메뉴 건너뛰기




Volumn 16, Issue 8, 2007, Pages 1667-1675

The role of protein homochirality in shaping the energy landscape of folding

Author keywords

Folding funnel; Lattice chain model; Protein design; Tacticity

Indexed keywords

ALANINE; POLYPEPTIDE;

EID: 34547572093     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.072867007     Document Type: Article
Times cited : (23)

References (52)
  • 1
    • 6044221427 scopus 로고    scopus 로고
    • Exploiting the right side of the Ramachandran plot: Substitution of glycines by D-alanine can significantly increase protein stability
    • Anil, B., Song, B., Tang, Y., and Raleigh, D.P. 2004. Exploiting the right side of the Ramachandran plot: Substitution of glycines by D-alanine can significantly increase protein stability. J. Am. Chem. Soc. 126: 13194-13195.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 13194-13195
    • Anil, B.1    Song, B.2    Tang, Y.3    Raleigh, D.P.4
  • 3
    • 33646585149 scopus 로고    scopus 로고
    • Dissecting the energetics of protein α-helix C-cap termination through chemical protein synthesis
    • Bang, D., Gribenko, A.V., Tereshko, V., Kossiakoff, A.A., Kent, S.B., and Makhatadze, G.I. 2006. Dissecting the energetics of protein α-helix C-cap termination through chemical protein synthesis. Nat. Chem. Biol. 2: 139-143.
    • (2006) Nat. Chem. Biol , vol.2 , pp. 139-143
    • Bang, D.1    Gribenko, A.V.2    Tereshko, V.3    Kossiakoff, A.A.4    Kent, S.B.5    Makhatadze, G.I.6
  • 4
    • 0001121381 scopus 로고
    • Deuterium exchange of poly-DL-alanine in aqueous solution
    • Berger, A. and Linderstrøm-Lang, K. 1957. Deuterium exchange of poly-DL-alanine in aqueous solution. Arch. Biochem. Biophys. 69: 106-118.
    • (1957) Arch. Biochem. Biophys , vol.69 , pp. 106-118
    • Berger, A.1    Linderstrøm-Lang, K.2
  • 5
    • 33947484491 scopus 로고
    • The configuration of random polypeptide chains
    • Brant, D.A. and Flory, P.J. 1965. The configuration of random polypeptide chains. 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
  • 6
    • 0025804130 scopus 로고
    • Large differences in the helix propensities of alanine and glycine
    • Chakrabartty, A., Schellman, 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    Schellman, J.A.2    Baldwin, R.L.3
  • 7
    • 0025906282 scopus 로고
    • Polymer principles in protein structure and stability
    • Chan, H.S. and Dill, K.A. 1991. Polymer principles in protein structure and stability. Annu. Rev. Biophys. Biophys. Chem. 20: 447-490.
    • (1991) Annu. Rev. Biophys. Biophys. Chem , vol.20 , pp. 447-490
    • Chan, H.S.1    Dill, K.A.2
  • 8
    • 0035471135 scopus 로고    scopus 로고
    • β-Peptides: From structure to function
    • Cheng, R.P., Gellman, S.H., and DeGrado, W.F. 2001. β-Peptides: From structure to function. Chem. Rev. 101: 3219-3232.
    • (2001) Chem. Rev , vol.101 , pp. 3219-3232
    • Cheng, R.P.1    Gellman, S.H.2    DeGrado, W.F.3
  • 9
    • 0017558860 scopus 로고
    • Helical structures of poly(D-L-peptides). A conformational energy analysis
    • Colonna-Cesari, F., Premilat, S., Heitz, F., Spach, G., and Lotz, B. 1977. Helical structures of poly(D-L-peptides). A conformational energy analysis. Macromolecules 10: 1284-1288.
