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Volumn 159, Issue 3, 2012, Pages 135-144

Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio

Author keywords

Citrate synthase; Constraint network analysis; Flexibility; Protein engineering; Rigidity theory; Thermostability

Indexed keywords

CITRATE SYNTHASE; CONSTRAINT NETWORKS; FLEXIBILITY; PROTEIN ENGINEERING; THERMOSTABILITY;

EID: 84860835198     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2012.01.027     Document Type: Article
Times cited : (41)

References (70)
  • 1
    • 33646799407 scopus 로고    scopus 로고
    • Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory
    • Ahmed A., Gohlke H. Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory. Proteins 2006, 63:1038-1051.
    • (2006) Proteins , vol.63 , pp. 1038-1051
    • Ahmed, A.1    Gohlke, H.2
  • 2
    • 0003156161 scopus 로고
    • Entropic analysis of random morphologies
    • Andraud C., Beghdadi A., Lafait J. Entropic analysis of random morphologies. Physica A 1994, 207:208-212.
    • (1994) Physica A , vol.207 , pp. 208-212
    • Andraud, C.1    Beghdadi, A.2    Lafait, J.3
  • 6
    • 34247215529 scopus 로고    scopus 로고
    • Discovery of a thermophilic protein complex stabilized by topologically interlinked chains
    • Boutz D.R., Cascio D., Whitelegge J., Perry L.J., Yeates T.O. Discovery of a thermophilic protein complex stabilized by topologically interlinked chains. J. Mol. Biol. 2007, 368:1332-1344.
    • (2007) J. Mol. Biol. , vol.368 , pp. 1332-1344
    • Boutz, D.R.1    Cascio, D.2    Whitelegge, J.3    Perry, L.J.4    Yeates, T.O.5
  • 7
    • 46149125316 scopus 로고    scopus 로고
    • Double-sigmoid model for fitting fatigue profiles in mouse fast- and slow-twitch muscle
    • Cairns S.P., Robinson D.M., Loiselle D.S. Double-sigmoid model for fitting fatigue profiles in mouse fast- and slow-twitch muscle. Exp. Physiol. 2008, 93:851-862.
    • (2008) Exp. Physiol. , vol.93 , pp. 851-862
    • Cairns, S.P.1    Robinson, D.M.2    Loiselle, D.S.3
  • 12
    • 0343742614 scopus 로고    scopus 로고
    • Automated design of the surface positions of protein helices
    • Dahiyat B.I., Gordon D.B., Mayo S.L. Automated design of the surface positions of protein helices. Protein Sci. 1997, 6:1333-1337.
    • (1997) Protein Sci. , vol.6 , pp. 1333-1337
    • Dahiyat, B.I.1    Gordon, D.B.2    Mayo, S.L.3
  • 13
    • 2442612037 scopus 로고    scopus 로고
    • Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling
    • Daidone I., Roccatano D., Hayward S. Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling. J. Mol. Biol. 2004, 339:515-525.
    • (2004) J. Mol. Biol. , vol.339 , pp. 515-525
    • Daidone, I.1    Roccatano, D.2    Hayward, S.3
  • 14
    • 33846823909 scopus 로고
    • Particle mesh Ewald: an N.log (N) method for Ewald sums in large systems
    • Darden T., York D., Pedersen L. Particle mesh Ewald: an N.log (N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98:10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 15
    • 0014963118 scopus 로고
    • A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile
    • Darland G., Brock T.D., Samsonoff W., Conti S.F. A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science 1970, 170:1416-1418.
    • (1970) Science , vol.170 , pp. 1416-1418
    • Darland, G.1    Brock, T.D.2    Samsonoff, W.3    Conti, S.F.4
  • 17
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • Dill K.A. Dominant forces in protein folding. Biochemistry 1990, 29:7133-7155.
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 20
    • 44849090619 scopus 로고    scopus 로고
    • Analysing the flexibility of RNA structures by constraint counting
    • Fulle S., Gohlke H. Analysing the flexibility of RNA structures by constraint counting. Biophys. J. 2008, 94:4202-4219.
    • (2008) Biophys. J. , vol.94 , pp. 4202-4219
    • Fulle, S.1    Gohlke, H.2
  • 21
    • 70349299861 scopus 로고    scopus 로고
    • Constraint counting on RNA structures: linking flexibility and function
    • Fulle S., Gohlke H. Constraint counting on RNA structures: linking flexibility and function. Methods 2009, 49:181-188.
    • (2009) Methods , vol.49 , pp. 181-188
    • Fulle, S.1    Gohlke, H.2
  • 22
    • 61649098586 scopus 로고    scopus 로고
    • Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding
    • Fulle S., Gohlke H. Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding. J. Mol. Biol. 2009, 387:502-517.
