메뉴 건너뛰기




Volumn 11, Issue 4, 2007, Pages 585-596

Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins

Author keywords

Amino acid frequency; Cold adaptation; Protein structure; Psychrophiles; Stability; Thermophiles

Indexed keywords

AMINO ACID; ARCHAEAL PROTEIN; BACTERIAL PROTEIN;

EID: 34347361558     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-007-0072-3     Document Type: Article
Times cited : (27)

References (53)
  • 3
    • 24644472817 scopus 로고    scopus 로고
    • Physics and evolution of thermophilic adaptation.
    • 36
    • Berezovsky IN, Shakhnovich EI (2005) Physics and evolution of thermophilic adaptation. Proc Natl Acad Sci USA 102(36):12742-12747
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 12742-12747
    • Berezovsky, I.N.1    Shakhnovich, E.I.2
  • 4
    • 34047232678 scopus 로고    scopus 로고
    • Positive and negative design in stability and thermal adaptation of natural proteins
    • doi: 10.1371/journal.pcbi.0030052.eor
    • Berezovsky IN, Zeldovich KB, Shakhnovich EI (2007) Positive and negative design in stability and thermal adaptation of natural proteins. PLOS Comput Biol doi: 10.1371/journal.pcbi.0030052.eor
    • (2007) PLOS Comput Biol
    • Berezovsky, I.N.1    Zeldovich, K.B.2    Shakhnovich, E.I.3
  • 6
    • 0031055738 scopus 로고    scopus 로고
    • Thermoanaerobacter brockii alcohol dehydrogenase: Characterization of the active site metal and its ligand amino acids.
    • 2
    • Bogin O, Peretz M, Burstein Y (1997) Thermoanaerobacter brockii alcohol dehydrogenase: characterization of the active site metal and its ligand amino acids. Protein Sci 6(2):450-458
    • (1997) Protein Sci , vol.6 , pp. 450-458
    • Bogin, O.1    Peretz, M.2    Burstein, Y.3
  • 7
    • 29244487908 scopus 로고    scopus 로고
    • Oligomeric protein structure networks: Insights into protein-protein interactions
    • Brinda KV, Vishveshwara S (2005) Oligomeric protein structure networks: insights into protein-protein interactions. BMC Bioinformatics (6):296
    • (2005) BMC Bioinformatics , Issue.6 , pp. 296
    • Brinda, K.V.1    Vishveshwara, S.2
  • 8
    • 0029900846 scopus 로고    scopus 로고
    • The magnitude of the backbone conformational entropy change in protein folding.
    • 2
    • D'Aquino JA, Gomez J, Hilser VJ, Lee KH, Amzel LM, Freire E (1996) The magnitude of the backbone conformational entropy change in protein folding. Proteins 25(2):143-156
    • (1996) Proteins , vol.25 , pp. 143-156
    • D'Aquino, J.A.1    Gomez, J.2    Hilser, V.J.3    Lee, K.H.4    Amzel, L.M.5    Freire, E.6
  • 10
    • 0036270790 scopus 로고    scopus 로고
    • Psychrophiles and polar regions.
    • 3
    • Deming JW (2002) Psychrophiles and polar regions. Curr Opin Microbiol 5(3):301-309
    • (2002) Curr Opin Microbiol , vol.5 , pp. 301-309
    • Deming, J.W.1
  • 11
    • 2542451914 scopus 로고    scopus 로고
    • Preferred amino acids and thermostability.
    • 4
    • Farias ST, Bonato MC (2003) Preferred amino acids and thermostability. Genet Mol Res 2(4):383-393
    • (2003) Genet Mol Res , vol.2 , pp. 383-393
    • Farias, S.T.1    Bonato, M.C.2
  • 12
    • 0033528657 scopus 로고    scopus 로고
    • Thermodynamic stability of a cold-active alpha-amylase from the Antarctic bacterium Alteromonas haloplanctis.
    • 14
    • Feller G, d'Amico D, Gerday C (1999) Thermodynamic stability of a cold-active alpha-amylase from the Antarctic bacterium Alteromonas haloplanctis. Biochemistry 38(14):4613-4619
    • (1999) Biochemistry , vol.38 , pp. 4613-4619
    • Feller, G.1    D'Amico, D.2    Gerday, C.3
  • 13
    • 1842509102 scopus 로고    scopus 로고
    • Psychrophilic enzymes: Hot topics in cold adaptation.
    • 3
    • Feller G, Gerday C (2003) Psychrophilic enzymes: hot topics in cold adaptation. Nat Rev Microbiol 1(3):200-208
    • (2003) Nat Rev Microbiol , vol.1 , pp. 200-208
    • Feller, G.1    Gerday, C.2
  • 14
    • 0030900384 scopus 로고    scopus 로고
    • Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes.
