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Volumn 8, Issue 4, 2016, Pages 994-1011

Functional divergence in teleost cardiac troponin paralogs guides variation in the interaction of TnI switch region with TnC

Author keywords

Functional divergence; Molecular coevolution; Protein interaction; Regulatory subfunctionalization; Structural subfunctionalization; Troponin

Indexed keywords

TROPONIN C; TROPONIN I;

EID: 85015351318     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evw044     Document Type: Article
Times cited : (11)

References (99)
  • 1
  • 2
    • 84942318924 scopus 로고    scopus 로고
    • Protein-protein interfaces from cytochrome c oxidase i evolve faster than nonbinding surfaces, yet negative selection is the driving force
    • Aledo JC, Valverde H, Ruiz-Camacho M, Morilla I, Lopez FD. 2014. Protein-protein interfaces from cytochrome c oxidase I evolve faster than nonbinding surfaces, yet negative selection is the driving force. Genome Biol Evol. 6:3064–3076.
    • (2014) Genome Biol Evol , vol.6 , pp. 3064-3076
    • Aledo, J.C.1    Valverde, H.2    Ruiz-Camacho, M.3    Morilla, I.4    Lopez, F.D.5
  • 3
    • 67650358909 scopus 로고    scopus 로고
    • QMEAN server for protein model quality estimation
    • Benkert P, Kunzli M, Schwede T. 2009. QMEAN server for protein model quality estimation. Nucleic Acids Res. 37:W510–W514.
    • (2009) Nucleic Acids Res , vol.37 , pp. W510-W514
    • Benkert, P.1    Kunzli, M.2    Schwede, T.3
  • 5
    • 0037270595 scopus 로고    scopus 로고
    • Maximum likelihood methods for detecting adaptive evolution after gene duplication
    • Bielawski JP, Yang Z. 2003. Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics. 3:201–212.
    • (2003) J Struct Funct Genomics , vol.3 , pp. 201-212
    • Bielawski, J.P.1    Yang, Z.2
  • 6
    • 84858126537 scopus 로고    scopus 로고
    • Automated protein structure modeling with SWISS-MODEL workspace and the protein model portal
    • Bordoli L, Schwede T. 2012. Automated protein structure modeling with SWISS-MODEL workspace and the protein model portal. Methods Mol Biol. 857:107–136.
    • (2012) Methods Mol Biol , vol.857 , pp. 107-136
    • Bordoli, L.1    Schwede, T.2
  • 7
    • 84901826570 scopus 로고    scopus 로고
    • Ca-regulatory function of the inhibitory peptide region of cardiac troponin i is aided by the C-terminus of cardiac troponin t: Effects of familial hy-pertrophic cardiomyopathy mutations cTnI R145G and cTnT R278C, alone and in combination, on filament sliding
    • Brunet NM, Chase PB, Mihajlovic G, Schoffstall B. 2014. Ca-regulatory function of the inhibitory peptide region of cardiac troponin I is aided by the C-terminus of cardiac troponin T: effects of familial hy-pertrophic cardiomyopathy mutations cTnI R145G and cTnT R278C, alone and in combination, on filament sliding. Arch Biochem Biophys. 552–553:11–20.
    • (2014) Arch Biochem Biophys , vol.552-553 , pp. 11-20
    • Brunet, N.M.1    Chase, P.B.2    Mihajlovic, G.3    Schoffstall, B.4
  • 8
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • Bussi G, Donadio D, Parrinello M. 2007. Canonical sampling through velocity rescaling. J Chem Phys. 126:014101.
    • (2007) J Chem Phys , vol.126 , pp. 014101
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 9
    • 79953048047 scopus 로고    scopus 로고
    • Identification of housekeeping genes suitable for gene expression analysis in the zebrafish
    • Casadei R, et al. 2011. Identification of housekeeping genes suitable for gene expression analysis in the zebrafish. Gene Expr Patterns. 11:271–276.
    • (2011) Gene Expr Patterns , vol.11 , pp. 271-276
    • Casadei, R.1
  • 10
    • 73349131117 scopus 로고    scopus 로고
    • Staggered mesh ewald: An extension of the smooth particle-mesh ewald method adding great versatility
    • Cerutti DS, Duke RE, Darden TA, Lybrand TP. 2009. Staggered mesh ewald: an extension of the smooth particle-mesh ewald method adding great versatility. J Chem Theory Comput. 5:2322.
