메뉴 건너뛰기




Volumn 348, Issue , 2014, Pages 55-64

Residue interaction network analysis of Dronpa and a DNA clamp

Author keywords

Communication pathway; Network theory; Protein topology; Small world

Indexed keywords

DNA DIRECTED DNA POLYMERASE BETA; DRONPA PROTEIN; GREEN FLUORESCENT PROTEIN; UNCLASSIFIED DRUG; BETA SUBUNIT, DNA POLYMERASE III; DNA DIRECTED DNA POLYMERASE GAMMA; PHOTOPROTEIN; PROTEIN;

EID: 84896335283     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2014.01.023     Document Type: Article
Times cited : (60)

References (53)
  • 1
    • 33745684683 scopus 로고    scopus 로고
    • Weighted and unweighted network of amino acids within protein
    • Aftabuddin M., Kundu S. Weighted and unweighted network of amino acids within protein. Physica A 2006, 396:895-904.
    • (2006) Physica A , vol.396 , pp. 895-904
    • Aftabuddin, M.1    Kundu, S.2
  • 2
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • Albert R., Jeong Hawoong., Barabási A.L. Error and attack tolerance of complex networks. Nature 2000, 406:378-382.
    • (2000) Nature , vol.406 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabási, A.L.3
  • 4
    • 65649138753 scopus 로고    scopus 로고
    • Perturbation Waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design
    • Antal M.A., Csaba B., Csermely P. Perturbation Waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design. Curr. Protein Pept. Sci. 2009, 10:161-172.
    • (2009) Curr. Protein Pept. Sci. , vol.10 , pp. 161-172
    • Antal, M.A.1    Csaba, B.2    Csermely, P.3
  • 6
    • 0346057951 scopus 로고    scopus 로고
    • Small-world communication of residues and significance for protein dynamics
    • Atilgan A.R., Akan P., Baysal C. Small-world communication of residues and significance for protein dynamics. Biophys. J. 2004, 86:85-91.
    • (2004) Biophys. J. , vol.86 , pp. 85-91
    • Atilgan, A.R.1    Akan, P.2    Baysal, C.3
  • 7
    • 9944223645 scopus 로고    scopus 로고
    • Network properties of protein structures
    • Bagler G., Sinha S. Network properties of protein structures. Phys. A: Stat. Mech. Appl. 2005, 346:27-33.
    • (2005) Phys. A: Stat. Mech. Appl. , vol.346 , pp. 27-33
    • Bagler, G.1    Sinha, S.2
  • 8
    • 34547909602 scopus 로고    scopus 로고
    • Assortative mixing in protein contact networks and protein folding kinetics
    • Bagler G., Sinha S. Assortative mixing in protein contact networks and protein folding kinetics. Bioinformatics 2007, 23:1760-1767.
    • (2007) Bioinformatics , vol.23 , pp. 1760-1767
    • Bagler, G.1    Sinha, S.2
  • 9
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I., Atilgan A.R., Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des. 1997, 2:173-181.
    • (1997) Fold Des. , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 10
    • 49749137012 scopus 로고    scopus 로고
    • Analysis of protein folds using protein contact networks
    • Barah P., Sinha S. Analysis of protein folds using protein contact networks. Pramana - J. Phys. 2008, 71:369-378.
    • (2008) Pramana - J. Phys. , vol.71 , pp. 369-378
    • Barah, P.1    Sinha, S.2
  • 11
    • 38049119840 scopus 로고    scopus 로고
    • The effect of backbone on the small-world properties of protein contact maps
    • Bartoli L., Fariselli P., Casadio R. The effect of backbone on the small-world properties of protein contact maps. Phys. Biol. 2007, 4:L1-L5.
    • (2007) Phys. Biol. , vol.4
    • Bartoli, L.1    Fariselli, P.2    Casadio, R.3
  • 14
    • 34250835708 scopus 로고    scopus 로고
    • From molecular to biological structure and back
    • Bonchev D., Buck G.A. From molecular to biological structure and back. J. Chem. Inf. Model. 2007, 47:909-917.
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 909-917
    • Bonchev, D.1    Buck, G.A.2
  • 15
    • 29244487908 scopus 로고    scopus 로고
    • Oligomeric protein structure networks: insights into protein-protein interactions
    • Brinda K.V., Vishveshwara S. Oligomeric protein structure networks: insights into protein-protein interactions. BMC Bioinformatics 2005, 6:296.
