메뉴 건너뛰기




Volumn 19, Issue 5, 2011, Pages 711-721

Tracing protein evolution through ancestral structures of fish galectin

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE; CONGERIN; GALECTIN; ISOPROTEIN; UNCLASSIFIED DRUG;

EID: 79955874187     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2011.02.014     Document Type: Article
Times cited : (13)

References (44)
  • 1
    • 0037012937 scopus 로고    scopus 로고
    • Evolution: Planetary biology - Paleontological, geological, and molecular histories of life
    • DOI 10.1126/science.1069863
    • S.A. Benner, M.D. Caraco, J.M. Thomson, and E.A. Gaucher Planetary biology-paleontological, geological, and molecular histories of life Science 296 2002 864 868 (Pubitemid 34464883)
    • (2002) Science , vol.296 , Issue.5569 , pp. 864-868
    • Benner, S.A.1    Caraco, M.D.2    Thomson, J.M.3    Gaucher, E.A.4
  • 2
    • 70349464621 scopus 로고    scopus 로고
    • An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
    • J.T. Bridgham, E.A. Ortlund, and J.W. Thornton An epistatic ratchet constrains the direction of glucocorticoid receptor evolution Nature 461 2009 515 519
    • (2009) Nature , vol.461 , pp. 515-519
    • Bridgham, J.T.1    Ortlund, E.A.2    Thornton, J.W.3
  • 6
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • CCP4 (Collaborative Computational Project, Number 4)
    • CCP4 (Collaborative Computational Project, Number 4) The CCP4 suite: programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50 1994 760 763
    • (1994) Acta Crystallogr. D Biol. Crystallogr. , vol.50 , pp. 760-763
  • 7
    • 33846823909 scopus 로고
    • Particle Mesh Ewald: An N Log(N) method for Ewald sums in large systems
    • T. Darden, D. York, and L. Pedersen Particle Mesh Ewald: an N Log(N) method for Ewald sums in large systems J. Chem. Phys. 103 1993 8577 8593
    • (1993) J. Chem. Phys. , vol.103 , pp. 8577-8593
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 8
    • 34548018528 scopus 로고    scopus 로고
    • Mechanistic approaches to the study of evolution: The functional synthesis
    • DOI 10.1038/nrg2160, PII NRG2160
    • A.M. Dean, and J.W. Thornton Mechanistic approaches to the study of evolution: the functional synthesis Nat. Rev. Genet. 8 2007 675 688 (Pubitemid 47281989)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.9 , pp. 675-688
    • Dean, A.M.1    Thornton, J.W.2
  • 9
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Y. Duan, C. Wu, S. Chowdhury, M.C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, and T. Lee A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 24 2003 1999 2012
    • (2003) J. Comput. Chem. , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.5    Zhang, W.6    Yang, R.7    Cieplak, P.8    Luo, R.9    Lee, T.10
  • 11
    • 0141828152 scopus 로고    scopus 로고
    • Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    • DOI 10.1038/nature01977
    • E.A. Gaucher, J.M. Thomson, M.F. Burgan, and S.A. Benner Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins Nature 425 2003 285 288 (Pubitemid 37158402)
    • (2003) Nature , vol.425 , Issue.6955 , pp. 285-288
    • Gaucher, E.A.1    Thomson, J.M.2    Burgan, M.F.3    Benner, S.A.4
  • 12
    • 0042027823 scopus 로고    scopus 로고
    • Frontal affinity chromatography as a tool for elucidation of sugar recognition properties of lectins
    • DOI 10.1016/S0076-6879(03)01025-5
    • J. Hirabayashi, Y. Arata, and K. Kasai Frontal affinity chromatography as a tool for elucidation of sugar recognition properties of lectins Methods Enzymol. 362 2003 353 368 (Pubitemid 36993059)
    • (2003) Methods in Enzymology , vol.362 , pp. 353-368
    • Hirabayashi, J.1    Arata, Y.2    Kasai, K.-I.3
  • 13
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • J.P. Huelsenbeck, and F. Ronquist MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 17 2001 754 755 (Pubitemid 32851390)
    • (2001) Bioinformatics , vol.17 , Issue.8 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 14
    • 15944381217 scopus 로고    scopus 로고
