Revisiting the myths of protein interior: Studying proteins with mass-fractal hydrophobicity-fractal and polarizability-fractal dimensions

PLoS ONE

Volumn 4, Issue 10, 2009, Pages

  Banerji, Anirban ^a   Ghosh, Indira ^b  

^a UNIVERSITY OF PUNE   (India)

^b JAWAHARLAL NEHRU UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALPHA HELIX; ANISOTROPY; ARTICLE; BETA SHEET; CONTROLLED STUDY; DIELECTRIC CONSTANT; FRACTAL ANALYSIS; HYDROPHOBICITY; POLARIZATION; PROTEIN ANALYSIS; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; ALGORITHM; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; HUMAN; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; STATIC ELECTRICITY; THEORETICAL MODEL; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; ANIMALS; ANISOTROPY; CRYSTALLOGRAPHY, X-RAY; FRACTALS; HUMANS; HYDROPHOBICITY; MODELS, BIOLOGICAL; MODELS, THEORETICAL; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 70449394017     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007361     Document Type: Article

References (87)

1. Richards FM (1997) Protein stability: still an unsolved problem. Cell Mol Life Sci 53: 790-802.
2. Rother K, Preissner R, Goede A, Frömmel C (2003) Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. Bioinformatics 19: 2112-2121.
3. Liang J, Dill KA (2001) Are proteins well-packed. Biophys J 81: 751-766.
4. Behe MJ, Lattman EE, Rose GD (1991) The protein-folding problem: The native fold determines packing, but does packing determine the native fold? Proc Nat Acad Sci USA 88: 4195-4199.
5. Perutz M (1978) Electrostatic effects in proteins. Science 201: 1187-1191.
6. Banerji A, Ghosh I (2009) A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in proteins; Eur. Biophys J 38: 577-587.
7. Vendruscolo M, Dokholyan NV, Paci E, Karplus M (2002) Small-world view of the amino acids that play a key role in protein folding. Phys Rev E 65: 061910.
8. Kaya H, Chan HS (2000) Energetic Components of Cooperative Protein Folding. Phys Rev Lett 85: 4823-4826.
9. Fitzkee NC, Fleming PJ, Gong H, Panasik N Jr, Street TO, et al. (2005) Are proteins made from a limited parts list? TRENDS in Biochemical Sciences 30: 73-80.
10. Tissen J, Fraaije J, Drenth J, Berendsen H (1994) Mesoscopic theories for protein crystal growth. Acta Cryst D 50: 569-571.
11. Steinbach PJ, Ansari A, Berendzen J, Braunstein D, Chu K, et al. (1991) Ligand binding to heme proteins: connection between dynamics and function. Biochemistry 30: 3988-4001.
12. Rasmussen BF, Stock AM, Ringe D, Petsko GA (1992) Crystalline ribonuclease A loses function below the dynamical transition at 220 K. Nature 357: 423-424.
13. Reuveni S, Granek R, Klafter J (2008) Proteins: Coexistence of Stability and Flexibility; Phys Rev Lett 100: 208101.
14. Phillips JC (2009) Scaling and self-organized criticality in proteins I. Proc Natl Acad Sci USA 106: 3107-3112.
15. Phillips JC (2009) Scaling and self-organized criticality in proteins II; Proc Natl Acad Sci USA 106: . pp 3113-3118.
16. Goldstein H (1962) Classical Mechanics. Addison-Wesley, Reading, MA. . pp 149-151.
17. Flory PJ (1953) Principles of Polymer Chemistry.Cornell University, . pp 428-429.
18. Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI (1998) Discrete molecular dynamics studies of the folding of a protein-like model. Fold Des 3: 577-587.
