메뉴 건너뛰기




Volumn 24, Issue 4, 2015, Pages 474-483

Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering

Author keywords

flexibility; mesophiles; normal mode analysis; protein engineering; thermophiles; thermostability; vibrational entropy

Indexed keywords

PROTEIN;

EID: 84940198458     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2592     Document Type: Article
Times cited : (24)

References (52)
  • 3
    • 0035836707 scopus 로고    scopus 로고
    • Directed evolution of polymerase function by compartmentalized self-replication
    • Ghadessy FJ, Ong JL, Holliger P, (2001) Directed evolution of polymerase function by compartmentalized self-replication. Proc Natl Acad Sci USA 98: 4552-4557.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 4552-4557
    • Ghadessy, F.J.1    Ong, J.L.2    Holliger, P.3
  • 4
    • 0036771287 scopus 로고    scopus 로고
    • Thermal stability: a means to assure tertiary structure in therapeutic proteins
    • Cauchy M, D'Aoust S, Dawson B, Rode H, Hefford MA, (2002) Thermal stability: a means to assure tertiary structure in therapeutic proteins. Biologicals 30: 175-185.
    • (2002) Biologicals , vol.30 , pp. 175-185
    • Cauchy, M.1    D'Aoust, S.2    Dawson, B.3    Rode, H.4    Hefford, M.A.5
  • 6
    • 0036968065 scopus 로고    scopus 로고
    • Extremophiles: developments of their special functions and potential resources
    • Fujiwara S, (2002) Extremophiles: developments of their special functions and potential resources. J Biosci Bioenegry 94: 518-525.
    • (2002) J Biosci Bioenegry , vol.94 , pp. 518-525
    • Fujiwara, S.1
  • 7
    • 0033066726 scopus 로고    scopus 로고
    • Extremophiles and their adaptation to hot environments
    • Stetter KO, (1999) Extremophiles and their adaptation to hot environments. FEBS Lett 452: 22-25.
    • (1999) FEBS Lett , vol.452 , pp. 22-25
    • Stetter, K.O.1
  • 9
    • 33645994444 scopus 로고    scopus 로고
    • Recent developments in the thermophilic microbiology of deep-sea hydrothermal vents
    • Miroshnichenko ML, Bonch-Osmolovskaya EA, (2006) Recent developments in the thermophilic microbiology of deep-sea hydrothermal vents. Extremophiles 10: 85-96.
    • (2006) Extremophiles , vol.10 , pp. 85-96
    • Miroshnichenko, M.L.1    Bonch-Osmolovskaya, E.A.2
  • 10
    • 0042021865 scopus 로고    scopus 로고
    • Extending the upper temperature limit for life
    • Kashefi K, Lovley DR, (2003) Extending the upper temperature limit for life. Science 301: 934-934.
    • (2003) Science , vol.301 , pp. 934
    • Kashefi, K.1    Lovley, D.R.2
  • 11
    • 0016771835 scopus 로고
    • Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2
    • Perutz MF, Raidt H, (1975) Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2. Nature 255: 256-259.
    • (1975) Nature , vol.255 , pp. 256-259
    • Perutz, M.F.1    Raidt, H.2
  • 12
    • 0024974452 scopus 로고
    • Engineering protein thermal stability. Sequence statistics point to residue substitutions in alpha-helices
    • Menéndez-Arias L, Argos P, (1989) Engineering protein thermal stability. Sequence statistics point to residue substitutions in alpha-helices. J Mol Biol 206: 397-406.
    • (1989) J Mol Biol , vol.206 , pp. 397-406
    • Menéndez-Arias, L.1    Argos, P.2
  • 13
    • 0025351922 scopus 로고
    • Proteins under extreme physical conditions
    • Jaenicke R, Závodszky P, (1990) Proteins under extreme physical conditions. FEBS Lett 268: 344-349.
    • (1990) FEBS Lett , vol.268 , pp. 344-349
    • Jaenicke, R.1    Závodszky, P.2
  • 14
    • 0026320508 scopus 로고
    • Protein stability and molecular adaptation to extreme conditions
    • Jaenicke R, (1991) Protein stability and molecular adaptation to extreme conditions. Eur J Biochem 202: 715-728.
    • (1991) Eur J Biochem , vol.202 , pp. 715-728
    • Jaenicke, R.1
  • 16
    • 0039116206 scopus 로고    scopus 로고
    • Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey
    • Szilágyi A, Závodszky P, (2000) Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure 8: 493-504.
    • (2000) Structure , vol.8 , pp. 493-504
    • Szilágyi, A.1    Závodszky, P.2
  • 18
    • 20444389830 scopus 로고    scopus 로고
    • Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability
    • Robinson-Rechavi M, Godzik A, (2005) Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability. Structure 13: 857-860.
    • (2005) Structure , vol.13 , pp. 857-860
    • Robinson-Rechavi, M.1    Godzik, A.2
  • 19
    • 32044454841 scopus 로고    scopus 로고
    • Effective factors in thermostability of thermophilic proteins
