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Volumn 304, Issue , 2012, Pages 211-218

Looking for a sequence based allostery definition: A statistical journey at different resolution scales

Author keywords

Allosteric drugs; Co evolution; Free energy transfer; Hydrophobicity; Recurrence quantification analysis

Indexed keywords

DATA SET; HYDROPHOBICITY; OPTIMIZATION; PROTEIN; STATISTICAL ANALYSIS;

EID: 84859931654     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2012.03.005     Document Type: Article
Times cited : (7)

References (48)
  • 1
    • 33847609615 scopus 로고    scopus 로고
    • A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase
    • Amaro R.E., Sethi A., Myers R.S., Davisson V.J., Luthey-Schulten Z.A. A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase. Biochemistry 2007, 46:2156-2173.
    • (2007) Biochemistry , vol.46 , pp. 2156-2173
    • Amaro, R.E.1    Sethi, A.2    Myers, R.S.3    Davisson, V.J.4    Luthey-Schulten, Z.A.5
  • 2
    • 84861192609 scopus 로고    scopus 로고
    • Ph.D, Computational and Experimental Investigation of Allosteric Communication in the Transcriptional Regulator NikR., Washington University in St. Louis.
    • Bradley, Michael John, Ph.D, Computational and Experimental Investigation of Allosteric Communication in the Transcriptional Regulator NikR., Washington University in St. Louis, 203 (2009) 3387550.
    • (2009) , vol.203 , pp. 3387550
    • Bradley, M.J.1
  • 5
    • 33749055796 scopus 로고    scopus 로고
    • Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES
    • Chennubhotla C., Bahar I. Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol. Syst. Biol. 2006, 2:1-13.
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 1-13
    • Chennubhotla, C.1    Bahar, I.2
  • 6
    • 70149085599 scopus 로고    scopus 로고
    • Simpler methods do it better: success of Recurrence Quantification Analysis as a general purpose data analysis tool
    • Charles L.Webber, Marwan Norbert, Facchini Angelo, Giuliani Alessandro Simpler methods do it better: success of Recurrence Quantification Analysis as a general purpose data analysis tool. Phys. Lett. A 2009, 373:3753-3756.
    • (2009) Phys. Lett. A , vol.373 , pp. 3753-3756
    • Charles, L.1    Marwan, N.2    Facchini, A.3    Giuliani, A.4
  • 8
    • 41149104308 scopus 로고    scopus 로고
    • Allostery: absence of a change in shape does not imply that allostery is not at play
    • Chung-Jung Tsai Antonio Del Sol, Nussinov Ruth Allostery: absence of a change in shape does not imply that allostery is not at play. J. Mol. Biol. 2008, 378(1):1-11.
    • (2008) J. Mol. Biol. , vol.378 , Issue.1 , pp. 1-11
    • Chung-Jung Tsai, A.D.S.1    Nussinov, R.2
  • 9
    • 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, 2:0019.
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 0019
    • Del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 10
    • 33947419241 scopus 로고    scopus 로고
    • Local motions in a benchmark of allosteric proteins
    • Daily M.D., Gray J.J. Local motions in a benchmark of allosteric proteins. Proteins 2007, 67:385-399.
    • (2007) Proteins , vol.67 , pp. 385-399
    • Daily, M.D.1    Gray, J.J.2
  • 11
    • 31344432159 scopus 로고    scopus 로고
    • Thirumalai Determination of network of residues that regulate allostery in protein families using sequence analysis
    • Dima Ruxandra I., Thirumalai Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci. 2006, 15:258-268.
    • (2006) Protein Sci. , vol.15 , pp. 258-268
    • Dima, R.I.1