19. Bachmann M, Jankeb W (2004) Thermodynamics of lattice heteropolymers; J. Chem Phys 120: 6779-6791.
20. Ba X, Wang H, Zhao M, Li M (2002) Conversion Dependence of the z-Average Mean Square Radii of Gyration for Hyperbranched Polymers with Excluded Volume Effect. Macromolecules 35: 4193-4197.
21. Barrett AJ, Skolnick J (1988) On the Apparent Radius of Gyration of Linear Polymers and the Experimental Determination of the Excluded-Volume Parameter. Macromolecules 21: 1141-1145.
22. Bonvin AM, Gunsteren WV (2000) â-hairpin stability and folding: molecular dynamics studies of the first â-hairpin of tendamistat. J Mol Biol 296: 255-268.
23. Dayantis J, Palierne JF (1994) Scaling exponents of the self-avoiding-walkproblem in three dimensions. Phys Rev B 49: 3217-3225.
24. Irbäck A, Sjunnesson F, Wallin S (2001) Hydrogen Bonds, Hydrophobicity Forces and the Character of the Collapse Transition. J Biol Phys 27(2-3): . pp 169-179.
25. Sosnick TR, Trewhella J (1992) Denatured states of ribonuclease A have compact dimensions and residual secondary structure. Biochemistry 31: 8329-8335.
26. Arteca GA (1995) A detailed shape characterization of regular polypeptide conformamtion; Canadin J Chem 73: 241-248.
27. Zhang J, Chen R, Chao T, Liang J (2003) Origin of scaling behavior of protein packing density: a sequential monte carlo study of compact long chain polymers. J Chem Phys 118: 6102-6109.
28. Akasaka K, Li H (2001) Low-Lying Excited States of Proteins Revealed from Nonlinear Pressure Shifts in 1H and 15N NMR. Biochemistry 40: . pp 8665-8671.
29. Zydney AL, Reis RV (2001) "High-Performance Tangential-Flow Filtration"; Membrane Separations in Biotechnology; ed Wang WK. CRC Press. pp 280-282.
30. Burke HB (2005) Proteomics: Analysis of Spectral Data. Cancer Inform 1: 15-24.
31. MacDonald M, Jan N (1986) Fractons and the fractal dimension of proteins. Canadian J Phys 64: 1353-1355.
32. Li H, Chen S, Zhao H (1998) Fractal mechanisms for the allosteric effects of proteins and enzymes; Biophys J 58: 1313-1320.
33. Lewis M, Rees DC (1985) Fractal Surfaces of Proteins. Science 230: 1163-1165.
34. Millhauser GL, Salpeter EE, Oswald RE (1988) Diffusion models of ion-channel gating and the origin of the power-law distributions from single-channel recordings. Proc Natl Acad Sci USA 85: 1503-1507.
35. Helman JS, Coniglio A, Tsallis C (1984) Fractals and the fractal structure of proteins. Phys Rev Lett 53: 1195-1197.
36. Dewey TG (1994) Fractal analysis of proton exchange kinetics in lysozyme (protein dynamics/fractal reaction kinetics) Proc Natl Acad Sci USA 91: 12101-12104.
37. Dewey TG (1999) Statistical Mechanics of Protein Sequences. Phys Rev E 60: 4652-4658.
38. Medini D, Widom A (2003) Atomic scale fractal dimensionality in proteins. J Chem Phys 118: 2405-2410.
39. Enright MB, Leitner DM (2005) Mass fractal dimension and the compactness of proteins. Phys Rev E 71: 011912.
40. Allen JP, Colvin JT, Stinson DG, Flynn CP, Stapelton HJ (1982) Protein conformation from electron spin relaxation data. Biophys J 38: 299-310.
41. Lee CY (2006) Mass fractal dimension of the ribosome and implication of its dynamic characteristics. Phys Rev E 73: 042901.
42. Andreeva A, Howorth D, Chandonia JM, Brenner S, Hubbard TJP, et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucl Acid Res 36: D419-D425.
43. Berman HM, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10: 980.
