Proteins as sponges: A statistical journey along protein structure organization principles (252 visite)
J Chem Inf Model (ISSN: 1549-9596), 2012 Feb 27; 52(2): 474-482.
Tipo di articolo: Journal Article,
Impact factor: 4.304, Impact factor a 5 anni: 4.067
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84857585657&partnerID=40&md5=b8f43eba7c73286ea4b1399c68f64af7
Parole chiave: Complex Networks, Fractal Analysis, Fractal-Shape, Hydrophobic Core, Hydrophobic Effect, Large Database, Order Parameter, Organizational Principles, Protein Data, Protein Structures, Hydrophobicity, Article, Chemical Phenomena, Chemistry, Protein Conformation, Protein Database, Hydrophobic And Hydrophilic Interactions,
Affiliazioni:
*** IBB - CNR ***
Università Campus Biomedico, via Alvaro del Portillo 21, 00128 Rome, Italy
CNR-Institute of Systems Analysis and Computer Science (IASI), BioMathLab, viale Manzoni 30, 00185 Rome, Italy
Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
Universit Campus Biomedico, via Alvaro del Portillo 21, 00128 Rome, Italy
Riferimenti:
Banerji, A., Ghosh, I., (2009) PloS One, 4, p. 736
Zbilut, J., Chua, G., Krishnan, A., Bossa, C., Rother, K., Webber, C., Giuliani, A., (2007) Proteins: Struct., Funct., Bioinf., 66, pp. 621-629
Natarajan, V., Koehl, P., Wang, Y., Hamann, B., Visual Analysis of Biomolecular Surfaces (2007) Mathematical Methods for Visualization in Medicine and Life Sciences, , In
Linsen, L. Hagen, H. Hamann, B. Mathematics and Visualization Series
Springer Verlag: Berlin
Wang, Y., (2004), Ph.D. Thesis, Department of Computer Science, Duke UniversityHopfinger, A., (1983) J. Med. Chem., 26, pp. 990-996
Arteca, G., (1993) Biopolymers, 33, pp. 1829-1841
Heckman, C., (1990) Cytometry, 11, pp. 771-783
Colafranceschi, M., Colosimo, A., Zbilut, J., Uversky, V., Giuliani, A., (2005) J. Chem. Inf. Model., 45, pp. 183-189
Emberly, E., Mukhopadhyay, R., Tang, C., Wingreen, N., (2004) Proteins: Struct., Funct., Bioinf., 55, pp. 91-98
Bloom, J., Drummond, D., Arnold, F., Wilke, C., (2006) Mol. Biol. Evol., 23, pp. 1751-1761
Benigni, R., Giuliani, A., (1994) Am. J. Physiol., 266, pp. 1697-R1704
Christie, O., (1995) Chemom. Intell. Lab. Syst., 29, pp. 177-188
Preisendorfer, R., (1988) Principal Component Analysis in Meteorology and Oceanography, , Elsevier
Dill, K., (1990) Biochemistry, 29, pp. 7133-7155
Vajda, S., Sippl, M., Novotny, J., (1997) Curr. Opin. Struct. Biol., 7, pp. 222-228
Giuliani, A., Di Paola, L., Setola, R., (2009) Curr. Proteomics, 6, pp. 235-245
Cotta-Ramusino, M., Benigni, R., Passerini, L., Giuliani, A., (2003) J. Chem. Inf. Comput. Sci., 43, pp. 248-254
Jackson, D., (1993) Ecology, 74, pp. 2204-2214
Takeda, M., Kirihara, S., Miyamoto, Y., Kazuaki, S., Honda, K., (2004) Phys. Rev. Lett., 92, p. 093902
Giuliani, A., Zbilut, J., Tomita, M., (2007) J. Proteome Res., 6, pp. 3924-3934
Kannan, N., Vishveshwara, S., (1999) J. Mol. Biol., 292, pp. 441-464
Amitai, G., Shemesh, A., Sitbon, E., Shklar, M., Netanely, D., Venger, I., Pietrokovski, S., (2004) J. Mol. Biol., 344, pp. 1135-1146
Gromiha, M.M., Selvaraj, S., (2004) Prog. Biophys. Mol. Biol., 86, pp. 235-277
Krishnan, A.A., Giuliani, A.J.Z., Tomita, M., (2008) PLoS ONE, 3, p. 2149