    • Thermostability of ancestral mutants of Caldococcus noboribetus isocitrate dehydrogenase
    • DOI 10.1016/j.femsle.2004.12.030
    • H. Iwabata, K. Watanabe, T. Ohkuri, S. Yokobori, and A. Yamagishi Thermostability of ancestral mutants of Caldococcus noboribetus isocitrate dehydrogenase FEMS Microbiol. Lett. 243 2005 393 398 (Pubitemid 40431205)
    • (2005) FEMS Microbiology Letters , vol.243 , Issue.2 , pp. 393-398
    • Iwabata, H.1    Watanabe, K.2    Ohkuri, T.3    Yokobori, S.-I.4    Yamagishi, A.5
  • 15
    • 0028895702 scopus 로고
    • Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily
    • T.M. Jermann, J.G. Opitz, J. Stackhouse, and S.A. Benner Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily Nature 374 1995 57 59
    • (1995) Nature , vol.374 , pp. 57-59
    • Jermann, T.M.1    Opitz, J.G.2    Stackhouse, J.3    Benner, S.A.4
  • 17
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • K. Katoh, K. Misawa, K. Kuma, and T. Miyata MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Res. 30 2002 3059 3066 (Pubitemid 34851225)
    • (2002) Nucleic Acids Research , vol.30 , Issue.14 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.-I.3    Miyata, T.4
  • 18
    • 35848954523 scopus 로고    scopus 로고
    • Reconstruction of a probable ancestral form of conger eel galectins revealed their rapid adaptive evolution process for specific carbohydrate recognition
    • DOI 10.1093/molbev/msm185
    • A. Konno, T. Ogawa, T. Shirai, and K. Muramoto Reconstruction of a probable ancestral form of conger eel galectins revealed their rapid adaptive evolution process for specific carbohydrate recognition Mol. Biol. Evol. 24 2007 2504 2514 (Pubitemid 350060453)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.11 , pp. 2504-2514
    • Konno, A.1    Ogawa, T.2    Shirai, T.3    Muramoto, K.4
  • 19
    • 77949472466 scopus 로고    scopus 로고
    • Protein engineering of conger eel galectins by tracing of molecular evolution using probable ancestral mutants
    • A. Konno, S. Yonemaru, A. Kitagawa, K. Muramoto, T. Shirai, and T. Ogawa Protein engineering of conger eel galectins by tracing of molecular evolution using probable ancestral mutants BMC Evol. Biol. 10 2010 43
    • (2010) BMC Evol. Biol. , vol.10 , pp. 43
    • Konno, A.1    Yonemaru, S.2    Kitagawa, A.3    Muramoto, K.4    Shirai, T.5    Ogawa, T.6
  • 20
    • 0035175679 scopus 로고    scopus 로고
    • PDBsum: Summaries and analyses of PDB structures
    • R.A. Laskowski PDBsum: summaries and analyses of PDB structures Nucleic Acids Res. 29 2001 221 222 (Pubitemid 32054453)
    • (2001) Nucleic Acids Research , vol.29 , Issue.1 , pp. 221-222
    • Laskowski, R.A.1
  • 21
    • 0025270813 scopus 로고
    • Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing
    • B.A. Malcolm, K.P. Wilson, B.W. Matthews, J.F. Kirsch, and A.C. Wilson Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing Nature 345 1990 86 89
    • (1990) Nature , vol.345 , pp. 86-89
    • Malcolm, B.A.1    Wilson, K.P.2    Matthews, B.W.3    Kirsch, J.F.4    Wilson, A.C.5
  • 23
    • 25844518483 scopus 로고    scopus 로고
    • Opsonic effect of congerin, a mucosal galectin of the Japanese conger, Conger myriaster (Brevoort)
    • DOI 10.1016/j.fsi.2005.06.004, PII S105046480500121X
    • O. Nakamura, H. Matsuoka, T. Ogawa, K. Muramoto, H. Kamiya, and T. Watanabe Opsonic effect of congerin, a mucosal galectin of the Japanese conger, Conger myriaster (Brevoort) Fish Shellfish Immunol. 20 2006 433 435 (Pubitemid 41392899)
    • (2006) Fish and Shellfish Immunology , vol.20 , Issue.3 , pp. 433-435
    • Nakamura, O.1    Matsuoka, H.2    Ogawa, T.3    Muramoto, K.4    Kamiya, H.5    Watanabe, T.6
  • 24
    • 0036483664 scopus 로고    scopus 로고
    • High-level expression and characterization of fully active recombinant conger eel galectins in Eschericia coli
    • T. Ogawa, C. Ishii, Y. Suda, H. Kamiya, and K. Muramoto High-level expression and characterization of fully active recombinant conger eel galectins in Eschericia coli Biosci. Biotechnol. Biochem. 66 2002 476 480 (Pubitemid 39251080)
