The severity of osteogenesis imperfecta: A comparison to the relative free energy differences of collagen model peptides

Biopolymers

Volumn 95, Issue 3, 2011, Pages 182-193

  Lee, Kyung Hoon ^a   Kuczera, Krzysztof ^b   Banaszak Holl, Mark M ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF KANSAS   (United States)

Author keywords

collagen like peptide; disulfide bond; free energy simulation; stochastic boundary molecular dynamics simulation; thermodynamic integration

Indexed keywords

COLLAGEN-LIKE PEPTIDES; DISULFIDE BONDS; FREE ENERGY SIMULATION; STOCHASTIC BOUNDARIES; THERMODYNAMIC INTEGRATION;

COLLAGEN; COMPUTER SIMULATION; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PEPTIDES; STOCHASTIC SYSTEMS;

FREE ENERGY;

COLLAGEN;

ARTICLE; DISEASE SEVERITY; ENERGY; MUTATION; OSTEOGENESIS IMPERFECTA; PROTEIN STABILITY; WILD TYPE;

AMINO ACID SEQUENCE; COLLAGEN; HUMANS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; OSTEOGENESIS IMPERFECTA; OXIDATION-REDUCTION; THERMODYNAMICS;

EID: 78650906757     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.21552     Document Type: Article

References (52)

