메뉴 건너뛰기




Volumn 1774, Issue 3, 2007, Pages 382-391

Conformational study of palindromic tripeptides (GPG, IPI and KPK) in HIV-1 protease-A density functional theory study

Author keywords

Amide capping; Density functional theory; PES; Proline; Pseudorotation

Indexed keywords

AMIDE; DIPROTIN A; GLYCYLPROLYLGLYCINE; LYSYLPROLYLLYSINE; PROLINE; PROTEINASE; PYRROLIDINE DERIVATIVE; TRIPEPTIDE; UNCLASSIFIED DRUG; VIRUS ENZYME;

EID: 33847680870     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2006.12.010     Document Type: Article
Times cited : (2)

References (55)
  • 3
    • 0028919502 scopus 로고
    • Prediction of protein secondary structures from their hydrophobic characters
    • Michael Gromiha M., and Ponnuswamy P.K. Prediction of protein secondary structures from their hydrophobic characters. Int. J. Pept. Protein Res. 45 (1995) 225
    • (1995) Int. J. Pept. Protein Res. , vol.45 , pp. 225
    • Michael Gromiha, M.1    Ponnuswamy, P.K.2
  • 4
    • 0025890946 scopus 로고
    • Influence of proline residues on protein conformation
    • MacArthur J., and Thornton M. Influence of proline residues on protein conformation. J. Mol. Biol. 218 (1991) 397
    • (1991) J. Mol. Biol. , vol.218 , pp. 397
    • MacArthur, J.1    Thornton, M.2
  • 5
    • 0030958758 scopus 로고    scopus 로고
    • Identification of membrane spanning β strands in bacterial porins
    • Michael Gromiha M., Majumdar R., and Ponnuswamy P.K. Identification of membrane spanning β strands in bacterial porins. Protein Eng. 10 (1997) 497
    • (1997) Protein Eng. , vol.10 , pp. 497
    • Michael Gromiha, M.1    Majumdar, R.2    Ponnuswamy, P.K.3
  • 6
    • 0032797505 scopus 로고    scopus 로고
    • A simple method for predicting transmembrane α helices with better accuracy
    • Gromiha M.M. A simple method for predicting transmembrane α helices with better accuracy. Protein Eng. 12 (1999) 557
    • (1999) Protein Eng. , vol.12 , pp. 557
    • Gromiha, M.M.1
  • 7
    • 0033752859 scopus 로고    scopus 로고
    • Beta and gamma turns in proteins revisited
    • Guruprasad K., and Rajkumar S. Beta and gamma turns in proteins revisited. J. Biosci. 25 (2000) 143
    • (2000) J. Biosci. , vol.25 , pp. 143
    • Guruprasad, K.1    Rajkumar, S.2
  • 9
    • 0015967881 scopus 로고
    • Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins
    • Chou Y., and Fasman G.D. Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins. Biochemistry 13 (1974) 211
    • (1974) Biochemistry , vol.13 , pp. 211
    • Chou, Y.1    Fasman, G.D.2
  • 10
    • 0030461902 scopus 로고    scopus 로고
    • Steric effects on the amide isomer equilibrium of prolyl peptides
    • Beausoleil E., and Lubell W.D. Steric effects on the amide isomer equilibrium of prolyl peptides. J. Am. Chem. Soc. 118 (1996) 12902
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 12902
    • Beausoleil, E.1    Lubell, W.D.2
  • 11
    • 0014932773 scopus 로고
    • Laser-Raman and infrared spectra of amino acids and their metal complexes. III. Proline and bisprolinato complexes
    • Herlinger A.W., and Long II T.V. Laser-Raman and infrared spectra of amino acids and their metal complexes. III. Proline and bisprolinato complexes. J. Am. Chem. Soc. 92 (1970) 6481
    • (1970) J. Am. Chem. Soc. , vol.92 , pp. 6481
    • Herlinger, A.W.1    Long II, T.V.2
  • 12
    • 0036462496 scopus 로고    scopus 로고
    • Quantum mechanical study of conformational behavior of proline and 4R hydroxyproline dipeptide analogues in vacuum and in aqueous solution
    • Benzi C., Improta R., Scalmani G., and Barone V. Quantum mechanical study of conformational behavior of proline and 4R hydroxyproline dipeptide analogues in vacuum and in aqueous solution. J. Comput. Chem. 23 (2002) 341
    • (2002) J. Comput. Chem. , vol.23 , pp. 341
