메뉴 건너뛰기




Volumn 51, Issue 28, 2012, Pages 5633-5641

Experimental assessment of the importance of amino acid positions identified by an entropy-based correlation analysis of multiple-sequence alignments

Author keywords

[No Author keywords available]

Indexed keywords

ANTHRANILATE; ARCHAEON; CATALYTIC EFFICIENCIES; CONFORMATIONAL STABILITIES; CORRELATION ANALYSIS; ENTROPY-BASED; ENZYME FUNCTIONS; EXPERIMENTAL ASSESSMENT; INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE; MUTANT PROTEINS; NON-CONSERVED RESIDUES; PHOSPHORIBOSYL TRANSFERASE; PROTEIN FUNCTIONS; SULFOLOBUS SOLFATARICUS; THERMAL UNFOLDING; WILD TYPES;

EID: 84863901189     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi300747r     Document Type: Article
Times cited : (13)

References (47)
  • 1
    • 34548133728 scopus 로고    scopus 로고
    • Predicting functionally important residues from sequence conservation
    • Capra, J. A. and Singh, M. (2007) Predicting functionally important residues from sequence conservation Bioinformatics 23, 1875-1882
    • (2007) Bioinformatics , vol.23 , pp. 1875-1882
    • Capra, J.A.1    Singh, M.2
  • 2
    • 33748505263 scopus 로고    scopus 로고
    • Incorporating background frequency improves entropy-based residue conservation measures
    • Wang, K. and Samudrala, R. (2006) Incorporating background frequency improves entropy-based residue conservation measures BMC Bioinf. 7, 385
    • (2006) BMC Bioinf. , vol.7 , pp. 385
    • Wang, K.1    Samudrala, R.2
  • 5
    • 0028295169 scopus 로고
    • Correlated mutations and residue contacts in proteins
    • Göbel, U., Sander, C., Schneider, R., and Valencia, A. (1994) Correlated mutations and residue contacts in proteins Proteins 18, 309-317
    • (1994) Proteins , vol.18 , pp. 309-317
    • Göbel, U.1    Sander, C.2    Schneider, R.3    Valencia, A.4
  • 6
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless, S. W. and Ranganathan, R. (1999) Evolutionarily conserved pathways of energetic connectivity in protein families Science 286, 295-299
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 7
    • 0037470597 scopus 로고    scopus 로고
    • Automatic methods for predicting functionally important residues
    • del Sol Mesa, A., Pazos, F., and Valencia, A. (2003) Automatic methods for predicting functionally important residues J. Mol. Biol. 326, 1289-1302
    • (2003) J. Mol. Biol. , vol.326 , pp. 1289-1302
    • Del Sol Mesa, A.1    Pazos, F.2    Valencia, A.3
  • 8
    • 0041821836 scopus 로고    scopus 로고
    • A perspective on enzyme catalysis
    • Benkovic, S. J. and Hammes-Schiffer, S. (2003) A perspective on enzyme catalysis Science 301, 1196-1202
    • (2003) Science , vol.301 , pp. 1196-1202
    • Benkovic, S.J.1    Hammes-Schiffer, S.2
  • 9
    • 12844268072 scopus 로고    scopus 로고
    • Statistical coevolution analysis and molecular dynamics: Identification of amino acid pairs essential for catalysis
    • Estabrook, R. A., Luo, J., Purdy, M. M., Sharma, V., Weakliem, P., Bruice, T. C., and Reich, N. O. (2005) Statistical coevolution analysis and molecular dynamics: Identification of amino acid pairs essential for catalysis Proc. Natl. Acad. Sci. U.S.A. 102, 994-999
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 994-999
    • Estabrook, R.A.1    Luo, J.2    Purdy, M.M.3    Sharma, V.4    Weakliem, P.5    Bruice, T.C.6    Reich, N.O.7
  • 10
    • 78649655423 scopus 로고    scopus 로고