    • 6
    • Galtier N, Lobry JR (1997) Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol 44(6):632-636
    • (1997) J Mol Evol , vol.44 , pp. 632-636
    • Galtier, N.1    Lobry, J.R.2
  • 16
    • 0034997442 scopus 로고    scopus 로고
    • Structural adaptation of enzymes to low temperatures.
    • 3
    • Gianese G, Argos P, Pascarella S (2001) Structural adaptation of enzymes to low temperatures. Protein Eng 14(3):141-148
    • (2001) Protein Eng , vol.14 , pp. 141-148
    • Gianese, G.1    Argos, P.2    Pascarella, S.3
  • 17
    • 0036425552 scopus 로고    scopus 로고
    • Role of cation-pi interactions to the stability of thermophilic proteins.
    • 4
    • Gromiha MM, Thomas S, Santhosh C (2002) Role of cation-pi interactions to the stability of thermophilic proteins. Prep Biochem Biotechnol 32(4):355-362
    • (2002) Prep Biochem Biotechnol , vol.32 , pp. 355-362
    • Gromiha, M.M.1    Thomas, S.2    Santhosh, C.3
  • 18
    • 0030970741 scopus 로고    scopus 로고
    • Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus.
    • 1
    • Haney P, Konisky J, Koretke KK, Luthey-Schulten Z, Wolynes PG (1997) Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus. Proteins 28(1):117-130
    • (1997) Proteins , vol.28 , pp. 117-130
    • Haney, P.1    Konisky, J.2    Koretke, K.K.3    Luthey-Schulten, Z.4    Wolynes, P.G.5
  • 20
    • 0035819839 scopus 로고    scopus 로고
    • High guanine-cytosine content is not an adaptation to high temperature: A comparative analysis amongst prokaryotes.
    • 1466
    • Hurst LD, Merchant AR (2001) High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes. Proc Biol Sci 268(1466):493-497
    • (2001) Proc Biol Sci , vol.268 , pp. 493-497
    • Hurst, L.D.1    Merchant, A.R.2
  • 21
    • 0032438190 scopus 로고    scopus 로고
    • The stability of proteins in extreme environments.
    • 6
    • Jaenicke R, Bohm G (1998) The stability of proteins in extreme environments. Curr Opin Struct Biol 8(6):738-748
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 738-748
    • Jaenicke, R.1    Bohm, G.2
  • 22
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features.
    • 12
    • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22(12):2577-2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 23
    • 0034495733 scopus 로고    scopus 로고
    • Aromatic clusters: A determinant of thermal stability of thermophilic proteins.
    • 11
    • Kannan N, Vishveshwara S (2000) Aromatic clusters: a determinant of thermal stability of thermophilic proteins. Protein Eng 13(11):753-761
    • (2000) Protein Eng , vol.13 , pp. 753-761
    • Kannan, N.1    Vishveshwara, S.2
  • 24
    • 0042021865 scopus 로고    scopus 로고
    • Extending the upper temperature limit for life.
    • 5635
    • Kashefi K, Lovley DR (2003) Extending the upper temperature limit for life. Science 301(5635):934
    • (2003) Science , vol.301 , pp. 934
    • Kashefi, K.1    Lovley, D.R.2
  • 25
    • 18244373419 scopus 로고    scopus 로고
    • Computational thermostabilization of an enzyme.
    • 5723
    • Korkegian A, Black ME, Baker D, Stoddard BL (2005) Computational thermostabilization of an enzyme. Science 308(5723):857-860
    • (2005) Science , vol.308 , pp. 857-860
    • Korkegian, A.1    Black, M.E.2    Baker, D.3    Stoddard, B.L.4
  • 26
    • 0035312933 scopus 로고    scopus 로고
    • Identification of thermophilic species by the amino acid compositions deduced from their genomes.
    • 7
    • Kreil DP, Ouzounis CA (2001) Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res 29(7):1608-1615
    • (2001) Nucleic Acids Res , vol.29 , pp. 1608-1615
    • Kreil, D.P.1    Ouzounis, C.A.2
  • 27
    • 0034855858 scopus 로고    scopus 로고
    • How do thermophilic proteins deal with heat.
    • 9
    • Kumar S, Nussinov R (2001) How do thermophilic proteins deal with heat. Cell Mol Life Sci 58(9):1216-1233
    • (2001) Cell Mol Life Sci , vol.58 , pp. 1216-1233
    • Kumar, S.1    Nussinov, R.2
  • 28
    • 0035960641 scopus 로고    scopus 로고