    • Sadeghi M, Naderi-Manesh H, Zarrabi M, Ranjbar B, (2006) Effective factors in thermostability of thermophilic proteins. Biophys Chem 119: 256-270.
    • (2006) Biophys Chem , vol.119 , pp. 256-270
    • Sadeghi, M.1    Naderi-Manesh, H.2    Zarrabi, M.3    Ranjbar, B.4
  • 20
    • 61649103550 scopus 로고    scopus 로고
    • Exploiting the link between protein rigidity and thermostability for data-driven protein engineering
    • Radestock S, Gohlke H, (2008) Exploiting the link between protein rigidity and thermostability for data-driven protein engineering. Eng Life Sci 8: 507-522.
    • (2008) Eng Life Sci , vol.8 , pp. 507-522
    • Radestock, S.1    Gohlke, H.2
  • 21
    • 77953674097 scopus 로고    scopus 로고
    • Flexibility and mobility in mesophilic and thermophilic homologous proteins from molecular dynamics and FoldUnfold method
    • Mamonova TB, Glyakina AV, Kurnikova MG, Galzitskaya OV, (2010) Flexibility and mobility in mesophilic and thermophilic homologous proteins from molecular dynamics and FoldUnfold method. J Bioinform Comput Biol 8: 377-394.
    • (2010) J Bioinform Comput Biol , vol.8 , pp. 377-394
    • Mamonova, T.B.1    Glyakina, A.V.2    Kurnikova, M.G.3    Galzitskaya, O.V.4
  • 22
    • 79952487469 scopus 로고    scopus 로고
    • Protein rigidity and thermophilic adaptation
    • Radestock S, Gohlke H, (2011) Protein rigidity and thermophilic adaptation. Proteins 79: 1089-1108.
    • (2011) Proteins , vol.79 , pp. 1089-1108
    • Radestock, S.1    Gohlke, H.2
  • 23
    • 84856833536 scopus 로고    scopus 로고
    • Thermophilic proteins: insight and perspective from in silico experiments
    • Sterpone F, Melchionna S, (2012) Thermophilic proteins: insight and perspective from in silico experiments. Chem Soc Rev 41: 1665-1676.
    • (2012) Chem Soc Rev , vol.41 , pp. 1665-1676
    • Sterpone, F.1    Melchionna, S.2
  • 24
    • 34548730241 scopus 로고    scopus 로고
    • Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms
    • Glyakina AV, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV, (2007) Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms. Bioinformatics 23: 2231-2238.
    • (2007) Bioinformatics , vol.23 , pp. 2231-2238
    • Glyakina, A.V.1    Garbuzynskiy, S.O.2    Lobanov, M.Y.3    Galzitskaya, O.V.4
  • 25
    • 77952507530 scopus 로고    scopus 로고
    • Discrimination of thermophilic and mesophilic proteins
    • Taylor TJ, Vaisman II, (2010) Discrimination of thermophilic and mesophilic proteins. BMC Struct Biol 10: S5.
    • (2010) BMC Struct Biol , vol.10 , pp. S5
    • Taylor, T.J.1    Vaisman, I.I.2
  • 27
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • Plaxco KW, Simons KT, Baker D, (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277: 985-994.
    • (1998) J Mol Biol , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 28
    • 0031467464 scopus 로고    scopus 로고
    • Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin
    • Lazaridis T, Lee I, Karplus M, (1997) Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin. Protein Sci 6: 2589-2605.
    • (1997) Protein Sci , vol.6 , pp. 2589-2605
    • Lazaridis, T.1    Lee, I.2    Karplus, M.3
  • 29
    • 84876551539 scopus 로고    scopus 로고
    • Constraint network analysis (CNA): a python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function
    • Pfleger C, Rathi PC, Klein DL, Radestock S, Gohlke H, (2013) Constraint network analysis (CNA): a python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function. J Chem Inf Model 53: 1007-1015.
    • (2013) J Chem Inf Model , vol.53 , pp. 1007-1015
    • Pfleger, C.1    Rathi, P.C.2    Klein, D.L.3    Radestock, S.4    Gohlke, H.5
  • 30
    • 84876532652 scopus 로고    scopus 로고
    • CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function
    • Krüger DM, Rathi PC, Pfleger C, Gohlke H, (2013) CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function. Nucl Acids Res 41: gkt292-W348.
    • (2013) Nucl Acids Res , vol.41 , pp. gkt292-W348
    • Krüger, D.M.1    Rathi, P.C.2    Pfleger, C.3    Gohlke, H.4
  • 31
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF, (2001) Protein flexibility predictions using graph theory. Proteins 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
  • 32
    • 0343742614 scopus 로고    scopus 로고
    • Automated design of the surface positions of protein helices
    • Dahiyat BI, Gordon DB, Mayo SL, (1997) Automated design of the surface positions of protein helices. Protein Sci 6: 1333-1337.
    • (1997) Protein Sci , vol.6 , pp. 1333-1337
    • Dahiyat, B.I.1    Gordon, D.B.2    Mayo, S.L.3
  • 35
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • Go N, Noguti T, Nishikawa T, (1983) Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Natl Acad Sci USA 80: 3696-3700.