    • (1977) Macromolecules , vol.10 , pp. 1284-1288
    • Colonna-Cesari, F.1    Premilat, S.2    Heitz, F.3    Spach, G.4    Lotz, B.5
  • 11
    • 0032835617 scopus 로고    scopus 로고
    • De novo design and structural characterization of proteins and metalloproteins
    • DeGrado, W.F., Summa, C.M., Pavone, V., Nastri, F., and Lombardi, A. 1999. De novo design and structural characterization of proteins and metalloproteins. Annu. Rev. Biochem. 68: 779-819.
    • (1999) Annu. Rev. Biochem , vol.68 , pp. 779-819
    • DeGrado, W.F.1    Summa, C.M.2    Pavone, V.3    Nastri, F.4    Lombardi, A.5
  • 12
    • 0026750901 scopus 로고
    • The helix-forming propensity of D-alanine in a right-handed α-helix
    • Fairman, R., Anthony-Cahill, S.J., and DeGrado, W.F. 1992. The helix-forming propensity of D-alanine in a right-handed α-helix. J. Am. Chem. Soc. 114: 5458-5459.
    • (1992) J. Am. Chem. Soc , vol.114 , pp. 5458-5459
    • Fairman, R.1    Anthony-Cahill, S.J.2    DeGrado, W.F.3
  • 13
    • 26844480393 scopus 로고    scopus 로고
    • Sterics and solvation winnow accessible conformational space for unfolded proteins
    • Fitzkee, N.C. and Rose, G.D. 2005. Sterics and solvation winnow accessible conformational space for unfolded proteins. J. Mol. Biol. 353: 873-887.
    • (2005) J. Mol. Biol , vol.353 , pp. 873-887
    • Fitzkee, N.C.1    Rose, G.D.2
  • 15
    • 0027703505 scopus 로고
    • Self-assembling organic nanotubes based on a cyclic peptide architecture
    • Ghadiri, M.R., Granja, J.R., Milligan, R.A., McRee, D.E., and Khazanovich, N. 1993. Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature 366: 324-327.
    • (1993) Nature , vol.366 , pp. 324-327
    • Ghadiri, M.R.1    Granja, J.R.2    Milligan, R.A.3    McRee, D.E.4    Khazanovich, N.5
  • 16
    • 0037432567 scopus 로고    scopus 로고
    • Local secondary structure content predicts folding rates for simple, two-state proteins
    • Gong, H., Isom, D.G., Srinivasan, R., and Rose, G.D. 2003. Local secondary structure content predicts folding rates for simple, two-state proteins. J. Mol. Biol. 327: 1149-1154.
    • (2003) J. Mol. Biol , vol.327 , pp. 1149-1154
    • Gong, H.1    Isom, D.G.2    Srinivasan, R.3    Rose, G.D.4
  • 18
    • 7744244288 scopus 로고
    • Sheet structures in alternating poly(D,L-peptides)
    • Heitz, F., Detriche, G., Vovelle, F., and Spach, G. 1981. Sheet structures in alternating poly(D,L-peptides). Macromolecules 14: 47-50.
    • (1981) Macromolecules , vol.14 , pp. 47-50
    • Heitz, F.1    Detriche, G.2    Vovelle, F.3    Spach, G.4
  • 19
    • 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
  • 20
    • 33947088903 scopus 로고
    • On the possible existence of α-helical structures of regular-sequence D,L copolymers of amino acids. Conformational energy calculations
    • Hesselink, F.T. and Scheraga, H.A. 1972. On the possible existence of α-helical structures of regular-sequence D,L copolymers of amino acids. Conformational energy calculations. Macromolecules 5: 455-463.
    • (1972) Macromolecules , vol.5 , pp. 455-463
    • Hesselink, F.T.1    Scheraga, H.A.2
  • 21
    • 0009364514 scopus 로고
    • Probability of initial ring closure in the restricted random-walk model of a macromolecule
    • Hiley, B.J. and Sykes,M.F. 1961. Probability of initial ring closure in the restricted random-walk model of a macromolecule. J. Chem. Phys. 34: 1531-1537.