    • Thermodynamic differences among homologous thermophilic and mesophilic proteins
    • 47
    • Kumar S, Tsai CJ, Nussinov R (2001) Thermodynamic differences among homologous thermophilic and mesophilic proteins. Biochemistry 40(47):14152-14165
    • (2001) Biochemistry , vol.40 , pp. 14152-14165
    • Kumar, S.1    Tsai, C.J.2    Nussinov, R.3
  • 29
    • 3042796482 scopus 로고    scopus 로고
    • Substitution of aspartic acid with glutamic acid increases the unfolding transition temperature of a protein
    • 3
    • Lee DY, Kim KA, Yu YG, Kim KS (2004) Substitution of aspartic acid with glutamic acid increases the unfolding transition temperature of a protein. Biochem Biophys Res Commun 320(3):900-906
    • (2004) Biochem Biophys Res Commun , vol.320 , pp. 900-906
    • Lee, D.Y.1    Kim, K.A.2    Yu, Y.G.3    Kim, K.S.4
  • 30
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences.
    • 13
    • Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13):1658-1659
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 31
    • 17644365489 scopus 로고    scopus 로고
    • Structural features of thermozymes.
    • 4
    • Li WF, Zhou XX, Lu P (2005) Structural features of thermozymes. Biotechnol Adv 23(4):271-281
    • (2005) Biotechnol Adv , vol.23 , pp. 271-281
    • Li, W.F.1    Zhou, X.X.2    Lu, P.3
  • 33
    • 4344666232 scopus 로고    scopus 로고
    • Correlations between genomic GC levels and optimal growth temperatures in prokaryotes.
    • 1-3
    • Musto H, Naya H, Zavala A, Romero H, Alvarez-Valin F, Bernardi G (2004) Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Lett 573(1-3):73-77
    • (2004) FEBS Lett , vol.573 , pp. 73-77
    • Musto, H.1    Naya, H.2    Zavala, A.3    Romero, H.4    Alvarez-Valin, F.5    Bernardi, G.6
  • 35
    • 0038583819 scopus 로고    scopus 로고
    • Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures.
    • 4
    • Nakashima H, Fukuchi S, Nishikawa K (2003) Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biochem (Tokyo) 133(4):507-513
    • (2003) J Biochem (Tokyo) , vol.133 , pp. 507-513
    • Nakashima, H.1    Fukuchi, S.2    Nishikawa, K.3
  • 36
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins.
    • 3
    • Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48(3):443-453
    • (1970) J Mol Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 37
    • 23844458318 scopus 로고    scopus 로고
    • Increased flexibility as a strategy for cold adaptation: A comparative molecular dynamics study of cold- and warm-active uracil DNA glycosylase.
    • 18
    • Olufsen M, Smalas AO, Moe E, Brandsdal BO (2005) Increased flexibility as a strategy for cold adaptation: a comparative molecular dynamics study of cold- and warm-active uracil DNA glycosylase. J Biol Chem 280(18):18042-18048
    • (2005) J Biol Chem , vol.280 , pp. 18042-18048
    • Olufsen, M.1    Smalas, A.O.2    Moe, E.3    Brandsdal, B.O.4
  • 38
    • 3142632218 scopus 로고    scopus 로고
    • Protein thermostability: Structure-based difference of amino acid between thermophilic and mesophilic proteins.
    • 3
    • Pack SP, Yoo YJ (2004) Protein thermostability: structure-based difference of amino acid between thermophilic and mesophilic proteins. J Biotechnol 111(3):269-277
    • (2004) J Biotechnol , vol.111 , pp. 269-277
    • Pack, S.P.1    Yoo, Y.J.2
  • 39
    • 16344393715 scopus 로고    scopus 로고
    • Packing-based difference of structural features between thermophilic and mesophilic proteins.
    • 3-4
    • Pack SP, Yoo YJ (2005) Packing-based difference of structural features between thermophilic and mesophilic proteins. Int J Biol Macromol 35(3-4):169-174
    • (2005) Int J Biol Macromol , vol.35 , pp. 169-174
    • Pack, S.P.1    Yoo, Y.J.2
  • 41
    • 32044454841 scopus 로고    scopus 로고
    • Effective factors in thermostability of thermophilic proteins.
    • 3
    • Sadeghi M, Naderi-Manesh H, Zarrabi M, Ranjbar B (2006) Effective factors in thermostability of thermophilic proteins. Biophys Chem 119(3):256-270
