A topologically related singularity suggests a maximum preferred size for protein domains

Proteins: Structure, Function and Genetics

Volumn 66, Issue 3, 2007, Pages 621-629

  Zbilut, Joseph P ^a   Chua, Gek Huey ^b   Krishnan, Arun ^c   Bossa, Cecilia ^d   Rother, Kristian ^e   Webber Jr , Charles L ^f   Giuliani, Alessandro ^d  

^a RUSH UNIVERSITY MEDICAL CENTER   (United States)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c KEIO UNIVERSITY   (Japan)

^d ISTITUTO SUPERIORE DI SANITÀ   (Italy)

^e HUMBOLDT UNIVERSITY   (Germany)

^f LOYOLA UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Compactness; Critical phenomena; Domain size; Folding; G factor; Hydrophobicity; Length dependency; Packing; Protein; Recurrence; Singularity

Indexed keywords

CONFERENCE PAPER; HYDROPHOBICITY; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; QUALITATIVE ANALYSIS; SURFACE PROPERTY;

BINDING SITES; KINETICS; MODELS, THEORETICAL; MOLECULAR WEIGHT; PROTEINS;

EID: 33846223291     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21179     Document Type: Conference Paper

References (21)

1. Liang J, Dill KA. Are proteins well packed? Biophys J 2001;81:751-766.
2. Sandelin E. On hydrophobicity and conformational specificity in proteins. Biophys J 2004;86:23-30.
3. Zhang J, Chen R, Tang C, Liang J. Origin of scaling behavior of protein packing density: a sequential Monte Carlo study of compact long chain polymers. J Chem Phys 2003;118:6102-6109.
4. Webber CL, Giuliani A, Zbilut JP, Colosimo A. Elucidating protein secondary structures using α carbon recurrence quantifications. Proteins: Struct Funct Genet 2001;44:292-303.
5. Hobohm U, Scharf M, Schneider R, Sander C. Selection of representative protein data sets. Protein Sci 1992;1:409-417.
6. Chan HS, Dill KA. Compact polymers. Macromolecules 1989;22:4559-4573.
7. Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:522-524.
8. Zbilut JP. Unstable singularities and randomness. Amsterdam: Elsevier; 2004.
9. Zak M, Zbilut JP, Meyers RE. From instability to intelligence. Berlin: Springer; 1997. Lecture notes in physics, New series M, Monographs, Vol. 49.
10. Engh RA, Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr A 1991;47:392-400.
11. Zavodszky MI, Kuhn LA. Side chain flexibility in protein ligand binding. Protein Sci 2005;14:1104-1114.
12. Donev A, Cisse I, Sachs D, Variano EA, Stillinger FH, Connelly R, Torquato S, Chaikin PM. Improving the density of jammed disordered packings using ellipsoids. Science 2004;303:990-993.
13. Rother K, Preissner R, Goede A, Frömmel C. Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. Bioinformatics 2003;19:2112-2121.
14. Shen M, Davis FP, Sali A. The optimal size of globular protein domain: a simple sphere-packing model. Chem Phys Lett 2005;405:224-228.
15. Zbilut JP, Colosimo A, Conti F, Colafranceschi M, Manetti C, Valerio MC, Webber CL, Jr, Giuliani A. Protein aggregation/folding: the role of deterministic singularities of sequence hydrophobicity as determined by nonlinear signal analysis of acylphosphatase and Aβ(1-40). Biophys J 2003;85:3544-3557.
16. Liang J, Zhang J, Chen E. Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method. J Chem Phys 2002;117:3511-3521.
17. Saini HK, Fischer D. Meta-DP: domain prediction meta-server. Bioinformatics 2005;21:2917-2920.
18. Kannan N, Vishveshwara S. Identification of side-chain clusters in protein structures by a graph spectral method. J Mol Biol 1999;292:441-464.
19. Vendovas C, Zemla A, Fidelis K, Moult J. Assessment of progress over the CASP experiments. Proteins: Struct Funct Genet 2003;53:585-595.
20. Chan HS, Dill KA. Origins of structure in globular protein. Proc Natl Acad Sci USA 1990;87:6388-6392.
21. Miao J, Klein-Seetharaman J, Meierovitch H. The optimal fraction of hydrophobic residues required to ensure protein collapse. J Mol Biol 2004;344:797-811.