메뉴 건너뛰기




Volumn 8, Issue , 2008, Pages

"Hot cores" in proteins: Comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms

Author keywords

[No Author keywords available]

Indexed keywords

METHYL GROUP; PROTEIN;

EID: 42149186292     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-8-14     Document Type: Article
Times cited : (18)

References (46)
  • 1
    • 33745726737 scopus 로고    scopus 로고
    • Lessons in stability from thermophilic proteins
    • 16815912. 10.1110/ps.062130306
    • Lessons in stability from thermophilic proteins. A Razvi JM Scholtz, Protein Sci 2006 15 1569 1578 16815912 10.1110/ps.062130306
    • (2006) Protein Sci , vol.15 , pp. 1569-1578
    • Razvi, A.1    Scholtz, J.M.2
  • 2
    • 0035931866 scopus 로고    scopus 로고
    • Life in extreme environments
    • 10.1038/35059215. 11234023
    • Life in extreme environments. JR Lynn RL Mancinelli, Nature 2001 409 1092 1101 10.1038/35059215 11234023
    • (2001) Nature , vol.409 , pp. 1092-1101
    • Lynn, J.R.1    Mancinelli, R.L.2
  • 3
    • 0035098779 scopus 로고    scopus 로고
    • Hyperthermophilic enzymes: Sources, uses, and molecular mechanisms for thermostability
    • 11238984. 10.1128/MMBR.65.1.1-43.2001
    • Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. C Vieille GJ Zeikus, Microbiol Mol Biol Rev 2001 65 1 43 11238984 10.1128/MMBR.65.1.1-43.2001
    • (2001) Microbiol Mol Biol Rev , vol.65 , pp. 1-43
    • Vieille, C.1    Zeikus, G.J.2
  • 4
    • 0030059689 scopus 로고    scopus 로고
    • Forces contributing to the conformational stability of proteins
    • 8566551
    • Forces contributing to the conformational stability of proteins. CN Pace BA Shirley M McNutt K Gajiwala, FASEB J 1996 10 75 83 8566551
    • (1996) FASEB J , vol.10 , pp. 75-83
    • Pace, C.N.1    Shirley, B.A.2    McNutt, M.3    Gajiwala, K.4
  • 5
    • 32044454841 scopus 로고    scopus 로고
    • Effective factors in thermostability of thermophilic proteins
    • 10.1016/j.bpc.2005.09.018. 16253416
    • Effective factors in thermostability of thermophilic proteins. M Sadeghi H Naderi-Manesh M Zarrabi B Ranjbar, Biophys Chem 2006 119 256 270 10.1016/j.bpc.2005.09.018 16253416
    • (2006) Biophys Chem , vol.119 , pp. 256-270
    • Sadeghi, M.1    Naderi-Manesh, H.2    Zarrabi, M.3    Ranjbar, B.4
  • 6
    • 0034017055 scopus 로고    scopus 로고
    • Factors enhancing protein thermostability
    • 10.1093/protein/13.3.179. 10775659
    • Factors enhancing protein thermostability. S Kumar CJ Tsai R Nussinov, Protein Engineering 2000 13 179 191 10.1093/protein/13.3.179 10775659
    • (2000) Protein Engineering , vol.13 , pp. 179-191
    • Kumar, S.1    Tsai, C.J.2    Nussinov, R.3
  • 7
    • 0034692902 scopus 로고    scopus 로고
    • Increasing the thermostability of staphylococcal nuclease: Implications for the origin of protein thermostability
    • 10.1006/jmbi.2000.4140. 11023780
    • Increasing the thermostability of staphylococcal nuclease: implications for the origin of protein thermostability. J Chen Z Lu J Sakon WE Stites, J Mol Biol 2000 303 125 130 10.1006/jmbi.2000.4140 11023780
    • (2000) J Mol Biol , vol.303 , pp. 125-130
    • Chen, J.1    Lu, Z.2    Sakon, J.3    Stites, W.E.4
  • 8
    • 0039116206 scopus 로고    scopus 로고
    • Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: Results of a comprehensive survey
    • 10.1016/S0969-2126(00)00133-7. 10801491
    • Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. A Szilagyi P Zavodszky, Structure Fold Des 2000 8 493 504 10.1016/S0969-2126(00) 00133-7 10801491
    • (2000) Structure Fold des , vol.8 , pp. 493-504
    • Szilagyi, A.1    Zavodszky, P.2
  • 9
    • 20444389830 scopus 로고    scopus 로고
    • Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability
    • 10.1016/j.str.2005.03.011. 15939017
    • Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability. M Robinson-Rechavi A Godzik, Structure 2005 13 857 860 10.1016/j.str.2005.03.011 15939017
    • (2005) Structure , vol.13 , pp. 857-860
    • Robinson-Rechavi, M.1    Godzik, A.2
  • 10
    • 0035876847 scopus 로고    scopus 로고
    • Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins
    • 10.1016/S0301-4622(01)00154-5. 11403885
    • Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins. MM Gromiha, Biophysical Chemistry 2001 91 71 77 10.1016/S0301-4622(01)00154-5 11403885
    • (2001) Biophysical Chemistry , vol.91 , pp. 71-77
    • Gromiha, M.M.1
  • 11
    • 0032502839 scopus 로고    scopus 로고
    • Contact order, transition state placement and the refolding rates of single domain proteins
    • 10.1006/jmbi.1998.1645
    • Contact order, transition state placement and the refolding rates of single domain proteins. KW Plaxco KT Simons D Baker, J Mol Biol 2001 277 985 994 10.1006/jmbi.1998.1645
    • (2001) J Mol Biol , vol.277 , pp. 985-994
    • Plaxco, K.W.1    Simons, K.T.2    Baker, D.3
  • 12
    • 30844449653 scopus 로고    scopus 로고
    • Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: Lessons from structural genomics of Thermotoga maritima
    • 10.1016/j.jmb.2005.11.065. 16375925
    • Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. M Robinson-Rechavi A Alibes A Godzik, J Mol Biol 2006 356 547 557 10.1016/j.jmb.2005.11.065 16375925
    • (2006) J Mol Biol , vol.356 , pp. 547-557
    • Robinson-Rechavi, M.1    Alibes, A.2    Godzik, A.3
  • 13
    • 0347089152 scopus 로고    scopus 로고
    • Sequence and structural analysis of cellular retinoic acid-binding proteins reveals a network of conserved hydrophobic interactions
    • 10.1002/prot.10520. 14696180
    • Sequence and structural analysis of cellular retinoic acid-binding proteins reveals a network of conserved hydrophobic interactions. K Gunasekaran AT Hagler LM Gierasch, Proteins 2004 54 179 194 10.1002/prot.10520 14696180
    • (2004) Proteins , vol.54 , pp. 179-194
    • Gunasekaran, K.1    Hagler, A.T.2    Gierasch, L.M.3
  • 15
    • 0028492437 scopus 로고
    • A measure of helical propensity for amino acids in membrane environments
    • 10.1038/nsb0694-368. 7664049
    • A measure of helical propensity for amino acids in membrane environments. SC Li CM Deber, Nature Struct Biol 1994 1 368 373 10.1038/nsb0694-368 7664049
    • (1994) Nature Struct Biol , vol.1 , pp. 368-373
    • Li, S.C.1    Deber, C.M.2
  • 16
    • 23944501630 scopus 로고    scopus 로고
    • Self-organization in protein folding and the hydrophobic interaction
    • 10.1063/1.1990110. 16108687
    • Self-organization in protein folding and the hydrophobic interaction. BS Gerstman PP Chapagain, J Chem Phys 2005 123 054901 10.1063/1.1990110 16108687
    • (2005) J Chem Phys , vol.123 , pp. 054901
    • Gerstman, B.S.1    Chapagain, P.P.2
  • 17
    • 0038441505 scopus 로고    scopus 로고
    • Designer proteins in biotechnology
    • 12671677. 10.1038/sj.embor.embor808
    • Designer proteins in biotechnology. H Lilie, EMBO reports 2003 4 346 351 12671677 10.1038/sj.embor.embor808
