 55:383-394. (Pubitemid 38437495)
    • (2004) Proteins: Structure, Function and Genetics , vol.55 , Issue.2 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 45
    • 73349094393 scopus 로고    scopus 로고
    • Reoptimization of the AMBER force field parameters for peptide bond (ω) torsions using accelerated molecular dynamics
    • Doshi, U., and D. Hamelberg. 2009. Reoptimization of the AMBER force field parameters for peptide bond (ω) torsions using accelerated molecular dynamics. J. Phys. Chem. B. 113:16590-16595.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 16590-16595
    • Doshi, U.1    Hamelberg, D.2
  • 46
    • 0017435119 scopus 로고
    • Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP
    • Zimmerman, S. S., M. S. Pottle, H. A. Scheraga. 1977. Conformational analysis of the 20 naturally occurring amino acid residues using ECEPP. Macromolecules. 10:1-9.
    • (1977) Macromolecules , vol.10 , pp. 1-9
    • Zimmerman, S.S.1    Pottle, M.S.2    Scheraga, H.A.3
  • 48
    • 77749316142 scopus 로고    scopus 로고
    • Optimizing the performance of bias-exchange metadynamics: Folding a 48-residue LysM domain using a coarse-grained model
    • Cossio, P., F. Marinelli, F. Pietrucci. 2010. Optimizing the performance of bias-exchange metadynamics: folding a 48-residue LysM domain using a coarse-grained model. J. Phys. Chem. B. 114:3259-3265.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 3259-3265
    • Cossio, P.1    Marinelli, F.2    Pietrucci, F.3
  • 49
    • 50449111518 scopus 로고    scopus 로고
    • The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins
    • Beck, D. A. C., D. O. V. Alonso, V. Daggett. 2008. The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins. Proc. Natl. Acad. Sci. USA. 105:12259-12264.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 12259-12264
    • Beck, D.A.C.1    Alonso, D.O.V.2    Daggett, V.3
  • 50
    • 0016106145 scopus 로고
    • Calculation of conformational properties of oligomers of L-proline
    • Tanaka, S., and H. A. Scheraga. 1974. Calculation of conformational properties of oligomers of L-proline. Macromolecules. 7:698-705.
    • (1974) Macromolecules , vol.7 , pp. 698-705
    • Tanaka, S.1    Scheraga, H.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.