Sol, A.D., Fujihashi, H., Amoros, D., Nussinov, R., (2006) Mol. Syst. Biol., 2, p. 0019
Alves, N., Aleksenko, V., Hansmann, U., (2005) J. Phys: Condens. Matter, 17, p. 1595
Enright, M.B., Leitner, D.M., (2005) Phys. Rev. e, 71, p. 011912
Russ, J., (1994) Fractal Surfaces, , Plenum Press: New York
Dewey, G., (1998) Fractals in Molecular Biophysics, , Oxford University Press, New York
Park, J., Barabasi, A., (2007) Proc. Natl. Acad. Sci. U.S.A., 104, pp. 17916-17920
Newman, M., (2006) Phys. Rev. e, 74, p. 056108
Elias-Kohav, T., Moshe, S., Avnir, D., (1991) Chem. Eng. Sci., 46, pp. 2787-2798
Giuliani, A., Colosimo, A., Benigni, R., Zbilut, J., (1998) Phys. Lett. A, 247, pp. 47-52
Roden, J., King, B., Trout, D., Mortazavi, A., Wold, B., Hart, C., (2006) BMC Bioinf., 7, p. 194
Gromiha, M. M., Selvaraj, S., (2004) Prog. Biophys. Mol. Biol., 86, pp. 235-277
Krishnan, A. A., Giuliani, A. J. Z., Tomita, M., (2008) PLoS ONE, 3, p. 2149
Sol, A. D., Fujihashi, H., Amoros, D., Nussinov, R., (2006) Mol. Syst. Biol., 2, p. 0019
Enright, M. B., Leitner, D. M., (2005) Phys. Rev. e, 71, p. 011912
J Chem Inf Model (ISSN: 1549-9596), 2012 Feb 27; 52(2): 474-482.
Tipo di articolo: Journal Article,
Impact factor: 4.304, Impact factor a 5 anni: 4.067
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84857585657&partnerID=40&md5=b8f43eba7c73286ea4b1399c68f64af7
Parole chiave: Complex Networks, Fractal Analysis, Fractal-Shape, Hydrophobic Core, Hydrophobic Effect, Large Database, Order Parameter, Organizational Principles, Protein Data, Protein Structures, Hydrophobicity, Article, Chemical Phenomena, Chemistry, Protein Conformation, Protein Database, Hydrophobic And Hydrophilic Interactions,
Affiliazioni:
*** IBB - CNR ***
Università Campus Biomedico, via Alvaro del Portillo 21, 00128 Rome, Italy
CNR-Institute of Systems Analysis and Computer Science (IASI), BioMathLab, viale Manzoni 30, 00185 Rome, Italy
Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
Universit Campus Biomedico, via Alvaro del Portillo 21, 00128 Rome, Italy
Riferimenti:
Banerji, A., Ghosh, I., (2009) PloS One, 4, p. 736
Zbilut, J., Chua, G., Krishnan, A., Bossa, C., Rother, K., Webber, C., Giuliani, A., (2007) Proteins: Struct., Funct., Bioinf., 66, pp. 621-629
Natarajan, V., Koehl, P., Wang, Y., Hamann, B., Visual Analysis of Biomolecular Surfaces (2007) Mathematical Methods for Visualization in Medicine and Life Sciences, , In
Linsen, L. Hagen, H. Hamann, B. Mathematics and Visualization Series
Springer Verlag: Berlin
Wang, Y., (2004), Ph.D. Thesis, Department of Computer Science, Duke UniversityHopfinger, A., (1983) J. Med. Chem., 26, pp. 990-996
Arteca, G., (1993) Biopolymers, 33, pp. 1829-1841
Heckman, C., (1990) Cytometry, 11, pp. 771-783
Colafranceschi, M., Colosimo, A., Zbilut, J., Uversky, V., Giuliani, A., (2005) J. Chem. Inf. Model., 45, pp. 183-189
Emberly, E., Mukhopadhyay, R., Tang, C., Wingreen, N., (2004) Proteins: Struct., Funct., Bioinf., 55, pp. 91-98
Bloom, J., Drummond, D., Arnold, F., Wilke, C., (2006) Mol. Biol. Evol., 23, pp. 1751-1761
Benigni, R., Giuliani, A., (1994) Am. J. Physiol., 266, pp. 1697-R1704
Christie, O., (1995) Chemom. Intell. Lab. Syst., 29, pp. 177-188
Preisendorfer, R., (1988) Principal Component Analysis in Meteorology and Oceanography, , Elsevier
