Proteins as sponges: A statistical journey along protein structure organization principles
CNR Ibb | back to homepage
▲NavBar
Ricerca avanzata▼
Contiene: [X]      Estesa     Autori: [X]  Tipo di lavoro: [X]   Data iniziale: Data finale: [X]      Sede: Affiliazione IBB     
    
[Pulisci modulo]


Proteins as sponges: A statistical journey along protein structure organization principles (134 visite)

Paola LD, Paci P, Santoni D, Ruvo MD, Giuliani A

J Chem Inf Model American Chemical Society (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.
Nessun risultato.
Nessun risultato.

Ricerca avanzata▼
Contiene: [X]      Estesa     Autori: [X]  Tipo di lavoro: [X]   Data iniziale: Data finale: [X]      Sede: Affiliazione IBB     
    
[Pulisci modulo]
Vai a fine pagina   Versione per copia e incolla facile   Esporta tutto in BibTeX   Esporta tutto in EndNote


Accardo A, Ringhieri P, Szekely N, Pipich V, Luchini A, Paduano L, Tesauro D
* Structural insights on nanoparticles containing gadolinium complexes as potential theranostic (108 visite)
COLLOID POLYM SCI (ISSN: 0303-402X), 2014 May; 292(5): 1121-1127.
Impact Factor: 1.865
Dettagli    Esporta in BibTeX    Esporta in EndNote

Roviello GN, Roviello GN, Musumeci D, Capasso D, Di Gaetano S, Costanzo M, Pedone C
* Synthesis and supramolecular assembly of 1, 3-bis(1 '-uracilyl)-2-propanone (133 visite)
RSC ADV (ISSN: 2046-2069), 2014; 4(54): 28691-28698.
Impact Factor: 3.84
Dettagli    Esporta in BibTeX    Esporta in EndNote

Sciacca MFM, Carbone V, Pappalardo M, Milardi D, La Rosa C, Grasso DM
* Interaction of human amylin with phosphatidylcholine and phosphatidylserine membranes (107 visite)
Mol Cryst Liq Cryst (ISSN: 1542-1406), 2009; 500: 73-81.
Impact Factor: 0.451
Dettagli    Esporta in BibTeX    Esporta in EndNote



3 Records (3 escludendo Abstract e Conferenze).
Impact factor totale: 6.156 (6.156 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 6.392 (6.392 escludendo Abstract e Conferenze).







    Esporta in BibTeX    Esporta in EndNote