    • Benzi, C.1    Improta, R.2    Scalmani, G.3    Barone, V.4
  • 13
    • 4644369698 scopus 로고    scopus 로고
    • Cis-trans isomerization and puckering of proline residue
    • Kang Y.K., and Choi H.Y. Cis-trans isomerization and puckering of proline residue. Biophys. Chem. 111 (2004) 135
    • (2004) Biophys. Chem. , vol.111 , pp. 135
    • Kang, Y.K.1    Choi, H.Y.2
  • 14
    • 2442443298 scopus 로고    scopus 로고
    • Ring flip of proline residue via the transition state with an envelope conformation
    • Kang Y.K. Ring flip of proline residue via the transition state with an envelope conformation. J. Phys. Chem. B 108 (2004) 5463
    • (2004) J. Phys. Chem. B , vol.108 , pp. 5463
    • Kang, Y.K.1
  • 15
    • 0001439872 scopus 로고    scopus 로고
    • Molecular mechanics parameters and conformational free energies of proline-containing peptides
    • McDonald Q.D., and Still W.C. Molecular mechanics parameters and conformational free energies of proline-containing peptides. J. Org. Chem. 61 (1996) 1385
    • (1996) J. Org. Chem. , vol.61 , pp. 1385
    • McDonald, Q.D.1    Still, W.C.2
  • 16
    • 0037126686 scopus 로고    scopus 로고
    • Proline cis-trans isomerization and protein folding
    • Wedemeyer W.J., Welker E., and Scheraga H.A. Proline cis-trans isomerization and protein folding. Biochemistry 41 (2002) 14637
    • (2002) Biochemistry , vol.41 , pp. 14637
    • Wedemeyer, W.J.1    Welker, E.2    Scheraga, H.A.3
  • 19
    • 33947436985 scopus 로고
    • The thermodynamics and molecular structure of cyclopentane1
    • Kilpatrick J.E., Pitzer K.S., and Spitzer R. The thermodynamics and molecular structure of cyclopentane1. J. Am. Chem. Soc. 69 (1947) 2483
    • (1947) J. Am. Chem. Soc. , vol.69 , pp. 2483
    • Kilpatrick, J.E.1    Pitzer, K.S.2    Spitzer, R.3
  • 20
    • 0021844602 scopus 로고
    • β-hairpin families in globular proteins
    • Sibanda B.L., and Thornton J.M. β-hairpin families in globular proteins. Nature 316 (1985) 170
    • (1985) Nature , vol.316 , pp. 170
    • Sibanda, B.L.1    Thornton, J.M.2
  • 21
    • 14944346760 scopus 로고    scopus 로고
    • Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains
    • Krieger F., Moglich A., and Kiefhaber T. Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains. J. Am. Chem. Soc. 127 (2005) 3346
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 3346
    • Krieger, F.1    Moglich, A.2    Kiefhaber, T.3
  • 23
    • 0001515201 scopus 로고    scopus 로고
    • Conformationally constrained peptide mimetics: the use of a small lactam ring as an HIV-1 antigen constraint
    • Long R.D., and Moeller K.D. Conformationally constrained peptide mimetics: the use of a small lactam ring as an HIV-1 antigen constraint. J. Am. Chem. Soc. 119 (1997) 12394
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 12394
    • Long, R.D.1    Moeller, K.D.2
  • 24
    • 0033986618 scopus 로고    scopus 로고
    • Deletion of the GPG motif in the HIV type 1 V3 loop does not abrogate infection in all cells
    • Su J., Palm A., Wu Y., Sandin S., Hoglund S., and Vahlne A. Deletion of the GPG motif in the HIV type 1 V3 loop does not abrogate infection in all cells. AIDS Res. Hum. Retroviruses 16 (2000) 37
    • (2000) AIDS Res. Hum. Retroviruses , vol.16 , pp. 37
    • Su, J.1    Palm, A.2    Wu, Y.3    Sandin, S.4    Hoglund, S.5    Vahlne, A.6
  • 26
    • 1842484196 scopus 로고    scopus 로고
    • Self-aggregation of reverse bis peptide conjugate derived from the unstructured region of the prion protein
    • Madhavaiah C., and Verma S. Self-aggregation of reverse bis peptide conjugate derived from the unstructured region of the prion protein. Chem. Commun. (2004) 638
    • (2004) Chem. Commun. , pp. 638
    • Madhavaiah, C.1    Verma, S.2
  • 28
    • 0033851469 scopus 로고    scopus 로고
