Protein specificity of charged sequences in polyanions and heparins

Biomacromolecules

Volumn 11, Issue 12, 2010, Pages 3325-3331

  Kayitmazer, A Basak ^a,c   Quinn, Bonnie ^b   Kimura, Kozue ^d   Ryan, Gillian L ^c,e   Tate, Angela J ^b   Pink, David A ^b   Dubin, Paul L ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

^b ST FRANCIS XAVIER UNIVERSITY   (Canada)

^c INDIANA UNIVERSITY   (United States)

^d Dalhousie University ^*  (United States)

^e DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AFFINITY BINDING; BINDING PROTEINS; CONFORMATIONAL FREEDOM; ELECTROSTATIC INTERACTIONS; ELECTROSTATIC MODELING; GLYCOSAMINOGLYCANS; HEPARAN SULFATES; MONTE CARLO SIMULATION; NON-SPECIFIC BINDING; POLYANIONS; POLYIONS; PROTEIN CHARGE; STRONG BINDING;

COMPUTER SIMULATION; ELECTROSTATICS; MONTE CARLO METHODS; POLYSACCHARIDES;

PROTEINS;

COPOLYMER; HEPARIN; POLYANION;

AMINO ACID SEQUENCE; ANISOTROPY; ARTICLE; BINDING AFFINITY; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN BINDING;

COMPUTER SIMULATION; HEPARIN; POLYMERS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; STATIC ELECTRICITY;

EID: 78650301020     PISSN: 15257797     EISSN: 15264602     Source Type: Journal    
DOI: 10.1021/bm1008074     Document Type: Article

References (56)