    • (2009) J Chem Theory Comput , vol.5 , pp. 2322
    • Cerutti, D.S.1    Duke, R.E.2    Darden, T.A.3    Lybrand, T.P.4
  • 11
    • 0028362401 scopus 로고
    • The effects of n helix deletion and mutant F29W on the Ca2+ binding and functional properties of chicken skeletal muscle troponin
    • Chandra M, et al. 1994. The effects of N helix deletion and mutant F29W on the Ca2+ binding and functional properties of chicken skeletal muscle troponin. J Biol Chem. 269:14988–14994.
    • (1994) J Biol Chem , vol.269 , pp. 14988-14994
    • Chandra, M.1
  • 12
    • 74549178560 scopus 로고    scopus 로고
    • MolProbity: All-atom structure validation for macromolecular crystallography
    • Chen VB, et al. 2010. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. 66:12–21.
    • (2010) Acta Crystallogr D Biol Crystallogr , vol.66 , pp. 12-21
    • Chen, V.B.1
  • 13
    • 67349201677 scopus 로고    scopus 로고
    • To investigate protein evolution by detecting suppressed epitope structures
    • Chong SM, Jin JP. 2009. To investigate protein evolution by detecting suppressed epitope structures. J Mol Evol. 68:448–460.
    • (2009) J Mol Evol , vol.68 , pp. 448-460
    • Chong, S.M.1    Jin, J.P.2
  • 16
    • 0242558200 scopus 로고    scopus 로고
    • Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish
    • Cresko WA, et al. 2003. Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish. Dev Dyn. 228:480–489.
    • (2003) Dev Dyn , vol.228 , pp. 480-489
    • Cresko, W.A.1
  • 17
    • 0033556236 scopus 로고    scopus 로고
    • Peptide folding: When simulation meets experiment
    • Daura X, et al. 1999. Peptide folding: when simulation meets experiment. Angew Chem Int Ed. 38:236–240.
    • (1999) Angew Chem Int Ed , vol.38 , pp. 236-240
    • Daura, X.1
  • 18
    • 77958150590 scopus 로고    scopus 로고
    • Sequencing the genome of the Atlantic salmon (Salmo salar)
    • Davidson WS, et al. 2010. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol. 11:403.
    • (2010) Genome Biol , vol.11 , pp. 403
    • Davidson, W.S.1
  • 19
    • 19344363466 scopus 로고    scopus 로고
    • Preferential duplication of conserved proteins in eukaryotic genomes
    • Davis JC, Petrov DA. 2004. Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol. 2:E55.
    • (2004) PLoS Biol , vol.2 , pp. E55
    • Davis, J.C.1    Petrov, D.A.2
  • 20
    • 84875225476 scopus 로고    scopus 로고
    • Emerging methods in protein coevolution
    • de Juan D, Pazos F, Valencia A. 2013. Emerging methods in protein coevolution. Nat Rev Genet. 14:249–261.
    • (2013) Nat Rev Genet , vol.14 , pp. 249-261
    • De Juan, D.1    Pazos, F.2    Valencia, A.3
  • 22
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • Drummond DA, Raval A, Wilke CO. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 23:327–337.
    • (2006) Mol Biol Evol , vol.23 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 23
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792–1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 24
    • 14644413494 scopus 로고    scopus 로고
    • Temperature sensitivity of calcium binding for parvalbumins from antarctic and temperate zone teleost fishes
    • Erickson JR, Sidell BD, Moerland TS. 2005. Temperature sensitivity of calcium binding for parvalbumins from Antarctic and temperate zone teleost fishes. Comp Biochem Physiol A Mol Integr Physiol. 140:179–185.
    • (2005) Comp Biochem Physiol A Mol Integr Physiol , vol.140 , pp. 179-185
    • Erickson, J.R.1    Sidell, B.D.2    Moerland, T.S.3
  • 25
    • 0032893932 scopus 로고    scopus 로고
    • Preservation of duplicate genes by complementary, degenerative mutations
    • Force A, et al. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531–1545.
    • (1999) Genetics , vol.151 , pp. 1531-1545
    • Force, A.1
  • 27
    • 66149160589 scopus 로고    scopus 로고
    • The molecular structures and expression patterns of zebrafish troponin i genes
    • Fu CY, Lee HC, Tsai HJ. 2009. The molecular structures and expression patterns of zebrafish troponin I genes. Gene Expr Patterns. 9:348–356.