    • Networks of high mutual information define the structural proximity of catalytic sites: Implications for catalytic residue identification
    • Marino Buslje, C., Teppa, E., Di Domenico, T., Delfino, J. M., and Nielsen, M. (2010) Networks of high mutual information define the structural proximity of catalytic sites: Implications for catalytic residue identification PLoS Comput. Biol. 6, e1000978
    • (2010) PLoS Comput. Biol. , vol.6 , pp. 1000978
    • Marino Buslje, C.1    Teppa, E.2    Di Domenico, T.3    Delfino, J.M.4    Nielsen, M.5
  • 12
    • 78049444976 scopus 로고    scopus 로고
    • Correlated mutations: A hallmark of phenotypic amino acid substitutions
    • Kowarsch, A., Fuchs, A., Frishman, D., and Pagel, P. (2010) Correlated mutations: A hallmark of phenotypic amino acid substitutions PLoS Comput. Biol. 6, e1000923
    • (2010) PLoS Comput. Biol. , vol.6 , pp. 1000923
    • Kowarsch, A.1    Fuchs, A.2    Frishman, D.3    Pagel, P.4
  • 13
    • 79957998371 scopus 로고    scopus 로고
    • Protein stability by number: High-throughput and statistical approaches to one of protein sciences most difficult problems
    • Magliery, T. J., Lavinder, J. J., and Sullivan, B. J. (2011) Protein stability by number: High-throughput and statistical approaches to one of protein sciences most difficult problems Curr. Opin. Chem. Biol. 15, 443-451
    • (2011) Curr. Opin. Chem. Biol. , vol.15 , pp. 443-451
    • Magliery, T.J.1    Lavinder, J.J.2    Sullivan, B.J.3
  • 15
    • 0023660022 scopus 로고
    • Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus
    • Altschuh, D., Lesk, A. M., Bloomer, A. C., and Klug, A. (1987) Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus J. Mol. Biol. 193, 693-707
    • (1987) J. Mol. Biol. , vol.193 , pp. 693-707
    • Altschuh, D.1    Lesk, A.M.2    Bloomer, A.C.3    Klug, A.4
  • 16
    • 0028125904 scopus 로고
    • How frequent are correlated changes in families of protein sequences?
    • Neher, E. (1994) How frequent are correlated changes in families of protein sequences? Proc. Natl. Acad. Sci. U.S.A. 91, 98-102
    • (1994) Proc. Natl. Acad. Sci. U.S.A. , vol.91 , pp. 98-102
    • Neher, E.1
  • 17
    • 0033977832 scopus 로고    scopus 로고
    • Correlations among amino acid sites in bHLH protein domains: An information theoretic analysis
    • Atchley, W. R., Wollenberg, K. R., Fitch, W. M., Terhalle, W., and Dress, A. W. (2000) Correlations among amino acid sites in bHLH protein domains: An information theoretic analysis Mol. Biol. Evol. 17, 164-178
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 164-178
    • Atchley, W.R.1    Wollenberg, K.R.2    Fitch, W.M.3    Terhalle, W.4    Dress, A.W.5
  • 18
    • 27944458910 scopus 로고    scopus 로고
    • Using information theory to search for co-evolving residues in proteins
    • Martin, L. C., Gloor, G. B., Dunn, S. D., and Wahl, L. M. (2005) Using information theory to search for co-evolving residues in proteins Bioinformatics 21, 4116-4124
    • (2005) Bioinformatics , vol.21 , pp. 4116-4124
    • Martin, L.C.1    Gloor, G.B.2    Dunn, S.D.3    Wahl, L.M.4
  • 19
    • 0034721944 scopus 로고    scopus 로고
    • Analysis of covariation in an SH3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions
    • Larson, S. M., Di Nardo, A. A., and Davidson, A. R. (2000) Analysis of covariation in an SH3 domain sequence alignment: Applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions J. Mol. Biol. 303, 433-446
    • (2000) J. Mol. Biol. , vol.303 , pp. 433-446
