ProCoCoA: A quantitative approach for analyzing protein core composition

Computational Biology and Chemistry

Volumn 43, Issue , 2013, Pages 29-34

  Bottini, Silvia ^a   Bernini, Andrea ^a   De Chiara, Matteo ^a   Garlaschelli, Diego ^c   Spiga, Ottavia ^a,b   Dioguardi, Marco ^a   Vannuccini, Elisa ^a   Tramontano, Anna ^d   Niccolai, Neri ^a,b  

^a UNIVERSITY OF SIENA   (Italy)

^b SienaBioGrafiX Srl   (Italy)

^c UNIVERSITEIT LEIDEN   (Netherlands)

^d SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Atom depth; Protein core composition; Protein folding

Indexed keywords

AMINO ACID COMPOSITIONS; AMINO ACID RESIDUES; CORE COMPOSITION; MOLECULAR MOIETIES; PROTEIN ARCHITECTURES; PROTEIN CORE; PROTEIN ENGINEERING; PROTEIN FOLDS; QUANTITATIVE APPROACH; QUANTITATIVE CHARACTERIZATION; STRUCTURAL STABILITIES; WEB INTERFACE;

AMINO ACIDS; GENETIC ENGINEERING; NETWORK ARCHITECTURE; PROTEIN FOLDING; PROTEINS; STABILITY;

STRUCTURE (COMPOSITION);

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE;

EID: 84872400601     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2012.12.007     Document Type: Article

References (27)

1. A.R. Atilgan, P. Akan, and C. Baysal Small-world communication of residues and significance for protein dynamics Biophysical Journal 86 1 2004 85 91 (Pubitemid 38067438)
2. F.C. Bernstein, T.F. Koetzle, G.J. Williams, E.F. Meyer, M.D. Brice, J.R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi The Protein Data Bank: a computer-based archival file for macromolecular structures Journal of Molecular Biology 112 3 1977 535 542 (Pubitemid 8109216)
3. C. Bode, I.A. Kovacs, M.S. Szalay, R. Palotai, T. Korcsmaros, and P. Csermely Network analysis of protein dynamics FEBS Letters 581 15 2007 2776 2782 (Pubitemid 46874391)
4. S. Chakravarty, and R. Varadarajan Residue depth: a novel parameter for the analysis of protein structure and stability Structure 7 7 1999 723 732 (Pubitemid 29329844)
5. M.S. Cheung, A.E. Garcia, and J.N. Onuchic Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse Proceedings of the National Academy of Sciences of the United States of America 99 2 2002 685 690 (Pubitemid 34106571)
6. C. Chipot, R. Jaffe, B. Maigret, D.A. Pearlman, and P.A. Kollman Benzene dimer: a good model for pi-pi interactions in proteins? A comparison between the benzene and the toluene dimers in the cas phase and in an aqueous solution Journal of the American Chemical Society 118 45 1996 11217 11224 (Pubitemid 26399745)
7. R.G. Coleman, and K.A. Sharp Travel depth, a new shape descriptor for macromolecules: application to ligand binding Journal of Molecular Biology 362 3 2006 441 458 (Pubitemid 44307154)
8. G. Fischer, U. Kosinska-Eriksson, C. Aponte-Santamaria, M. Palmgren, C. Geijer, K. Hedfalk, S. Hohmann, B.L. de Groot, R. Neutze, and K. Lindkvist-Petersson Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism PLoS Biology 7 6 2009 e1000130
9. L.C. Freeman A set of measures of centrality. Based on betweenness Sociometry 40 1 1977 35 44
10. M. Gerstein, and R.B. Altman Average core structures and variability measures for protein families-application to the immunoglobulins Journal of Molecular Biology 251 1 1995 161 175
11. Y. Isogai Native protein sequences are designed to destabilize folding intermediates Biochemistry 45 8 2006 2488 2492
12. D. Lama, and R. Sankararamakrishnan Identification of core structural residues in the sequentially diverse and structurally homologous Bcl-2 Family of proteins Biochemistry 49 11 2010 2574 2584
13. A. Madhumalar, D.J. Smith, and C. Verma Stability of the core domain of p53: insights from computer simulations BMC Bioinformatics 9 1 2008 S17
14. K. Mizuguchi, C.M. Deane, T.L. Blundell, and J.P. Overington HOMSTRAD: a database of protein structure alignments for homologous families Protein Science 7 11 1998 2469 2471 (Pubitemid 28506965)
15. C.A. Orengo, A.D. Michie, S. Jones, D.T. Jones, M.B. Swindells, and J.M. Thornton CATH-a hierarchic classification of protein domain structures Structure 5 8 1997 1093 1108 (Pubitemid 27393093)
16. A. Pintar, O. Carugo, and S. Pongor Atom depth as a descriptor of the protein interior Biophysical Journal 84 4 2003 2553 2561 (Pubitemid 36373575)
17. A. Pintar, O. Carugo, and S. Pongor DPX: for the analysis of the protein core Bioinformatics 19 2 2003 313 314 (Pubitemid 36181929)
18. N. Prudhomme, and J. Chomilier Prediction of the protein folding core: application to the immunoglobulin fold Biochimie 91 11-12 2009 1465 1474
19. S. Raimondi, F. Guglielmi, S. Giorgetti, S. Di Gaetano, A. Arciello, A. Relini, S.M. Doglia, A. Natalello, P. Pucci, P. Mangione, L. Obici, G. Merlini, M. Stoppini, G.G. Tartaglia, M. Vendruscolo, R. Piccoli, and V. Bellotti Effects of disease-associated mutations on the aggregation process of the 93-residue N-terminal fragment of human apolipoprotein A-I Amyloid 17 2010 39 40
20. C. Sander, and R. Schneider Database of homology-derived protein structures and the structural meaning of sequence alignment Proteins 9 1 1991 56 68
21. W. Sheffler, and D. Baker RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation Protein Science 18 1 2009 229 239
22. V. Soundararajan, R. Raman, S. Raguram, V. Sasisekharan, and R. Sasisekharan Atomic interaction networks in the core of protein domains and their native folds PLoS ONE 5 2 2010 e9391
23. M.B. Swindells A procedure for the automatic-determination of hydrophobic cores in protein structures Protein Science 4 1 1995 93 102
24. D. Varrazzo, A. Bernini, O. Spiga, A. Ciutti, S. Chiellini, V. Venditti, L. Bracci, and N. Niccolai Three-dimensional computation of atom depth in complex molecular structures Bioinformatics 21 12 2005 2856 2860 (Pubitemid 40862284)
25. M. Vendruscolo, N.V. Dokholyan, E. Paci, and M. Karplus Small-world view of the amino acids that play a key role in protein folding Physical Review E: Statistical, Nonlinear, and Soft Matter Physics 65 6 Pt 1 2002 061910
26. M. Vendruscolo, E. Paci, C.M. Dobson, and M. Karplus Three key residues form a critical contact network in a protein folding transition state Nature 409 6820 2001 641 645 (Pubitemid 32154819)
27. T. Yoda, Y. Sugita, and Y. Okamoto Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations Biophysical Journal 99 5 2010 1637 1644