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Volumn 31, Issue 2, 2013, Pages 142-157

Light on the structural communication in Ras GTPases

Author keywords

Communication paths; Guanine nucleotide binding proteins; Molecular dynamics simulations; Protein structure network analysis

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR 1; AMINO ACID; H RAS PROTEIN; NUCLEOTIDE; RAS PROTEIN; RHOA GUANINE NUCLEOTIDE BINDING PROTEIN; SEC4 PROTEIN; UNCLASSIFIED DRUG;

EID: 84875191768     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.698379     Document Type: Article
Times cited : (19)

References (61)
  • 3
    • 79953726279 scopus 로고    scopus 로고
    • Conserved amino acids participate in the structure networks deputed to intramolecular communication in the lutropin receptor
    • Angelova, K., Felline, A., Lee, M., Patel, M., Puett, D., & Fanelli, F. (2011). Conserved amino acids participate in the structure networks deputed to intramolecular communication in the lutropin receptor. Cellular and Molecular Life Sciences, 68, 1227-1239.
    • (2011) Cellular and Molecular Life Sciences , vol.68 , pp. 1227-1239
    • Angelova, K.1    Felline, A.2    Lee, M.3    Patel, M.4    Puett, D.5    Fanelli, F.6
  • 4
    • 36549043024 scopus 로고    scopus 로고
    • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    • Bahar, I., Chennubhotla, C., & Tobi, D. (2007). Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Current Opinion in Structural Biology, 17, 633-640.
    • (2007) Current Opinion in Structural Biology , vol.17 , pp. 633-640
    • Bahar, I.1    Chennubhotla, C.2    Tobi, D.3
  • 6
    • 77949907106 scopus 로고    scopus 로고
    • Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks
    • Bhattacharyya, M., Ghosh, A., Hansia, P., & Vishveshwara, S. (2010). Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks. Proteins, 78, 506-517.
    • (2010) Proteins , Issue.78 , pp. 506-517
    • Bhattacharyya, M.1    Ghosh, A.2    Hansia, P.3    Vishveshwara, S.4
  • 8
    • 0024376173 scopus 로고
    • Ras oncogenes in human cancer: A review
    • Bos, J.L. (1989). Ras oncogenes in human cancer: A review. Cancer Research, 49, 4682-4689.
    • (1989) Cancer Research , vol.49 , pp. 4682-4689
    • Bos, J.L.1
  • 9
    • 26844503957 scopus 로고    scopus 로고
    • Insights into the quaternary association of proteins through structure graphs: A case study of lectins
    • Brinda, K.V., Surolia, A., & Vishveshwara, S. (2005). Insights into the quaternary association of proteins through structure graphs: A case study of lectins. Biochemical Journal, 391, 1-15.
    • (2005) Biochemical Journal , vol.391 , pp. 1-15
    • Brinda, K.V.1    Surolia, A.2    Vishveshwara, S.3
  • 10
    • 28444453011 scopus 로고    scopus 로고
    • A network representation of protein structures: Implications for protein stability
    • Brinda, K.V., & Vishveshwara, S. (2005). A network representation of protein structures: Implications for protein stability. Biophysical Journal, 89, 4159-4170.
    • (2005) Biophysical Journal , vol.89 , pp. 4159-4170
    • Brinda, K.V.1    Vishveshwara, S.2
  • 13
    • 33749055796 scopus 로고    scopus 로고
    • Markov propagation of allosteric effects in biomolecular systems: Application to GroEL-GroES
    • Chennubhotla, C., & Bahar, I. (2006). Markov propagation of allosteric effects in biomolecular systems: Application to GroEL-GroES. Molecular Systems Biology, 2, 1-13.
    • (2006) Molecular Systems Biology , vol.2 , pp. 1-13
    • Chennubhotla, C.1    Bahar, I.2
  • 14
    • 34848882812 scopus 로고    scopus 로고
    • Signal propagation in proteins and relation to equilibrium fluctuations
    • Chennubhotla, C., & Bahar, I. (2007). Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Computational Biology, 3, 1716-1726.
