Binding free energy calculations between bovine β-lactoglobulin and four fatty acids using the MMGBSA method

Biopolymers

Volumn 101, Issue 10, 2014, Pages 1010-1018

  Bello, Martiniano ^a  

^a INSTITUTO POLITÉCNICO NACIONAL   (Mexico)

Author keywords

capric acid; caprylic acid; free energy calculation; lactoglobulin; molecular dynamics; myristic acid; stearic acid

Indexed keywords

FREE ENERGY; LIGANDS; MAMMALS; MOLECULAR DYNAMICS; PROTEINS; SATURATED FATTY ACIDS; STEARIC ACID;

CAPRIC ACID; CAPRYLIC ACID; FREE-ENERGY CALCULATIONS; LACTOGLOBULIN; MYRISTIC ACID;

BINDING ENERGY;

BETA LACTOGLOBULIN; DECANOIC ACID; MYRISTIC ACID; OCTANOIC ACID; STEARIC ACID; FATTY ACID; LACTOGLOBULIN; PROTEIN BINDING;

ANIMAL EXPERIMENT; ARTICLE; BINDING AFFINITY; BIOENERGY; CATTLE; CHEMICAL INTERACTION; CLINICAL EVALUATION; COMPLEX FORMATION; DECOMPOSITION; ENERGY; ENERGY METABOLISM; FREE ENERGY CALCULATION; HYDROGEN BOND; HYDROPHOBICITY; LIGAND BINDING; MATHEMATICAL ANALYSIS; MATHEMATICAL PHENOMENA; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULAR MECHANICS GENERALIZED BORN SURFACE AREA; NONHUMAN; STATIC ELECTRICITY; THERMODYNAMICS; ANIMAL; BOVINE; METABOLISM; X RAY CRYSTALLOGRAPHY;

ANIMALS; CATTLE; CRYSTALLOGRAPHY, X-RAY; FATTY ACIDS; LACTOGLOBULINS; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; THERMODYNAMICS;

EID: 84904604662     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.22483     Document Type: Article

References (48)