    • (1961) J. Chem. Phys , vol.34 , pp. 1531-1537
    • Hiley, B.J.1    Sykes, M.F.2
  • 22
    • 0001842441 scopus 로고    scopus 로고
    • Adding backbone to protein folding: Why proteins are polypeptides
    • Honig, B. and Cohen, F.E. 1996. Adding backbone to protein folding: Why proteins are polypeptides. Fold. Des. 1: R17-R20.
    • (1996) Fold. Des , vol.1
    • Honig, B.1    Cohen, F.E.2
  • 23
    • 0027992140 scopus 로고
    • The origins of protein secondary structure. Effects of packing density and hydrogen bonding studied by a fast conformational search
    • Hunt, N.G., Gregoret, L.M., and Cohen, F.E. 1994. The origins of protein secondary structure. Effects of packing density and hydrogen bonding studied by a fast conformational search. J. Mol. Biol. 241: 214-225.
    • (1994) J. Mol. Biol , vol.241 , pp. 214-225
    • Hunt, N.G.1    Gregoret, L.M.2    Cohen, F.E.3
  • 24
    • 0036345270 scopus 로고    scopus 로고
    • Enumerating designing sequences in the HP model
    • Irback, A. and Troein, C. 2002. Enumerating designing sequences in the HP model. J. Biol. Phys. 28: 1-15.
    • (2002) J. Biol. Phys , vol.28 , pp. 1-15
    • Irback, A.1    Troein, C.2
  • 26
    • 0037062978 scopus 로고    scopus 로고
    • The antiquity of RNA-based evolution
    • Joyce, G.F. 2002. The antiquity of RNA-based evolution. Nature 418: 214-221.
    • (2002) Nature , vol.418 , pp. 214-221
    • Joyce, G.F.1
  • 28
    • 0023372377 scopus 로고
    • The case for an ancestral genetic system involving simple analogues of the nucleotides
    • Joyce, G.F., Schwartz, A.W., Miller, S.L., and Orgel, L.E. 1987. The case for an ancestral genetic system involving simple analogues of the nucleotides. Proc. Natl. Acad. Sci. 84: 4398-4402.
    • (1987) Proc. Natl. Acad. Sci , vol.84 , pp. 4398-4402
    • Joyce, G.F.1    Schwartz, A.W.2    Miller, S.L.3    Orgel, L.E.4
  • 29
    • 0025345233 scopus 로고
    • Structural characteristics of α-helical peptide molecules containing aib residues
    • Karle, I.L. and Balaram, P. 1990. Structural characteristics of α-helical peptide molecules containing aib residues. Biochemistry 29: 6747-6756.
    • (1990) Biochemistry , vol.29 , pp. 6747-6756
    • Karle, I.L.1    Balaram, P.2
  • 30
    • 0042631521 scopus 로고    scopus 로고
    • Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences
    • Kaya, H. and Chan, H.S. 2003. Contact order dependent protein folding rates: Kinetic consequences of a cooperative interplay between favorable nonlocal interactions and local conformational preferences. Proteins 52: 524-533.
    • (2003) Proteins , vol.52 , pp. 524-533
    • Kaya, H.1    Chan, H.S.2
  • 32
    • 0037214137 scopus 로고    scopus 로고
    • Protein hydrogen exchange mechanism: Local fluctuations
    • Maity, H., Lim, W.K., Rumbley, J.N., and Englander, S.W. 2003. Protein hydrogen exchange mechanism: Local fluctuations. Protein Sci. 12: 153-160.
    • (2003) Protein Sci , vol.12 , pp. 153-160
    • Maity, H.1    Lim, W.K.2    Rumbley, J.N.3    Englander, S.W.4
  • 33
    • 33750036386 scopus 로고    scopus 로고
    • Effects of the alternating backbone configuration on the secondary structure and self-assembly of β-peptides
    • Martinek, T.A., Mandity, I.M., Fulop, L., Toth, G.K., Vass, E., Hollosi, M., Forro, E., and Fulop, F. 2006. Effects of the alternating backbone configuration on the secondary structure and self-assembly of β-peptides. J. Am. Chem. Soc. 128: 13539-13544.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 13539-13544
    • Martinek, T.A.1    Mandity, I.M.2    Fulop, L.3    Toth, G.K.4    Vass, E.5    Hollosi, M.6    Forro, E.7    Fulop, F.8
  • 34
    • 0002830680 scopus 로고
    • Random-coil configurations of polypeptide copolymers
    • Miller, W.G., Brant, D.A., and Flory, P.J. 1967. Random-coil configurations of polypeptide copolymers. J. Mol. Biol. 23: 67-80.
