메뉴 건너뛰기




Volumn 373, Issue 1, 2007, Pages 211-218

Increasing Protein Conformational Stability by Optimizing β-Turn Sequence

Author keywords

glycine; proline; protein conformational stability; turn

Indexed keywords

GLYCINE; PROLINE; PROTEIN DERIVATIVE;

EID: 34548567337     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.07.061     Document Type: Article
Times cited : (128)

References (55)
  • 1
    • 0025420076 scopus 로고
    • Measuring and increasing protein stability
    • Pace C.N. Measuring and increasing protein stability. Trends Biotechnol. 8 (1990) 93-98
    • (1990) Trends Biotechnol. , vol.8 , pp. 93-98
    • Pace, C.N.1
  • 2
    • 0030863786 scopus 로고    scopus 로고
    • Stabilization of protein
    • Imoto T. Stabilization of protein. Cell Mol. Life Sci. 53 (1997) 215-223
    • (1997) Cell Mol. Life Sci. , vol.53 , pp. 215-223
    • Imoto, T.1
  • 3
    • 0026654252 scopus 로고
    • Mutational studies of protein structures and their stabilities
    • Shortle D. Mutational studies of protein structures and their stabilities. Quart. Rev. Biophys. 25 (1992) 205-250
    • (1992) Quart. Rev. Biophys. , vol.25 , pp. 205-250
    • Shortle, D.1
  • 4
    • 0028968018 scopus 로고
    • Studies on protein stability with T4 lysozyme
    • Matthews B.W. Studies on protein stability with T4 lysozyme. Advan. Protein Chem. 46 (1995) 249-278
    • (1995) Advan. Protein Chem. , vol.46 , pp. 249-278
    • Matthews, B.W.1
  • 5
    • 0028918594 scopus 로고
    • Engineering the stability and function of gene V protein
    • Terwilliger T.C. Engineering the stability and function of gene V protein. Advan. Protein Chem. 46 (1995) 177-215
    • (1995) Advan. Protein Chem. , vol.46 , pp. 177-215
    • Terwilliger, T.C.1
  • 6
    • 0026553768 scopus 로고
    • The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
    • Serrano L., Kellis Jr. J.T., Cann P., Matouschek A., and Fersht A.R. The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J. Mol. Biol. 224 (1992) 783-804
    • (1992) J. Mol. Biol. , vol.224 , pp. 783-804
    • Serrano, L.1    Kellis Jr., J.T.2    Cann, P.3    Matouschek, A.4    Fersht, A.R.5
  • 7
    • 0030220763 scopus 로고    scopus 로고
    • Engineering enzymes for stability
    • Shaw A., and Bott R. Engineering enzymes for stability. Curr. Opin. Struct. Biol. 6 (1996) 546-550
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 546-550
    • Shaw, A.1    Bott, R.2
  • 8
    • 0030059689 scopus 로고    scopus 로고
    • Forces contributing to the conformational stability of proteins
    • Pace C.N., Shirley B.A., McNutt M., and Gajiwala K. Forces contributing to the conformational stability of proteins. FASEB J. 10 (1996) 75-83
    • (1996) FASEB J. , vol.10 , pp. 75-83
    • Pace, C.N.1    Shirley, B.A.2    McNutt, M.3    Gajiwala, K.4
  • 9
    • 0025019350 scopus 로고
    • Conformational stability of globular proteins
    • Pace C.N. Conformational stability of globular proteins. Trends Biochem. Sci. 15 (1990) 14-17
    • (1990) Trends Biochem. Sci. , vol.15 , pp. 14-17
    • Pace, C.N.1
  • 10
    • 0035424955 scopus 로고    scopus 로고
    • Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution
    • Lehmann M., and Wyss M. Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution. Curr. Opin. Biotechnol. 12 (2001) 371-35
    • (2001) Curr. Opin. Biotechnol. , vol.12 , pp. 371-335
    • Lehmann, M.1    Wyss, M.2
  • 11
    • 0021107512 scopus 로고
    • Interior turns in globular proteins
    • Rose G.D., Young W.B., and Gierasch L.M. Interior turns in globular proteins. Nature 304 (1983) 654-657