    • (1983) Proc Natl Acad Sci USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 36
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor
    • Brooks B, Karplus M, (1983) Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 80: 6571-6575.
    • (1983) Proc Natl Acad Sci USA , vol.80 , pp. 6571-6575
    • Brooks, B.1    Karplus, M.2
  • 37
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt M, Sander C, Stern PS, (1985) Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol 181: 423-447.
    • (1985) J Mol Biol , vol.181 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stern, P.S.3
  • 39
    • 0019774669 scopus 로고
    • Molecular dynamics of hydrogen bonds in bovine pancreatic trypsin inhibitor protein
    • Levitt M, (1981) Molecular dynamics of hydrogen bonds in bovine pancreatic trypsin inhibitor protein. Nature 294: 379-380.
    • (1981) Nature , vol.294 , pp. 379-380
    • Levitt, M.1
  • 40
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus M, Kushick JN, (1981) Method for estimating the configurational entropy of macromolecules. Macromolecules 14: 325-332.
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 41
    • 33646943202 scopus 로고    scopus 로고
    • Molecular dynamics: survey of methods for simulating the activity of proteins
    • Adcock SA, McCammon JA, (2006) Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev 106: 1589-1615.
    • (2006) Chem Rev , vol.106 , pp. 1589-1615
    • Adcock, S.A.1    McCammon, J.A.2
  • 42
    • 4143087050 scopus 로고    scopus 로고
    • Calculating potentials of mean force from steered molecular dynamics simulations
    • Park S, Schulten K, (2004) Calculating potentials of mean force from steered molecular dynamics simulations. J Chem Phys 120: 5946-5961.
    • (2004) J Chem Phys , vol.120 , pp. 5946-5961
    • Park, S.1    Schulten, K.2
  • 44
    • 0037079578 scopus 로고    scopus 로고
    • Dynamics of large proteins through hierarchical levels of coarse-grained structures
    • Doruker P, Jernigan RL, Bahar I, (2002) Dynamics of large proteins through hierarchical levels of coarse-grained structures. J Comput Chem 23: 119-127.
    • (2002) J Comput Chem , vol.23 , pp. 119-127
    • Doruker, P.1    Jernigan, R.L.2    Bahar, I.3
  • 45
    • 0034308140 scopus 로고    scopus 로고
    • Building-block approach for determining low-frequency normal modes of macromolecules
    • Tama F, Gadea FX, Marques O, Sanejouand YH, (2000) Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 41: 1-7.
    • (2000) Proteins , vol.41 , pp. 1-7
    • Tama, F.1    Gadea, F.X.2    Marques, O.3    Sanejouand, Y.H.4
  • 46
    • 84901355476 scopus 로고    scopus 로고
    • A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations
    • Frappier V, Najmanovich RJ, (2014) A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations. PLoS Comput Biol 10: e1003569.
    • (2014) PLoS Comput Biol , vol.10
    • Frappier, V.1    Najmanovich, R.J.2
  • 47
    • 0037452894 scopus 로고    scopus 로고
    • Discrimination of native protein structures using atom-atom contact scoring
    • McConkey B, Sobolev V, Edelman M, (2003) Discrimination of native protein structures using atom-atom contact scoring. Proc Natl Acad Sci USA 100: 3215-3220.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 3215-3220
    • McConkey, B.1    Sobolev, V.2    Edelman, M.3
  • 48
    • 0034663710 scopus 로고    scopus 로고
    • Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor
    • Doruker P, Atilgan AR, Bahar I, (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor. Proteins 40: 512-524.
    • (2000) Proteins , vol.40 , pp. 512-524
    • Doruker, P.1    Atilgan, A.R.2    Bahar, I.3
  • 49
    • 0034855858 scopus 로고    scopus 로고
    • How do thermophilic proteins deal with heat?
    • Kumar S, Nussinov R, (2001) How do thermophilic proteins deal with heat? Cell Mol Life Sci 58: 1216-1233.
    • (2001) Cell Mol Life Sci , vol.58 , pp. 1216-1233
    • Kumar, S.1    Nussinov, R.2
  • 50
    • 0033596744 scopus 로고    scopus 로고
    • Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme
    • Beadle BM, Baase WA, Wilson DB, Gilkes NR, Shoichet BK, (1999) Comparing the thermodynamic stabilities of a related thermophilic and mesophilic enzyme. Biochemistry 38: 2570-2576.
    • (1999) Biochemistry , vol.38 , pp. 2570-2576
    • Beadle, B.M.1    Baase, W.A.2    Wilson, D.B.3    Gilkes, N.R.4    Shoichet, B.K.5
  • 52
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: a protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J, (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.