    • (2002) Bioscience, Biotechnology and Biochemistry , vol.66 , Issue.2 , pp. 476-480
    • Ogawa, T.1    Ishii, C.2    Suda, Y.3    Kamiya, H.4    Muramoto, K.5
  • 26
    • 34548040966 scopus 로고    scopus 로고
    • Crystal structure of an ancient protein: Evolution by conformational epistasis
    • DOI 10.1126/science.1142819
    • E.A. Ortlund, J.T. Bridgham, M.R. Redinbo, and J.W. Thornton Crystal structure of an ancient protein: evolution by conformational epistasis Science 317 2007 1544 1548 (Pubitemid 47417432)
    • (2007) Science , vol.317 , Issue.5844 , pp. 1544-1548
    • Ortlund, E.A.1    Bridgham, J.T.2    Redinbo, M.R.3    Thornton, J.W.4
  • 27
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • DOI 10.1016/S0076-6879(97)76066-X
    • Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology, Volume 276: Macromolecular Crystallography, part A, J.C.W. Carter and R.M. Sweet, eds., pp. 307-326. (Pubitemid 27085611)
    • (1997) Methods in Enzymology , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 28
    • 0031959770 scopus 로고    scopus 로고
    • Galectins: Versatile modulators of cell adhesion, cell proliferation, and cell death
    • DOI 10.1007/s001090050232
    • N.L. Perillo, M.E. Marcus, and L.G. Baum Galectins: versatile modulators of cell adhesion, cell proliferation, and cell death J. Mol. Med. 76 1998 402 412 (Pubitemid 28218642)
    • (1998) Journal of Molecular Medicine , vol.76 , Issue.6 , pp. 402-412
    • Perillo, N.L.1    Marcus, M.E.2    Baum, L.G.3
  • 30
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • J.-P. Ryckaert, G. Ciccotti, and H.J.C. Berendsen Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 31
    • 0033570024 scopus 로고    scopus 로고
    • High-resolution structure of the conger eel galectin, congerin I, in lactose-liganded and ligand-free forms: Emergence of a new structure class by accelerated evolution
    • DOI 10.1016/S0969-2126(00)80056-8
    • T. Shirai, C. Mitsuyama, Y. Niwa, Y. Matsui, H. Hotta, T. Yamane, H. Kamiya, C. Ishii, T. Ogawa, and K. Muramoto High-resolution structure of the conger eel galectin, congerin I, in lactose-liganded and ligand-free forms: emergence of a new structure class by accelerated evolution Structure 7 1999 1223 1233 (Pubitemid 29482984)
    • (1999) Structure , vol.7 , Issue.10 , pp. 1223-1233
    • Shirai, T.1    Mitsuyama, C.2    Niwa, Y.3    Matsui, Y.4    Hotta, H.5    Yamane, T.6    Kamiya, H.7    Ishii, C.8    Ogawa, T.9    Muramoto, K.10
  • 32
    • 0036384139 scopus 로고    scopus 로고
    • Crystal structure of a conger eel galectin (congerin II) at 1.45A resolution: Implication for the accelerated evolution of a new ligand-binding site following gene duplication
    • T. Shirai, Y. Matsui, C. Shionyu-Mitsuyama, T. Yamane, H. Kamiya, C. Ishii, T. Ogawa, and K. Muramoto Crystal structure of a conger eel galectin (congerin II) at 1.45A resolution: implication for the accelerated evolution of a new ligand-binding site following gene duplication J. Mol. Biol. 321 2002 879 889
    • (2002) J. Mol. Biol. , vol.321 , pp. 879-889
    • Shirai, T.1    Matsui, Y.2    Shionyu-Mitsuyama, C.3    Yamane, T.4    Kamiya, H.5    Ishii, C.6    Ogawa, T.7    Muramoto, K.8
  • 33
    • 33846218264 scopus 로고    scopus 로고
    • Ancestral sequence evolutionary trace and crystal structure analyses of alkaline α-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins
    • DOI 10.1002/prot.21255
    • T. Shirai, K. Igarashi, T. Ozawa, H. Hagihara, T. Kobayashi, K. Ozaki, and S. Ito Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins Proteins 66 2007 600 610 (Pubitemid 46106764)
    • (2007) Proteins: Structure, Function and Genetics , vol.66 , Issue.3 , pp. 600-610
    • Shirai, T.1    Igarashi, K.2    Ozawa, T.3    Hagihara, H.4    Kobayashi, T.5    Ozaki, K.6    Ito, S.7
  • 34
    • 0021175076 scopus 로고
    • Cell surface phenotypes and expression of viral antigens of various human cell lines carrying human T-cell leukemia virus
