메뉴 건너뛰기




Volumn 14, Issue 10, 2006, Pages 1499-1510

Assessing Computational Amino Acid β-Turn Propensities with a Phage-Displayed Combinatorial Library and Directed Evolution

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

EID: 33749257494     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2006.08.006     Document Type: Article
Times cited : (26)

References (39)
  • 2
    • 0034635340 scopus 로고    scopus 로고
    • beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat
    • Bonvin A.M., and van Gunsteren W.F. beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat. J. Mol. Biol. 296 (2000) 255-268
    • (2000) J. Mol. Biol. , vol.296 , pp. 255-268
    • Bonvin, A.M.1    van Gunsteren, W.F.2
  • 3
    • 0028284549 scopus 로고
    • Linking an easily detectable phenotype to the folding of a common structural motif. Selection of rare turn mutations that prevent the folding of Rop
    • Castagnoli L., Vetriani C., and Cesareni G. Linking an easily detectable phenotype to the folding of a common structural motif. Selection of rare turn mutations that prevent the folding of Rop. J. Mol. Biol. 237 (1994) 378-387
    • (1994) J. Mol. Biol. , vol.237 , pp. 378-387
    • Castagnoli, L.1    Vetriani, C.2    Cesareni, G.3
  • 6
    • 0024278597 scopus 로고
    • Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn
    • Dyson H.J., Rance M., Houghten R.A., Lerner R.A., and Wright P.E. Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn. J. Mol. Biol. 201 (1988) 161-200
    • (1988) J. Mol. Biol. , vol.201 , pp. 161-200
    • Dyson, H.J.1    Rance, M.2    Houghten, R.A.3    Lerner, R.A.4    Wright, P.E.5
  • 7
    • 0000691365 scopus 로고
    • Chain reversals in model peptides: studies of cystine-containing cyclic peptide. 3. Conformational free energies of cyclization of tetrapeptides of sequence Ac-Cys-Pro-X-Cys-NHMe
    • Falcomer C., Meinwald Y., Choudhary I., Talluri S., Milburn P., Clady J., and Scheraga H. Chain reversals in model peptides: studies of cystine-containing cyclic peptide. 3. Conformational free energies of cyclization of tetrapeptides of sequence Ac-Cys-Pro-X-Cys-NHMe. J. Am. Chem. Soc. 114 (1992) 4036-4042
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 4036-4042
    • Falcomer, C.1    Meinwald, Y.2    Choudhary, I.3    Talluri, S.4    Milburn, P.5    Clady, J.6    Scheraga, H.7
  • 8
    • 0033533387 scopus 로고    scopus 로고
    • Core-directed protein design. II. Rescue of a multiply mutated and destabilized variant of ubiquitin
    • Finucane M.D., and Woolfson D.N. Core-directed protein design. II. Rescue of a multiply mutated and destabilized variant of ubiquitin. Biochemistry 38 (1999) 11613-11623
    • (1999) Biochemistry , vol.38 , pp. 11613-11623
    • Finucane, M.D.1    Woolfson, D.N.2
  • 9
    • 0033533503 scopus 로고    scopus 로고
    • Core-directed protein design. I. An experimental method for selecting stable proteins from combinatorial libraries
    • Finucane M.D., Tuna M., Lees J.H., and Woolfson D.N. Core-directed protein design. I. An experimental method for selecting stable proteins from combinatorial libraries. Biochemistry 38 (1999) 11604-11612
    • (1999) Biochemistry , vol.38 , pp. 11604-11612
    • Finucane, M.D.1    Tuna, M.2    Lees, J.H.3    Woolfson, D.N.4
  • 10
    • 13944275960 scopus 로고    scopus 로고
    • The Protein Coil Library: a structural database of nonhelix, nonstrand fragments derived from the PDB
    • Fitzkee N.C., Fleming P.J., and Rose G.D. The Protein Coil Library: a structural database of nonhelix, nonstrand fragments derived from the PDB. Proteins 58 (2005) 852-854
    • (2005) Proteins , vol.58 , pp. 852-854
    • Fitzkee, N.C.1    Fleming, P.J.2    Rose, G.D.3
  • 11
    • 0033536659 scopus 로고    scopus 로고
    • Dissecting the stability of a beta-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the beta-turn and beta-strand contributions to folding
    • Griffiths-Jones S.R., Maynard A.J., and Searle M.S. Dissecting the stability of a beta-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the beta-turn and beta-strand contributions to folding. J. Mol. Biol. 292 (1999) 1051-1069
    • (1999) J. Mol. Biol. , vol.292 , pp. 1051-1069
    • Griffiths-Jones, S.R.1    Maynard, A.J.2    Searle, M.S.3
  • 12
    • 0028566270 scopus 로고
    • A revised set of potentials for beta-turn formation in proteins
    • Hutchinson E.G., and Thornton J.M. A revised set of potentials for beta-turn formation in proteins. Protein Sci. 3 (1994) 2207-2216
    • (1994) Protein Sci. , vol.3 , pp. 2207-2216