44. Haney PJ, Badger JH, Buldak GL, Reich CI, Woese CR, et al. (1999) Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc Natl Acad Sci USA 96: 3578-3583.
45. Kuhn LA, Swanson CA, Pique ME, Tainer JA, Getzoff ED (1995) Atomic and residue hydrophilicity in the context of folded protein structures. Prot Struct Funct Genet 23: 536-547.
46. Olumee Z, Vertes A (1998) Protonation of Glyn Homologues in Matrix-Assisted Laser Desorption Ionization. J Phys Chem B 102: 6118-6122.
47. Song XJ (2002) An inhomogeneous model of protein dielectric properties: Intrinsic polarizabilities of amino acids. J Chem Phys 116: 9359-9363.
48. Elking D, Darden T, Woods RJ (2007) Gaussian Induced Dipole Polarization Model. J Comput Chem 28: 1261-1274.
49. Voges D, Karshikoff A (1998) A model of a local dielectric constant in proteins. J Chem Phys 108: 2219-2227.
50. Galzitskaya O, Reifsnyder D, Bogatyreva N, Ivankov D, Garbuzynskiy S (2008) More compact protein globules exhibit slower folding rates. Proteins 70: 329-332.
51. Koshi, JM, Goldstein RA (1997) Mutation matrices and physical-chemical properties: correlations and implications. Proteins 27: 336-344.
52. Finucane MD, Tuna M, Lees JH, Woolfson DN (1999) Core-directed Protein Design. I. An Experimental Method For Selecting Stable Proteins from Combinatorial Libraries. Biochemistry 38: 11613-11623.
53. Karplus M (2000) Aspects of Protein Reaction Dynamics: Deviations from Simple Behavior. J Phys Chem B 104: 11-27.
54. Hecht MH, Nelson HCM, Sauer RT (1983) Mutations in lambda Repressor's Amino-Terminal Domain: Implications for Protein Stability and DNA Binding. Proc Natl Acad Sci USA 80: 2676-2680.
55. Reidhaar-Olson JF, Sauer RT (1988) Combinatorial Cassette Mutagenesis as a Probe of the Informational Content of Protein Sequences. Science 241: 53-57.
56. Karpusas M, Baase WA, Matsumara M, Matthews BW (1989) Hydrophobic packing in T4 lysozyme probed by cavity-filling mutants. Proc Natl Acad Sci USA 86: 8237-8241.
57. Lim WA, Sauer RT (1989) Alternative Packing Arrangements in the Hydrophobic Core of l Repressor. Nature (London) 339: 31-36.
58. Hubbard SJ, Argos P (1995) Evidence on close packing and cavities in proteins. Curr Opin Biotechnol 6: 375-381.
59. Munson M, Balasubramanian S, Fleming KG, Nagi AD, O'Brien R, et al. (1996) What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties. Prot Sci 5: 1584-1593.
60. Carter CW Jr, LeFebvre BC, Cammer SA, Tropsha A, Edgell MH (2001) Fourbody Potentials Reveal Protein-specific Correlations to Stability Changes Caused by Hydrophobic Core Mutations. J Mol Biol 311: 625-638.
61. Pande VS, Rokhsar DS (1999) Molecular dynamics simulations of unfolding and refolding of a a ̊-hairpin fragment of protein G. Proc. Natl Acad Sci USA 96: 9062-9067.
62. Shude Y, Grzegorz G, Koki M, Valentina T, Akiko K, et al. (2007) Hydrophobic Surface Burial Is the Major Stability Determinant of a Flat, Single-layer â-Sheet. J Mol Biol 368: 230-243.
63. Dwyer DS (2005) Electronic properties of amino acid side chains: quantum mechanics calculation of substituent effects. BMC Chemical Biology 5: 2.
64. Gao J, Li Z (2008) Inter-residue interactions in protein structures exhibit powerlaw behavior. Biopolymers 2008 89: 1174-1178.
65. Russo D, Peŕez J, Zanotti JM, Desmadril M, Durand D (2002) Dynamic transition associated with the thermal denaturation of a small Beta protein; Biophys J 83: 2792-2800.