    • Larson, S.M.1    Di Nardo, A.A.2    Davidson, A.R.3
  • 20
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • Süel, G. M., Lockless, S. W., Wall, M. A., and Ranganathan, R. (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins Nat. Struct. Biol. 10, 59-69
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 59-69
    • Süel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 21
    • 3543089710 scopus 로고    scopus 로고
    • A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments
    • Dekker, J. P., Fodor, A., Aldrich, R. W., and Yellen, G. (2004) A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments Bioinformatics 20, 1565-1572
    • (2004) Bioinformatics , vol.20 , pp. 1565-1572
    • Dekker, J.P.1    Fodor, A.2    Aldrich, R.W.3    Yellen, G.4
  • 22
    • 0037433701 scopus 로고    scopus 로고
    • Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
    • Tillier, E. R. and Lui, T. W. (2003) Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments Bioinformatics 19, 750-755
    • (2003) Bioinformatics , vol.19 , pp. 750-755
    • Tillier, E.R.1    Lui, T.W.2
  • 23
    • 42449127565 scopus 로고    scopus 로고
    • H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments
    • Merkl, R. and Zwick, M. (2007) H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments BMC Bioinf. 9, 151
    • (2007) BMC Bioinf. , vol.9 , pp. 151
    • Merkl, R.1    Zwick, M.2
  • 24
    • 79957521422 scopus 로고    scopus 로고
    • New methods to measure residues coevolution in proteins
    • Gao, H., Dou, Y., Yang, J., and Wang, J. (2011) New methods to measure residues coevolution in proteins BMC Bioinf. 12, 206
    • (2011) BMC Bioinf. , vol.12 , pp. 206
    • Gao, H.1    Dou, Y.2    Yang, J.3    Wang, J.4
  • 26
    • 67049100569 scopus 로고    scopus 로고
    • Activation of anthranilate phosphoribosyltransferase from Sulfolobus solfataricus by removal of magnesium inhibition and acceleration of product release
    • Schlee, S., Deuss, M., Bruning, M., Ivens, A., Schwab, T., Hellmann, N., Mayans, O., and Sterner, R. (2009) Activation of anthranilate phosphoribosyltransferase from Sulfolobus solfataricus by removal of magnesium inhibition and acceleration of product release Biochemistry 48, 5199-5209
    • (2009) Biochemistry , vol.48 , pp. 5199-5209
    • Schlee, S.1    Deuss, M.2    Bruning, M.3    Ivens, A.4    Schwab, T.5    Hellmann, N.6    Mayans, O.7    Sterner, R.8
  • 27
    • 0036645661 scopus 로고    scopus 로고
    • Structural analysis of two enzymes catalysing reverse metabolic reactions implies common ancestry
    • Mayans, O., Ivens, A., Nissen, L. J., Kirschner, K., and Wilmanns, M. (2002) Structural analysis of two enzymes catalysing reverse metabolic reactions implies common ancestry EMBO J. 21, 3245-3254
    • (2002) EMBO J. , vol.21 , pp. 3245-3254
    • Mayans, O.1    Ivens, A.2    Nissen, L.J.3    Kirschner, K.4    Wilmanns, M.5
  • 28
    • 0028994307 scopus 로고
    • 2.0 structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus: Possible determinants of protein stability
    • Hennig, M., Darimont, B., Sterner, R., Kirschner, K., and Jansonius, J. N. (1995) 2.0 structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus: Possible determinants of protein stability Structure 3, 1295-1306
    • (1995) Structure , vol.3 , pp. 1295-1306
    • Hennig, M.1    Darimont, B.2    Sterner, R.3    Kirschner, K.4    Jansonius, J.N.5
  • 29