    • (1967) J. Mol. Biol , vol.23 , pp. 67-80
    • Miller, W.G.1    Brant, D.A.2    Flory, P.J.3
  • 35
    • 0026686436 scopus 로고
    • Total chemical synthesis of a D-enzyme: The enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected]
    • Milton, R.C., Milton, S.C., and Kent, S.B. 1992. Total chemical synthesis of a D-enzyme: The enantiomers of HIV-1 protease show reciprocal chiral substrate specificity [corrected]. Science 256: 1445-1448.
    • (1992) Science , vol.256 , pp. 1445-1448
    • Milton, R.C.1    Milton, S.C.2    Kent, S.B.3
  • 36
    • 0035005366 scopus 로고    scopus 로고
    • Preorganized secondary structure as an important determinant of fast protein folding
    • Myers, J.K. and Oas, T.G. 2001. Preorganized secondary structure as an important determinant of fast protein folding. Nat. Struct. Biol. 8: 552-558.
    • (2001) Nat. Struct. Biol , vol.8 , pp. 552-558
    • Myers, J.K.1    Oas, T.G.2
  • 37
    • 7744230016 scopus 로고    scopus 로고
    • Simulated evolution of emergent chiral structures in polyalanine
    • Nanda, V. and DeGrado, W.F. 2004. Simulated evolution of emergent chiral structures in polyalanine. J. Am. Chem. Soc. 126: 14459-14467.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 14459-14467
    • Nanda, V.1    DeGrado, W.F.2
  • 38
    • 31444449249 scopus 로고    scopus 로고
    • Computational design of heterochiral peptides against a helical target
    • Nanda, V. and DeGrado, W.F. 2006. Computational design of heterochiral peptides against a helical target. J. Am. Chem. Soc. 128: 809-816.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 809-816
    • Nanda, V.1    DeGrado, W.F.2
  • 39
    • 0025222978 scopus 로고
    • A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids
    • O'Neil, K.T. and DeGrado, W.F. 1990. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 250: 646-651.
    • (1990) Science , vol.250 , pp. 646-651
    • O'Neil, K.T.1    DeGrado, W.F.2
  • 40
    • 0033730431 scopus 로고    scopus 로고
    • The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding
    • Pappu, R.V., Srinivasan, R., and Rose, G.D. 2000. The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding. Proc. Natl. Acad. Sci. 97: 12565-12570.
    • (2000) Proc. Natl. Acad. Sci , vol.97 , pp. 12565-12570
    • Pappu, R.V.1    Srinivasan, R.2    Rose, G.D.3
  • 41
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single-domain proteins
    • Plaxco, K.W., Simons, K.T., and Baker, D. 1998. Contact order, transition state placement and the refolding rates of single-domain proteins. J. Mol. Biol. 277: 985-994.
    • (1998) J. Mol. Biol , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 42
    • 33744822163 scopus 로고    scopus 로고
    • The link between sequence and conformation in protein structures appears to be stereochemically established
    • Ramakrishnan, V., Ranbhor, R., Kumar, A., and Durani, S. 2006. The link between sequence and conformation in protein structures appears to be stereochemically established. J. Phys. Chem. B 110: 9314-9323.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 9314-9323
    • Ramakrishnan, V.1    Ranbhor, R.2    Kumar, A.3    Durani, S.4
  • 43
    • 33845197716 scopus 로고    scopus 로고
    • The interplay of sequence and stereochemistry in defining conformation in proteins and polypeptides
    • Ranbhor, R., Ramakrishnan, V., Kumar, A., and Durani, S. 2006. The interplay of sequence and stereochemistry in defining conformation in proteins and polypeptides. Biopolymers 83: 537-545.