    • (2009) Gene Expr Patterns , vol.9 , pp. 348-356
    • Fu, C.Y.1    Lee, H.C.2    Tsai, H.J.3
  • 28
    • 84884177243 scopus 로고    scopus 로고
    • Adult teleost heart expresses two distinct troponin c paralogs: Cardiac TnC and a novel and teleost-specific ssTnC in a chamber- and temperature-dependent manner
    • Genge CE, Davidson WS, Tibbits GF. 2013. Adult teleost heart expresses two distinct troponin C paralogs: cardiac TnC and a novel and teleost-specific ssTnC in a chamber- and temperature-dependent manner. Physiol Genomics. 45:866–875.
    • (2013) Physiol Genomics , vol.45 , pp. 866-875
    • Genge, C.E.1    Davidson, W.S.2    Tibbits, G.F.3
  • 30
    • 25144468303 scopus 로고    scopus 로고
    • Increasing mammalian cardiomyocyte contractility with residues identified in trout troponin
    • Gillis TE, Liang B, Chung F, Tibbits GF. 2005. Increasing mammalian cardiomyocyte contractility with residues identified in trout troponin. Physiol Genomics. 22:1–7.
    • (2005) Physiol Genomics , vol.22 , pp. 1-7
    • Gillis, T.E.1    Liang, B.2    Chung, F.3    Tibbits, G.F.4
  • 31
    • 37449015457 scopus 로고    scopus 로고
    • Functional and evolutionary relationships of troponin c
    • Gillis TE, Marshall CR, Tibbits GF. 2007. Functional and evolutionary relationships of troponin C. Physiol Genomics. 32:16–27.
    • (2007) Physiol Genomics , vol.32 , pp. 16-27
    • Gillis, T.E.1    Marshall, C.R.2    Tibbits, G.F.3
  • 33
    • 0034059761 scopus 로고    scopus 로고
    • Regulation of contraction in striated muscle
    • Gordon AM, Homsher E, Regnier M. 2000. Regulation of contraction in striated muscle. Physiol Rev. 80:853–924.
    • (2000) Physiol Rev , vol.80 , pp. 853-924
    • Gordon, A.M.1    Homsher, E.2    Regnier, M.3
  • 34
    • 84940111566 scopus 로고    scopus 로고
    • Maintenance and loss of duplicated genes by dosage subfunctionalization
    • Gout JF, Lynch M. 2015. Maintenance and loss of duplicated genes by dosage subfunctionalization. Mol Biol Evol. 32:2141–2148.
    • (2015) Mol Biol Evol , vol.32 , pp. 2141-2148
    • Gout, J.F.1    Lynch, M.2
  • 35
    • 0242666374 scopus 로고    scopus 로고
    • Functional divergence prediction from evolutionary analysis: A case study of vertebrate hemoglobin
    • Gribaldo S, Casane D, Lopez P, Philippe H. 2003. Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol Biol Evol. 20:1754–1759.
    • (2003) Mol Biol Evol , vol.20 , pp. 1754-1759
    • Gribaldo, S.1    Casane, D.2    Lopez, P.3    Philippe, H.4
  • 36
    • 0035211809 scopus 로고    scopus 로고
    • A site-specific measure for rate difference after gene duplication or speciation
    • Gu X. 2001a. A site-specific measure for rate difference after gene duplication or speciation. Mol Biol Evol. 18:2327–2330.
    • (2001) Mol Biol Evol , vol.18 , pp. 2327-2330
    • Gu, X.1
  • 37
    • 0035061686 scopus 로고    scopus 로고
    • Maximum-likelihood approach for gene family evolution under functional divergence
    • Gu X. 2001b. Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol. 18:453–464.
    • (2001) Mol Biol Evol , vol.18 , pp. 453-464
    • Gu, X.1
  • 38
    • 84878925597 scopus 로고    scopus 로고
    • An update of DIVERGE software for functional divergence analysis of protein family
    • Gu X, et al. 2013. An update of DIVERGE software for functional divergence analysis of protein family. Mol Biol Evol. 30:1713–1719.
    • (2013) Mol Biol Evol , vol.30 , pp. 1713-1719
    • Gu, X.1
  • 39
    • 0024582850 scopus 로고
    • Influence of temperature on the calcium sensitivity of the myofilaments of skinned ventricular muscle from the rabbit
    • Harrison SM, Bers DM. 1989. Influence of temperature on the calcium sensitivity of the myofilaments of skinned ventricular muscle from the rabbit. J Gen Physiol. 93:411–428.