1. Cooper, C. L.; Dubin, P. L.; Kayitmazer, A. B.; Turksen, S. Curr. Opin. Colloid Interface Sci. 2005, 10, 52-78
2. Evers, O. A.; Fleer, G. J.; Scheutjens, J. M. H. M. J. Colloid Interface Sci. 1986, 111, 446-454
3. Muthukumar, M. J. Chem. Phys. 1987, 86, 7230-7235
4. Record, M. T.; Lohman, T. M.; Dehaseth, P. J. Mol. Biol. 1976, 107, 145-158
5. Darling, R. J.; Kuchibhotla, U.; Glaesner, W.; Micanovic, R.; Witcher, D. R.; Beals, J. M. Biochemistry 2002, 41, 14524-14531
6. Lohman, T. M.; DeHaseth, P.; Record, M. T. J. Biochemistry 1980, 19, 3522-3530
7. Olson, S. T.; Bjork, I.; Sheffer, R.; Craig, P. A.; Shore, J. D.; Choay, J. J. Biol. Chem. 1992, 267, 12528-12538
8. Capila, I.; Lindhardt, R. J. Angew. Chem., Int. Ed. 2002, 41, 390-412
9. Conrad, H. E. Heparin-Binding Proteins; Academic Press: San Diego, CA, 1998.
10. Iozzo, R. V. Annu. Rev. Biochem. 1998, 67, 609-652
11. Sugahara, K.; Kitagawa, H. IUBMB Life 2002, 54, 163-175
12. Jin, L.; Abrahams, J. P.; Skinner, R.; Petitou, M.; Pike, R. N.; Carrell, R. W. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 14683-14688
13. Grootenhuis, P. D. J.; Van Boeckel, C. A. A. J. Am. Chem. Soc. 1991, 113, 2743-2747
14. Margalit, H.; Fischer, N.; Ben-Sasson, S. A. J. Biol. Chem. 1993, 268, 19228-19231
15. Seyrek, E.; Dubin, P. L.; Tribet, C.; Gamble, E. A. Biomacromolecules 2003, 4, 273-282
16. Park, J. M.; Muhoberac, B. B.; Dubin, P. L.; Xia, J. Macromolecules 1992, 25, 290-295
17. Catlow, K. R.; Deakin, J. A.; Wei, Z.; Delehedde, M.; Fernig, D. G.; Gherardi, E.; Gallagher, J. T.; Pavao, M. S. G.; Lyon, M. J. Biol. Chem. 2008, 283, 5235-5248
18. Pye, D. A.; Vives, R. R.; Hyde, P.; Gallagher, J. T. Glycobiology 2000, 10, 1183-1192
19. Sarrazin, S.; Bonnaffe, D.; Lubineau, A.; Lortat-Jacob, H. J. Biol. Chem. 2005, 280, 37558-37564
20. Lander, A. D. Matrix Biol. 1998, 17, 465-472
21. Deakin, J. A.; Blaum, B.; Gallagher, J. T.; Uhrin, D.; Lyon, M. J. Biol. Chem. 2009, 284, 6311-6321
22. Jones, L. S.; Yazzie, B.; Middaugh, C. R. Mol. Cell. Proteomics 2004, 3, 746-769
23. Rudd, T. R.; Yates, E. A. Mol. BioSyst. 2010, 6, 902-908
24. Henry, B. L.; Connell, J.; Liang, A. Y.; Krishnasamy, C.; Desai, U. R. J. Biol. Chem. 2009, 284, 20897-20908
25. Tamada, Y.; Murata, M.; Hayashi, T.; Goto, K. Biomaterials 2002, 23, 1375-1382
26. Cooper, C. L.; Goulding, A.; Kayitmazer, A. B.; Ulrich, S.; Stoll, S.; Turksen, S.; Yusa, S. I.; Kumar, A.; Dubin, P. L. Biomacromolecules 2006, 7, 1025-1035
27. Carter, D. C.; Ho, J. X. Adv. Protein Chem. 1994, 45, 153-203
28. Tanford, C.; Swanson, S. A.; Shore, W. S. J. Am. Chem. Soc. 1955, 77, 6414-6421
29. Gao, J. Y.; Dubin, P. L.; Sato, T.; Morishima, Y. J. Chromatogr., A 1997, 766, 233-236
30. Grymonpre, K. R.; Staggemeier, B. A.; Dubin, P. L.; Mattison, K. W. Biomacromolecules 2001, 2, 422-429
31. Tanford, C.; Kirkwood, J. G. J. Am. Chem. Soc. 1957, 79, 5333-5339
32. Hattori, T.; Kimura, K.; Seyrek, E.; Dubin, P. L. Anal. Biochem. 2001, 295, 158-167
33. Bertonati, C.; Honig, B.; Alexov, E. Biophys. J. 2007, 92, 1891-1899
34. Honig, B.; Sharp, K.; Yang, A.-S. J. Phys. Chem. 1993, 97, 1101-1109
35. Schutz, C. N.; Warshel, A. Protein: Struct. Funct. Genet. 2001, 44, 400-417
36. Carmesin, I.; Kremer, K. Macromolecules 1988, 21, 2819-2823
37. Zajac, R.; Chakrabarti, A. J. Chem. Phys. 1996, 104, 2418-2437
38. Zhang, H.; Lai, L.; Wang, L.; Han, Y.; Tang, Y. Biopolymers 1997, 41, 61-72
39. Deserno, M.; Holm, C.; May, S. Macromolecules 2000, 33, 199-206
40. Pink, D. A.; Hanna, C. B.; Quinn, B. E.; Levadny, V.; Ryan, G. L.; Filion, L.; Paulson, A. T. Food Res. Int. 2006, 39, 1031-1045
41. Vlachy, V. Annu. Rev. Phys. Chem. 1999, 50, 145-165
42. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. Chem. Phys. 1953, 21, 1087-1092
43. Binder, K.; Mueller, M.; Baschnagel, J. In Simulation Methods for Polymers; Kotelyanski, M.; Theodoru, D. N., Eds.; Marcel Dekker: New York, 2004; pp 125 - 146.
44. Xia, J.; Dubin, P. L.; Kim, Y.; Muhoberac, B. B.; Klimkowski, V. J. J. Phys. Chem. 1993, 97, 4528-4534
45. Kaibara, K.; Okazaki, T.; Bohidar, H. B.; Dubin, P. L. Biomacromolecules 2000, 1, 100-107
46. McQuigg, D. W.; Kaplan, J. I.; Dubin, P. L. J. Phys. Chem. 1992, 96, 1973-1978
47. Zhang, H. W.; Ohbu, K.; Dubin, P. L. Langmuir 2000, 16, 9082-9086
48. Powell, A. K.; Yates, E. A.; Fernig, D. G.; Turnbull, J. E. Glycobiology 2004, 14, 17R-30R
49. de Vries, R.; Weinbreck, F.; de Kruif, C. G. J. Chem. Phys. 2003, 118, 4649-4659
50. Pavlov, G.; Finet, S.; Tatarenko, K.; Korneeva, E.; Ebel, C. Eur. Biophys. J. 2003, 32, 437-449
51. Casu, B.; Petitou, M.; Provasoli, M.; Sinay, P. Trends Biochem. Sci. 1988, 13, 221-225
52. Canales, A.; Angulo, J.; Ojeda, R.; Bruix, M.; Fayos, R.; Lozano, R.; Gimenez-Gallego, G.; Martin-Lomas, M.; Nieto, P. M.; Jimenez-Barbero, J. J. Am. Chem. Soc. 2005, 127, 5778-5779
53. Higman, V. A.; Blundell, C. D.; Mahoney, D. J.; Redfield, C.; Noble, M. E. M.; Day, A. J. J. Mol. Biol. 2007, 371, 669-684
54. Hricovini, M.; Guerrini, M.; Bisio, A.; Torri, G.; Petitou, M.; Casu, B. Biochem. J. 2001, 359, 265-272
55. Odian, G. In Principles of Polymerization, 4th ed.; Wiley-Interscience: Hoboken, NJ, 2004; pp 481 - 484.
56. Abzalimov, R. R.; Dubin, P. L.; Kaltashov, I. A. Anal. Chem. 2007, 79, 6055-6063