    • (2007) PLoS Computational Biology , vol.3 , pp. 1716-1726
    • Chennubhotla, C.1    Bahar, I.2
  • 15
    • 41049092674 scopus 로고    scopus 로고
    • Coupling between global dynamics and signal transduction pathways: A mechanism of allostery for chaperonin GroEL
    • Chennubhotla, C., Yang, Z., & Bahar, I. (2008). Coupling between global dynamics and signal transduction pathways: A mechanism of allostery for chaperonin GroEL. Molecular BioSystems, 4, 287-292.
    • (2008) Molecular BioSystems , vol.4 , pp. 287-292
    • Chennubhotla, C.1    Yang, Z.2    Bahar, I.3
  • 16
    • 16644370412 scopus 로고    scopus 로고
    • Human RAS superfamily proteins and related GTPases
    • re13
    • Colicelli, J. (2004). Human RAS superfamily proteins and related GTPases. Sci Signal, re13.
    • (2004) Sci Signal
    • Colicelli, J.1
  • 17
    • 77957231785 scopus 로고    scopus 로고
    • Induced fit, conformational selection and independent dynamic segments: An extended view of binding events
    • Csermely, P., Palotai, R., & Nussinov, R. (2010). Induced fit, conformational selection and independent dynamic segments: An extended view of binding events. Trends in Biochemical Sciences, 35, 539-546.
    • (2010) Trends in Biochemical Sciences , vol.35 , pp. 539-546
    • Csermely, P.1    Palotai, R.2    Nussinov, R.3
  • 18
    • 33745461893 scopus 로고    scopus 로고
    • Residues crucial for maintaining short paths in network communication mediate signaling in proteins
    • 2006.0019
    • del Sol, A., Fujihashi, H., Amoros, D., & Nussinov, R. (2006). Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Molecular Systems Biology, 2, 2006.0019.
    • (2006) Molecular Systems Biology , vol.2
    • Del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 19
    • 34147120474 scopus 로고
    • A note on two problems in connexion with graphs
    • Dijkstra, E.W. (1959). A note on two problems in connexion with graphs. Numerische Mathematik, 1, 269-271.
    • (1959) Numerische Mathematik , vol.1 , pp. 269-271
    • Dijkstra, E.W.1
  • 20
    • 33846474121 scopus 로고    scopus 로고
    • G-protein-coupled receptors and cancer
    • Dorsam, R.T., & Gutkind, J.S. (2007). G-protein-coupled receptors and cancer. Nature Reviews Cancer, 7, 79-94.
    • (2007) Nature Reviews Cancer , vol.7 , pp. 79-94
    • Dorsam, R.T.1    Gutkind, J.S.2
  • 21
    • 79953194763 scopus 로고    scopus 로고
    • Dimerization and ligand binding affect the structure network of A(2A) adenosine receptor
    • Fanelli, F., & Felline, A. (2011). Dimerization and ligand binding affect the structure network of A(2A) adenosine receptor. Biochimica et Biophysica Acta, 1808, 1256-1266.
    • (2011) Biochimica et Biophysica Acta , vol.1808 , pp. 1256-1266
    • Fanelli, F.1    Felline, A.2
  • 22
    • 77956626759 scopus 로고    scopus 로고
    • Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants
    • Fanelli, F., & Seeber, M. (2010). Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants. FASEB Journal, 24, 3196-3209.
    • (2010) FASEB Journal , vol.24 , pp. 3196-3209
    • Fanelli, F.1    Seeber, M.2
  • 23
    • 79960052850 scopus 로고    scopus 로고
    • Ras in cancer and developmental diseases
    • Fernandez-Medarde, A., & Santos, E. (2011). Ras in cancer and developmental diseases. Genes Cancer, 2, 344-358.
    • (2011) Genes Cancer , vol.2 , pp. 344-358
    • Fernandez-Medarde, A.1    Santos, E.2
  • 24
    • 34047195261 scopus 로고    scopus 로고
    • Dynamics of lysozyme structure network: Probing the process of unfolding
    • Ghosh, A., Brinda, K.V., & Vishveshwara, S. (2007). Dynamics of lysozyme structure network: Probing the process of unfolding. Biophysical Journal, 92, 2523-2535.