    • (1989) J Gen Physiol , vol.93 , pp. 411-428
    • Harrison, S.M.1    Bers, D.M.2
  • 40
    • 15544389841 scopus 로고    scopus 로고
    • Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution
    • He X, Zhang J. 2005. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169:1157–1164.
    • (2005) Genetics , vol.169 , pp. 1157-1164
    • He, X.1    Zhang, J.2
  • 41
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • Hess B, Berendsen BH, Fraaije HJ, 1997. LINCS: a linear constraint solver for molecular simulations. J Comput Chem. 18:1463–1472.
    • (1997) J Comput Chem , vol.18 , pp. 1463-1472
    • Hess, B.1    Berendsen, B.H.2    Fraaije, H.J.3
  • 43
    • 0033279838 scopus 로고    scopus 로고
    • 2+ signaling of contractility
    • 2+ signaling of contractility. J Mol Evol. 49:780–788.
    • (1999) J Mol Evol , vol.49 , pp. 780-788
    • Huang, Q.Q.1    Jin, J.P.2
  • 44
    • 0028342845 scopus 로고
    • The evolution of functionally novel proteins after gene duplication
    • Hughes AL. 1994. The evolution of functionally novel proteins after gene duplication. Proc Biol Sci. 256:119–124.
    • (1994) Proc Biol Sci , vol.256 , pp. 119-124
    • Hughes, A.L.1
  • 46
    • 70349119250 scopus 로고
    • Regression and time-series model selection in small samples
    • Hurvich CM, Tsai CL. 1989. Regression and time-series model selection in small samples. Biometrika 76:297–307.
    • (1989) Biometrika , vol.76 , pp. 297-307
    • Hurvich, C.M.1    Tsai, C.L.2
  • 47
    • 75549087305 scopus 로고    scopus 로고
    • The evolution of gene duplications: Classifying and distinguishing between models
    • Innan H, Kondrashov F. 2010. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 11:97–108.
    • (2010) Nat Rev Genet , vol.11 , pp. 97-108
    • Innan, H.1    Kondrashov, F.2
  • 48
    • 80053256684 scopus 로고    scopus 로고
    • Expression of olfactory receptors in different life stages and life histories of wild Atlantic salmon (Salmo salar)
    • Johnstone KA, Lubieniecki KP, Koop BF, Davidson WS. 2011. Expression of olfactory receptors in different life stages and life histories of wild Atlantic salmon (Salmo salar). Mol Ecol. 20:4059–4069.
    • (2011) Mol Ecol , vol.20 , pp. 4059-4069
    • Johnstone, K.A.1    Lubieniecki, K.P.2    Koop, B.F.3    Davidson, W.S.4
  • 49
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275–282.
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 51
    • 68149176813 scopus 로고    scopus 로고
    • Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
    • Kassahn KS, Dang VT, Wilkins SJ, Perkins AC, Ragan MA. 2009. Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates. Genome Res. 19:1404–1418.
    • (2009) Genome Res , vol.19 , pp. 1404-1418
    • Kassahn, K.S.1    Dang, V.T.2    Wilkins, S.J.3    Perkins, A.C.4    Ragan, M.A.5
  • 52
    • 34547567980 scopus 로고    scopus 로고
    • OligoCalc: An online oligonucleotide properties calculator
    • Kibbe WA. 2007. OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res. 35:W43–W46.
    • (2007) Nucleic Acids Res , vol.35 , pp. W43-W46
    • Kibbe, W.A.1
  • 53
    • 84859145291 scopus 로고    scopus 로고
    • Toward a general model for the evolutionary dynamics of gene duplicates
    • Konrad A, Teufel AI, Grahnen JA, Liberles DA. 2011. Toward a general model for the evolutionary dynamics of gene duplicates. Genome Biol Evol. 3:1197–1209.
    • (2011) Genome Biol Evol , vol.3 , pp. 1197-1209
    • Konrad, A.1    Teufel, A.I.2    Grahnen, J.A.3    Liberles, D.A.4
  • 54
    • 84904964377 scopus 로고    scopus 로고
    • G_mmpbsa – A GROMACS tool for high-throughput MM-PBSA calculations
    • Open Source Drug Discovery C
    • Kumari R, Kumar R, Open Source Drug Discovery C, Lynn A. 2014. g_mmpbsa–a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model. 54:1951–1962.