    • Conformational and topological considerations in designing agonist peptodomimetics from peptide leads
    • Hruby V.J., and Balse P.M. Conformational and topological considerations in designing agonist peptodomimetics from peptide leads. Curr. Med. Chem. 7 (2000) 945
    • (2000) Curr. Med. Chem. , vol.7 , pp. 945
    • Hruby, V.J.1    Balse, P.M.2
  • 31
    • 0034940390 scopus 로고    scopus 로고
    • Conformational landscapes in amino acids: infrared and ultraviolet ion dip spectroscopy of tryptophan
    • Snoek L.C., Kroemer R.T., Hockridge M.R., and Simons J.P. Conformational landscapes in amino acids: infrared and ultraviolet ion dip spectroscopy of tryptophan. Phys. Chem. Chem. Phys. 3 (2001) 1819
    • (2001) Phys. Chem. Chem. Phys. , vol.3 , pp. 1819
    • Snoek, L.C.1    Kroemer, R.T.2    Hockridge, M.R.3    Simons, J.P.4
  • 32
    • 3042559897 scopus 로고    scopus 로고
    • β-sheet model systems in the gas phase: Structures and vibrations of Ac-Phe-NHMe and its dimer (Ac-Phe-NHMe)2
    • Gerhards M., Unterberg C., Gerlach A., and Jansen A. β-sheet model systems in the gas phase: Structures and vibrations of Ac-Phe-NHMe and its dimer (Ac-Phe-NHMe)2. Phys. Chem. Chem. Phys. 6 (2004) 2682
    • (2004) Phys. Chem. Chem. Phys. , vol.6 , pp. 2682
    • Gerhards, M.1    Unterberg, C.2    Gerlach, A.3    Jansen, A.4
  • 33
    • 84961973279 scopus 로고    scopus 로고
    • A quantum mechanical study of proline, hydroxyproline, and fluoroproline dipeptide analogues in aqueous solution
    • Improta R., Benzi C., and Barone V. A quantum mechanical study of proline, hydroxyproline, and fluoroproline dipeptide analogues in aqueous solution. J. Am. Chem. Soc. 123 (2001) 12568
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 12568
    • Improta, R.1    Benzi, C.2    Barone, V.3
  • 34
    • 0024272758 scopus 로고
    • Conformational preferences of sequential fragments of the hinge region of human IgA1 immunoglobulin molecule: II
    • Burton J., Wood S.G., Pedyczak A., and Siemion I.Z. Conformational preferences of sequential fragments of the hinge region of human IgA1 immunoglobulin molecule: II. Biophys. Chem. 33 (1989) 39
    • (1989) Biophys. Chem. , vol.33 , pp. 39
    • Burton, J.1    Wood, S.G.2    Pedyczak, A.3    Siemion, I.Z.4
  • 35
    • 0001203833 scopus 로고    scopus 로고
    • Influence of medium and long range interactions in protein folding
    • Gromiha M.M., and Selvaraj S. Influence of medium and long range interactions in protein folding. Prep. Biochem. Biotechnol. 29 4 (1999) 339
    • (1999) Prep. Biochem. Biotechnol. , vol.29 , Issue.4 , pp. 339
    • Gromiha, M.M.1    Selvaraj, S.2
  • 37
    • 0034056585 scopus 로고    scopus 로고
    • Class of potent hiv-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease
    • Munshi S., Chen Z., Yan Y., Li Y., Olsen D.B., Schock H.B., Galvin B.B., Dorsey B., and Kuo L.C. Class of potent hiv-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease. Acta Crystallogr. 56 (2000) 381
    • (2000) Acta Crystallogr. , vol.56 , pp. 381
    • Munshi, S.1    Chen, Z.2    Yan, Y.3    Li, Y.4    Olsen, D.B.5    Schock, H.B.6    Galvin, B.B.7    Dorsey, B.8    Kuo, L.C.9
  • 38
    • 0028846226 scopus 로고
    • Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme
    • Kim E.E., Baker C.T., Dwyer M.D., Murcko M.A., Rao B.G., Tung R.D., and Navia M.A. Crystal structure of HIV-1 protease in complex with VX-478, a potent and orally bioavailable inhibitor of the enzyme. J. Am. Chem. Soc. 117 (1995) 1181
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 1181
    • Kim, E.E.1    Baker, C.T.2    Dwyer, M.D.3    Murcko, M.A.4    Rao, B.G.5    Tung, R.D.6    Navia, M.A.7
  • 39
    • 0034860870 scopus 로고    scopus 로고
    • Large-scale ab initio quantum chemical calculations on biological systems
