메뉴 건너뛰기




Volumn 1, Issue 5, 1994, Pages 334-340

Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; HYDROCARBON;

EID: 0028429178     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb0594-334     Document Type: Article
Times cited : (302)

References (32)
  • 1
    • 0014885326 scopus 로고
    • Studies on the conformation of amino acids. XI. Analysis of the observed side group conformations in proteins. Int
    • Chandrasekaran, R & Ramachandran, G.N. Studies on the conformation of amino acids. XI. Analysis of the observed side group conformations in proteins. Int. J. prof. Res. 2, 223-233 (1970).
    • (1970) J. Prof. Res , vol.2 , pp. 223-233
    • Chandrasekaran, R.1    Ramachandran, G.N.2
  • 2
    • 0018115846 scopus 로고
    • Conformations of amino acid sidechains in proteins. 7. molec
    • Janin, J., Wodak, S., Levitt, M. & Maigret, B. Conformations of amino acid sidechains in proteins. 7. molec. Biol. 125, 357-386 (1978).
    • (1978) Biol , vol.125 , pp. 357-386
    • Janin, J.1    Wodak, S.2    Levitt, M.3    Maigret, B.4
  • 3
    • 0023155210 scopus 로고
    • Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes
    • Ponder, J.W. & Richards, F.M. Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. molec. Biol. 193, 775-792 (1987).
    • (1987) J. Molec. Biol , vol.193 , pp. 775-792
    • Ponder, J.W.1    Richards, F.M.2
  • 5
    • 0020787793 scopus 로고
    • &Scheraga, H.A. Statistical and energetic analysis of side-chain conformations in oligopeptides
    • Benedetti, E., Morelli, G., Nemethy, G. &Scheraga, H.A. Statistical and energetic analysis of side-chain conformations in oligopeptides. Int. J. Peptide Protein Res. 22, 1-15 (1983).
    • (1983) Int. J. Peptide Protein Res , vol.22 , pp. 1-15
    • Benedetti, E.1    Morelli, G.2    Nemethy, G.3
  • 6
    • 0026179489 scopus 로고
    • A new approach to the rapid determination of protein side chain conformations. ?. biomolec. Struct
    • Tuffery, R, Etchebest, C., Hazout, S. & Lavery, R. A new approach to the rapid determination of protein side chain conformations. ?. biomolec. Struct. Dyn. 8, 1267-1289 (1991).
    • (1991) Dyn , vol.8 , pp. 1267-1289
    • Tuffery, R.1    Etchebest, C.2    Hazout, S.3    Lavery, R.4
  • 7
    • 0023521842 scopus 로고
    • Analysis of the relationship between sidechain conformation and secondary structure in globular proteins
    • McGregor, M.J., Islam, S.A. & Sternberg, M.J.E. Analysis of the relationship between sidechain conformation and secondary structure in globular proteins. J. molec. Biol. 198, 295-310 (1987).
    • (1987) J. Molec. Biol , vol.198 , pp. 295-310
    • McGregor, M.J.1    Islam, S.A.2    Sternberg, M.J.E.3
  • 8
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins: Application to sidechain prediction
    • Dunbrack, R.L., Jr & Karplus, M. Backbone-dependent rotamer library for proteins: Application to sidechain prediction. J. molec. Biol. 230, 543-571 (1993).
    • (1993) J. Molec. Biol , vol.230 , pp. 543-571
    • Dunbrack, R.L.1    Karplus, M.2
  • 9
    • 0027208112 scopus 로고
    • Rotamers: To be or not to be? An analysis of amino acid sidechain conformations in globular proteins
    • Schrauber, H., Eisenhaber, F. & Argos, P Rotamers: To be or not to be? An analysis of amino acid sidechain conformations in globular proteins. J. molec. Biol. 230, 592-612 (1993).
    • (1993) J. Molec. Biol , vol.230 , pp. 592-612
    • Schrauber, H.1    Eisenhaber, F.2    Argos, P.3
  • 11
    • 0027185404 scopus 로고
    • Method to configure protein sidechains from the mainchain trace in homology modeling
    • Eisenmenger, F., Argos, P. & Abagyan, R. A method to configure protein sidechains from the mainchain trace in homology modeling. J. molec. Biol. 231, 849-860 (1993).
    • (1993) J. Molec. Biol , vol.231 , pp. 849-860
    • Eisenmenger, F.1    Argos, P.2    Abagyan, R.A.3
  • 12
    • 0026019108 scopus 로고
    • Prediction of protein sidechain conformation by packing optimization
    • Lee, C. & Subbiah, S. Prediction of protein sidechain conformation by packing optimization. J. molec. Biol. 217, 373-388 (1991).
    • (1991) J. Molec. Biol , vol.217 , pp. 373-388
    • Lee, C.1    Subbiah, S.2
  • 13
    • 0026589733 scopus 로고
    • The dead-end elimination theorem and its use in protein sidechain positioning
    • Desmet, J., DeMaeyer, M., Hazes, B. & Lasters, I. The dead-end elimination theorem and its use in protein sidechain positioning. Nature 356, 539-542 (1992).
    • (1992) Nature , vol.356 , pp. 539-542
    • Desmet, J.1    Demaeyer, M.2    Hazes, B.3    Lasters, I.4
  • 17
    • 0018780591 scopus 로고
    • Sidechain torsional potentials: Effect of dipeptide, protein, and solvent environment
    • Gelin, B.R. & Karplus, M. Sidechain torsional potentials: Effect of dipeptide, protein, and solvent environment. Biochemistry 18, 1256-1268 (1979).
