"Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids

Journal of Molecular Modeling

Volumn 16, Issue 7, 2010, Pages 1269-1282

  Prymula, Katarzyna ^a,b   Salapa, Kinga ^a   Roterman, Irena ^a  

^a JAGIELLONIAN UNIVERSITY MEDICAL COLLEGE   (Poland)

^b JAGIELLONIAN UNIVERSITY   (Poland)

Author keywords

Active site recognition; Biological activity; Hydrophobicity deficiency; Proteins of unknown function; Small proteins

Indexed keywords

AMINO ACID; DNA; RNA;

ARTICLE; BINDING SITE; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; THREE DIMENSIONAL IMAGING;

ALGORITHMS; AMINO ACIDS; ANTIFREEZE PROTEINS; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; GROWTH HORMONE; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR CHAPERONES; MOLECULAR WEIGHT; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SERINE PROTEINASE INHIBITORS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77955092811     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-009-0639-2     Document Type: Article

References (66)

1. Rosenberg M, Goldblum A (2006) Computational protein design: a novel path to future protein drugs. Curr Pharm Des 12:3973-3997
2. Deng Y, Zheng Q, Ketas TJ, Moore JP, Lu M (2007) Protein design of a bacterially expressed HIV-1 gp41 fusion inhibitor. Biochemistry 46:4360-4369
3. Antikainen NM, Martin SF (2005) Altering protein specificity: techniques and applications. Bioorg Med Chem 13:2701-2716
4. Patrick WM, Firth AE (2005) Strategies and computational tools for improving randomized protein libraries. Biomol Eng 22:105-112
5. Chaparro-Riggers JF, Polizzi KM, Bommarius AS (2007) Better library design:data-driven protein engineering. J Biotechnol 2:180-191
6. Fowler SB, Poon S, Muff R, Chiti F, Dobson CM, Zurdo J (2005) Rational design of aggregation-resistant bioactive peptides: Reengineering human calcitonin. Proc Natl Acad Sci USA 102:10105-10110
7. Shao Z, Arnold FH (1996) Engineering new functions and altering existing functions. Curr Opin Struct Biol 6:513-518
8. Eijsink VGH, Bjørk A, Gäseidnes S, Sireväg R, Synstad B, van den Burg B, Vriend G (2004) Rational engineering of enzyme stability. J Biotechnol 113:105-120
9. Chiarabelli C, Vrijbloed JW, Thomas RM, Luisi PL (2006) Investigation of de novo totally random biosequences. Part I: A general method for in vitro selection of folded domains from a random polypeptide library displayed on phage. Chem Biodivers 3:827-839
10. Chiarabelli C, Vrijbloed JW, Lucrezia DD, Thomas RM, Stano P, Polticelli F, Ottone T, Papa E, Luisi PL (2006) Investigation of de novo totally random biosequences. Part II: On the folding frequency in a totally random library of de novo proteins obtained by phage display. Chem Biodivers 3:840-859 (Pubitemid 44362040)
11. EUChinaGRID project.http://www.euchinagrid.org/
12. Bonneau R, Strauss CEM, Rohl CA, Chivian D, Bradley P, Malmström L, Robertson T, Baker D (2002) De novo prediction of three-dimensional structures for major protein families. J Mol Biol 322:65-78
13. Konieczny L, Brylinski M, Roterman I (2006) Gauss-functionbased model of hydrophobicity density in proteins. In Silico Biol 6:15-22
14. Brylinski M, Konieczny L, Roterman I (2006) Fuzzy-oil-drop hydrophobic force field-a model to represent late-stage folding (in silico) of lysozyme. J Biomol Struct Dyn 23:519-528
15. Brylinski M, Konieczny L, Roterman I (2006) Hydrophobic collapse in (in silico) protein folding. Comput Biol Chem 30:255-267
16. Brylinski M, Konieczny L, Roterman I (2006) Hydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor. Biochimie 88:1229-1239
17. Brylinski M, Konieczny L, Roterman I (2007) Is the protein folding an aim-oriented process? Human haemoglobin as example. Int J Bioinform Res Appl 3:234-260