    • (2009) J. Mol. Biol. , vol.387 , pp. 502-517
    • Fulle, S.1    Gohlke, H.2
  • 23
    • 3042806330 scopus 로고    scopus 로고
    • Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach
    • Gohlke H., Kuhn L.A., Case D.A. Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach. Proteins 2004, 56:322-337.
    • (2004) Proteins , vol.56 , pp. 322-337
    • Gohlke, H.1    Kuhn, L.A.2    Case, D.A.3
  • 24
    • 33748448490 scopus 로고    scopus 로고
    • A natural coarse graining for simulating large biomolecular motion
    • Gohlke H., Thorpe M.F. A natural coarse graining for simulating large biomolecular motion. Biophys. J. 2006, 91:2115-2120.
    • (2006) Biophys. J. , vol.91 , pp. 2115-2120
    • Gohlke, H.1    Thorpe, M.F.2
  • 25
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • Greene L.H., Higman V.A. Uncovering network systems within protein structures. J. Mol. Biol. 2003, 334:781-791.
    • (2003) J. Mol. Biol. , vol.334 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 26
    • 0032715527 scopus 로고    scopus 로고
    • Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins
    • Gromiha M.M., Oobatake M., Sarai A. Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys. Chem. 1999, 82:51-67.
    • (1999) Biophys. Chem. , vol.82 , pp. 51-67
    • Gromiha, M.M.1    Oobatake, M.2    Sarai, A.3
  • 27
    • 0037411739 scopus 로고    scopus 로고
    • Developments in industrially important thermostable enzymes: a review
    • Haki G.D., Rakshit S.K. Developments in industrially important thermostable enzymes: a review. Bioresour. Technol. 2003, 89:17-34.
    • (2003) Bioresour. Technol. , vol.89 , pp. 17-34
    • Haki, G.D.1    Rakshit, S.K.2
  • 28
    • 68749107059 scopus 로고    scopus 로고
    • Protein sectors: evolutionary units of three-dimensional structure
    • Halabi N., Rivoire O., Leibler S., Ranganathan R. Protein sectors: evolutionary units of three-dimensional structure. Cell 2009, 138:774-786.
    • (2009) Cell , vol.138 , pp. 774-786
    • Halabi, N.1    Rivoire, O.2    Leibler, S.3    Ranganathan, R.4
  • 29
    • 9144263145 scopus 로고    scopus 로고
    • Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus
    • Hespenheide B.M., Jacobs D.J., Thorpe M.F. Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus. J. Phys.: Condens. Matter 2004, 16:S5055-S5064.
    • (2004) J. Phys.: Condens. Matter , vol.16
    • Hespenheide, B.M.1    Jacobs, D.J.2    Thorpe, M.F.3
  • 30
    • 0036888379 scopus 로고    scopus 로고
    • Identifying protein folding cores from the evolution of flexible regions during unfolding
    • Hespenheide B.M., Rader A.J., Thorpe M.F., Kuhn L.A. Identifying protein folding cores from the evolution of flexible regions during unfolding. J. Mol. Graph. Model. 2002, 21:195-207.
    • (2002) J. Mol. Graph. Model. , vol.21 , pp. 195-207
    • Hespenheide, B.M.1    Rader, A.J.2    Thorpe, M.F.3    Kuhn, L.A.4
  • 32
    • 0032493601 scopus 로고    scopus 로고
    • Generic rigidity in three-dimensional bond-bending networks
    • Jacobs D.J. Generic rigidity in three-dimensional bond-bending networks. J. Phys. A: Math. Gen. 1998, 31:6653-6668.
    • (1998) J. Phys. A: Math. Gen. , vol.31 , pp. 6653-6668
    • Jacobs, D.J.1
  • 33
    • 21244483843 scopus 로고    scopus 로고
    • Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity
    • Jacobs D.J., Dallakyan S. Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity. Biophys. J. 2005, 88:903-915.
    • (2005) Biophys. J. , vol.88 , pp. 903-915
    • Jacobs, D.J.1    Dallakyan, S.2
  • 34
    • 1542285840 scopus 로고    scopus 로고
    • Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems
    • Jacobs D.J., Dallakyan S., Wood G.G., Heckathorne A. Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems. Phys. Rev. E: Stat. Nonlin. Soft Matter Phys. 2003, 68:061109.
    • (2003) Phys. Rev. E: Stat. Nonlin. Soft Matter Phys. , vol.68 , pp. 061109
    • Jacobs, D.J.1    Dallakyan, S.2    Wood, G.G.3    Heckathorne, A.4
  • 35
    • 0031281604 scopus 로고    scopus 로고
    • An algorithm for two-dimensional rigidity percolation: the pebble game
    • Jacobs D.J., Hendrickson B. An algorithm for two-dimensional rigidity percolation: the pebble game. J. Comput. Phys. 1997, 137:346-365.
    • (1997) J. Comput. Phys. , vol.137 , pp. 346-365
    • Jacobs, D.J.1    Hendrickson, B.2
  • 36