    • (2006) Biophys Chem , vol.119 , pp. 256-270
    • Sadeghi, M.1    Naderi-Manesh, H.2    Zarrabi, M.3    Ranjbar, B.4
  • 42
    • 0027488713 scopus 로고
    • Stabilization of creatinase from Pseudomonas putida by random mutagenesis.
    • 10
    • Schumann J, Bohm G, Schumacher G, Rudolph R, Jaenicke R (1993) Stabilization of creatinase from Pseudomonas putida by random mutagenesis. Protein Sci 2(10):1612-1620
    • (1993) Protein Sci , vol.2 , pp. 1612-1620
    • Schumann, J.1    Bohm, G.2    Schumacher, G.3    Rudolph, R.4    Jaenicke, R.5
  • 44
    • 33745609527 scopus 로고    scopus 로고
    • Role of lysine versus arginine in enzyme cold-adaptation: Modifying lysine to homo-arginine stabilizes the cold-adapted alpha-amylase from Pseudoalteramonas haloplanktis.
    • 2
    • Siddiqui KS, Poljak A, Guilhaus M, De Francisci D, Curmi PM, Feller G, D'Amico S, Gerday C, Uversky VN, Cavicchioli R (2006) Role of lysine versus arginine in enzyme cold-adaptation: modifying lysine to homo-arginine stabilizes the cold-adapted alpha-amylase from Pseudoalteramonas haloplanktis. Proteins 64(2):486-501
    • (2006) Proteins , vol.64 , pp. 486-501
    • Siddiqui, K.S.1    Poljak, A.2    Guilhaus, M.3    De Francisci, D.4    Curmi, P.M.5    Feller, G.6    D'Amico, S.7    Gerday, C.8    Uversky, V.N.9    Cavicchioli, R.10
  • 45
    • 0033745103 scopus 로고    scopus 로고
    • Nucleotide bias causes a genomewide bias in the amino acid composition of proteins.
    • 11
    • Singer GA, Hickey DA (2000) Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol 17(11):1581-1588
    • (2000) Mol Biol Evol , vol.17 , pp. 1581-1588
    • Singer, G.A.1    Hickey, D.A.2
  • 46
    • 0242290154 scopus 로고    scopus 로고
    • Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content.
    • 1-2
    • Singer GAC, Hickey DA (2003) Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 317(1-2):39-47
    • (2003) Gene , vol.317 , pp. 39-47
    • Singer, G.A.C.1    Hickey, D.A.2
  • 47
    • 0037059027 scopus 로고    scopus 로고
    • Potential of mean force between two hydrophobic solutes in water.
    • Southall NT, Dill KA (2002) Potential of mean force between two hydrophobic solutes in water. Biophys Chem 101-102:295-307
    • (2002) Biophys Chem , vol.101-102 , pp. 295-307
    • Southall, N.T.1    Dill, K.A.2
  • 48
    • 0022591495 scopus 로고
    • The classification of amino acid conservation.
    • 2
    • Taylor WR (1986) The classification of amino acid conservation. J Theor Biol 119(2):205-218
    • (1986) J Theor Biol , vol.119 , pp. 205-218
    • Taylor, W.R.1
  • 49
    • 0033538553 scopus 로고    scopus 로고
    • Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability.
    • 2
    • Thompson MJ, Eisenberg D (1999) Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. J Mol Biol 290(2):595-604
    • (1999) J Mol Biol , vol.290 , pp. 595-604
    • Thompson, M.J.1    Eisenberg, D.2
  • 50
    • 33644622447 scopus 로고    scopus 로고
    • On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: Data quality and confounding factors.
    • 3
    • Wang HC, Susko E, Roger AJ (2006) On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors. Biochem Biophys Res Commun 342(3):681-684
    • (2006) Biochem Biophys Res Commun , vol.342 , pp. 681-684
    • Wang, H.C.1    Susko, E.2    Roger, A.J.3
  • 51
    • 0031591389 scopus 로고    scopus 로고
    • The refined crystal structure of bacillus cereus oligo-1,6-glucosidase at 2.0 a resolution: Structural characterization of proline-substitution sites for protein thermostabilization.
    • 1
    • Watanabe K, Hata Y, Kizaki H, Katsube Y, Suzuki Y (1997) The refined crystal structure of bacillus cereus oligo-1,6-glucosidase at 2.0 A resolution: structural characterization of proline-substitution sites for protein thermostabilization. J Mol Biol 269(1):142-153
    • (1997) J Mol Biol , vol.269 , pp. 142-153
    • Watanabe, K.1    Hata, Y.2    Kizaki, H.3    Katsube, Y.4    Suzuki, Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.