    • (1979) Biochemistry , vol.18 , pp. 1256-1268
    • Gelin, B.R.1    Karplus, M.2
  • 18
    • 0014979318 scopus 로고
    • Studies on the conformation of amino acids. IX. Conformations of butyl, seryl, threonyl, cysteinyl, andvalyl residues in a dipeptide unit
    • Ponnuswamy, P.K. & Sasisekharan, V. Studies on the conformation of amino acids. IX. Conformations of butyl, seryl, threonyl, cysteinyl, andvalyl residues in a dipeptide unit. Biopolymers 10, 565-582 (1971).
    • (1971) Biopolymers , vol.10 , pp. 565-582
    • Ponnuswamy, P.K.1    Sasisekharan, V.2
  • 19
    • 84987317310 scopus 로고
    • Energy parameters in polypeptides. VI. Conformational energy analysis of the N-Acetyl N'-methyl amides of the twenty naturally occurring amino acids. Israel
    • Lewis, P.N., Momany, F.A. & Scheraga, H.A. Energy parameters in polypeptides. VI. Conformational energy analysis of the N-Acetyl N'-methyl amides of the twenty naturally occurring amino acids. Israel. J. Chem. 11, 121-152 (1973).
    • (1973) J. Chem , vol.11 , pp. 121-152
    • Lewis, P.N.1    Momany, F.A.2    Scheraga, H.A.3
  • 21
    • 33847087644 scopus 로고
    • Low-frequency Raman spectrum and asymmetric potential function for internal rotation of gaseous n-butane
    • Compton, D.A.C., Montero, S. & Murphy, W.F. Low-frequency Raman spectrum and asymmetric potential function for internal rotation of gaseous n-butane. J. phys. Chem. 84, 3587-3591 (1980).
    • (1980) J. Phys. Chem , vol.84 , pp. 3587-3591
    • Compton, D.A.C.1    Montero, S.2    Murphy, W.F.3
  • 22
    • 36849125469 scopus 로고
    • The vibration frequencies and thermodynamic functions of long chain hydrocarbons
    • Pitzer, K.S. The vibration frequencies and thermodynamic functions of long chain hydrocarbons. J. chem. Phys. 8, 711-720 (1940).
    • (1940) J. Chem. Phys , vol.8 , pp. 711-720
    • Pitzer, K.S.1
  • 23
    • 33845279881 scopus 로고
    • Rotational barriers. 2. Energies of alkane rotamers. An examination of gauche interactions
    • Wiberg, K.B. & Murcko, M.A. Rotational barriers. 2. Energies of alkane rotamers. An examination of gauche interactions.?. Am. chem. Soc. 110, 8029-8038(1988).
    • (1988) Am. Chem. Soc , vol.8029 , pp. 110
    • Wiberg, K.B.1    Murcko, M.A.2
  • 24
    • 36849131794 scopus 로고
    • Unperturbed mean-square end-to-end distance in polyethylene
    • Hoeve, C.A.J. Unperturbed mean-square end-to-end distance in polyethylene. J. chem. Phys. 35, 1266-1267 (1961).
    • (1961) J. Chem. Phys , vol.35 , pp. 1266-1267
    • Hoeve, C.A.J.1
  • 25
    • 33947333633 scopus 로고
    • Conformational energies of n-alkanes and the random configuration of higher homologs Including polymethylene. J
    • Abe, A., Jernigan, R.L. & Flory, P.J. Conformational energies of n-alkanes and the random configuration of higher homologs Including polymethylene. J. Am. chem. Soc. 88, 631-639 (1966).
    • (1966) Am. Chem. Soc , vol.88 , pp. 631-639
    • Abe, A.1    Jernigan, R.L.2    Flory, P.J.3
  • 26
    • 33947445123 scopus 로고
    • Chemical equilibria, free energies, and heat contents for gaseous hydrocarbons
    • Pitzer, K.S. Chemical equilibria, free energies, and heat contents for gaseous hydrocarbons. Chem. Rev. 27, 39-57 (1940).
    • (1940) Chem. Rev , vol.27 , pp. 39-57
    • Pitzer, K.S.1
  • 27
    • 0000711866 scopus 로고
    • The barrierto internal rotation in ethane. Accts. chem
    • Pitzer, R.M. The barrierto internal rotation in ethane. Accts. chem. Res. 16, 201-210 (1983).
    • (1983) Res , vol.16 , pp. 201-210
    • Pitzer, R.M.1
  • 28
    • 33646271477 scopus 로고
    • A notation for the study of certain stereochemical problems. J
    • Newman, M S. A notation for the study of certain stereochemical problems. J. chem. Ed. 32, 344-347 (1955).
    • (1955) Chem. Ed. , vol.32 , pp. 344-347
    • Newman, M.S.1
  • 29
    • 0021755525 scopus 로고
    • Intrahelical hydrogen bonding of serine, threonine, and cysteine residues with ct-helices and its relevance to membrane-bound proteins
    • Gray, T.M. & Matthews, B.W. Intrahelical hydrogen bonding of serine, threonine, and cysteine residues with ct-helices and its relevance to membrane-bound proteins. J. molec. Biol. 175, 75-81 (1984).
    • (1984) J. Molec. Biol , vol.175 , pp. 75-81
    • Gray, T.M.1    Matthews, B.W.2
  • 30
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
    • Brooks, B.R. et at. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. comp. Chem. 4, 187-217 (1983).
    • (1983) J. Comp. Chem , vol.4 , pp. 187-217
    • Brooks, B.R.1
  • 32
    • 0023977089 scopus 로고
    • Eta/. The MIDAS display system. J, molec
    • Ferrin, T.E. eta/. The MIDAS display system. J, molec. Graphics 6, 13-27 (1988).
    • (1988) Graphics , vol.6 , pp. 13-27
    • Ferrin, T.E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.