    • (2014) J Chem Inf Model , vol.54 , pp. 1951-1962
    • Kumari, R.1    Kumar, R.2    Lynn, A.3
  • 55
    • 0000243829 scopus 로고
    • Procheck—a program to check the stereochemical quality of protein structures
    • Laskowski RA, Macarthur MW, Moss DS, Thornton JM. 1993. Procheck—a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 26:283–291.
    • (1993) J Appl Crystallogr , vol.26 , pp. 283-291
    • Laskowski, R.A.1    Macarthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 56
    • 20444476656 scopus 로고    scopus 로고
    • Structural divergence and distant relationships in proteins: Evolution of the globins
    • Lecomte JT, Vuletich DA, Lesk AM. 2005. Structural divergence and distant relationships in proteins: evolution of the globins. Curr Opin Struct Biol. 15:290–301.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 290-301
    • Lecomte, J.T.1    Vuletich, D.A.2    Lesk, A.M.3
  • 57
    • 0033614841 scopus 로고    scopus 로고
    • Binding of cardiac troponin-I147-163 induces a structural opening in human cardiac troponin-C
    • Li MX, Spyracopoulos L, Sykes BD. 1999. Binding of cardiac troponin-I147-163 induces a structural opening in human cardiac troponin-C. Biochemistry 38:8289–8298.
    • (1999) Biochemistry , vol.38 , pp. 8289-8298
    • Li, M.X.1    Spyracopoulos, L.2    Sykes, B.D.3
  • 58
    • 84921473973 scopus 로고    scopus 로고
    • Effects of HCM cTnI mutation R145G on troponin structure and modulation by PKA phosphorylation elucidated by molecular dynamics simulations
    • Lindert S, Cheng Y, Kekenes-Huskey P, Regnier M, McCammon JA. 2015. Effects of HCM cTnI Mutation R145G on troponin structure and modulation by PKA phosphorylation elucidated by molecular dynamics simulations. Biophys J. 108:395–407.
    • (2015) Biophys J , vol.108 , pp. 395-407
    • Lindert, S.1    Cheng, Y.2    Kekenes-Huskey, P.3    Regnier, M.4    McCammon, J.A.5
  • 59
    • 77953513118 scopus 로고    scopus 로고
    • Improved side-chain torsion potentials for the amber ff99SB protein force field
    • Lindorff-Larsen K, et al. 2010. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78:1950–1958.
    • (2010) Proteins , vol.78 , pp. 1950-1958
    • Lindorff-Larsen, K.1
  • 60
    • 84859812469 scopus 로고    scopus 로고
    • Evolution of mitochondrial-encoded cytochrome oxidase subunits in endothermic fish: The importance of taxon-sampling in codon-based models
    • Little AG, Lougheed SC, Moyes CD. 2012. Evolution of mitochondrial-encoded cytochrome oxidase subunits in endothermic fish: the importance of taxon-sampling in codon-based models. Mol Phylogenet Evol. 63:679–684.
    • (2012) Mol Phylogenet Evol , vol.63 , pp. 679-684
    • Little, A.G.1    Lougheed, S.C.2    Moyes, C.D.3
  • 61
    • 0037441653 scopus 로고    scopus 로고
    • Structure validation by calpha geometry: Phi,psi and cbeta deviation
    • Lovell SC, et al. 2003. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50:437–450.
    • (2003) Proteins , vol.50 , pp. 437-450
    • Lovell, S.C.1
  • 62
    • 0033972072 scopus 로고    scopus 로고
    • The probability of duplicate gene preservation by subfunctionalization
    • Lynch M, Force A. 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459–473.
    • (2000) Genetics , vol.154 , pp. 459-473
    • Lynch, M.1    Force, A.2
  • 63
    • 84926677816 scopus 로고    scopus 로고
    • The effect of species representation on the detection of positive selection in primate gene data sets
    • McBee RM, Rozmiarek SA, Meyerson NR, Rowley PA, Sawyer SL. 2015. The effect of species representation on the detection of positive selection in primate gene data sets. Mol Biol Evol. 32:1091–1096.