    • (2005) BMC Bioinformatics , vol.6 , pp. 296
    • Brinda, K.V.1    Vishveshwara, S.2
  • 16
    • 28444453011 scopus 로고    scopus 로고
    • A network representation of protein structures: implications for protein stability
    • Brinda K.V., Vishveshwara.S. A network representation of protein structures: implications for protein stability. Biophys. J. 2005, 89:4159-4170.
    • (2005) Biophys. J. , vol.89 , pp. 4159-4170
    • Brinda, K.V.1    Vishveshwara, S.2
  • 18
    • 84861779036 scopus 로고    scopus 로고
    • Topological analysis and interactive visualization of biological networks and protein structures
    • Doncheva N.T., Assenov Y., Domingues F.S., Albrecht M. Topological analysis and interactive visualization of biological networks and protein structures. Nat. Protoc. 2012, 7:670-685.
    • (2012) Nat. Protoc. , vol.7 , pp. 670-685
    • Doncheva, N.T.1    Assenov, Y.2    Domingues, F.S.3    Albrecht, M.4
  • 19
    • 84863114942 scopus 로고    scopus 로고
    • Residue centrality in alpha helical polytopic transmembrane protein structures
    • Emerson I.A., Gothandam K.M. Residue centrality in alpha helical polytopic transmembrane protein structures. J. Theor. Biol. 2012, 309:78-87.
    • (2012) J. Theor. Biol. , vol.309 , pp. 78-87
    • Emerson, I.A.1    Gothandam, K.M.2
  • 20
    • 80455143537 scopus 로고    scopus 로고
    • Network analysis of transmembrane protein structures
    • Emerson I.A., Gothandam K.M. Network analysis of transmembrane protein structures. Phys. A: Stat. Mech. Appl. 2012, 391:905-916.
    • (2012) Phys. A: Stat. Mech. Appl. , vol.391 , pp. 905-916
    • Emerson, I.A.1    Gothandam, K.M.2
  • 21
    • 84879416017 scopus 로고    scopus 로고
    • Fast approximate method of identifying paths of allosteric communication in proteins
    • Erman B.A. Fast approximate method of identifying paths of allosteric communication in proteins. Proteins 2013, 81:1097-1101.
    • (2013) Proteins , vol.81 , pp. 1097-1101
    • Erman, B.A.1
  • 22
    • 77749318502 scopus 로고    scopus 로고
    • Universality in protein residue networks
    • Estrada E. Universality in protein residue networks. Biophys. J. 2010, 98:890-900.
    • (2010) Biophys. J. , vol.98 , pp. 890-900
    • Estrada, E.1
  • 23
    • 77951079392 scopus 로고    scopus 로고
    • Investigation of proteins folding rates and their properties of amino acid networks
    • Fang Y.P., Ma D.C., Li M.L., Wen Z.N., Diao Y.B. Investigation of proteins folding rates and their properties of amino acid networks. Chemometrics Intell. Lab. Syst. 2010, 101:123-129.
    • (2010) Chemometrics Intell. Lab. Syst. , vol.101 , pp. 123-129
    • Fang, Y.P.1    Ma, D.C.2    Li, M.L.3    Wen, Z.N.4    Diao, Y.B.5
  • 24
    • 35648944297 scopus 로고    scopus 로고
    • A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
    • Ghosh A., Vishveshwara S. A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:15711-15716.
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 15711-15716
    • Ghosh, A.1    Vishveshwara, S.2
  • 25
    • 84870336885 scopus 로고    scopus 로고
    • Protein structure networks
    • Greene L.H. Protein structure networks. Brief. Funct. Genomics 2012, 11:469-478.
    • (2012) Brief. Funct. Genomics , vol.11 , pp. 469-478
    • Greene, L.H.1
  • 26
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • Greene L.H., Higman V.A. Uncovering network systems within protein structures. J. Mol. Biol. 2003, 334:781-791.
    • (2003) J. Mol. Biol. , vol.334 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 27
    • 38549092067 scopus 로고    scopus 로고
    • HotSprint: database of computational hot spots in protein interfaces
    • Guney E., Tuncbag N., Keskin O., Gursoy A. HotSprint: database of computational hot spots in protein interfaces. Nucleic Acids Res. 2008, 36:D662-666.
    • (2008) Nucleic Acids Res. , vol.36
    • Guney, E.1    Tuncbag, N.2    Keskin, O.3    Gursoy, A.4
  • 28
    • 84856456583 scopus 로고    scopus 로고