Dill, K., (1990) Biochemistry, 29, pp. 7133-7155
Vajda, S., Sippl, M., Novotny, J., (1997) Curr. Opin. Struct. Biol., 7, pp. 222-228
Giuliani, A., Di Paola, L., Setola, R., (2009) Curr. Proteomics, 6, pp. 235-245
Cotta-Ramusino, M., Benigni, R., Passerini, L., Giuliani, A., (2003) J. Chem. Inf. Comput. Sci., 43, pp. 248-254
Jackson, D., (1993) Ecology, 74, pp. 2204-2214
Takeda, M., Kirihara, S., Miyamoto, Y., Kazuaki, S., Honda, K., (2004) Phys. Rev. Lett., 92, p. 093902
Giuliani, A., Zbilut, J., Tomita, M., (2007) J. Proteome Res., 6, pp. 3924-3934
Kannan, N., Vishveshwara, S., (1999) J. Mol. Biol., 292, pp. 441-464
Amitai, G., Shemesh, A., Sitbon, E., Shklar, M., Netanely, D., Venger, I., Pietrokovski, S., (2004) J. Mol. Biol., 344, pp. 1135-1146
Gromiha, M.M., Selvaraj, S., (2004) Prog. Biophys. Mol. Biol., 86, pp. 235-277
Krishnan, A.A., Giuliani, A.J.Z., Tomita, M., (2008) PLoS ONE, 3, p. 2149
Sol, A.D., Fujihashi, H., Amoros, D., Nussinov, R., (2006) Mol. Syst. Biol., 2, p. 0019
Alves, N., Aleksenko, V., Hansmann, U., (2005) J. Phys: Condens. Matter, 17, p. 1595
Enright, M.B., Leitner, D.M., (2005) Phys. Rev. e, 71, p. 011912
Russ, J., (1994) Fractal Surfaces, , Plenum Press: New York
Dewey, G., (1998) Fractals in Molecular Biophysics, , Oxford University Press, New York
Park, J., Barabasi, A., (2007) Proc. Natl. Acad. Sci. U.S.A., 104, pp. 17916-17920
Newman, M., (2006) Phys. Rev. e, 74, p. 056108
Elias-Kohav, T., Moshe, S., Avnir, D., (1991) Chem. Eng. Sci., 46, pp. 2787-2798
Giuliani, A., Colosimo, A., Benigni, R., Zbilut, J., (1998) Phys. Lett. A, 247, pp. 47-52
Roden, J., King, B., Trout, D., Mortazavi, A., Wold, B., Hart, C., (2006) BMC Bioinf., 7, p. 194
Gromiha, M. M., Selvaraj, S., (2004) Prog. Biophys. Mol. Biol., 86, pp. 235-277
Krishnan, A. A., Giuliani, A. J. Z., Tomita, M., (2008) PLoS ONE, 3, p. 2149
Sol, A. D., Fujihashi, H., Amoros, D., Nussinov, R., (2006) Mol. Syst. Biol., 2, p. 0019
Enright, M. B., Leitner, D. M., (2005) Phys. Rev. e, 71, p. 011912
The analysis of a large database of protein structures by means of topological and shape indexes inspired by complex network and fractal analysis shed light on some organizational principles of proteins. Proteins appear much more similar to "fractal" sponges than to closely packed spheres, casting doubts on the tenability of the hydrophobic core concept. Principal component analysis highlighted three main order parameters shaping the protein universe: (1) "size", with the consequent generation of progressively less dense and more empty structures at an increasing number of residues, (2) "microscopic structuring", linked to the existence of a spectrum going from the prevalence of heterologous (different hydrophobicity) to the prevalence of homologous (similar hydrophobicity) contacts, and (3) "fractal shape", an organizing protein data set along a continuum going from approximately linear to very intermingled structures. Perhaps the time has come for seriously taking into consideration the real relevance of time-honored principles like the hydrophobic core and hydrophobic effect. © 2012 American Chemical Society.
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