    • (2015) Mol Biol Evol , vol.32 , pp. 1091-1096
    • McBee, R.M.1    Rozmiarek, S.A.2    Meyerson, N.R.3    Rowley, P.A.4    Sawyer, S.L.5
  • 64
    • 0032733930 scopus 로고    scopus 로고
    • Gene and genome duplications in vertebrates: The one-to-four (-to-eight in fish) rule and the evolution of novel gene functions
    • Meyer A, Schartl M. 1999. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr Opin Cell Biol. 11:699–704.
    • (1999) Curr Opin Cell Biol , vol.11 , pp. 699-704
    • Meyer, A.1    Schartl, M.2
  • 65
    • 84871840207 scopus 로고    scopus 로고
    • Integrating sequence variation and protein structure to identify sites under selection
    • Meyer AG, Wilke CO. 2013. Integrating sequence variation and protein structure to identify sites under selection. Mol Biol Evol. 30:36–44.
    • (2013) Mol Biol Evol , vol.30 , pp. 36-44
    • Meyer, A.G.1    Wilke, C.O.2
  • 66
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, Yang Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929–936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 67
    • 0021953047 scopus 로고
    • 2+, ionic strength and pH
    • 2+, ionic strength and pH. J Biol Chem. 97:1011–1023.
    • (1985) J Biol Chem , vol.97 , pp. 1011-1023
    • Ogawa, Y.1
  • 68
    • 84888294449 scopus 로고    scopus 로고
    • A flexible algorithm for calculating pair interactions on SIMD architectures
    • Pall S, Hess B. 2013. A flexible algorithm for calculating pair interactions on SIMD architectures. Comput Phys Commun. 184:2641–2650.
    • (2013) Comput Phys Commun , vol.184 , pp. 2641-2650
    • Pall, S.1    Hess, B.2
  • 69
    • 77955438444 scopus 로고    scopus 로고
    • Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutations
    • Palpant NJ, et al. 2010. Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutations. Physiol Genomics. 42:287–299.
    • (2010) Physiol Genomics , vol.42 , pp. 287-299
    • Palpant, N.J.1
  • 70
    • 84859386743 scopus 로고    scopus 로고
    • PH-responsive titratable inotropic performance of histidine-modified cardiac troponin i
    • Palpant NJ, Houang EM, Sham YY, Metzger JM. 2012. pH-responsive titratable inotropic performance of histidine-modified cardiac troponin I. Biophys J. 102:1570–1579.
    • (2012) Biophys J , vol.102 , pp. 1570-1579
    • Palpant, N.J.1    Houang, E.M.2    Sham, Y.Y.3    Metzger, J.M.4
  • 71
    • 4444221565 scopus 로고    scopus 로고
    • UCSF chimera – A visualization system for exploratory research and analysis
    • Pettersen EF, et al. 2004. UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem. 25:1605–1612.
    • (2004) J Comput Chem , vol.25 , pp. 1605-1612
    • Pettersen, E.F.1
  • 72
    • 84934969890 scopus 로고    scopus 로고
    • Structure and dynamics of the acidosis-resistant A162H mutant of the switch region of troponin i bound to the regulatory domain of troponin c
    • Pineda-Sanabria SE, Robertson IM, Sykes BD. 2015. Structure and dynamics of the acidosis-resistant A162H mutant of the switch region of troponin I bound to the regulatory domain of troponin C. Biochemistry. 54:3583–3593.
    • (2015) Biochemistry , vol.54 , pp. 3583-3593
    • Pineda-Sanabria, S.E.1    Robertson, I.M.2    Sykes, B.D.3
  • 73
    • 84875592758 scopus 로고    scopus 로고
    • GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
    • Pronk S, et al. 2013. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29:845–854.
    • (2013) Bioinformatics , vol.29 , pp. 845-854
    • Pronk, S.1
  • 74
    • 21344439563 scopus 로고    scopus 로고
    • Subfunctionalization of duplicated genes as a transition state to neofunctionalization
    • Rastogi S, Liberles DA. 2005. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol Biol. 5:28.
    • (2005) BMC Evol Biol , vol.5 , pp. 28
    • Rastogi, S.1    Liberles, D.A.2
  • 76
    • 84863146631 scopus 로고    scopus 로고
    • Elucidation of isoform-dependent pH sensitivity of troponin i by NMR spectroscopy
    • Robertson IM, et al. 2012. Elucidation of isoform-dependent pH sensitivity of troponin I by NMR spectroscopy. J Biol Chem. 287:4996–5007.