18. Prymula K, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, Evangelista G, Minervini G, Polticelli F, Wisniowski Z, Salapa K, Matczynska E, Roterman I (in press) In silico structural study of random amino acid sequence proteins not present in nature. Chem Biodivers
19. Brylinski M, Konieczny L, Roterman I (2006) Ligation site in proteins recognized in silico. Bioinformation 1:127-129
20. Brylinski M, Kochanczyk M, Konieczny L, Roterman I (2006) Sequence-structure-function relation characterized in silico. In Silico Biol 6:589-600
21. Brylinski M, Kochanczyk M, Broniatowska E, Roterman I (2007) Localization of ligand binding site in proteins identified in silico. J Mol Model 13:665-675
22. BrylinskiM, Prymula K, JurkowskiW,KochanczykM, Stawowczyk E, Konieczny L, Roterman I (2007) Prediction of functional sites based on the fuzzy oil drop model. PLoS Comput Biol 3:e94
23. Prymula K, Roterman I (2009) Functional characteristics of small proteins (70 amino acid residues) forming protein-nucleic acid complexes. J Biomol Struct Dyn 26:663-677
24. Prymula K, Roterman I (2009) Structural entropy to characterize small proteins (70 aa) and their interactions. Entropy 11:62-84
25. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C (2002) The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 58:899-907
26. Jia Z, DeLuca CI, Chao H, Davies PL (1996) Structural basis for the binding of a globular antifreeze protein to ice. Nature 384:285-288
27. Wisniewska M, Bossenmaier B, Georges G, Hesse F, Dangl M, Künkele KP, Ioannidis I, Huber R, Engh RA (2005) The 1.1 A resolution crystal structure of the p130cas SH3 domain and ramifications for ligand selectivity. J Mol Biol 347:1005-1014
28. Mokranjac D, Bourenkov G, Hell K, Neupert W, Groll M (2006) Structure and function of Tim14 and Tim16, the J and J-like components of the mitochondrial protein import motor. EMBO J 25:4675-4685
29. Werner MH, Wemmer DE (1992) Three-dimensional structure of soybean trypsin/chymotrypsin Bowman-Birk inhibitor in solution. Biochemistry 31:999-1010
30. Cierpicki T, Otlewski J (2000) Determination of a high precision structure of a novel protein, Linum usitatissimum trypsin inhibitor (LUTI), using computer-aided assignment of NOESY cross-peaks. Mol Biol 302:1179-1192
31. Hyberts SG, Goldberg MS, Havel TF, Wagner G (1992) The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures. Protein Sci 1:736-751
32. Christendat D et al (2000) Structural proteomics of an archaeon. Nat Struct Biol 7:903-909
33. Kohda D, Hatanaka H, Odaka M, Mandiyan V, Ullrich A, Schlessinger J, Inagaki F (1993) Solution structure of the sh3 domain of phospholipase c-gamma. Cell 72:953-960
34. Sönnichsen FD, DeLuca CI, Davies PL, Sykes BD (1996) Refined solution structure of type III antifreeze protein:hydrophobic groups may be involved in the energetics of the protein-ice interaction. Structure 4:1325-1337
35. Schaffer ML, Deshayes K, Nakamura G, Sidhu S, Skelton NJ (2003) Complex with a phage display-derived peptide provides insight into the function of insulin-like growth factor I. Biochemistry 42:9324-9334
36. Yee A et al (2002) An NMR approach to structural proteomics. Proc Natl Acad Sci USA 99:1825-1830
37. Pineda-Lucena A, Liao J, Wu B, Yee A, Cort JR, Kennedy MA, Edwards AM, Arrowsmith CH (2002) NMR structure of the hypothetical protein encoded by the YjbJ gene from Escherichia coli. Proteins 47:572-574
38. Abajian C, Yatsunyk LA, Ramirez BE, Rosenzweig AC (2004) Yeast cox17 solution structure and copper(I) binding. J Biol Chem 279:53584-53592
39. Arnesano F, Balatri E, Banci L, Bertini I, Winge DR (2005) Folding studies of cox17 reveal an important interplay of cysteine oxidation and copper binding. Structure 13:713-722