    • (2007) Biophysical Journal , vol.92 , pp. 2523-2535
    • Ghosh, A.1    Brinda, K.V.2    Vishveshwara, S.3
  • 25
    • 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. (2007). A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis. Proceedings of the National Academy of Sciences of the United States of America, 104, 15711-15716.
    • (2007) Proceedings of the National Academy of Sciences of the United States of America , vol.104 , pp. 15711-15716
    • Ghosh, A.1    Vishveshwara, S.2
  • 26
    • 55249123363 scopus 로고    scopus 로고
    • Variations in clique and community patterns in protein structures during allosteric communication: Investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes
    • Ghosh, A., & Vishveshwara, S. (2008). Variations in clique and community patterns in protein structures during allosteric communication: Investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes. Biochemistry, 47, 11398-11407.
    • (2008) Biochemistry , vol.47 , pp. 11398-11407
    • Ghosh, A.1    Vishveshwara, S.2
  • 27
    • 0032538317 scopus 로고    scopus 로고
    • Structural basis for activation of ARF GTPase: Mechanisms of guanine nucleotide exchange and GTP-myristoyl switching
    • Goldberg, J. (1998). Structural basis for activation of ARF GTPase: Mechanisms of guanine nucleotide exchange and GTP-myristoyl switching. Cell, 95, 237-248.
    • (1998) Cell , vol.95 , pp. 237-248
    • Goldberg, J.1
  • 28
    • 78649801418 scopus 로고    scopus 로고
    • Conformational selection in G-proteins: Lessons from Ras and Rho
    • Grant, B.J., McCammon, J.A., & Gorfe, A.A. (2010). Conformational selection in G-proteins: Lessons from Ras and Rho. Biophysical Journal, 99, L87-L89.
    • (2010) Biophysical Journal , vol.99
    • Grant, B.J.1    McCammon, J.A.2    Gorfe, A.A.3
  • 31
    • 0032729435 scopus 로고    scopus 로고
    • Exploring expression data: Identification and analysis of coexpressed genes
    • Heyer, L.J., Kruglyak, S., & Yooseph, S. (1999). Exploring expression data: Identification and analysis of coexpressed genes. Genome Research, 9, 1106-1115.
    • (1999) Genome Research , vol.9 , pp. 1106-1115
    • Heyer, L.J.1    Kruglyak, S.2    Yooseph, S.3
  • 32
    • 33646628771 scopus 로고    scopus 로고
    • Protein folds and their recognition from sequence
    • M.J.E. Sternberg (Ed.), Oxford: Oxford University Press
    • Jones, D.T., Orengo, C.A., & Thornton, J.M. (1996). Protein folds and their recognition from sequence. In M.J.E. Sternberg (Ed.), Protein structure prediction a practical approach (pp. 173-204). Oxford: Oxford University Press.
    • (1996) Protein Structure Prediction A Practical Approach , pp. 173-204
    • Jones, D.T.1    Orengo, C.A.2    Thornton, J.M.3
  • 33
    • 0033578690 scopus 로고    scopus 로고
    • Identification of sidechain clusters in protein structures by a graph spectral method
    • Kannan, N., & Vishveshwara, S. (1999). Identification of sidechain clusters in protein structures by a graph spectral method. Journal of Molecular Biology, 292, 441-464.
    • (1999) Journal of Molecular Biology , vol.292 , pp. 441-464
    • Kannan, N.1    Vishveshwara, S.2
  • 35
    • 33644847828 scopus 로고    scopus 로고
    • Generalized correlation for biomolecular dynamics
    • Lange, O.F., & Grubmuller, H. (2006). Generalized correlation for biomolecular dynamics. Proteins, 62, 1053-1061.
    • (2006) Proteins , vol.62 , pp. 1053-1061
    • Lange, O.F.1    Grubmuller, H.2
  • 36
    • 78650845707 scopus 로고    scopus 로고
    • G protein-coupled receptors: Novel targets for drug discovery in cancer
    • Lappano, R., & Maggiolini, M. (2011). G protein-coupled receptors: Novel targets for drug discovery in cancer. Nature Reviews Drug Discovery, 10, 47-60.
