Differences between apo and three holo forms of the intestinal fatty acid binding protein seen by molecular dynamics computer calculations

Biophysical Journal

Volumn 78, Issue 2, 2000, Pages 608-625

  Woolf, Thomas B ^a   Grossfield, Alan ^a   Tychko, Michael ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APOPROTEIN; FATTY ACID BINDING PROTEIN;

ARTICLE; BINDING AFFINITY; COMPUTER SIMULATION; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 0034076542     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(00)76621-5     Document Type: Article

References (41)

1. Åqvist, J., C. Medina, and J.-E. Samuelsson. 1994. A new method for predicting binding affinity in computer-aided drug design. Prot. Eng. 7:385.
2. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comp. Chem. 4:187-217.
3. Brown, M. L., R. M. Venable, and R. W. Pastor. 1995. A method for characterizing transition concertedness from polymer dynamics computer simulations. Biopolymers. 35:31-46.
4. Brünger, A., III, C. L. Brooks, and M. Karplus. 1984. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett. 105:495-500.
5. Cistola, D. P., and K. B. Hall. 1995. Probing internal water molecules in proteins using two-dimensional 19F-1H NMR. J. Biomol. NMR. 5:415-419.
6. Cistola, D. P., J. C. Sacchettini, L. J. Banaszak, M. T. Walsh, and J. I. Gordon. 1989. Fatty acid interactions with rat intestinal and liver fatty acid-binding proteins expressed in Escherichia Coli: a comparative 13C NMR study. J. Biol. Chem. 264:2700-2710.
7. Cistola, D. P., J. C. Sacchettini, and J. I. Gordon. 1990. 13C NMR studies of fatty acid-protein interactions: comparison of homologous fatty acid-binding proteins produced in the intestinal epithelium. Mol. Cell Biochem. 98:101-110.
8. Dill, K. A. 1997. Additivity principles in biochemistry. J. Biol. Chem. 272:701-704.
9. Eads, J., J. C. Sacchettini, A. Kromminga, and J. I. Gordon. 1993. Escherichia coli-derived rat intestinal fatty acid binding protein with bound myristate at 1.5 Å resolution and I-FABP (Arg 106-G1n) with bound oleate at 1.74 Å resolution. J. Biol Chem. 268:26375-26385.
10. Frieden, C., N. Jiang, and D. P. Cistola. 1995. Intestinal fatty acid binding protein: Folding of fluorescein-modified proteins. Biochemistry. 34: 2724-2730.
11. Frolov, A., and F. Schroeder. 1997. Time-resolved fluorescence of intestinal and liver fatty acid binding proteins: role of fatty acyl CoA and fatty acid. Biochemistry. 36:505-517.
12. Gilson, M., K. A. Sharp, and B. Honig. 1988. Calculating the electrostatic potential of molecules in solution. J. Comp. Chem. 9:327-335.
13. Hodsdon, M. E., and D. P. Cistola, D. P. 1997a. Discrete backbone disorder in the nuclear magnetic resonance structure of apo intestinal fatty acid binding protein: implications for the mechanism of ligand entry. Biochemistry. 36:1450-1460.
14. Hodsdon, M. E., and D. P. Cistola. 1997b. Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange. Biochemistry. 36: 2278-2290.
15. Hodsdon, M. E., J. J. Toner, and D. P. Cistola. 1995. 1H, 13C and 15N assignments and chemical shift-derived secondary structure of intestinal fatty acid-binding protein. J. Biomol. NMR. 6:198-210.
16. Hodsdon, M. E., J. W. Ponder, and D. P. Cistola, D. P. 1996. The NMR solution structure of intestinal fatty acid-binding protein complexed with palmitate: application of a novel distance geometry algorithm. J. Mol. Biol. 264:585-602.
17. Kim, K., D. P. Cistola, and C. Frieden. 1996. Intestinal fatty acid binding protein: The structure and stability of a helix-less variant. Biochemistry. 35:7553-7558.
18. Kirk, W. R., E. Kurian, and F. G. Prendergast. 1996. Characterization of the sources of protein-ligand affinity: 1-sulfonato-8-(1′) anilinonaphthalene binding to intestinal fatty acid binding protein. Biophys. J. 70: 69-83.
19. Kurian, E., W. R. Kirk, and F. G. Prendergast. 1996. Affinity of fatty acid for rat intestinal fatty acid binding protein: further examination. Biochemistry. 35:3865-3874.
20. LaLonde, J. M., D. A. Bernlohr, and L. J. Banaszak. 1994. The up-and-down Beta-barrel proteins. FASEB J. 8:1240-1247.