    • (2006) Biopolymers , vol.83 , pp. 537-545
    • Ranbhor, R.1    Ramakrishnan, V.2    Kumar, A.3    Durani, S.4
  • 44
    • 0032054585 scopus 로고    scopus 로고
    • The design of efficient α-helical C-capping auxiliaries
    • Schneider, J.P. and DeGrado, W.F. 1998. The design of efficient α-helical C-capping auxiliaries. J. Am. Chem. Soc. 120: 2764-2767.
    • (1998) J. Am. Chem. Soc , vol.120 , pp. 2764-2767
    • Schneider, J.P.1    DeGrado, W.F.2
  • 45
    • 0036606453 scopus 로고    scopus 로고
    • Ab initio prediction of protein structure using LINUS
    • Srinivasan, R. and Rose, G.D. 2002. Ab initio prediction of protein structure using LINUS. Proteins 47: 489-495.
    • (2002) Proteins , vol.47 , pp. 489-495
    • Srinivasan, R.1    Rose, G.D.2
  • 46
    • 0014504439 scopus 로고
    • Solution, phase coexistence, and related proton nuclear magnetic resonance studies on poly-L- and poly-DL-alanine in helix-random-coil interconverting media
    • Takahashi, A., Mandelkern, L., and Glick, R.E. 1969. Solution, phase coexistence, and related proton nuclear magnetic resonance studies on poly-L- and poly-DL-alanine in helix-random-coil interconverting media. Biochemistry 8: 1673-1684.
    • (1969) Biochemistry , vol.8 , pp. 1673-1684
    • Takahashi, A.1    Mandelkern, L.2    Glick, R.E.3
  • 47
    • 0015100247 scopus 로고
    • The gramicidin A transmembrane channel: Characteristics of head-to-head dimerized Pi(L,D) helices
    • Urry, D.W., Goodall, M.C., Glickson, J.D., and Mayers, D.F. 1971. The gramicidin A transmembrane channel: Characteristics of head-to-head dimerized Pi(L,D) helices. Proc. Natl. Acad. Sci. 68: 1907-1911.
    • (1971) Proc. Natl. Acad. Sci , vol.68 , pp. 1907-1911
    • Urry, D.W.1    Goodall, M.C.2    Glickson, J.D.3    Mayers, D.F.4
  • 48
  • 49
    • 1842399980 scopus 로고
    • Origin of optical activity
    • Wald, G. 1957. Origin of optical activity. Ann. N. Y. Acad. Sci. 69: 352-368.
    • (1957) Ann. N. Y. Acad. Sci , vol.69 , pp. 352-368
    • Wald, G.1
  • 50
    • 0028124611 scopus 로고
    • Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry
    • Yee, D.P., Chan, H.S., Havel, T.F., and Dill, K.A. 1994. Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry. J. Mol. Biol. 241: 557-573.
    • (1994) J. Mol. Biol , vol.241 , pp. 557-573
    • Yee, D.P.1    Chan, H.S.2    Havel, T.F.3    Dill, K.A.4
  • 51
    • 0028317634 scopus 로고
    • 3(10)-Helix versus α-helix - a molecular-dynamics study of conformational preferences of aib and alanine
    • Zhang, L. and Hermans, J. 1994. 3(10)-Helix versus α-helix - a molecular-dynamics study of conformational preferences of aib and alanine. J. Am. Chem. Soc. 116: 11915-11921.
    • (1994) J. Am. Chem. Soc , vol.116 , pp. 11915-11921
    • Zhang, L.1    Hermans, J.2
  • 52
    • 3142729196 scopus 로고    scopus 로고
    • Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models
    • Zhang, J.F., Chen, Y., Chen, R., and Liang, J. 2004. Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models. J. Chem. Phys. 121: 592-603.
    • (2004) J. Chem. Phys , vol.121 , pp. 592-603
    • Zhang, J.F.1    Chen, Y.2    Chen, R.3    Liang, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.