    • (2012) J Biol Chem , vol.287 , pp. 4996-5007
    • Robertson, I.M.1
  • 77
    • 33847214241 scopus 로고    scopus 로고
    • Evolution after gene duplication: Models, mechanisms, sequences, systems, and organisms
    • Roth C, et al. 2007. Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. J Exp Zool B Mol Dev Evol. 308:58–73.
    • (2007) J Exp Zool B Mol Dev Evol , vol.308 , pp. 58-73
    • Roth, C.1
  • 78
    • 0033990048 scopus 로고    scopus 로고
    • Primer3 on the WWW for general users and for biologist programmers
    • Rozen S, Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 132:356–386.
    • (2000) Methods Mol Biol , vol.132 , pp. 356-386
    • Rozen, S.1    Skaletsky, H.2
  • 79
    • 77952490857 scopus 로고    scopus 로고
    • Phylogenomics with incomplete taxon coverage: The limits to inference
    • Sanderson MJ, McMahon MM, Steel M. 2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evol Biol. 10:155.
    • (2010) BMC Evol Biol , vol.10 , pp. 155
    • Sanderson, M.J.1    McMahon, M.M.2    Steel, M.3
  • 80
    • 46149123448 scopus 로고    scopus 로고
    • Preferential subfunctionalization of slow-evolving genes after allopolyploidization in xenopus laevis
    • Semon M, Wolfe KH. 2008. Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis. Proc Natl Acad Sci U S A. 105:8333–8338.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 8333-8338
    • Semon, M.1    Wolfe, K.H.2
  • 81
    • 0000300663 scopus 로고
    • Effect of acute and chronic temperature transition on enzymes of cardiac metabolism in white perch (Morone-Americana), yellow perch (Perca-flavescens), and smallmouth bass (Micropterus-dolomieui)
    • Sephton DH, Driedzic WR. 1991. Effect of acute and chronic temperature transition on enzymes of cardiac metabolism in white perch (Morone-Americana), yellow Perch (Perca-Flavescens), and smallmouth bass (Micropterus-Dolomieui). Can J Zool. 69:258–262.
    • (1991) Can J Zool , vol.69 , pp. 258-262
    • Sephton, D.H.1    Driedzic, W.R.2
  • 82
    • 77955730763 scopus 로고    scopus 로고
    • Evolution of the regulatory control of vertebrate striated muscle: The roles of troponin i and myosin binding protein-C
    • Shaffer JF, Gillis TE. 2010. Evolution of the regulatory control of vertebrate striated muscle: the roles of troponin I and myosin binding protein-C. Physiol Genomics. 42:406–419.
    • (2010) Physiol Genomics , vol.42 , pp. 406-419
    • Shaffer, J.F.1    Gillis, T.E.2
  • 83
    • 84942909519 scopus 로고    scopus 로고
    • The cardiac transcriptome and dilated cardiomyopathy genes in zebrafish
    • Shih YH, et al. 2015. The cardiac transcriptome and dilated cardiomyopathy genes in zebrafish. Circ Cardiovasc Genet. 8:261–9.
    • (2015) Circ Cardiovasc Genet , vol.8 , pp. 261-269
    • Shih, Y.H.1
  • 84
    • 84908154345 scopus 로고    scopus 로고
    • Biophysics of protein evolution and evolutionary protein biophysics
    • Sikosek T, Chan HS. 2014. Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface. 11:20140419.
    • (2014) J R Soc Interface , vol.11 , pp. 20140419
    • Sikosek, T.1    Chan, H.S.2
  • 85
    • 77958523252 scopus 로고    scopus 로고
    • Distinct troponin c isoform requirements in cardiac and skeletal muscle
    • Sogah VM, et al. 2010. Distinct troponin C isoform requirements in cardiac and skeletal muscle. Dev Dyn. 239:3115–3123.
    • (2010) Dev Dyn , vol.239 , pp. 3115-3123
    • Sogah, V.M.1
  • 86
    • 0031576345 scopus 로고    scopus 로고
    • Structural details of a calcium-induced molecular switch: X-ray crystallographic analysis of the calcium-saturated N-terminal domain of troponin c at 1.75 a resolution
    • Strynadka NC, et al. 1997. Structural details of a calcium-induced molecular switch: X-ray crystallographic analysis of the calcium-saturated N-terminal domain of troponin C at 1.75 A resolution. J Mol Biol. 273:238–255.