    • (2011) Nature Reviews Drug Discovery , vol.10 , pp. 47-60
    • Lappano, R.1    Maggiolini, M.2
  • 37
    • 0037495965 scopus 로고    scopus 로고
    • Development of polyphosphate parameters for use with the AMBER force field
    • Meagher, K.L., Redman, L.T., & Carlson, H.A. (2003). Development of polyphosphate parameters for use with the AMBER force field. Journal of Computational Chemistry, 24, 1016-1025.
    • (2003) Journal of Computational Chemistry , vol.24 , pp. 1016-1025
    • Meagher, K.L.1    Redman, L.T.2    Carlson, H.A.3
  • 39
    • 67349190989 scopus 로고    scopus 로고
    • The charge-dipole pocket: A defining feature of signaling pathway GTPase on/off switches
    • Neuwald, A.F. (2009). The charge-dipole pocket: A defining feature of signaling pathway GTPase on/off switches. Journal of Molecular Biology, 390, 142-153.
    • (2009) Journal of Molecular Biology , vol.390 , pp. 142-153
    • Neuwald, A.F.1
  • 40
    • 33750702165 scopus 로고    scopus 로고
    • Structural basis of function in heterotrimeric G proteins
    • Oldham, W.M., & Hamm, H.E. (2006). Structural basis of function in heterotrimeric G proteins. Quarterly Reviews of Biophysics, 39, 117-166.
    • (2006) Quarterly Reviews of Biophysics , vol.39 , pp. 117-166
    • Oldham, W.M.1    Hamm, H.E.2
  • 41
    • 0036866606 scopus 로고    scopus 로고
    • Arf, Arl, Arp and Sar proteins: A family of GTP-binding proteins with a structural device for "front-back" communication
    • Pasqualato, S., Renault, L., & Cherfils, J. (2002). Arf, Arl, Arp and Sar proteins: A family of GTP-binding proteins with a structural device for "front-back" communication. EMBO Reports, 3, 1035-1041.
    • (2002) EMBO Reports , vol.3 , pp. 1035-1041
    • Pasqualato, S.1    Renault, L.2    Cherfils, J.3
  • 43
    • 77649134951 scopus 로고    scopus 로고
    • Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily
    • Raimondi, F., Orozco, M., & Fanelli, F. (2010). Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily. Structure, 18, 402-414.
    • (2010) Structure , vol.18 , pp. 402-414
    • Raimondi, F.1    Orozco, M.2    Fanelli, F.3
  • 46
    • 33244482490 scopus 로고    scopus 로고
    • Correlation of the side-chain hubs with the functional residues in DNA binding protein structures
    • Sathyapriya, R., Brinda, K.V., & Vishveshwara, S. (2006). Correlation of the side-chain hubs with the functional residues in DNA binding protein structures. Journal of Chemical Information and Modeling, 46, 123-129.
    • (2006) Journal of Chemical Information and Modeling , vol.46 , pp. 123-129
    • Sathyapriya, R.1    Brinda, K.V.2    Vishveshwara, S.3
  • 48
    • 79952498871 scopus 로고    scopus 로고
    • Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
    • Seeber, M., Felline, A., Raimondi, F., Muff, S., Friedman, R., Rao, F., ⋯ Fanelli, F. (2011). Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Journal of Computational Chemistry, 32, 1183-1194.
    • (2011) Journal of Computational Chemistry , vol.32 , pp. 1183-1194
    • Seeber, M.1    Felline, A.2    Raimondi, F.3    Muff, S.4    Friedman, R.5    Rao, F.6    Fanelli, F.7
  • 49
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
    • Sorin, E.J., & Pande, V.S. (2005). Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophysical Journal, 88, 2472-2493.
    • (2005) Biophysical Journal , vol.88 , pp. 2472-2493
    • Sorin, E.J.1    Pande, V.S.2
  • 50
    • 79958164854 scopus 로고    scopus 로고
    • A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks
    • Stein, A., Rueda, M., Panjkovich, A., Orozco, M., & Aloy, P. (2011). A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks. Structure, 19, 881-889.