    • (1983) Nature , vol.304 , pp. 654-657
    • Rose, G.D.1    Young, W.B.2    Gierasch, L.M.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
    • 0033752859 scopus 로고    scopus 로고
    • Beta-and gamma-turns in proteins revisited: a new set of amino acid turn-type dependent positional preferences and potentials
    • Guruprasad K., and Rajkumar S. Beta-and gamma-turns in proteins revisited: a new set of amino acid turn-type dependent positional preferences and potentials. J. Biosci. 25 (2000) 143-156
    • (2000) J. Biosci. , vol.25 , pp. 143-156
    • Guruprasad, K.1    Rajkumar, S.2
  • 14
    • 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
  • 16
    • 0034713833 scopus 로고    scopus 로고
    • Role of amino acid residues at turns in the conformational stability and folding of human lysozyme
    • Takano K., Yamagata Y., and Yutani K. Role of amino acid residues at turns in the conformational stability and folding of human lysozyme. Biochemistry 39 (2000) 8655-8665
    • (2000) Biochemistry , vol.39 , pp. 8655-8665
    • Takano, K.1    Yamagata, Y.2    Yutani, K.3
  • 17
    • 0030062459 scopus 로고    scopus 로고
    • Amino-acid substitutions in a surface turn modulate protein stability
    • Predki P.F., Agrawal V., Brunger A.T., and Regan L. Amino-acid substitutions in a surface turn modulate protein stability. Nature Struct. Biol. 3 (1996) 54-58
    • (1996) Nature Struct. Biol. , vol.3 , pp. 54-58
    • Predki, P.F.1    Agrawal, V.2    Brunger, A.T.3    Regan, L.4
  • 18
    • 0031022599 scopus 로고    scopus 로고
    • Beta-turn propensities as paradigms for the analysis of structural motifs to engineer protein stability
    • Ohage E.C., Graml W., Walter M.M., Steinbacher S., and Steipe B. Beta-turn propensities as paradigms for the analysis of structural motifs to engineer protein stability. Protein Sci. 6 (1997) 233-241
    • (1997) Protein Sci. , vol.6 , pp. 233-241
    • Ohage, E.C.1    Graml, W.2    Walter, M.M.3    Steinbacher, S.4    Steipe, B.5
  • 19
    • 0029926618 scopus 로고    scopus 로고
    • In vitro evolution of thermodynamically stable turns
    • Zhou H.X., Hoess R.H., and DeGrado W.F. In vitro evolution of thermodynamically stable turns. Nature Struct. Biol. 3 (1996) 446-451
    • (1996) Nature Struct. Biol. , vol.3 , pp. 446-451
    • Zhou, H.X.1    Hoess, R.H.2    DeGrado, W.F.3
  • 20
    • 0028111743 scopus 로고
    • Sequence statistics reliably predict stabilizing mutations in a protein domain
    • Steipe B., Schiller B., Pluckthun A., and Steinbacher S. Sequence statistics reliably predict stabilizing mutations in a protein domain. J. Mol. Biol. 240 (1994) 188-192
    • (1994) J. Mol. Biol. , vol.240 , pp. 188-192
    • Steipe, B.1    Schiller, B.2    Pluckthun, A.3    Steinbacher, S.4
  • 21
    • 0026526263 scopus 로고
    • Thermostabilization of Escherichia coli ribonuclease HI by replacing left-handed helical Lys95 with Gly or Asn
    • Kimura S., Kanaya S., and Nakamura H. Thermostabilization of Escherichia coli ribonuclease HI by replacing left-handed helical Lys95 with Gly or Asn. J. Biol. Chem. 267 (1992) 22014-22017
    • (1992) J. Biol. Chem. , vol.267 , pp. 22014-22017
    • Kimura, S.1    Kanaya, S.2    Nakamura, H.3
  • 22
    • 0037427477 scopus 로고    scopus 로고
    • Identification of a key structural element for protein folding within beta-hairpin turns
    • Kim J., Brych S.R., Lee J., Logan T.M., and Blaber M. Identification of a key structural element for protein folding within beta-hairpin turns. J. Mol. Biol. 328 (2003) 951-961