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 13
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 14
    • 0031759422 scopus 로고    scopus 로고
    • Proteolytic selection for protein folding using filamentous bacteriophages
    • Kristensen P., and Winter G. Proteolytic selection for protein folding using filamentous bacteriophages. Fold. Des. 3 (1998) 321-328
    • (1998) Fold. Des. , vol.3 , pp. 321-328
    • Kristensen, P.1    Winter, G.2
  • 15
    • 3543101355 scopus 로고    scopus 로고
    • Protein backbone angle prediction with machine learning approaches
    • 10.1093/bioinformatics/bth136 Published online February 26, 2004
    • Kuang R., Leslie C.S., and Yang A.S. Protein backbone angle prediction with machine learning approaches. Bioinformatics 20 (2004) 1612-1621 10.1093/bioinformatics/bth136 Published online February 26, 2004
    • (2004) Bioinformatics , vol.20 , pp. 1612-1621
    • Kuang, R.1    Leslie, C.S.2    Yang, A.S.3
  • 16
    • 0030976150 scopus 로고    scopus 로고
    • Bacteriophage display and discovery of peptide leads for drug development
    • Lowman H.B. Bacteriophage display and discovery of peptide leads for drug development. Annu. Rev. Biophys. Biomol. Struct. 26 (1997) 401-424
    • (1997) Annu. Rev. Biophys. Biomol. Struct. , vol.26 , pp. 401-424
    • Lowman, H.B.1
  • 17
    • 0028176595 scopus 로고
    • Measurement of the beta-sheet-forming propensities of amino acids
    • Minor Jr. D.L., and Kim P.S. Measurement of the beta-sheet-forming propensities of amino acids. Nature 367 (1994) 660-663
    • (1994) Nature , vol.367 , pp. 660-663
    • Minor Jr., D.L.1    Kim, P.S.2
  • 18
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of beta-hairpin formation
    • Munoz V., Thompson P.A., Hofrichter J., and Eaton W.A. Folding dynamics and mechanism of beta-hairpin formation. Nature 390 (1997) 196-199
    • (1997) Nature , vol.390 , pp. 196-199
    • Munoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 19
    • 0034846826 scopus 로고    scopus 로고
    • Construction of high-complexity combinatorial phage display peptide libraries
    • Noren K.A., and Noren C.J. Construction of high-complexity combinatorial phage display peptide libraries. Methods 23 (2001) 169-178
    • (2001) Methods , vol.23 , pp. 169-178
    • Noren, K.A.1    Noren, C.J.2
  • 20
    • 26844466961 scopus 로고    scopus 로고
    • Hydrogen-bonded turns in proteins: the case for a recount
    • Panasik Jr. N., Fleming P.J., and Rose G.D. Hydrogen-bonded turns in proteins: the case for a recount. Protein Sci. 14 (2005) 2910-2914
    • (2005) Protein Sci. , vol.14 , pp. 2910-2914
    • Panasik Jr., N.1    Fleming, P.J.2    Rose, G.D.3
  • 21
    • 0033529908 scopus 로고    scopus 로고
    • Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G
    • Pande V.S., and Rokhsar D.S. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc. Natl. Acad. Sci. USA 96 (1999) 9062-9067
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9062-9067
    • Pande, V.S.1    Rokhsar, D.S.2
  • 22
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson J.S. 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
  • 23
    • 0036409329 scopus 로고    scopus 로고
    • Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries
    • Rodi D.J., Soares A.S., and Makowski L. Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries. J. Mol. Biol. 322 (2002) 1039-1052
    • (2002) J. Mol. Biol. , vol.322 , pp. 1039-1052
    • Rodi, D.J.1    Soares, A.S.2    Makowski, L.3
  • 25
    • 0025008168 scopus 로고
    • Sequence logos: a new way to display consensus sequences
    • Schneider T.D., and Stephens R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18 (1990) 6097-6100
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 26
    • 24144500637 scopus 로고    scopus 로고
    • Efficient construction of a large collection of phage-displayed combinatorial peptide libraries
    • Scholle M.D., Kehoe J.W., and Kay B.K. Efficient construction of a large collection of phage-displayed combinatorial peptide libraries. Comb. Chem. High Throughput Screen. 8 (2005) 545-551
    • (2005) Comb. Chem. High Throughput Screen. , vol.8 , pp. 545-551
    • Scholle, M.D.1    Kehoe, J.W.2    Kay, B.K.3
  • 27
    • 1942531291 scopus 로고    scopus 로고
    • Insights into stabilizing weak interactions in designed peptide beta-hairpins
    • Searle M.S. Insights into stabilizing weak interactions in designed peptide beta-hairpins. Biopolymers 76 (2004) 185-195
    • (2004) Biopolymers , vol.76 , pp. 185-195
    • Searle, M.S.1
  • 28
    • 4143070403 scopus 로고    scopus 로고