    • (2003) EMBO Reports , vol.4 , pp. 346-351
    • Lilie, H.1
  • 18
    • 0036968784 scopus 로고    scopus 로고
    • Sequence conservation in families whose members have little or no sequence similarity: The four-helical cytokines and cytochromes
    • 10.1016/S0022-2836(02)00653-8. 12215425
    • Sequence conservation in families whose members have little or no sequence similarity: the four-helical cytokines and cytochromes. EE Hill V Morea C Chothia, J Mol Biol 2002 322 205 233 10.1016/S0022-2836(02)00653-8 12215425
    • (2002) J Mol Biol , vol.322 , pp. 205-233
    • Hill, E.E.1    Morea, V.2    Chothia, C.3
  • 19
    • 23144434732 scopus 로고    scopus 로고
    • CAMPO, SCR_FIND and CHC_FIND: A suite of web tools for computational structural biology
    • 10.1093/nar/gki416
    • CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology. A Paiardini F Bossa S Pascarella, Nucleic Acids Res 2005 33 50 55 10.1093/nar/gki416
    • (2005) Nucleic Acids Res , vol.33 , pp. 50-55
    • Paiardini, A.1    Bossa, F.2    Pascarella, S.3
  • 20
    • 24644472817 scopus 로고    scopus 로고
    • Physics and evolution of thermophilic adaptation
    • 16120678. 10.1073/pnas.0503890102
    • Physics and evolution of thermophilic adaptation. IN Berezovsky EI Shakhnovich, Proc Natl Acad Sci USA 2005 102 12742 12747 16120678 10.1073/pnas.0503890102
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 12742-12747
    • Berezovsky, I.N.1    Shakhnovich, E.I.2
  • 21
    • 0032573431 scopus 로고    scopus 로고
    • The stability of salt bridges at high temperatures: Implications for hyperthermophilic proteins
    • 10.1006/jmbi.1998.2159. 9813132
    • The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins. AH Elcock, J Mol Biol 1998 284 489 502 10.1006/jmbi.1998.2159 9813132
    • (1998) J Mol Biol , vol.284 , pp. 489-502
    • Elcock, A.H.1
  • 22
    • 0030781507 scopus 로고    scopus 로고
    • Insights into thermal resistance of proteins from the intrinsic stability of their alpha-helices
    • 10.1002/(SICI)1097-0134(199711)29:3<309::AID-PROT5>3.0.CO;2-5. 9365986
    • Insights into thermal resistance of proteins from the intrinsic stability of their alpha-helices. M Petukhov Y Kil S Kuramitsu V Lanzov, Proteins 1997 29 309 320 10.1002/(SICI)1097-0134(199711)29:3<309::AID-PROT5>3.0.CO;2-5 9365986
    • (1997) Proteins , vol.29 , pp. 309-320
    • Petukhov, M.1    Kil, Y.2    Kuramitsu, S.3    Lanzov, V.4
  • 23
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: Towards fully automated sequence selection
    • 10.1126/science.278.5335.82. 9311930
    • De novo protein design: towards fully automated sequence selection. BI Dahiyat CA Sarisky SL Mayo, Science 1997 278 82 87 10.1126/science.278.5335.82 9311930
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Sarisky, C.A.2    Mayo, S.L.3
  • 24
    • 0031779918 scopus 로고    scopus 로고
    • Design, structure and stability of a hyperthermophilic protein variant
    • 10.1038/nsb0698-470. 9628485
    • Design, structure and stability of a hyperthermophilic protein variant. SM Malakauskas SL Mayo, Nat Struct Biol 1998 5 470 475 10.1038/nsb0698-470 9628485
    • (1998) Nat Struct Biol , vol.5 , pp. 470-475
    • Malakauskas, S.M.1    Mayo, S.L.2
  • 25
    • 29944442954 scopus 로고    scopus 로고
    • Interactions between hydrophobic side chains within alpha-helices
    • 10.1007/s00709-005-0136-0. 16389492