    • (1997) J Mol Biol , vol.273 , pp. 238-255
    • Strynadka, N.C.1
  • 87
    • 84863843952 scopus 로고    scopus 로고
    • Metabolism in the age of “omes
    • Suarez RK, Moyes CD. 2012. Metabolism in the age of “omes.” J Exp Biol. 215:2351–2357.
    • (2012) J Exp Biol , vol.215 , pp. 2351-2357
    • Suarez, R.K.1    Moyes, C.D.2
  • 88
    • 36349031141 scopus 로고    scopus 로고
    • Cardiac troponin i threonine 144: Role in myofilament length dependent activation
    • Tachampa K, Wang H, Farman GP, de Tombe PP. 2007. Cardiac troponin I threonine 144: role in myofilament length dependent activation. Circ Res. 101:1081–1083.
    • (2007) Circ Res , vol.101 , pp. 1081-1083
    • Tachampa, K.1    Wang, H.2    Farman, G.P.3    De Tombe, P.P.4
  • 89
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using naximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using naximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731–2739.
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1
  • 90
    • 84901257307 scopus 로고    scopus 로고
    • Molecular determinants of cardiac myocyte performance as conferred by isoform-specific TnI residues
    • Thompson BR, Houang EM, Sham YY, Metzger JM. 2014. Molecular determinants of cardiac myocyte performance as conferred by isoform-specific TnI residues. Biophys J. 106:2105–2114.
    • (2014) Biophys J , vol.106 , pp. 2105-2114
    • Thompson, B.R.1    Houang, E.M.2    Sham, Y.Y.3    Metzger, J.M.4
  • 91
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • RESEARCH0034
    • Vandesompele J, et al. 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3:RESEARCH0034.
    • (2002) Genome Biol , vol.3
    • Vandesompele, J.1
  • 92
    • 84862892391 scopus 로고    scopus 로고
    • An improved likelihood ratio test for detecting site-specific functional divergence among clades of protein-coding genes
    • Weadick CJ, Chang BS. 2012. An improved likelihood ratio test for detecting site-specific functional divergence among clades of protein-coding genes. Mol Biol Evol. 29:1297–1300.
    • (2012) Mol Biol Evol , vol.29 , pp. 1297-1300
    • Weadick, C.J.1    Chang, B.S.2
  • 93
    • 77955574001 scopus 로고    scopus 로고
    • Signatures of protein biophysics in coding sequence evolution
    • Wilke CO, Drummond DA. 2010. Signatures of protein biophysics in coding sequence evolution. Curr Opin Struct Biol. 20:385–389.
    • (2010) Curr Opin Struct Biol , vol.20 , pp. 385-389
    • Wilke, C.O.1    Drummond, D.A.2
  • 94
    • 0034687371 scopus 로고    scopus 로고
    • The proteins of linked genes evolve at similar rates
    • Williams EJ, Hurst LD. 2000. The proteins of linked genes evolve at similar rates. Nature 407:900–903.
    • (2000) Nature , vol.407 , pp. 900-903
    • Williams, E.J.1    Hurst, L.D.2
  • 95
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586–1591.
    • (2007) Mol Biol Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 96
    • 24744438019 scopus 로고    scopus 로고
    • Gene expression evolves faster in narrowly than in broadly expressed mammalian genes
    • Yang J, Su AI, Li WH. 2005. Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol. 22:2113–2118.
    • (2005) Mol Biol Evol , vol.22 , pp. 2113-2118
    • Yang, J.1    Su, A.I.2    Li, W.H.3
  • 97
    • 16344378246 scopus 로고    scopus 로고
    • Bayes empirical bayes inference of amino acid sites under positive selection
    • Yang Z, Wong WS, Nielsen R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22:1107–1118.
    • (2005) Mol Biol Evol , vol.22 , pp. 1107-1118
    • Yang, Z.1    Wong, W.S.2    Nielsen, R.3
  • 98
    • 36949019322 scopus 로고    scopus 로고
    • Detecting coevolution in and among protein domains
    • Yeang CH, Haussler D. 2007. Detecting coevolution in and among protein domains. PLoS Comput Biol. 3:e211.
    • (2007) PLoS Comput Biol , vol.3 , pp. e211
    • Yeang, C.H.1    Haussler, D.2
  • 99
    • 27844439855 scopus 로고    scopus 로고
    • Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    • Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 22:2472–2479.
    • (2005) Mol Biol Evol , vol.22 , pp. 2472-2479
    • Zhang, J.1    Nielsen, R.2    Yang, Z.3


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