    • 33746371711 scopus 로고    scopus 로고
    • Structural and mutational analysis of substrate complexation by anthranilate phosphoribosyltransferase from Sulfolobus solfataricus
    • Marino, M., Deuss, M., Svergun, D. I., Konarev, P. V., Sterner, R., and Mayans, O. (2006) Structural and mutational analysis of substrate complexation by anthranilate phosphoribosyltransferase from Sulfolobus solfataricus J. Biol. Chem. 281, 21410-21421
    • (2006) J. Biol. Chem. , vol.281 , pp. 21410-21421
    • Marino, M.1    Deuss, M.2    Svergun, D.I.3    Konarev, P.V.4    Sterner, R.5    Mayans, O.6
  • 30
    • 0036308014 scopus 로고    scopus 로고
    • The catalytic mechanism of indole-3-glycerol phosphate synthase: Crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product
    • Hennig, M., Darimont, B. D., Jansonius, J. N., and Kirschner, K. (2002) The catalytic mechanism of indole-3-glycerol phosphate synthase: Crystal structures of complexes of the enzyme from Sulfolobus solfataricus with substrate analogue, substrate, and product J. Mol. Biol. 319, 757-766
    • (2002) J. Mol. Biol. , vol.319 , pp. 757-766
    • Hennig, M.1    Darimont, B.D.2    Jansonius, J.N.3    Kirschner, K.4
  • 31
    • 38349132546 scopus 로고    scopus 로고
    • A rationally designed monomeric variant of anthranilate phosphoribosyltransferase from Sulfolobus solfataricus is as active as the dimeric wild-type enzyme but less thermostable
    • Schwab, T., Skegro, D., Mayans, O., and Sterner, R. (2008) A rationally designed monomeric variant of anthranilate phosphoribosyltransferase from Sulfolobus solfataricus is as active as the dimeric wild-type enzyme but less thermostable J. Mol. Biol. 376, 506-516
    • (2008) J. Mol. Biol. , vol.376 , pp. 506-516
    • Schwab, T.1    Skegro, D.2    Mayans, O.3    Sterner, R.4
  • 33
    • 58149178579 scopus 로고    scopus 로고
    • NCBI Reference Sequences: Current status, policy and new initiatives
    • Pruitt, K. D., Tatusova, T., Klimke, W., and Maglott, D. R. (2009) NCBI Reference Sequences: Current status, policy and new initiatives Nucleic Acids Res. 37, D32-D36
    • (2009) Nucleic Acids Res. , vol.37
    • Pruitt, K.D.1    Tatusova, T.2    Klimke, W.3    Maglott, D.R.4
  • 34
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: Improvement in accuracy of multiple sequence alignment
    • Katoh, K., Kuma, K., Toh, H., and Miyata, T. (2005) MAFFT version 5: Improvement in accuracy of multiple sequence alignment Nucleic Acids Res. 33, 511-518
    • (2005) Nucleic Acids Res. , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 35
    • 0025325983 scopus 로고
    • The "megaprimer" method of site-directed mutagenesis
    • Sarkar, G. and Sommer, S. S. (1990) The "megaprimer" method of site-directed mutagenesis BioTechniques 8, 404-407
    • (1990) BioTechniques , vol.8 , pp. 404-407
    • Sarkar, G.1    Sommer, S.S.2
  • 36
    • 0024520745 scopus 로고
    • Site-directed mutagenesis by overlap extension using the polymerase chain reaction
    • Ho, S. N., Hunt, H. D., Horton, R. M., Pullen, J. K., and Pease, L. R. (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction Gene 77, 51-59
    • (1989) Gene , vol.77 , pp. 51-59
    • Ho, S.N.1    Hunt, H.D.2    Horton, R.M.3    Pullen, J.K.4    Pease, L.R.5
  • 39
    • 0028871804 scopus 로고
    • How to measure and predict the molar absorption coefficient of a protein
    • Pace, C. N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995) How to measure and predict the molar absorption coefficient of a protein Protein Sci. 4, 2411-2423