    • Interactions between hydrophobic side chains within alpha-helices. R Jarosch, Protoplasma 2005 227 37 46 10.1007/s00709-005-0136-0 16389492
    • (2005) Protoplasma , vol.227 , pp. 37-46
    • Jarosch, R.1
  • 26
    • 0026665778 scopus 로고
    • Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities
    • 1631077. 10.1073/pnas.89.13.5937
    • Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities. TP Creamer GD Rose, Proc Natl Acad Sci USA 1992 89 5937 5941 1631077 10.1073/pnas.89.13.5937
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 5937-5941
    • Creamer, T.P.1    Rose, G.D.2
  • 27
    • 0032562654 scopus 로고    scopus 로고
    • Position dependence of non-polar amino acid intrinsic helical propensities
    • 10.1006/jmbi.1998.1682. 9571050
    • Position dependence of non-polar amino acid intrinsic helical propensities. M Petukhov V Munoz N Yumoto S Yoshikawa L Serrano, J Mol Biol 1998 278 279 289 10.1006/jmbi.1998.1682 9571050
    • (1998) J Mol Biol , vol.278 , pp. 279-289
    • Petukhov, M.1    Munoz, V.2    Yumoto, N.3    Yoshikawa, S.4    Serrano, L.5
  • 28
    • 0033616712 scopus 로고    scopus 로고
    • Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species
    • 10097079. 10.1073/pnas.96.7.3578
    • Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. PJ Haney JH Badger GL Buldak CI Reich CR Woese GJ Olsen, Proc Natl Acad Sci USA 1999 96 3578 3583 10097079 10.1073/pnas.96.7.3578
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 3578-3583
    • Haney, P.J.1    Badger, J.H.2    Buldak, G.L.3    Reich, C.I.4    Woese, C.R.5    Olsen, G.J.6
  • 29
    • 0037172796 scopus 로고    scopus 로고
    • Elucidation of factors responsible for enhanced thermal stability of proteins: A structural genomics based study
    • 10.1021/bi025523t. 12069608
    • Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. S Chakravarty R Varadarajan, Biochemistry 2002 41 8152 8161 10.1021/bi025523t 12069608
    • (2002) Biochemistry , vol.41 , pp. 8152-8161
    • Chakravarty, S.1    Varadarajan, R.2
  • 30
    • 0029077857 scopus 로고
    • Interactions between hydrophobic side chains within alpha-helices
    • 7670373
    • Interactions between hydrophobic side chains within alpha-helices. TP Creamer GD Rose, Protein Sci 1995 4 1305 1314 7670373
    • (1995) Protein Sci , vol.4 , pp. 1305-1314
    • Creamer, T.P.1    Rose, G.D.2
  • 31
    • 0031808074 scopus 로고    scopus 로고
    • A helix propensity scale based on experimental studies of peptides and proteins
    • 9649402
    • A helix propensity scale based on experimental studies of peptides and proteins. CN Pace JM Scholtz, Biophys J 1998 75 422 427 9649402
    • (1998) Biophys J , vol.75 , pp. 422-427
    • Pace, C.N.1    Scholtz, J.M.2
  • 32
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • 14404936
    • Some factors in the interpretation of protein denaturation. W Kauzmann, Adv Protein Chem 1959 14 1 63 14404936
    • (1959) Adv Protein Chem , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 33
    • 0025370815 scopus 로고
    • Dominant forces in protein folding
    • 10.1021/bi00483a001. 2207096
    • Dominant forces in protein folding. KA Dill, Biochemistry 1990 29 7133 7155 10.1021/bi00483a001 2207096
    • (1990) Biochemistry , vol.29 , pp. 7133-7155
    • Dill, K.A.1
  • 34
    • 0026189147 scopus 로고
    • Solvent reorganization contribution to the transfer thermodynamics of small nonpolar molecules
    • 10.1002/bip.360310809. 1782360