    • (2003) J. Mol. Biol. , vol.328 , pp. 951-961
    • Kim, J.1    Brych, S.R.2    Lee, J.3    Logan, T.M.4    Blaber, M.5
  • 23
    • 0034495135 scopus 로고    scopus 로고
    • Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II′ region of the Ramachandran plot
    • Vega M.C., Martinez J.C., and Serrano L. Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II′ region of the Ramachandran plot. Protein Sci. 9 (2000) 2322-2328
    • (2000) Protein Sci. , vol.9 , pp. 2322-2328
    • Vega, M.C.1    Martinez, J.C.2    Serrano, L.3
  • 24
    • 0030039296 scopus 로고    scopus 로고
    • PROMOTIF-a program to identify and analyze structural motifs in proteins
    • Hutchinson E.G., and Thornton J.M. PROMOTIF-a program to identify and analyze structural motifs in proteins. Protein Sci. 5 (1996) 212-220
    • (1996) Protein Sci. , vol.5 , pp. 212-220
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 27
    • 0032542062 scopus 로고    scopus 로고
    • Contribution of a conserved asparagine to the conformational stability of ribonucleases Sa, Ba, and T1
    • Hebert E.J., Giletto A., Sevcik J., Urbanikova L., Wilson K.S., Dauter Z., and Pace C.N. Contribution of a conserved asparagine to the conformational stability of ribonucleases Sa, Ba, and T1. Biochemistry 37 (1998) 16192-16200
    • (1998) Biochemistry , vol.37 , pp. 16192-16200
    • Hebert, E.J.1    Giletto, A.2    Sevcik, J.3    Urbanikova, L.4    Wilson, K.S.5    Dauter, Z.6    Pace, C.N.7
  • 28
    • 0033852796 scopus 로고    scopus 로고
    • Charge-charge interactions influence the denatured state ensemble and contribute to protein stability
    • Pace C.N., Alston R.W., and Shaw K.L. Charge-charge interactions influence the denatured state ensemble and contribute to protein stability. Protein Sci. 9 (2000) 1395-1398
    • (2000) Protein Sci. , vol.9 , pp. 1395-1398
    • Pace, C.N.1    Alston, R.W.2    Shaw, K.L.3
  • 29
    • 0037138712 scopus 로고    scopus 로고
    • Probing the structural determinants of type II′ beta-turn formation in peptides and proteins
    • Gibbs A.C., Bjorndahl T.C., Hodges R.S., and Wishart D.S. Probing the structural determinants of type II′ beta-turn formation in peptides and proteins. J. Am. Chem. Soc. 124 (2002) 1203-1213
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 1203-1213
    • Gibbs, A.C.1    Bjorndahl, T.C.2    Hodges, R.S.3    Wishart, D.S.4
  • 30
    • 13144249171 scopus 로고    scopus 로고
    • Conformational stability and thermodynamics of folding of ribonucleases Sa, Sa2 and Sa3
    • Pace C.N., Hebert E.J., Shaw K.L., Schell D., Both V., Krajcikova D., et al. Conformational stability and thermodynamics of folding of ribonucleases Sa, Sa2 and Sa3. J. Mol. Biol. 279 (1998) 271-286
    • (1998) J. Mol. Biol. , vol.279 , pp. 271-286
    • Pace, C.N.1    Hebert, E.J.2    Shaw, K.L.3    Schell, D.4    Both, V.5    Krajcikova, D.6
  • 34
    • 0035009229 scopus 로고    scopus 로고
    • The effect of net charge on the solubility, activity, and stability of ribonuclease Sa
    • Shaw K.L., Grimsley G.R., Yakovlev G.I., Makarov A.A., and Pace C.N. The effect of net charge on the solubility, activity, and stability of ribonuclease Sa. Protein Sci. 10 (2001) 1206-1215
    • (2001) Protein Sci. , vol.10 , pp. 1206-1215
    • Shaw, K.L.1    Grimsley, G.R.2    Yakovlev, G.I.3    Makarov, A.A.4    Pace, C.N.5
  • 36
    • 0035895356 scopus 로고    scopus 로고
    • Polar group burial contributes more to protein stability than nonpolar group burial