    • (2011) Structure , vol.19 , pp. 881-889
    • Stein, A.1    Rueda, M.2    Panjkovich, A.3    Orozco, M.4    Aloy, P.5
  • 51
    • 0034624037 scopus 로고    scopus 로고
    • Crystal structures of a Rab protein in its inactive and active conformations
    • Stroupe, C., & Brunger, A.T. (2000). Crystal structures of a Rab protein in its inactive and active conformations. Journal of Molecular Biology, 304, 585-598.
    • (2000) Journal of Molecular Biology , vol.304 , pp. 585-598
    • Stroupe, C.1    Brunger, A.T.2
  • 53
    • 78751662442 scopus 로고    scopus 로고
    • The role of G proteincoupled receptors in the pathology of Alzheimer's disease
    • Thathiah, A., & De Strooper, B. (2011). The role of G proteincoupled receptors in the pathology of Alzheimer's disease. Nature Reviews Neuroscience, 12, 73-87.
    • (2011) Nature Reviews Neuroscience , vol.12 , pp. 73-87
    • Thathiah, A.1    De Strooper, B.2
  • 54
    • 0025908897 scopus 로고
    • The ras protein family: Evolutionary tree and role of conserved amino acids
    • Valencia, A., Chardin, P., Wittinghofer, A., & Sander, C. (1991). The ras protein family: Evolutionary tree and role of conserved amino acids. Biochemistry, 30, 4637-4648.
    • (1991) Biochemistry , vol.30 , pp. 4637-4648
    • Valencia, A.1    Chardin, P.2    Wittinghofer, A.3    Sander, C.4
  • 55
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues form a critical contact network in a protein folding transition state
    • Vendruscolo, M., Paci, E., Dobson, C.M., & Karplus, M. (2001). Three key residues form a critical contact network in a protein folding transition state. Nature, 409, 641-645.
    • (2001) Nature , vol.409 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 56
    • 0035834388 scopus 로고    scopus 로고
    • The guanine nucleotide-binding switch in three dimensions
    • Vetter, I.R., & Wittinghofer, A. (2001). The guanine nucleotide-binding switch in three dimensions. Science, 294, 1299-1304.
    • (2001) Science , vol.294 , pp. 1299-1304
    • Vetter, I.R.1    Wittinghofer, A.2
  • 57
    • 78649883885 scopus 로고    scopus 로고
    • Interaction energy based protein structure networks
    • Vijayabaskar, M.S., & Vishveshwara, S. (2010a). Interaction energy based protein structure networks. Biophysical Journal, 99, 3704-3715.
    • (2010) Biophysical Journal , vol.99 , pp. 3704-3715
    • Vijayabaskar, M.S.1    Vishveshwara, S.2
  • 58
    • 75149155238 scopus 로고    scopus 로고
    • Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks
    • Vijayabaskar, M.S., & Vishveshwara, S. (2010b). Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks. Biophys J BMC Bioinformatics, 11(Suppl 1), S49.
    • (2010) Biophys J BMC Bioinformatics , vol.11 , Issue.SUPPL. 1
    • Vijayabaskar, M.S.1    Vishveshwara, S.2
  • 60
    • 65649089458 scopus 로고    scopus 로고
    • Intra and inter-molecular communications through protein structure network
    • Vishveshwara, S., Ghosh, A., & Hansia, P. (2009). Intra and inter-molecular communications through protein structure network. Current Protein and Peptide Science, 10, 146-160.
    • (2009) Current Protein and Peptide Science , vol.10 , pp. 146-160
    • Vishveshwara, S.1    Ghosh, A.2    Hansia, P.3
  • 61
    • 79959393264 scopus 로고    scopus 로고
    • Structure-function relationships of the G domain, a canonical switch motif
    • Wittinghofer, A., & Vetter, I.R. (2011). Structure-function relationships of the G domain, a canonical switch motif. Annual Review of Biochemistry, 80, 943-971.
    • (2011) Annual Review of Biochemistry , Issue.80 , pp. 943-971
    • Wittinghofer, A.1    Vetter, I.R.2


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