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • Jacobs D.J., Rader A.J., Kuhn L.A., Thorpe M.F. Protein flexibility predictions using graph theory. Proteins 2001, 44:150-165.
    • (2001) Proteins , vol.44 , pp. 150-165
    • Jacobs, D.J.1    Rader, A.J.2    Kuhn, L.A.3    Thorpe, M.F.4
  • 37
    • 0000785338 scopus 로고
    • Generic rigidity percolation: the pebble game
    • Jacobs D.J., Thorpe M.F. Generic rigidity percolation: the pebble game. Phys. Rev. Lett. 1995, 75:4051-4054.
    • (1995) Phys. Rev. Lett. , vol.75 , pp. 4051-4054
    • Jacobs, D.J.1    Thorpe, M.F.2
  • 38
    • 0032438190 scopus 로고    scopus 로고
    • The stability of proteins in extreme environments
    • Jaenicke R., Böhm G. The stability of proteins in extreme environments. Curr. Opin. Struct. Biol. 1998, 8:738-748.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 738-748
    • Jaenicke, R.1    Böhm, G.2
  • 40
    • 0034495733 scopus 로고    scopus 로고
    • Aromatic clusters: a determinant of thermal stability of thermophilic proteins
    • Kannan N., Vishveshwara S. Aromatic clusters: a determinant of thermal stability of thermophilic proteins. Protein Eng. 2000, 13:753-761.
    • (2000) Protein Eng. , vol.13 , pp. 753-761
    • Kannan, N.1    Vishveshwara, S.2
  • 41
    • 84860835970 scopus 로고    scopus 로고
    • Analyzing protein rigidity for understanding and improving thermal adaptation
    • CRC Press Taylor & Francis Group, Boca Raton, S. Sen, L. Nilsson (Eds.)
    • Klein D.L., Radestock S., Gohlke H. Analyzing protein rigidity for understanding and improving thermal adaptation. Thermophilic Proteins: Structural Stability and Design Strategies 2011, 47-67. CRC Press Taylor & Francis Group, Boca Raton. S. Sen, L. Nilsson (Eds.).
    • (2011) Thermophilic Proteins: Structural Stability and Design Strategies , pp. 47-67
    • Klein, D.L.1    Radestock, S.2    Gohlke, H.3
  • 43
    • 0035424955 scopus 로고    scopus 로고
    • Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution
    • Lehmann M., Wyss M. Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution. Curr. Opin. Biotechnol. 2001, 12:371-375.
    • (2001) Curr. Opin. Biotechnol. , vol.12 , pp. 371-375
    • Lehmann, M.1    Wyss, M.2
  • 44
    • 34250799148 scopus 로고    scopus 로고
    • Protein engineering: opportunities and challenges
    • Leisola M., Turunen O. Protein engineering: opportunities and challenges. Appl. Microbiol. Biotechnol. 2007, 75:1225-1232.
    • (2007) Appl. Microbiol. Biotechnol. , vol.75 , pp. 1225-1232
    • Leisola, M.1    Turunen, O.2
  • 45
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless S.W., Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 1999, 286:295-299.
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 47
    • 0015955554 scopus 로고
    • Description of Thermus thermophilus (Yoshida and Oshima) comb. nov., a nonsporulating thermophilic bacterium from a Japanese thermal spa
    • Oshima T., Imahori K. Description of Thermus thermophilus (Yoshida and Oshima) comb. nov., a nonsporulating thermophilic bacterium from a Japanese thermal spa. Int. J. Syst. Bacteriol. 1974, 24:102-112.
    • (1974) Int. J. Syst. Bacteriol. , vol.24 , pp. 102-112
    • Oshima, T.1    Imahori, K.2
  • 49
    • 0024199422 scopus 로고
    • Stability of protein structure and hydrophobic interaction
    • Privalov P.L., Gill S.J. Stability of protein structure and hydrophobic interaction. Adv. Protein Chem. 1988, 39:191-234.
    • (1988) Adv. Protein Chem. , vol.39 , pp. 191-234
    • Privalov, P.L.1    Gill, S.J.2
  • 50
    • 0037223885 scopus 로고    scopus 로고
    • Aromatic stacking as a determinant of the thermal stability of CYP119 from Sulfolobus solfataricus
    • Puchkaev A.V., Koo L.S., Ortiz de Montellano P.R. Aromatic stacking as a determinant of the thermal stability of CYP119 from Sulfolobus solfataricus. Arch. Biochem. Biophys. 2003, 409:52-58.
    • (2003) Arch. Biochem. Biophys. , vol.409 , pp. 52-58
    • Puchkaev, A.V.1    Koo, L.S.2    Ortiz de Montellano, P.R.3
  • 51
    • 0346492917 scopus 로고    scopus 로고
    • Folding core predictions from network models of proteins
    • Rader A.J., Bahar I. Folding core predictions from network models of proteins. Polymer 2004, 45:659-668.
    • (2004) Polymer , vol.45 , pp. 659-668
    • Rader, A.J.1    Bahar, I.2
  • 54
    • 61649103550 scopus 로고    scopus 로고