    • Solvent reorganization contribution to the transfer thermodynamics of small nonpolar molecules. B Lee, Biopolymers 1991 31 993 1008 10.1002/bip.360310809 1782360
    • (1991) Biopolymers , vol.31 , pp. 993-1008
    • Lee, B.1
  • 35
    • 0026553768 scopus 로고
    • The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
    • 10.1016/0022-2836(92)90562-X. 1569557
    • The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. L Serrano J Kellis P Cann A Matouschek A Fersht, J Mol Biol 1992 224 783 804 10.1016/0022-2836(92) 90562-X 1569557
    • (1992) J Mol Biol , vol.224 , pp. 783-804
    • Serrano, L.1    Kellis, J.2    Cann, P.3    Matouschek, A.4    Fersht, A.5
  • 37
    • 0030010970 scopus 로고    scopus 로고
    • Entrez: Molecular biology database and retrieval system
    • 8743683
    • Entrez: molecular biology database and retrieval system. GD Schuler JA Epstein H Ohkawa JA Kans, Methods Enzymol 1996 266 141 162 8743683
    • (1996) Methods Enzymol , vol.266 , pp. 141-162
    • Schuler, G.D.1    Epstein, J.A.2    Ohkawa, H.3    Kans, J.A.4
  • 38
    • 1042263811 scopus 로고    scopus 로고
    • PGTdb: A database providing growth temperatures of prokaryotes
    • 10.1093/bioinformatics/btg403. 14734322
    • PGTdb: a database providing growth temperatures of prokaryotes. SL Huang LC Wu HK Laing KT Pan JT Horng, Bioinformatics 2004 20 276 278 10.1093/bioinformatics/btg403 14734322
    • (2004) Bioinformatics , vol.20 , pp. 276-278
    • Huang, S.L.1    Wu, L.C.2    Laing, H.K.3    Pan, K.T.4    Horng, J.T.5
  • 39
    • 23144438711 scopus 로고    scopus 로고
    • PISCES: Recent improvements to a PDB sequence culling server
    • 10.1093/nar/gki402
    • PISCES: recent improvements to a PDB sequence culling server. G Wang RL Dunbrack, Nucleic Acids Res 2005 33 94 98 10.1093/nar/gki402
    • (2005) Nucleic Acids Res , vol.33 , pp. 94-98
    • Wang, G.1    Dunbrack, R.L.2
  • 42
    • 0029046744 scopus 로고
    • An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zone revisited
    • 10.1006/jmbi.1995.0340. 7602593
    • An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. G Vogt T Etzold P Argos, J Mol Biol 1995 249 816 831 10.1006/jmbi.1995.0340 7602593
    • (1995) J Mol Biol , vol.249 , pp. 816-831
    • Vogt, G.1    Etzold, T.2    Argos, P.3
  • 43
    • 0032771019 scopus 로고    scopus 로고
    • Clustering of non-polar contacts in proteins
    • 10.1093/bioinformatics/15.6.501. 10383474
    • Clustering of non-polar contacts in proteins. F Drabløs, Bioinformatics 1999 15 501 509 10.1093/bioinformatics/15.6.501 10383474
    • (1999) Bioinformatics , vol.15 , pp. 501-509
    • Drabløs, F.1
  • 44
    • 0035222012 scopus 로고    scopus 로고
    • A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization
    • 11262947
    • A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization. CE Guda D Scheeff PE Bourne IN Shindyalov, Pac Symp Biocomput 2001 275 86 11262947
    • (2001) Pac Symp Biocomput , pp. 275-86
    • Guda, C.E.1    Scheeff, D.2    Bourne, P.E.3    Shindyalov, I.N.4
  • 45
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • 10.1002/bip.360221211. 6667333
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. W Kabsch C Sander, Biopolymers 1983 22 2577 2637 10.1002/bip.360221211 6667333
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 46
    • 42149090043 scopus 로고    scopus 로고
    • MAXIT. http://sw-tools.pdb.org/apps/MAXIT/
    • MAXIT


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.