66. Bullock AN, Fersht AR (2001) Rescuing the function of mutant p53. Nature 1: 1.
67. Sivaraman T, Kumar TK, Jayaraman G, Han CC, Yu C (1997) Characterization of a partially structured state in an all-beta-sheet protein. Biochem J 321: 457-464.
68. Samuel D, Kumar TKS, Srimathi T, Hsieh HC, Yu C (2000) Identification and characterization of an equilibrium intermediate in the unfolding pathway of an all â-barrel protein. J Biol Chem 275: 34968-34975.
69. Dabora JM, Pelton JG, Marqusee S (1996) Structure of the acid state of E. coli ribonuclease HI; Biochemistry 35: 11951-11958.
70. West MW, Hecht MH (1995) Binary patterning of polar and nonpolar amino acids in the sequences and structures of native proteins. Prot Sci 4: 2032-2039.
71. Havranek JJ, Harbury PH (2002) Automated design of specificity in molecular recognition. Nat Struct Biol 10: 45-52.
72. Hecht MH, Das A, Go A, Bradley LH, Wei Y (2004) De novo proteins from designed combinatorial libraries. Prot Sci 13: 1711-1723.
73. Kajander T, LehtiöL, Schlm̈ann M, Goldman A (2003) The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: Co-evolution of structure and dynamics with the dehalogenation function Prot Sci 12: 1855-1864.
74. Higo J, Umeyama H (1997) Protein dynamics determined by backbone conformation and atom packing. Prot Eng 10: 373-380.
75. McCammon JA, Lee CY, Northrup SH (1983) Side-chain rotational isomerization in proteins: a mechanism involving gating and transient packing defects. J Am Chem Soc 105: 2232-2237.
76. Hildebrand PW, Rother K, Goede A, Preissner R, Frommel C (2005) Molecular Packing and Packing Defects in Helical Membrane Proteins. Biophys J 88: 1970-1977.
77. Lumry R, Rosenberg A (1976) The mobile-defect hypothesis of protein function. Coll Int CNRS LEau Syst Biol 246: 55-63.
78. Englander SW, Kallenbach NR (1984) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q Rev Biophys 16: 521-655.
79. Taverna DM, Goldstein RA (2002) Why Are Proteins Marginally Stable? Prot: Struct Func, and Gen 46: 105-109.
80. Vogl T, Jatzke C, Hinz HJ, Benz J, Huber R (1997) Thermodynamic stability of annexin V E17G: Equilibrium parameters from an irreversible unfolding reaction. Biochemistry 36: 1657-1668.
81. Privalov PL, Khechinashvili NN (1974) A thermodynamic approach to the problem of stabilization of globular protein structure: A calorimetric study. J Mol Biol 86: 665-684.
82. Chakrabarti P, Pal D (2001) The interrelationships of side-chain and main-chain conformations in proteins. Prog in Biophys Mol Biol 76: 1-102.
83. Guo HH, Choe J, Loeb LA (2004) Protein tolerance to random amino acid change. Proc Natl Acad Sci USA 101: 9205-9210.
84. Bowie JU, Reidhaar-Olson JF, Lim WA, Sauer RT (1990) Deciphering the Message in Protein Sequences: Tolerance to Amino Acid Substitutions. Science 247: 1306-1310.
85. Glyakina AV, Lobanov M, Galzitskaya OV (2007) Search for Structural Factors Responsible for the Stability of Proteins from Thermophilic Organisms. Mol Biol J 41: 4.
86. Jaenicke R, Bohm G (1998) The stability of proteins in extreme environments. Curr Opin Struct Biol 8: 738-748.
87. Jefferson E, Walsh T, Barton G (2006) Biological Units and their Effect upon the Properties and Prediction of Protein-Protein Interactions. J Mol Biol 364: 6111-1129.