Molecular dynamics simulation study on the effect of water on the thermal stability of collagen polypeptide

Journal of the American Leather Chemists Association

Volumn 104, Issue 7, 2009, Pages 244-250

  Zhang, Wenhua ^a   He, Qiang ^a   Liao, Xuepin ^a   Shi, Bi ^b  

^a SICHUAN UNIVERSITY   (China)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID RESIDUES; COLLAGEN POLYPEPTIDES; EFFECT OF WATER; INITIAL CONFIGURATION; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR MECHANICALS; PRESENCE OF WATER; RISING TEMPERATURES; ROOT MEAN SQUARE; ROOT MEAN SQUARE DEVIATIONS; STRUCTURAL STABILITIES; THERMAL STABILITY; TRIPLE HELIXES; VALENCE FORCE FIELDS; X-RAY CRYSTALLOGRAPHIC STRUCTURES;

AMINATION; AMINES; AMINO ACIDS; BINDING SITES; COLLAGEN; HYDROGEN; HYDROGEN BONDS; MOLECULAR DYNAMICS; ORGANIC ACIDS; THERMODYNAMIC STABILITY;

CRYSTAL STRUCTURE;

EID: 69549126816     PISSN: 00029726     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (31)

1. Gary, D. F., Andre's, R.; Collagen structure: the molecular source of the tendon magic angle effect. J. Magne. Reson. Imag. 25, 345-361, 2007.
2. Kenji, O., Hirotaka, N., Tatsuya, K., Keiichi, N., Yuji, T., Norikazu, N.; Unique side chain conformation of a leu residue in a triple-helical structure. Biopolymers 86, 212-221,2007.
3. Barbara, B., Geetha, T., Balaraman, M., Karunakar, K..; Triple-helical peptides: an approach to collagen conformation, stability, and self-association. Biopolymers 89,345-353, 2007.
4. Meek, K. M., Chapman, J. A., Hardcastle, R. A.; The staining pattern of collagen fibrils. I. J. Biol. Chem. 254, 10710-10714, 1979.
5. Brodsky, B., Eikenberry, E. F.; Characterisation of fibrous forms of collagen. Methods Enzymol. 82, 127-174, 1982.
6. Barbara, B., Anton, V. P.; Molecular structure of the collagen triple helix. Adv. Pro. Chem. 70, 301-339, 2005.
7. Usha, R., Ramasami, T.; The effects of urea and n-propanol on collagen denaturation:using DSC, circular dicroism and viscosity. Thermo. Acta. 409,201-206, 2004.
8. Usha, R., Ramasami, T.; Effect of crosslinking agents (basic chromium sulfate and formaldehyde) on the thermal and thermomechanical stability of rat tail tendon collagen fibre. Thermo. Acta. 356,59-66, 2000.
9. Manich, A. M., Bosch, T., Carilla, J., Cot, J., Marsal, A., Sala, J., Celma, P. J.; Determination of the collagen thermal transitions in chrome leather by TMA. JALCA 98, 279-284, 2003.
10. Nishtar, N. F., Murugan, C. B., Jonnalagadda, R. R., Balachandran, U. N.; Stabilization of type I collagen against collagenases (type I) and thermal degradation using iron complex. J. Inorg. Biochem. 100,1774-1780, 2006.
11. Angela, M., Teresita S., Takeshi, Y., Ravish, A., Slawomir, L., Massayori, I., Barbara, B.; Mechanism of stabilization of a bacterial collagen triple helix in the absence of hydroxyl- proline. J. Biol. Chem. 282, 29757-29765, 2007.
12. Rault, I., Frei, V., Herbage, D., Abdul-Malak, N., Hue, A.; Evaluation of different chemical methods for cross-linking collagen gel, films and sponges. J.Mater.Sci. Mater.Med. 7,215-221, 1996.
13. Christopher, A. M., Nicholas, C. A., Victor, V. R. and Allen, J. B.; The increase in denaturation temperature following cross-linking of collagen is caused by dehydration of the fibres. J. Mol. Biol. 346, 551-556, 2005.
14. Ding, K. Y., Taylor, M. M., Brown, Eleanor M.; Tanning effects of aluminum-genipin or -vegetable tannin combinations. JALCA 103,377-382, 2008.
15. Covington, A.D., Inaganti, P., Leather, H., Wren, S., Hammond, R.; Chrome tanning: exploding the perceived myths, preconceptions and received wisdom. JALCA 96,467-480, 2001.
16. Holmgren, S.K., Taylor, K.M., Bretscher, L.E., Raines, R.T.; Code for collagen's stability deciphered. Nature 392,666-667,1998.
17. Kramer, R.Z., Bella, J., Mayville P., Brodsky, B., Berman, H.M.; Sequence dependent conformational variations of collagen triple-helical structure. Nat. Struct. Biol. 6, 454-457,1999.
18. Rochdi, A., Foucat, L., Renou, J. P.; Effect of thermal denaturation on water-collagen interactions: NMR relaxation and differential scanning calorimetry analysis. Biopolymers 50, 690-696,1999.
19. Miles, C. A., Ghelashvili, M.; Polymer-in-a-box mechanism for the thermal stabilization of collagen molecules in fibres. Biophys. J. 76,3243-3252,1999.
20. Miles, C. A., Burjanadze, T. V.; Thermal stability of collagen fibres in ethylene glycol. Biophys. J. 80,1480-1486,2001.
21. Magne, O., Bjorn, O. B., Arne, O. S.; Comparative unfolding studies of psychrophilic and mesophilic uracil DNA glycosylase: MD simulations show reduced thermal stability of the cold-adapted enzyme. J. Mol. Graph. Model. 26,124-134,2007.
22. Jian, Y., Donnell, B., William, M. S.; Barnase thermal titration via molecular dynamics simulations:Detection of early denaturation sites. J. Mol. Graph. Model. 24,233-243,2006.
23. Mogilner, I. G., Ruderman, G., Grigera, J. R.; Collagen stability, hydration and native state. J. Mol. Graph. Model. 21,209-213,2002.
24. Simona, B., Chiara, C, Susanna, M.; Understanding the structural and binding properties of collagen: a theoretical perspective. J.Phys.Chem. B 108,10101-10112,2004.
25. 3. JBiochem.(Tokyo) 138,135-144,2005.
26. Brown, E.M., Chen, J.M., Feairheller, S.H.; Predicted interactions of ionizable side chains in a fragment of the three-dimensional energy-minimized model for calf skin type I collagen microfibril. JALCA 83, 2-11,1993.
27. Fietzek, P.P., Kuehn, K.; The covalent structure of collagen: amino-acid sequence of the cyanogen-bromide peptides alpha-1-CB2, alpha-1-CB4 and alpha-1-CB5 from calf-skin collagen. Eur. J. Biochem. 52,77-82,1975.
28. Fietzek, P.P., Rexrodt, F.W.; The covalent structure of collagen. The amino-acid sequence of alpha2-CB4 from calf-skin collagen. Eur. J. Biochem. 59,113-118,1975.
29. Daggett, V.; Molecular dynamics simulations of the protein unfolding/folding reaction. Acc. Chem. Res. 35, 422-429, 2002.
30. Alemayehu, A. Gorfe, Amedeo, C, Ilian, J.; The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis. J. Mol. Recognit. 17,120-131,2004.
31. Purmonen, M., Valjakka, J., Takkinen, K.., Laitinen, T., Rouvinen J.; Molecular dynamics studies on the thermostability of family 11 xylanases. Protein Engineering, Design & Selection 20,551-559,2007.