1. Rich, A.,;, Crick, F. H. C., J Mol Biol 1961, 3, 483-506.
2. Fraser, R. D. B.,;, MacRae, T. P.,;, Suzuki, E., J Mol Biol 1979, 129, 463-481.
3. Prockop, D. J.,;, Kivirikko, K. I., Annu Rev Biochem 1995, 64, 403-434.
4. Engel, J.,;, Chen, H.-T.,;, Prockop, D. J., Biopolymers 1977, 16, 601-622.
5. Ramachandran, N. G.,;, Kartha, G., Nature 1955, 176, 593-594.
6. Ahmed, M.,;, Liu, Z. J.,;, Lukyanov, A. N.,;, Signoretti, S.,;, Horkan, C.,;, Monsky, W. L.,;, Torchilin, V. P.,;, Goldberg, S. N., Radiology 2005, 235, 469-477.
7. Byers, P. H., Disorders of Collagen Biosynthesis and Structure; McGraw-Hill: New York, 1989.
8. Byers, P. H.,;, Tsipouras, P.,;, Bonadio, J. F.,;, Starman, B.,;, Schwartz, R. C., Am J Hum Genet 1988, 42, 237-248.
9. Byers, P. H.,;, Steiner, R. D., Annu Rev Med 1992, 43, 269-282.
10. Byers, P. H., Connective Tissue and Its Heritable Disorders; Wiley-Liss: New York, 1993.
11. Bachiner, H. P.,;, Morris, N. P.,;, Davis, J. M., Am J Med Genet 1993, 45, 152-162.
12. Wang, Q.,;, Orrison, B. M.,;, Marini, J. C., J Biol Chem 1993, 268, 25162-25167.
13. Dalgleish, R., Nucleic Acids Res 1998, 26, 253-255.
14. Bodian, D. L.,;, Madhan, B.,;, Brodsky, B.,;, Klein, T. E., Biochemistry 2008, 47, 5424-5432.
15. Radmer, R. J.,;, Klein, T. E., Biochemistry 2004, 43, 5314-5323.
16. Bachiner, H. P.,;, Davis, J. M., Int J Biol Macromol 1991, 13, 152-156.
17. Mooney, S. D.,;, Huang, C. C.,;, Kollman, P. A.,;, Klein, T. E., Biopolymers 2001, 58, 347-353.
18. Beck, K.,;, Chan, V. C.,;, Shenoy, N.,;, Kirkpatrick, A.,;, Ramshaw, J. A. M.,;, Brodsky, B., Proc Natl Acad Sci USA 2000, 97, 4273-4278.
19. Ottl, J.,;, Battistuta, R.,;, Pieper, M.,;, Tschesche, H.,;, Bode, W.,;, Kuhn, K.,;, Moroder, L., FEBS Lett 1996, 398, 31-36.
20. Gauba, V.,;, Hartgerink, J. D., J Am Chem Soc 2008, 130, 7509-7515.
21. Gauba, V.,;, Hartgerink, J. D., J Am Chem Soc 2007, 129, 15034-15041.
22. Brooks, B. R.,;, Bruccoleri, R.,;, Olafson, B.,;, States, D.,;, Swaminathan, S.,;, Karplus, M., J Comput Chem 1983, 4, 187-217.
23. MacKerell, A. D.,;, Bashford, D.,;, Bellott, M.,;, Dunbrack, R. L. J.,;, Evanseck, J. D.,;, Field, M. J.,;, Fischer, S.,;, Gao, J.,;, Guo, H.,;, Ha, S.,;, Joseph-McCarthy, D.,;, Kuchnir, L.,;, Kuczera, K.,;, Lau, F. T. K.,;, Mattos, C.,;, Michnick, S.,;, Ngo, T.,;, Nguyen, D. T.,;, Prodhom, B.,;, Reiher, W. E.,;, III Roux, B.,;, Schlenkrich, M.,;, Smith, J. C.,;, Stote, R.,;, Straub, J.,;, Watanabe, M.,;, Wiorkiewicz-Kuczera, J.,;, Karplus, M., J Phys Chem B 1998, 102, 3386-3616.
24. Bella, J.,;, Eaton, M.,;, Brodsky, B.,;, Berman, H. M., Science 1994, 266, 75-81.
25. Jorgensen, W. L.,;, Chandrasekhar, J.,;, Madura, J. D.,;, Impey, R. W.,;, Klein, M. L., J Chem Phys 1983, 79, 926-935.
26. Brooks, C. L.,;, Karplus, M., J Mol Biol 1983, 208, 159-181.
27. Beveridge, D.,;, DiCapua, F., Annu Rev Biophys Chem 1989, 18, 431-492.
28. Straatsma, T. P.,;, McCammon, J. A., Annu Rev Phys Chem 1992, 43, 407-435.
29. Kollman, P. A., Chem Rev 1993, 93, 2395-2417.
30. Brooks, C. L.,;, Karplus, M.,;, Pettitt, B. M., Adv Chem Phys 1988, 71, 1-249.
31. Bevington, P. R., Data Reduction and Error Analysis for the Physical Sciences; McGraw-Hill: New York, 1992.
32. Swart, M.,;, Van Duijnen, P. T.,;, Snijders, J. G., J Comput Chem 2001, 22, 79-88.
33. Boresch, S.,;, Archontis, G.,;, Karplus, M., Proteins: Structure, Function and Genetics; 1994, 20, 25-33.
34. Boresch, S.,;, Karplus, M., J Mol Biol 1995, 254, 801-807.
35. Mark, A. E.,;, van Gunsteren, W. F., J Mol Biol 1994, 240, 167-176.
36. Brady, G. P.,;, Sharp, K. A., J Mol Biol 1995, 254, 77-85.
37. Bella, J.,;, Brodsky, B.,;, Berman, H. M., Structure 1995, 3, 893-906.
38. Bogaert, R.,;, Tiller, G. E.,;, Weis, M. A.,;, Gruber, H. E.,;, Rimoin, D. L.,;, Cohn, D. H.,;, Eyre, D. R., J Biol Chem 1992, 267, 22522-22526.
39. Vogel, B. E.,;, Doelz, R.,;, Kadler, K. E.,;, Hojima, Y.,;, Engel, J.,;, Prockop, D. J., J Biol Chem 1988, 263, 19249-19255.
40. Lightfoot, S. J.,;, Holmes, D. F.,;, Brass, A.,;, Grant, M. E.,;, Byers, P. H.,;, Kadler, K. E., J Biol Chem 1992, 267, 25521-25528.
41. Matsumura, M.,;, Becktel, W. J.,;, Levitt, M.,;, Matthews, B. W., Proc Natl Acad Sci USA 1989, 86, 6562-6566.
42. Perry, L. J.,;, Wetzel, R., Science 1984, 226, 555-557.
43. Starman, B. J.,;, Eyre, D.,;, Charbonneau, H.,;, Harrylock, M.,;, Weis, M. A.,;, Weiss, L.,;, Graham, J. M.,;, Byers, P. H., J Clin Invest 1989, 84, 1206-1214.
44. Gautieri, A.,;, Vesentini, S.,;, Redaelli, A.,;, Buehler, M. J., Protein Sci 2009, 18, 161-168.
45. Gautieri, A.,;, Uzel, S.,;, Vesentini, S.,;, Redaelli, A.,;, Buehler, M. J., Biophys J 2009, 97, 847-865.
46. Sasaki, N.,;, Odajima, S., J Biomech 1996, 29, 655-658.
47. Sun, Y. L.,;, Luo, Z. P.,;, Fertala, A.,;, An, K. N., J Biomech 2004, 37, 1665-1669.
48. Berendsen, H. J. C.,;, van der Spoel, D.,;, van Drunen, R., Comp Phys Commun 1995, 91, 43-56.
49. Lindahl, E.,;, Hess, B.,;, van der Spoel, D., J Mol Mod 2001, 7, 306-317.
50. Raghunath, M.,;, Bruckner, P.,;, Steinmann, B., J Mol Biol 1994, 236, 940-949.
51. Traub, W.,;, Arad, T.,;, Vetter, U.,;, Weiner, S., Matrix Biol 1994, 14, 337-345.
52. Cohen-Solal, L.,;, Zylberberg, L.,;, Sangalli, A.,;, Lira, M. G.,;, Mottes, M., J Biol Chem 1994, 269, 14751-14758.