    • Exploiting the link between protein rigidity and thermostability for data-driven protein engineering
    • Radestock S., Gohlke H. Exploiting the link between protein rigidity and thermostability for data-driven protein engineering. Eng. Life Sci. 2008, 8:507-522.
    • (2008) Eng. Life Sci. , vol.8 , pp. 507-522
    • Radestock, S.1    Gohlke, H.2
  • 55
    • 79952487469 scopus 로고    scopus 로고
    • Protein rigidity and thermophilic adaptation
    • Radestock S., Gohlke H. Protein rigidity and thermophilic adaptation. Proteins 2011, 79:1089-1108.
    • (2011) Proteins , vol.79 , pp. 1089-1108
    • Radestock, S.1    Gohlke, H.2
  • 57
    • 33845288649 scopus 로고    scopus 로고
    • Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability
    • Reetz M.T., Carballeira J.D., Vogel A. Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew. Chem. Int. Ed. Engl. 2006, 45:7745-7751.
    • (2006) Angew. Chem. Int. Ed. Engl. , vol.45 , pp. 7745-7751
    • Reetz, M.T.1    Carballeira, J.D.2    Vogel, A.3
  • 58
    • 0020483375 scopus 로고
    • Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7Å resolution
    • Remington S., Wiegand G., Huber R. Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7Å resolution. J. Mol. Biol. 1982, 158:111-152.
    • (1982) J. Mol. Biol. , vol.158 , pp. 111-152
    • Remington, S.1    Wiegand, G.2    Huber, R.3
  • 59
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
    • Ryckaert J.P., Ciccotti G., Berendsen H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23:327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 60
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A., Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234:779-815.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 61
    • 0030834850 scopus 로고    scopus 로고
    • Temperature, stability, and the hydrophobic interaction
    • Schellman J.A. Temperature, stability, and the hydrophobic interaction. Biophys. J. 1997, 73:2960-2964.
    • (1997) Biophys. J. , vol.73 , pp. 2960-2964
    • Schellman, J.A.1
  • 62
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling C., Strockbine B., Roitberg A.E. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 2002, 124:11258-11259.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 63
    • 0002353040 scopus 로고
    • Temperature adaptation of enzymes: biological optimization through structure-function compromises
    • Somero G.N. Temperature adaptation of enzymes: biological optimization through structure-function compromises. Annu. Rev. Ecol. Syst. 1978, 9:1-29.
    • (1978) Annu. Rev. Ecol. Syst. , vol.9 , pp. 1-29
    • Somero, G.N.1
  • 64
    • 70449727646 scopus 로고    scopus 로고
    • Functional metagenomics for enzyme discovery: challenges to efficient screening
    • Uchiyama T., Miyazaki K. Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr. Opin. Biotechnol. 2009, 20:616-622.
    • (2009) Curr. Opin. Biotechnol. , vol.20 , pp. 616-622
    • Uchiyama, T.1    Miyazaki, K.2
  • 65
    • 0037590011 scopus 로고    scopus 로고
    • Extremophiles as a source for novel enzymes
    • Van den Burg B. Extremophiles as a source for novel enzymes. Curr. Opin. Microbiol. 2003, 6:213-218.
    • (2003) Curr. Opin. Microbiol. , vol.6 , pp. 213-218
    • Van den Burg, B.1
  • 66
    • 0035098779 scopus 로고    scopus 로고
    • Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability
    • Vieille C., Zeikus G.J. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol. Mol. Biol. Rev. 2001, 65:1-43.
    • (2001) Microbiol. Mol. Biol. Rev. , vol.65 , pp. 1-43
    • Vieille, C.1    Zeikus, G.J.2
  • 69
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word J.M., Lovell S.C., Richardson J.S., Richardson D.C. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 1999, 285:1735-1747.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 70
    • 0018928663 scopus 로고
    • The Sulfolobus-Caldariella group: taxonomy on the basis of the structure of DNA-dependent RNA polymerases
    • Zillig W., Stetter K.O., Wunderl S., Schulz W., Priess H., Scholz I. The Sulfolobus-Caldariella group: taxonomy on the basis of the structure of DNA-dependent RNA polymerases. Arch. Microbiol. 1980, 125:259-269.
    • (1980) Arch. Microbiol. , vol.125 , pp. 259-269
    • Zillig, W.1    Stetter, K.O.2    Wunderl, S.3    Schulz, W.4    Priess, H.5    Scholz, I.6


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