    • Pace C.N. Polar group burial contributes more to protein stability than nonpolar group burial. Biochemistry 40 (2001) 310-313
    • (2001) Biochemistry , vol.40 , pp. 310-313
    • Pace, C.N.1
  • 37
    • 0041856175 scopus 로고    scopus 로고
    • The contribution of polar group burial to protein stability is strongly context-dependent
    • Takano K., Scholtz J.M., Sacchettini J.C., and Pace C. N. The contribution of polar group burial to protein stability is strongly context-dependent. J. Biol. Chem. 278 (2003) 31790-31795
    • (2003) J. Biol. Chem. , vol.278 , pp. 31790-31795
    • Takano, K.1    Scholtz, J.M.2    Sacchettini, J.C.3    Pace, C. N.4
  • 38
    • 22244458003 scopus 로고    scopus 로고
    • Charge-charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa
    • Trefethen J.M., Pace C.N., Scholtz J.M., and Brems D. N. Charge-charge interactions in the denatured state influence the folding kinetics of ribonuclease Sa. Protein Sci. 14 (2005) 1934-1938
    • (2005) Protein Sci. , vol.14 , pp. 1934-1938
    • Trefethen, J.M.1    Pace, C.N.2    Scholtz, J.M.3    Brems, D. N.4
  • 39
    • 33846374339 scopus 로고    scopus 로고
    • Amino acid contribution to protein solubility: Asp, Glu, and Ser contribute more favorably than the other hydrophilic amino acids in RNase Sa
    • Trevino S.R., Scholtz J.M., and Pace C.N. Amino acid contribution to protein solubility: Asp, Glu, and Ser contribute more favorably than the other hydrophilic amino acids in RNase Sa. J. Mol. Biol. 366 (2007) 449-460
    • (2007) J. Mol. Biol. , vol.366 , pp. 449-460
    • Trevino, S.R.1    Scholtz, J.M.2    Pace, C.N.3
  • 40
    • 0023430560 scopus 로고
    • Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding
    • Matthews B.W., Nicholson H., and Becktel W.J. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc. Natl Acad. Sci. USA 84 (1987) 6663-6667
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 6663-6667
    • Matthews, B.W.1    Nicholson, H.2    Becktel, W.J.3
  • 41
    • 0032516409 scopus 로고    scopus 로고
    • Protein thermostabilization by proline substitutions
    • Watanabe K., and Suzuki Y. Protein thermostabilization by proline substitutions. J. Mol. Catal. B Enz. 4 (1998) 167-180
    • (1998) J. Mol. Catal. B Enz. , vol.4 , pp. 167-180
    • Watanabe, K.1    Suzuki, Y.2
  • 42
    • 0028130117 scopus 로고
    • Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule
    • Watanabe K., Masuda T., Ohashi H., Mihara H., and Suzuki Y. Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule. Eur. J. Biochem. 226 (1994) 277-283
    • (1994) Eur. J. Biochem. , vol.226 , pp. 277-283
    • Watanabe, K.1    Masuda, T.2    Ohashi, H.3    Mihara, H.4    Suzuki, Y.5
  • 43
    • 33745698181 scopus 로고    scopus 로고
    • Generation and analysis of proline mutants in protein G
    • Choi E.J., and Mayo S.L. Generation and analysis of proline mutants in protein G. Protein Eng. Des. Sel. 19 (2006) 285-289
    • (2006) Protein Eng. Des. Sel. , vol.19 , pp. 285-289
    • Choi, E.J.1    Mayo, S.L.2
  • 45
    • 0035889693 scopus 로고    scopus 로고
    • Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein
    • Takano K., Yamagata Y., and Yutani K. Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein. Proteins: Struct. Funct. Genet. 45 (2001) 274-280
    • (2001) Proteins: Struct. Funct. Genet. , vol.45 , pp. 274-280
    • Takano, K.1    Yamagata, Y.2    Yutani, K.3
  • 46
    • 0034530687 scopus 로고    scopus 로고
    • Relationship between local structure and stability in hen egg white lysozyme mutant with alanine substituted for glycine