    • Design of beta-sheet systems for understanding the thermodynamics and kinetics of protein folding
    • Searle M.S., and Ciani B. Design of beta-sheet systems for understanding the thermodynamics and kinetics of protein folding. Curr. Opin. Struct. Biol. 14 (2004) 458-464
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 458-464
    • Searle, M.S.1    Ciani, B.2
  • 29
    • 0031729179 scopus 로고    scopus 로고
    • Selecting proteins with improved stability by a phage-based method
    • Sieber V., Pluckthun A., and Schmid F.X. Selecting proteins with improved stability by a phage-based method. Nat. Biotechnol. 16 (1998) 955-960
    • (1998) Nat. Biotechnol. , vol.16 , pp. 955-960
    • Sieber, V.1    Pluckthun, A.2    Schmid, F.X.3
  • 30
    • 23744501900 scopus 로고    scopus 로고
    • Engineering enhanced protein stability through beta-turn optimization: insights for the design of stable peptide beta-hairpin systems
    • Simpson E.R., Meldrum J.K., Bofill R., Crespo M.D., Holmes E., and Searle M.S. Engineering enhanced protein stability through beta-turn optimization: insights for the design of stable peptide beta-hairpin systems. Angew. Chem. Int. Ed. Engl. 44 (2005) 4939-4944
    • (2005) Angew. Chem. Int. Ed. Engl. , vol.44 , pp. 4939-4944
    • Simpson, E.R.1    Meldrum, J.K.2    Bofill, R.3    Crespo, M.D.4    Holmes, E.5    Searle, M.S.6
  • 31
    • 0021818675 scopus 로고
    • Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface
    • Smith G.P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228 (1985) 1315-1317
    • (1985) Science , vol.228 , pp. 1315-1317
    • Smith, G.P.1
  • 32
    • 0000825481 scopus 로고
    • A statistical method for evaluation systematic relationships
    • Sokal R.R., and Michener C.D. A statistical method for evaluation systematic relationships. Univ. Kans. Sci. Bull. 28 (1958) 1409-1438
    • (1958) Univ. Kans. Sci. Bull. , vol.28 , pp. 1409-1438
    • Sokal, R.R.1    Michener, C.D.2
  • 33
    • 0028091659 scopus 로고
    • Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks
    • Tatusov R.L., Altschul S.F., and Koonin E.V. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl. Acad. Sci. USA 91 (1994) 12091-12095
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 12091-12095
    • Tatusov, R.L.1    Altschul, S.F.2    Koonin, E.V.3
  • 34
    • 0029918575 scopus 로고    scopus 로고
    • A strategy to locate cysteine residues in proteins by specific chemical cleavage followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
    • Wu J., Gage D.A., and Watson J.T. A strategy to locate cysteine residues in proteins by specific chemical cleavage followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal. Biochem. 235 (1996) 161-174
    • (1996) Anal. Biochem. , vol.235 , pp. 161-174
    • Wu, J.1    Gage, D.A.2    Watson, J.T.3
  • 35
    • 0036948143 scopus 로고    scopus 로고
    • Structure-dependent sequence alignment for remotely related proteins
    • Yang A.S. Structure-dependent sequence alignment for remotely related proteins. Bioinformatics 18 (2002) 1658-1665
    • (2002) Bioinformatics , vol.18 , pp. 1658-1665
    • Yang, A.S.1
  • 36
    • 0034682851 scopus 로고    scopus 로고
    • An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments
    • Yang A.S., and Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. J. Mol. Biol. 301 (2000) 691-712
    • (2000) J. Mol. Biol. , vol.301 , pp. 691-712
    • Yang, A.S.1    Honig, B.2
  • 37
    • 0036952917 scopus 로고    scopus 로고
    • Local structure-based sequence profile database for local and global protein structure predictions
    • Yang A.S., and Wang L. Local structure-based sequence profile database for local and global protein structure predictions. Bioinformatics 18 (2002) 1650-1657
    • (2002) Bioinformatics , vol.18 , pp. 1650-1657
    • Yang, A.S.1    Wang, L.2
  • 38
    • 0037818341 scopus 로고    scopus 로고
    • Local structure prediction with local structure-based sequence profiles
    • Yang A.S., and Wang L. Local structure prediction with local structure-based sequence profiles. Bioinformatics 19 (2003) 1267-1274
    • (2003) Bioinformatics , vol.19 , pp. 1267-1274
    • Yang, A.S.1    Wang, L.2
  • 39
    • 0030596522 scopus 로고    scopus 로고
    • Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding
    • Yang A.S., Hitz B., and Honig B. Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding. J. Mol. Biol. 259 (1996) 873-882
    • (1996) J. Mol. Biol. , vol.259 , pp. 873-882
    • Yang, A.S.1    Hitz, B.2    Honig, B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.