1. Kontopidis, G.,;, Holt, C.,;, Sawyer L., J. Dairy Sci 2004, 87, 85-796.
2. Zimmerman, A. W.,;, Veerkamp, J. H., Cell Mol Life Sci 2002, 59, 1096-1116.
3. Bello, M.,;, Gutiérrez, G.,;, García-Hernández, E., Biophys Chem 2012, 165-166, 79-86.
4. Bello, M,;, García-Hernández, E., Biopolymers 2013, DOI: 10.1002/bip.22454.
5. Sawyer, L., β-lactoglobulin, In Advanced Dairy Chemistry;, Fox, P. F.,;, McSweeney, P. L. H.,; Eds., 3rd ed. New York: Kluwer Academic/Plenum Publishers, 2003, pp 319-386.
6. Loch, J. I.,;, Polit, A.,;, Bonarek, P.,;, Olszewska, D.,;, Kurpiewska, K.,;, Dziedzicka-Wasylewska, M.,;, Lewiński, K., Int J Biol Macromol 2012, 50, 1095-102.
7. Bello, M.,;, Portillo-Téllez, M. D.,;, García- Hernández E., Biochemistry 2011, 50, 151-161.
8. Collini, M.,;, D'Alfonso, L.,;, Molinari, H.,;, Ragona, L.,;, Catalano, M.,;, Baldini, G., Protein Sci 2003, 12, 1596-1603.
9. Ragona, L.,;, Fogolari, F.,;, Zetta, L.,;, Perez, D. M.,;, Puyol, P.,;, De Kruif, K.,:, Lohr, F.,;, Ruterjans, H.,;, Molinari, H., Protein Sci 2000, 9, 1347-1356.
10. Barbiroli, A.,;, Beringhelli, T.,;, Bonomi, F.,;, Donghi, D.,;, Ferranti, P.,;, Galliano, M.,;, Iametti, S.,;, Maggioni, D.,;, Rasmussen, P.,;, Scanu, S.,;, Vilardo, M. C., Biol Chem 2000, 391, 21-32.
11. Jiang, H. R., Liu, N., J. Dairy Sci 2010, 9, 3931-3939.
12. Sali, A.,;, Blundell, T. L., J Mol Biol 1993, 234, 779-815.
13. Lovell, S. C.,;, Davis, I. W.,;, Arendall III, W. B.,;, de Bakker, P. I. W.,;, Word, J. M.,;, Prisant, M. G.,;, Richardson, J. S.,;, Richardson D. C., Proteins 2002, 50, 437-450.
14. Case, D. A.,;, Cheatham, T. E.,;, Darden, T.,;, Gohlke, H.,;, Luo, R.,;, Merz, K. M.,;, Onufriev, A.,;, Simmerling, C.,;, Wang, B.,;, Woods, R., J Comput Chem 2005, 26, 1668-1688.
15. Duan, Y.,;, Wu, C.,;, Chowdhury, S.,;, Lee, M. C.,;, Xiong, G.,;, Zhang, W.,;, Yang, R.,;, Cieplak, P.,;, Luo, R.,;, Lee, T., J Comput Chem 2003, 24, 1999-2012.
16. Wang, J.,;, Wolf, R. M.,;, Caldwell, J. W.,;, Kollman, P. A.,;, Case, D. A., J Comput Chem 2004, 25, 1157-1174.
17. Jakalian, A.,;, Jack, D. B.,;, Bayly, C. I., J Comput Chem 2002, 23, 1623-1641.
18. Jorgensen, W. L.,;, Chandrasekhar, J.,;, Madura, J. D.,;, Impey, R. W.,;, Klein, M. L., J Chem Phys 1983, 79, 926-935.
19. Van Gunsteren, W. F.,;, Berendsen H. J. C., Mol Phys 1977, 34, 1311-1327.
20. Darden, T.,;, York, D.,;, Pedersen, L., J Chem Phys 1993, 98, 10089-10092.
21. Berendsen, H. J. C.,;, Postma, J. P. M.,;, van Gunsteren W. F.,;, DiNola A.,;, Haak J. R., J Chem Phys 1984, 81, 3684-3690.
22. Case, D. A.,;, Darden, T. A.,;, Cheatham, T. E., III,;, Simmerling, C. L.,;, Wang, J.,;, Duke, R. E.,;, Luo, R.,;, Walker, R. C.,;, Zhang, W.,;, Merz, K. M.,;, Roberts, B. P.,;, Hayik, S.,;, Roitberg, A. E.,;, Seabra, G.,;, Swails, J. M.,;, Kolossváry, I.,;, Wong, K. F.,;, Paesani, F.,;, Vanicek, J.,;, Wolf, R. M.,;, Liu, J.,;, Wu, X.,;, Brozell, S. R.,;, Steinbrecher, T.,;, Gohlke, H.,;, Cai, Q.,;, Ye, X.,;, Wang, J.,;, Hsieh, M.-J.,;, Cui, G.,;, Roe, D. R.,;, Mathews, D. H.,;, Seetin, M. G.,;, Salomon-Ferrer, R.,;, Sagui, C.,;, Babin, V.,;, Luchko, T.,;, Gusarov, S.,;, Kovalenko, A.,;, Kollman, P. A., AMBER 12; University of California: San Francisco, CA, 2012.
23. DeLano, W. L., The PyMOL Molecular Graphics System, DeLano Scientific, 2002, San Carlos, CA, USA. Available at: http://www.pymol.org. Last accessed date March 1, 2014.
24. Miller, B. R.,;, McGee, T. D.,;, Swails, J. M.,;, Homeyer, N.,;, Gohlke, H.,;, Roitberg, A. E., J Chem Theory Comput 2012, 8, 3314-3321.
25. Hou, T.,;, Yu, R., J Med Chem 2007, 50, 1177-1188.
26. Gohlke, H.,;, Kiel, C.,;, Case, D. A., J Mol Biol 2003, 330, 891-913.
27. Sanner, M. F.,;, Olson, A. J.,;, Spehner, J. C., Biopolymers, 1996, 38, 305-320.
28. Weiser, J.,;, Shenkin, P. S.,;, Still, W. C., J Comput Chem, 1999, 20, 217-230.
29. Hawkins, G. D.,;, Cramer, C. J.,;, Truhlar, D. G., J Phys Chem 1996, 100, 19824-19839.
30. Konuma, T.,;, Sakurai, K.,;, Goto, Y., J Mol Biol 2007, 368, 209-218.
31. Sakurai, K.,;, Konuma, T.,;, Yagi M.,;, Goto, Y., Biochimica et Biophysica Acta 2009, 1790, 527-537.
32. Loch, J.,;, Polit, A.,;, Gorecki, A.,;, Bonarek, P.,;, Kurpiewska, K.,;, Dziedzicka-Wasylewska, M.,;, Lewinski, K., J Mol Recognit 2011, 24, 341-349.
33. Kuhn, B.,;, Gerber, P.,;, Schulz-Gasch, T.,;, Stahl, M., J Med Chem 2005, 48, 4040-4048.
34. Yan, C.,;, Xiu, Z.,;, Li, X.,;, Li, S.,;, Hao, C.,;, Teng, H., Proteins 2008, 73, 134-149.
35. Wang, J.,;, Hou, T.,;, Xu, X., Curr Comput Aided Drug Des 2006, 2, 287-306.
36. Kuhn, B.,;, Kollman P. A., J Med Chem 2000, 20, 3786-3791.
37. Huo, S.,;, Wang, J.,;, Cieplak, P.,;, Kollman, P. A.,;, Kuntz, I. D., J Med Chem. 2002, 45, 1412-1419.
38. Hou, T.,;, Zhang, W.,;, Case, D. A.,;, Wang, W., J Mol Biol. 2008, 376, 1201-1214.
39. Hou, T.,;, Wang, J.,;, Li, Y.,;, Wang, W., J Comput Chem 2011, 32, 866-877.
40. Hou, T.,;, Li, N.,;, Li, Y.,;, Wang, W., J Proteome Res 2012, 11, 2982-2995.
41. Li, L.,;, Li, Y.,;, Zhang, L.,;, Hou, T., J Chem Inf Model 2012, 52, 2715-2729.
42. Kollman, P. A.,;, Massova, I.,;, Reyes, C.,;, Kuhn, B.,;, Huo, S., et al. Acc Chem Res 2000, 33, 889-897.
43. Hou, T.,;, Wang, J.,;, Li, Y.,;, Wang, W., J Chem Inform Modeling 2011, 51, 69-82.
44. Singh, N.,;, Warshel, A., Proteins 2010, 78, 1705-1723.
45. Skerra, A., Biochim Biophys Acta 2000, 1482, 337-350.
46. Wallace, A. C.,;, Laskowski, R. A.,;, Thornton, J. M., Protein Eng 1995, 8, 127-134.
47. Schmidt, A. M.,;, Bloss, I.,;, Skerra, A., Protein Eng 1998, 7, 601-607.
48. Chan, H. S., 2002. Amino Acid Side-chain Hydrophobicity. eLS. DOI: 10.1038/npg.els.0003005.