  • 12
    • 73349121291 scopus 로고    scopus 로고
    • Structure-based predictive models for allosteric hot spots
    • Demerdash Omar N.A., Daily Michael D., Mitchell Julie C. Structure-based predictive models for allosteric hot spots. PLoS Comput. Biol. 2009, 5(10):e1000531.
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.10
    • Demerdash, O.N.A.1    Daily, M.D.2    Mitchell, J.C.3
  • 14
    • 0035951105 scopus 로고    scopus 로고
    • Engineered disulfide linking the hinge regions within lactose repressor dimer increases operator affinity decreases sequence selectivity and alters allostery
    • Falcon C.M., Matthews K.S. Engineered disulfide linking the hinge regions within lactose repressor dimer increases operator affinity decreases sequence selectivity and alters allostery. Biochemistry 2001, 40:15650-15659.
    • (2001) Biochemistry , vol.40 , pp. 15650-15659
    • Falcon, C.M.1    Matthews, K.S.2
  • 15
    • 6344219895 scopus 로고    scopus 로고
    • Is allostery an intrinsic property of all dynamic proteins? Proteins: structure
    • Gunasekaran K., Ma B., Nussinov R. Is allostery an intrinsic property of all dynamic proteins? Proteins: structure. Funct. Bioinf. 2004, 57:433-443.
    • (2004) Funct. Bioinf. , vol.57 , pp. 433-443
    • Gunasekaran, K.1    Ma, B.2    Nussinov, R.3
  • 16
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular motions
    • Gerstein M., Krebs W.G. A database of macromolecular motions. Nucleic Acids Res. 1998, 26:4280-4290.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.G.2
  • 17
    • 0036467156 scopus 로고    scopus 로고
    • Recurrence quantification analysis reveals interaction patterns in paramyxoviridae envelope glycoproteins
    • Giuliani A., Tomasi M. Recurrence quantification analysis reveals interaction patterns in paramyxoviridae envelope glycoproteins. Proteins 2002, 46:171-176.
    • (2002) Proteins , vol.46 , pp. 171-176
    • Giuliani, A.1    Tomasi, M.2
  • 18
    • 0037402099 scopus 로고    scopus 로고
    • Large contact surface interaction between proteins detected by time series analysis methods: case study on C-phycocyanins
    • Giuliani A., Benigni R., Colafranceschi M., Chandrashekar I., Cowsik S.M. Large contact surface interaction between proteins detected by time series analysis methods: case study on C-phycocyanins. Proteins 2003, 51:299-310.
    • (2003) Proteins , vol.51 , pp. 299-310
    • Giuliani, A.1    Benigni, R.2    Colafranceschi, M.3    Chandrashekar, I.4    Cowsik, S.M.5
  • 20
    • 0036558478 scopus 로고    scopus 로고
    • Nonlinear signal analysis methods in the elucidation of protein sequence/structure relationships
    • Giuliani A., Benigni R., Zbilut J.P., Webber C.L., Sirabella P., Colosimo A. Nonlinear signal analysis methods in the elucidation of protein sequence/structure relationships. Chem. Rev. 2002, 102:1471-1491.
    • (2002) Chem. Rev. , vol.102 , pp. 1471-1491
    • Giuliani, A.1    Benigni, R.2    Zbilut, J.P.3    Webber, C.L.4    Sirabella, P.5    Colosimo, A.6
  • 21
    • 0030580089 scopus 로고    scopus 로고
    • Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors
    • Hilser V.J., Freire E. Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J. Mol. Biol. 1996, 262:756-772.
    • (1996) J. Mol. Biol. , vol.262 , pp. 756-772
    • Hilser, V.J.1    Freire, E.2
  • 24
    • 84861192610 scopus 로고    scopus 로고
    • http://www.drgutman.org/ORIGINAL_PAPERS/%2314.pdf.
  • 25
    • 84861202190 scopus 로고    scopus 로고
    • http://onlinelibrary.wiley.com/doi/10.1002/bip.20607/full.