    • (1995) Protein Sci. , vol.4 , pp. 2411-2423
    • Pace, C.N.1    Vajdos, F.2    Fee, L.3    Grimsley, G.4    Gray, T.5
  • 40
    • 79959702279 scopus 로고    scopus 로고
    • Stabilization of a metabolic enzyme by library selection in Thermus thermophilus
    • Schwab, T. and Sterner, R. (2011) Stabilization of a metabolic enzyme by library selection in Thermus thermophilus ChemBioChem 12, 1581-1588
    • (2011) ChemBioChem , vol.12 , pp. 1581-1588
    • Schwab, T.1    Sterner, R.2
  • 41
    • 0031863441 scopus 로고    scopus 로고
    • Mutational analysis of the active site of indoleglycerol phosphate synthase from Escherichia coli
    • Darimont, B., Stehlin, C., Szadkowski, H., and Kirschner, K. (1998) Mutational analysis of the active site of indoleglycerol phosphate synthase from Escherichia coli Protein Sci. 7, 1221-1232
    • (1998) Protein Sci. , vol.7 , pp. 1221-1232
    • Darimont, B.1    Stehlin, C.2    Szadkowski, H.3    Kirschner, K.4
  • 42
    • 77957969243 scopus 로고    scopus 로고
    • Enhancing the stability and solubility of the glucocorticoid receptor ligand-binding domain by high-throughput library screening
    • Seitz, T., Thoma, R., Schoch, G. A., Stihle, M., Benz, J., DArcy, B., Wiget, A., Ruf, A., Hennig, M., and Sterner, R. (2010) Enhancing the stability and solubility of the glucocorticoid receptor ligand-binding domain by high-throughput library screening J. Mol. Biol. 403, 562-577
    • (2010) J. Mol. Biol. , vol.403 , pp. 562-577
    • Seitz, T.1    Thoma, R.2    Schoch, G.A.3    Stihle, M.4    Benz, J.5    Darcy, B.6    Wiget, A.7    Ruf, A.8    Hennig, M.9    Sterner, R.10
  • 43
    • 84862203724 scopus 로고    scopus 로고
    • Stabilizing Proteins from Sequence Statistics: The Interplay of Conservation and Correlation in Triosephosphate Isomerase Stability
    • Sullivan, B. J., Nguyen, T., Durani, V., Mathur, D., Rojas, S., Thomas, M., Syu, T., and Magliery, T. J. (2012) Stabilizing Proteins from Sequence Statistics: The Interplay of Conservation and Correlation in Triosephosphate Isomerase Stability J. Mol. Biol. 420, 384-399
    • (2012) J. Mol. Biol. , vol.420 , pp. 384-399
    • Sullivan, B.J.1    Nguyen, T.2    Durani, V.3    Mathur, D.4    Rojas, S.5    Thomas, M.6    Syu, T.7    Magliery, T.J.8
  • 44
    • 0035104227 scopus 로고    scopus 로고
    • Stabilization of hen egg white lysozyme by a cavity-filling mutation
    • Ohmura, T., Ueda, T., Ootsuka, K., Saito, M., and Imoto, T. (2001) Stabilization of hen egg white lysozyme by a cavity-filling mutation Protein Sci. 10, 313-320
    • (2001) Protein Sci. , vol.10 , pp. 313-320
    • Ohmura, T.1    Ueda, T.2    Ootsuka, K.3    Saito, M.4    Imoto, T.5
  • 45
    • 1542267781 scopus 로고    scopus 로고
    • Thermodynamics of core hydrophobicity and packing in the hyperthermophile proteins Sac7d and Sso7d
    • Clark, A. T., McCrary, B. S., Edmondson, S. P., and Shriver, J. W. (2004) Thermodynamics of core hydrophobicity and packing in the hyperthermophile proteins Sac7d and Sso7d Biochemistry 43, 2840-2853
    • (2004) Biochemistry , vol.43 , pp. 2840-2853
    • Clark, A.T.1    McCrary, B.S.2    Edmondson, S.P.3    Shriver, J.W.4
  • 46
    • 84872212394 scopus 로고    scopus 로고
    • Schrödinger, Inc. Portland, OR
    • PyMOL (2010) Schrödinger, Inc., Portland, OR.
    • (2010) PyMOL


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.