40. Cooke RM, Harvey TS, Campbell ID (1991) Solution structure of human insulin-like growth factor 1: a nuclear magnetic resonance and restrained molecular dynamics study. Biochemistry 30:5484-5491
41. Dalgarno DC, Botfield MC, Rickles RJ (1997) SH3 domains and drug design:ligands, structure, biological function. Biopolymers 43:383-400
42. Huang X, Miller W (1991) A time-efficient, linear-space local similarity algorithm. Adv Appl Math 12:337-357
43. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444-2448
44. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R,Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X, version 2.0. Bioinformatics 23:2947-2948
45. Holm L, Park J (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16:566-567
46. Levitt M (1976) A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 104:59-107
47. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105-132
48. Eisenberg D, Weiss RM, Terwilliger TC, Wilcox W (1982) Hydrophobic moments and protein structure. Faraday Symp Chem Soc 17:109-120
49. Engelman DM, Zaccai G (1986) Bacteriorhodopsin is an insideout protein. Proc Natl Acad Sci USA 77:5894-5898
50. Hopp TP, Woods KR (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci USA 78:3824-3828
51. Rose GD, Geselowitz AR, Lesser GJ, Lee RH, Zehfus MH (1985) Hydrophobicity of amino acid residues in globular proteins. Science 229:834-838
52. Wimley WC, White SH (1996) Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nat Struct Biol 3:842-848
53. Wolfender R, Anderson L, Cullis PM, Soulhgate CC (1981) Affinities of amino acids side chains for solvent water. Biochemistry 20:846-855
54. http://www.statsoft.com/?kw=spss&gclid=ck3ik-namzscfcitzaodhfy-ig
55. Spearman C (1906) General intelligence, objectively determined and measured. Am J Psychol 6:201-293
56. Vajdos FF, Ultsch M, Schaffer ML, Deshayes KD, Liu J, Skelton NJ, de Vos AM (2001) Crystal structure of human insulin-like growth factor-1:detergent binding inhibits binding protein interactions. Biochemistry 40:11022-11029
57. Koepke J, Ermler U, Warkentin E, Wenzl G, Flecker P (2000) Crystal structure of cancer chemopreventive bowman-birk inhibitor in ternary complex with bovine trypsin at 2.3 a resolution. Structural basis of janus-faced serine protease inhibitor specificity. J Mol Biol 298:477-491
58. Raymond JA, DeVries AL (1972) Freezing behavior of fish blood glycoproteins with antifreeze properties. Cryobiology 9:541-547
59. Raymond JA, DeVries AL (1977) Adsorption inhibition as a mechanism of freezing resistance in polar fishes. Proc Natl Acad Sci USA 74:2589-2593
60. Li Q, Luo L (1993) The kinetic theory of thermal hysteresis of a macromolecule solution. Chem Phys Lett 216:453-457
61. Li Q, Luo L (1994) Further discussion on the thermal hysteresis of the ice growth inhibitor. Chem Phys Lett 223:181-184
62. Hall DG, Lips A (1999) Phenomenology and mechanism of antifreeze peptide activity. Langmuir 15:1905-1912
63. Kristiansen E, Zachariassen KE (2005) The mechanism by which fish antifreeze proteins cause thermal hysteresis. Cryobiology 51:262-328
64. Chao H, Sönnichsen FD, DeLuca CI, Sykes BD, Davies PL (1994) Structure-function relationship in the globular type iii antifreeze protein: identification of a cluster of surface residues required for binding to ice. Protein Sci 3:1760-1769
65. Kauzmann W (1959) Some factors in the interpretation of protein denaturation. Adv Protein Chem 14:1-63
66. Minervini G, Evangelista G, Polticelli F, Piwowar M, Kochanczyk M, Flis L, Malawski M, Szepieniec T, Wisniowski Z, Matczynska E, Prymula K, Roterman I (2008) Never born proteins as a test case for ab initio protein structures prediction. Bioinformation 3:177-179