  • 26
    • 0035810165 scopus 로고    scopus 로고
    • Functional proteins from a random-sequence library
    • Keefe A.D., Szostak J.V. Functional proteins from a random-sequence library. Nature 2001, 410:715-718.
    • (2001) Nature , vol.410 , pp. 715-718
    • Keefe, A.D.1    Szostak, J.V.2
  • 27
    • 0036468436 scopus 로고    scopus 로고
    • The modular logic of signaling proteins: building allosteric switches from simple binding domains
    • Lim W.A. The modular logic of signaling proteins: building allosteric switches from simple binding domains. Curr. Opin. Struct. Biol. 2002, 12:61-68.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 61-68
    • Lim, W.A.1
  • 28
    • 31944447675 scopus 로고    scopus 로고
    • Ensemble-based signatures of energy propagation in proteins: a new view of an old phenomenon
    • Liu T., Whitten S.T., Hilser V.J. Ensemble-based signatures of energy propagation in proteins: a new view of an old phenomenon. Proteins: Struct. Funct. Bioinf. 2006, 62:728-738.
    • (2006) Proteins: Struct. Funct. Bioinf. , vol.62 , pp. 728-738
    • Liu, T.1    Whitten, S.T.2    Hilser, V.J.3
  • 29
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionary conserved pathways of energetic connectivity in protein families
    • Lockless S.W., Ranganathan R. Evolutionary conserved pathways of energetic connectivity in protein families. Science 1999, 286:295-299.
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 30
    • 73649152457 scopus 로고
    • Allosteric proteins and cellular control systems
    • Monod J., Changeux J.P., Jacob F. Allosteric proteins and cellular control systems. J. Mol. Biol. 1963, 20:306-329.
    • (1963) J. Mol. Biol. , vol.20 , pp. 306-329
    • Monod, J.1    Changeux, J.P.2    Jacob, F.3
  • 32
    • 33846338227 scopus 로고    scopus 로고
    • Recurrence plots for the analysis of complex systems
    • Marwan N., Carmen R.M., Thiel M., Kurths J. Recurrence plots for the analysis of complex systems. Phys. Rep. 2007, 438:237-329.
    • (2007) Phys. Rep. , vol.438 , pp. 237-329
    • Marwan, N.1    Carmen, R.M.2    Thiel, M.3    Kurths, J.4
  • 34
    • 81755184126 scopus 로고    scopus 로고
    • Allo-network drugs: harnessing allostery in cellular networks
    • Nussinov R., Tsai C.J., Csermely P. Allo-network drugs: harnessing allostery in cellular networks. Trends Pharmacol. Sci. 2011, 32(12):686-693.
    • (2011) Trends Pharmacol. Sci. , vol.32 , Issue.12 , pp. 686-693
    • Nussinov, R.1    Tsai, C.J.2    Csermely, P.3
  • 35
    • 22444450449 scopus 로고    scopus 로고
    • Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
    • Ota N., Agard D.A. Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J. Mol. Biol. 2005, 351:345-354.
    • (2005) J. Mol. Biol. , vol.351 , pp. 345-354
    • Ota, N.1    Agard, D.A.2
  • 36
    • 2442499615 scopus 로고    scopus 로고
    • Discrimination of single amino acid mutations of the p53 protein by means of deterministic singularities of Recurrence Quantification Analysis
    • Porrello A., Soddu S., Zbilut J.P., Crescenzi M., Giuliani A. Discrimination of single amino acid mutations of the p53 protein by means of deterministic singularities of Recurrence Quantification Analysis. Proteins: Struct. Funct. Bioinf. 2004, 55:743-755.
    • (2004) Proteins: Struct. Funct. Bioinf. , vol.55 , pp. 743-755
    • Porrello, A.1    Soddu, S.2    Zbilut, J.P.3    Crescenzi, M.4    Giuliani, A.5
  • 40
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • (Publication PDF at 〈〉).