    • The harmonic analysis of cylindrically symmetric proteins: a comparison of Dronpa and a DNA sliding clamp
    • Hu G., Michielssens S., Moors S.L.C., Ceulemans A. The harmonic analysis of cylindrically symmetric proteins: a comparison of Dronpa and a DNA sliding clamp. J. Mol. Gr. Model. 2012, 34:28-37.
    • (2012) J. Mol. Gr. Model. , vol.34 , pp. 28-37
    • Hu, G.1    Michielssens, S.2    Moors, S.L.C.3    Ceulemans, A.4
  • 29
    • 84878604130 scopus 로고    scopus 로고
    • The Topology and dynamics of protein complexes: insights from intra- molecular network theory
    • Hu G., Zhou J., Yan W., Chen J., Shen B. The Topology and dynamics of protein complexes: insights from intra- molecular network theory. Curr. Protein Pept. Sci. 2013, 14:121-132.
    • (2013) Curr. Protein Pept. Sci. , vol.14 , pp. 121-132
    • Hu, G.1    Zhou, J.2    Yan, W.3    Chen, J.4    Shen, B.5
  • 30
    • 84055221808 scopus 로고    scopus 로고
    • Scoring function based on weighted residue network
    • Jiao X., Chang S. Scoring function based on weighted residue network. Int. J. Mol. Sci. 2011, 12:8773-8786.
    • (2011) Int. J. Mol. Sci. , vol.12 , pp. 8773-8786
    • Jiao, X.1    Chang, S.2
  • 31
    • 0033578690 scopus 로고    scopus 로고
    • Identification of side-chain clusters in protein structures by a graph spectral method
    • Kannan.N., Vishveshwara S. Identification of side-chain clusters in protein structures by a graph spectral method. J. Mol. Biol. 1999, 292:441-464.
    • (1999) J. Mol. Biol. , vol.292 , pp. 441-464
    • Kannan, N.1    Vishveshwara, S.2
  • 32
    • 0026717535 scopus 로고
    • Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp
    • Kong X.P., Onrust R., O'Donnell M., Kuriyan J. Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell 1992, 69:425-437.
    • (1992) Cell , vol.69 , pp. 425-437
    • Kong, X.P.1    Onrust, R.2    O'Donnell, M.3    Kuriyan, J.4
  • 34
    • 9944232975 scopus 로고    scopus 로고
    • Amino acids network within protein
    • Kundu S. Amino acids network within protein. Physica A 2005, 346:104-109.
    • (2005) Physica A , vol.346 , pp. 104-109
    • Kundu, S.1
  • 35
    • 79960149420 scopus 로고    scopus 로고
    • RING: networking interacting residues, evolutionary information and energetics in protein structures
    • Martin A.J., Vidotto M., Boscariol F., Di Domenico T., Walsh I., Tosatto S.C.E. RING: networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics 2011, 27:2003-2005.
    • (2011) Bioinformatics , vol.27 , pp. 2003-2005
    • Martin, A.J.1    Vidotto, M.2    Boscariol, F.3    Di Domenico, T.4    Walsh, I.5    Tosatto, S.C.E.6
  • 36
    • 84867738584 scopus 로고    scopus 로고
    • Structural and functional analysis of hemoglobin and serum albumin through protein long-range interaction networks
    • Paci P., Di Paola L., Santoni D., De Ruvo M., Giuliani A. Structural and functional analysis of hemoglobin and serum albumin through protein long-range interaction networks. Curr. Proteomics 2012, 9:160-166.
    • (2012) Curr. Proteomics , vol.9 , pp. 160-166
    • Paci, P.1    Di Paola, L.2    Santoni, D.3    De Ruvo, M.4    Giuliani, A.5
  • 37
    • 84875170915 scopus 로고    scopus 로고
    • Protein contact networks: an emerging paradigm in chemistry
    • Paola L.D., Ruvo M.D., Paci P., Santoni D., Giuliani A. Protein contact networks: an emerging paradigm in chemistry. Chem. Rev. 2013, 113:1598-1613.
    • (2013) Chem. Rev. , vol.113 , pp. 1598-1613
    • Paola, L.D.1    Ruvo, M.D.2    Paci, P.3    Santoni, D.4    Giuliani, A.5
  • 38
    • 84877736250 scopus 로고    scopus 로고
    • A mixed protein structure network and elastic network model approach to predict the structural communication in biomolecular systems
    • Raimondi F., Felline A., Seeber M., Mariani S., Fanelli F. A mixed protein structure network and elastic network model approach to predict the structural communication in biomolecular systems. J. Chem. Theory Computation 2013, 9:2504-2518.
    • (2013) J. Chem. Theory Computation , vol.9 , pp. 2504-2518