    • Friesner R.A., and Dunietz B.D. Large-scale ab initio quantum chemical calculations on biological systems. Acc. Chem. Res. 34 (2001) 351
    • (2001) Acc. Chem. Res. , vol.34 , pp. 351
    • Friesner, R.A.1    Dunietz, B.D.2
  • 40
    • 0036024488 scopus 로고    scopus 로고
    • Recent applications of density functional theory calculations to biomolecules
    • ban F., Kathryn Rankin N., James Gauld W., and Boyd R. Recent applications of density functional theory calculations to biomolecules. J. Theor. Chem. Acc. 108 (2002) 1
    • (2002) J. Theor. Chem. Acc. , vol.108 , pp. 1
    • ban, F.1    Kathryn Rankin, N.2    James Gauld, W.3    Boyd, R.4
  • 42
    • 0345491105 scopus 로고
    • Development of colle-solvetti correlational energy formula into a functional of electron density
    • Lee C., Yang W., and Parr R.G. Development of colle-solvetti correlational energy formula into a functional of electron density. Phys. Rev. B 37 (1988) 785
    • (1988) Phys. Rev. B , vol.37 , pp. 785
    • Lee, C.1    Yang, W.2    Parr, R.G.3
  • 44
    • 0000189651 scopus 로고
    • Density functional thermochemistry III
    • Becke A.D. Density functional thermochemistry III. J. Chem. Phys. 98 (1993) 5648
    • (1993) J. Chem. Phys. , vol.98 , pp. 5648
    • Becke, A.D.1
  • 45
    • 0038506965 scopus 로고    scopus 로고
    • Ab initio analysis of the conformational changes of the prolyl-proline model peptide
    • Hudaky I., and Perczel A. Ab initio analysis of the conformational changes of the prolyl-proline model peptide. J. Mol. Struct. (THEOCHEM) 630 (2003) 135
    • (2003) J. Mol. Struct. (THEOCHEM) , vol.630 , pp. 135
    • Hudaky, I.1    Perczel, A.2
  • 49
    • 0027066845 scopus 로고
    • Difference in amino acid distributions of 3(10) helices and alpha helices
    • Karpen M.E., De Haseth P.L., and Neet K.E. Difference in amino acid distributions of 3(10) helices and alpha helices. Protein Sci. 1 (1992) 1333
    • (1992) Protein Sci. , vol.1 , pp. 1333
    • Karpen, M.E.1    De Haseth, P.L.2    Neet, K.E.3
  • 50
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
    • Némethy G., Gibson K.D., Palmer K.A., Yoon C.N., Paterline G., Zagari A., Rumsey S., and Scheraga H.A. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 96 (1992) 6472
    • (1992) J. Phys. Chem. , vol.96 , pp. 6472
    • Némethy, G.1    Gibson, K.D.2    Palmer, K.A.3    Yoon, C.N.4    Paterline, G.5    Zagari, A.6    Rumsey, S.7    Scheraga, H.A.8
  • 51
    • 0024279235 scopus 로고
    • Analysis and prediction of the different types of beta-turn in proteins
    • Wilmot C.M., and Thornton J.M. Analysis and prediction of the different types of beta-turn in proteins. J. Mol. Biol. 203 (1988) 221
    • (1988) J. Mol. Biol. , vol.203 , pp. 221
    • Wilmot, C.M.1    Thornton, J.M.2
  • 53
    • 0017250408 scopus 로고
    • Infrared spectra and resonance interactions of amide-I and II vibration of alpha-helix
    • Chirgadze, and Nevskaya. Infrared spectra and resonance interactions of amide-I and II vibration of alpha-helix. Biopolymers 15 4 (1976) 637
    • (1976) Biopolymers , vol.15 , Issue.4 , pp. 637
    • Chirgadze1    Nevskaya2
  • 55
    • 1642533605 scopus 로고    scopus 로고
    • Molecular orbital analysis of the effect of d- and l-alanyl residues on the glycine chirality within the tripeptide N-Ac-Ala-Gly-Ala-NH-Me
    • Jack Liao C.C., Gregory Chass A., David Setiadi H., and Imre Csizmadia G. Molecular orbital analysis of the effect of d- and l-alanyl residues on the glycine chirality within the tripeptide N-Ac-Ala-Gly-Ala-NH-Me. J. Mol. Struct. (THEOCHEM) 666-667 (2003) 321
    • (2003) J. Mol. Struct. (THEOCHEM) , vol.666-667 , pp. 321
    • Jack Liao, C.C.1    Gregory Chass, A.2    David Setiadi, H.3    Imre Csizmadia, G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.