    • Tamura K., Dudley J., Nei M., Kumar S., MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24 (2007) 1596-1599. (Publication PDF at 〈〉). http://www.kumarlab.net/publications.
    • (2007) Molecular Biology and Evolution , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 42
    • 0035799336 scopus 로고    scopus 로고
    • Reaction path of phosphofructo-1-kinase is altered by mutagenesis and alternative substrates
    • Wang X., Kemp R.G. Reaction path of phosphofructo-1-kinase is altered by mutagenesis and alternative substrates. Biochemistry 2001, 40:3938-3942.
    • (2001) Biochemistry , vol.40 , pp. 3938-3942
    • Wang, X.1    Kemp, R.G.2
  • 43
    • 15444362906 scopus 로고    scopus 로고
    • Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins
    • Whitten S.T., Garcia-Moreno B., Hilser V.J. Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins. Proc. Nat. Acad. Sci. U.S.A. 2005, 102:4282-4287.
    • (2005) Proc. Nat. Acad. Sci. U.S.A. , vol.102 , pp. 4282-4287
    • Whitten, S.T.1    Garcia-Moreno, B.2    Hilser, V.J.3
  • 44
    • 13844276692 scopus 로고    scopus 로고
    • Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model
    • Zheng W.J., Brooks B. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. J. Mol. Biol. 2005, 346:745-759.
    • (2005) J. Mol. Biol. , vol.346 , pp. 745-759
    • Zheng, W.J.1    Brooks, B.2
  • 45
    • 34248586875 scopus 로고    scopus 로고
    • Toward the mechanism of dynamical couplings and translocation in Hepatitis C Virus NS3 helicase using elastic network model
    • Zheng W.J., Liao J.C., Brooks B.R., Doniach S. Toward the mechanism of dynamical couplings and translocation in Hepatitis C Virus NS3 helicase using elastic network model. Proteins: Struct. Funct. Bioinf. 2007, 67:886-896.
    • (2007) Proteins: Struct. Funct. Bioinf. , vol.67 , pp. 886-896
    • Zheng, W.J.1    Liao, J.C.2    Brooks, B.R.3    Doniach, S.4
  • 46
    • 0042639046 scopus 로고    scopus 로고
    • Detecting deterministic signals in exceptionally noisy environments using Cross-Recurrence Quantification
    • Zbilut J.P., Giuliani A., Webber C.L. Detecting deterministic signals in exceptionally noisy environments using Cross-Recurrence Quantification. Phys. Lett. A 1998, 246:122-128.
    • (1998) Phys. Lett. A , vol.246 , pp. 122-128
    • Zbilut, J.P.1    Giuliani, A.2    Webber, C.L.3
  • 47
    • 0042639046 scopus 로고    scopus 로고
    • Detecting deterministic signals in exceptionally noisy environments using Cross-Recurrence Quantification
    • Zbilut J.P., Giuliani A., Webber C.L. Detecting deterministic signals in exceptionally noisy environments using Cross-Recurrence Quantification. Phys. Lett. A 1998, 246:122-128.
    • (1998) Phys. Lett. A , vol.246 , pp. 122-128
    • Zbilut, J.P.1    Giuliani, A.2    Webber, C.L.3
  • 48
    • 11144308782 scopus 로고    scopus 로고
    • Charge and hydrophobicity patterning along the sequence predicts the folding mechanism and aggregation of proteins: a computational approach
    • Zbilut J.P., Giuliani A., Colosimo A., Mitchell J.C., Colafrancesch M., Marwan N., Webber C.L., Uversky V. Charge and hydrophobicity patterning along the sequence predicts the folding mechanism and aggregation of proteins: a computational approach. J. Proteome Res. 2004, 3:1243-1253.
    • (2004) J. Proteome Res. , vol.3 , pp. 1243-1253
    • Zbilut, J.P.1    Giuliani, A.2    Colosimo, A.3    Mitchell, J.C.4    Colafrancesch, M.5    Marwan, N.6    Webber, C.L.7    Uversky, V.8


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