    • Masumoto K., Ueda T., Motoshima H., and Imoto T. Relationship between local structure and stability in hen egg white lysozyme mutant with alanine substituted for glycine. Protein Eng. 13 (2000) 691-695
    • (2000) Protein Eng. , vol.13 , pp. 691-695
    • Masumoto, K.1    Ueda, T.2    Motoshima, H.3    Imoto, T.4
  • 47
    • 0028014680 scopus 로고
    • Evidence for strained interactions between side-chains and the polypeptide backbone
    • Stites W.E., Meeker A.K., and Shortle D. Evidence for strained interactions between side-chains and the polypeptide backbone. J. Mol. Biol. 235 (1994) 27-32
    • (1994) J. Mol. Biol. , vol.235 , pp. 27-32
    • Stites, W.E.1    Meeker, A.K.2    Shortle, D.3
  • 48
    • 0024455131 scopus 로고
    • Contributions of left-handed helical residues to the structure and stability of bacteriophage T4 lysozyme
    • Nicholson H., Soderlind E., Tronrud D.E., and Matthews B.W. Contributions of left-handed helical residues to the structure and stability of bacteriophage T4 lysozyme. J. Mol. Biol. 210 (1989) 181-193
    • (1989) J. Mol. Biol. , vol.210 , pp. 181-193
    • Nicholson, H.1    Soderlind, E.2    Tronrud, D.E.3    Matthews, B.W.4
  • 49
    • 0026099553 scopus 로고
    • Role of conserved proline residues in stabilizing tryptophan synthase alpha subunit: analysis by mutants with alanine or glycine
    • Yutani K., Hayashi S., Sugisaki Y., and Ogasahara K. Role of conserved proline residues in stabilizing tryptophan synthase alpha subunit: analysis by mutants with alanine or glycine. Proteins: Struct. Funct. Genet. 9 (1991) 90-98
    • (1991) Proteins: Struct. Funct. Genet. , vol.9 , pp. 90-98
    • Yutani, K.1    Hayashi, S.2    Sugisaki, Y.3    Ogasahara, K.4
  • 50
    • 0023668221 scopus 로고
    • Temperature-sensitive mutations of bacteriophage T4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein
    • Alber T., Sun D.P., Nye J.A., Muchmore D.C., and Matthews B.W. Temperature-sensitive mutations of bacteriophage T4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein. Biochemistry 26 (1987) 3754-3758
    • (1987) Biochemistry , vol.26 , pp. 3754-3758
    • Alber, T.1    Sun, D.P.2    Nye, J.A.3    Muchmore, D.C.4    Matthews, B.W.5
  • 51
    • 0027255479 scopus 로고
    • Structural and genetic analysis of protein stability
    • Matthews B.W. Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 62 (1993) 139-160
    • (1993) Annu. Rev. Biochem. , vol.62 , pp. 139-160
    • Matthews, B.W.1
  • 52
    • 0032900496 scopus 로고    scopus 로고
    • Prediction of the location and type of beta-turns in proteins using neural networks
    • Shepherd A.J., Gorse D., and Thornton J.M. Prediction of the location and type of beta-turns in proteins using neural networks. Protein Sci. 8 (1999) 1045-1055
    • (1999) Protein Sci. , vol.8 , pp. 1045-1055
    • Shepherd, A.J.1    Gorse, D.2    Thornton, J.M.3
  • 54
    • 0002846347 scopus 로고    scopus 로고
    • Measuring the conformational stability of a protein
    • Creighton T.E. (Ed), IRL Press, Oxford
    • Pace C.N., and Scholtz J.M. Measuring the conformational stability of a protein. In: Creighton T.E. (Ed). Protein Structure: A Practical Approach (1997), IRL Press, Oxford 299-321
    • (1997) Protein Structure: A Practical Approach , pp. 299-321
    • Pace, C.N.1    Scholtz, J.M.2
  • 55
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling
    • Guex N., and Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18 (1997) 2714-2723
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.