    • K. Sugamura, M. Fujii, M. Kannagi, M. Sakitani, M. Takeuchi, and Y. Hinuma Cell surface phenotypes and expression of viral antigens of various human cell lines carrying human T-cell leukemia virus Int. J. Cancer 34 1984 221 228 (Pubitemid 14053144)
    • (1984) International Journal of Cancer , vol.34 , Issue.2 , pp. 221-228
    • Sugamura, K.1    Fujii, M.2    Kannagi, M.3
  • 35
    • 0024592555 scopus 로고
    • Monoclonal antibody defining a molecule possibly identical to the p75 subunit of interleukin 2 receptor
    • DOI 10.1084/jem.169.4.1323
    • T. Takeshita, Y. Goto, K. Tada, K. Nagata, H. Asao, and K. Sugamura Monoclonal antibody defining a molecule possibly identical to the p75 subunit of interleukin 2 receptor J. Exp. Med. 169 1989 1323 1332 (Pubitemid 19104965)
    • (1989) Journal of Experimental Medicine , vol.169 , Issue.4 , pp. 1323-1332
    • Takeshita, T.1    Goto, Y.2    Tada, K.3    Nagata, K.4    Asao, H.5    Sugamura, K.6
  • 36
    • 0028205953 scopus 로고
    • Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site
    • Y. Tateno, N. Takezaki, and M. Nei Relative efficiencies of the maximum-likelihood, neighbor-joining, and\ maximum-parsimony methods when substitution rate varies with site Mol. Biol. Evol. 11 1994 261 277 (Pubitemid 24075751)
    • (1994) Molecular Biology and Evolution , vol.11 , Issue.2 , pp. 261-277
    • Tateno, Y.1    Takezaki, N.2    Nei, M.3
  • 38
    • 0035826690 scopus 로고    scopus 로고
    • Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions
    • DOI 10.1073/pnas.091553298
    • J.W. Thornton Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions Proc. Natl. Acad. Sci. USA 98 2001 5671 5676 (Pubitemid 32435700)
    • (2001) Proceedings of the National Academy of Sciences of the United States of America , vol.98 , Issue.10 , pp. 5671-5676
    • Thornton, J.W.1
  • 39
    • 1942531303 scopus 로고    scopus 로고
    • Resurrecting ancient genes: Experimental analysis of extinct molecules
    • DOI 10.1038/nrg1324
    • J.W. Thornton Resurrecting ancient genes: experimental analysis of extinct molecules Nat. Rev. Genet. 5 2004 366 375 (Pubitemid 38529408)
    • (2004) Nature Reviews Genetics , vol.5 , Issue.5 , pp. 366-375
    • Thornton, J.W.1
  • 40
    • 19244366496 scopus 로고    scopus 로고
    • Evolution of coral pigments recreated
    • DOI 10.1126/science.1099597
    • J.A. Ugalde, B.S. Chang, and M.V. Matz Evolution of coral pigments recreated Science 305 2004 1433 (Pubitemid 39167655)
    • (2004) Science , vol.305 , Issue.5689 , pp. 1433
    • Ugalde, J.A.1    Chang, B.S.W.2    Matz, M.V.3
  • 41
    • 29144522906 scopus 로고    scopus 로고
    • Designing thermostable proteins: Ancestral mutants of 3-isopropylmalate dehydrogenase designed by using a phylogenetic tree
    • DOI 10.1016/j.jmb.2005.10.011, PII S0022283605012416
    • K. Watanabe, T. Ohkuri, S. Yokobori, and A. Yamagishi Designing thermostable proteins: ancestral mutants of 3-isopropylmalate dehydrogenase designed by using a phylogenetic tree J. Mol. Biol. 355 2006 664 674 (Pubitemid 41817627)
    • (2006) Journal of Molecular Biology , vol.355 , Issue.4 , pp. 664-674
    • Watanabe, K.1    Ohkuri, T.2    Yokobori, S.-I.3    Yamagishi, A.4
  • 42
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • S.J. Weiner, P.A. Kollman, D.T. Nguyen, and D.A. Case An all atom force field for simulations of proteins and nucleic acids J. Comput. Chem. 7 1986 230 252
    • (1986) J. Comput. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 43
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • DOI 10.1093/molbev/msm088
    • Z. Yang PAML 4: phylogenetic analysis by maximum likelihood Mol. Biol. Evol. 24 2007 1586 1591 (Pubitemid 47236688)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1586-1591
    • Yang, Z.1
  • 44
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Z. Yang, R. Nielsen, N. Goldman, and A.M. Pedersen Codon-substitution models for heterogeneous selection pressure at amino acid sites Genetics 155 2000 431 449 (Pubitemid 30257141)
    • (2000) Genetics , vol.155 , Issue.1 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.-M.K.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.