    • Raimondi, F.1    Felline, A.2    Seeber, M.3    Mariani, S.4    Fanelli, F.5
  • 40
    • 12944331889 scopus 로고    scopus 로고
    • Small-world network approach to identify key residues in protein-protein interaction
    • del Sol A., O'Meara P. Small-world network approach to identify key residues in protein-protein interaction. Proteins 2004, 58:672-682.
    • (2004) Proteins , vol.58 , pp. 672-682
    • del Sol, A.1    O'Meara, P.2
  • 41
    • 33745461893 scopus 로고    scopus 로고
    • Residues crucial for maintaining short paths in network communication mediate signaling in proteins
    • del Sol A., Fujihashi H., Amoros D., Nussinov R. Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol. Syst. Biol. 2006, 2(2006):0019.
    • (2006) Mol. Syst. Biol. , vol.2 , Issue.2006 , pp. 0019
    • del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 42
    • 79955715044 scopus 로고    scopus 로고
    • From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation
    • Sun W., He J. From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation. PLoS One 2011, 6:e19238.
    • (2011) PLoS One , vol.6
    • Sun, W.1    He, J.2
  • 43
    • 58149119413 scopus 로고    scopus 로고
    • Cutoff variation induces different topological properties: A new discovery of amino acid network within protein
    • Tao Y., Zou X.Q., Huang S.Y., Zou X.W. Cutoff variation induces different topological properties: A new discovery of amino acid network within protein. J. Theor. Biol. 2009, 256:408-413.
    • (2009) J. Theor. Biol. , vol.256 , pp. 408-413
    • Tao, Y.1    Zou, X.Q.2    Huang, S.Y.3    Zou, X.W.4
  • 44
    • 84896337730 scopus 로고    scopus 로고
    • Small world network strategies for studying protein structures and binding
    • Taylor N.R. Small world network strategies for studying protein structures and binding. Computational Struct. Biotechnol. J. 2013, 5:e201302006.
    • (2013) Computational Struct. Biotechnol. J. , vol.5
    • Taylor, N.R.1
  • 45
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 1996, 77:1905-1908.
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 48
    • 41349118690 scopus 로고    scopus 로고
    • Small-world view of the amino acids that play a key role in protein folding
    • 061910:1-061910:4
    • Vendruscolo M., Dokholyan N.V., Paci E., Karplus M. Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E 2002, 65:061910:1-061910:4.
    • (2002) Phys. Rev. E , vol.65
    • Vendruscolo, M.1    Dokholyan, N.V.2    Paci, E.3    Karplus, M.4
  • 49
    • 65649089458 scopus 로고    scopus 로고
    • Intra and inter-molecular communications through protein structure network
    • Vishveshwara S., Ghosh A., Hansia P. Intra and inter-molecular communications through protein structure network. Curr. Protein Pept. Sci. 2009, 10:146-160.
    • (2009) Curr. Protein Pept. Sci. , vol.10 , pp. 146-160
    • Vishveshwara, S.1    Ghosh, A.2    Hansia, P.3
  • 50
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of small-world networks
    • Watts D.J., Strogatz S.H. Collective dynamics of small-world networks. Nature 1998, 393:440-442.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 52
    • 84895515580 scopus 로고    scopus 로고
    • SVR-CAF: an integrated score function for detecting native protein structures among decoys. Proteins, (in press).
    • Zhou, J., Yan, W., Hu, G., Shen, B., SVR_CAF: an integrated score function for detecting native protein structures among decoys. Proteins, (in press). http://dx.doi.org/10.1002/prot.24421.
    • Zhou, J.1    Yan, W.2    Hu, G.3    Shen, B.4
  • 53
    • 84896357579 scopus 로고    scopus 로고
    • Amino acid network for the discrimination of native protein structures from decoys
    • (accepted for publication).
    • Zhou J., Yan W., Hu G., Shen B. Amino acid network for the discrimination of native protein structures from decoys. Curr. Protein Pept. Sci. 2014, (accepted for publication).
    • (2014) Curr. Protein Pept. Sci.
    • Zhou, J.1    Yan, W.2    Hu, G.3    Shen, B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.