21. Lee, F. S., Z. T. Chu, M. B. Bolger, and A. Warshel. 1992. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Protein Eng. 5:215-228.
22. Lipari, G., and A. Szabo. 1982. Model-free approach to the interpretation of nuclear magnetic resoance relaxation in macromolecules. I. Theory and range of validity. J. Am. Chem. Soc. 104:4546-4559.
23. Lucke, C., C. Ludwig, M. Rademacher, D. Fushman, J. C. Sacchettini, and H. Ruterjans. 1997. Conformational flexibility concurs with ligand binding in fatty acid binding proteins. The Third International Conference on Lipid-Binding Proteins Poster:26.
24. Mesgarzadeh, A., S. Pfeiffer, J. Engelke, D. Lassen, and H. Ruterjans. 1998. Bound water in apo and holo bovine heard fatty-acid-binding protein determined by heteronuclear NMR spectroscopy. Eur. J. Biochem. 251:781-786.
25. Richieri, G. V., R. T. Ogata, and A. M. Kleinfeld. 1992. A fluorescently labeled intestinal fatty acid binding protein: interactions with fatty acids and its use in monitoring tree tatty acids. J. Biol. Chem. 267: 23495-23501.
26. Richieri, G. V., R. T. Ogata, and A. M. Kleinfeld. 1994. Equilibrium constants for the binding of fatty acids with fatty acid-binding proteins from adipocyte, intestine, heart, and liver measured with the fluorescent probe ADIFAB. J. Biol. Chem. 269:23918-23930.
27. Richieri, G. V., R. T. Ogata, and A. M. Kleinfeld. 1995. Thermodynamics of fatty acid binding to fatty acid binding proteins and fatty acid partition between water and membranes measured using the fluorescent probe ADIFAB. J. Biol. Chem. 270:15076-15084.
28. Richieri, G. V., R. T. Ogata, and A. M. Kleinfeld. 1996. Kinetics of fatty acid interactions with fatty acid binding proteins from adipocyte, heart, and intestine. J. Biol. Chem. 271:11291-11300.
29. Richieri, G. V., P. J. Low, R. T. Ogata, and A. M. Kleinfeld. 1997. Mutants of rat intestinal fatly acid binding protein illustrate the critical role played by enthalpy-entropy compensation in ligand binding. J. Biol. Chem. 272:16737-16740.
30. Richieri, G. V., P. J. Low, R. T. Ogata, and A. M. Kleinfeld. 1998. Thermodynamics of fatty acid binding to engineered mutants of the adipocyte and intestinal fatty acid-binding proteins. J. Biol. Chem. 273:7397-7405.
31. Sacchettini, J. C., and J. I. Gordon. 1993. Rat intestinal fatty acid binding protein: A model system for analyzing the forces that can bind fatty acids to proteins. J. Biol. Chem. 268:18399-18402.
32. Sacchettini, J. C., J. I. Gordon, and L. J. Banaszak. 1989. Crystal structure of rat intestinal fatty-acid-binding protein. J. Mol. Biol. 208:327-339.
33. Sacchettini, J. C., G. Scapin, D. Gopaul, and J. I. Gordon. 1992. Refinement of the structure of Escherichia coli-derived rat intestinal fatty acid binding protein with bound oleate to 1.75-Å resolution. J. Biol. Chem. 267:23534-23545.
34. Scapin, G., J. I. Gordon, and J. C. Sacchettini. 1992. Refinement of the structure of recombinant rat intestinal fatty acid binding apoprotein at 1.2-Å resolution. J. Biol. Chem. 267:4253-4269.
35. Schlenkrich, M., J. Brickmann, A. D. MacKerell, Jr., and M. Karplus. 1996. An empirical potential energy function for phospholipids: criteria for parameter optimization and applications. In Biological Membranes: A Molecular Perspective from Computation and Experiment. K. M. Merz, Jr., and B. Roux, eds. Birkhauser Press. 31-81.
36. Tjandra, N., S. E. Feller, R. W. Pastor, and A. Bax. 1995. Rotational diffusion anisotropy of human ubiquitin from 15N NMR relaxation. J. Am. Chem. Soc. 117:12562-12566.
37. Woolf, T. B. 1998. Simulations of fatty acid-binding proteins suggest sites important for function. I. Stearic acid. Biophys. J. 74:681-693.
38. Woolf, T. B., and M. Tychko. 1998. Simulations of fatty acid-binding proteins II: Sites for discrimination of monounsaturated ligands. Biophys. J. 74:694-707.
39. Wrabl, J., D. Shortle, and T. B. Woolf. 1998. Molecular dynamics simulations of native and denatured staphylococcal nuclease. Biophys. J. 74:A171.
40. Zhang, F., C. Lucke, L. J. Baier, J. C. Sacchettini, and J. A. Hamilton. 1997. Solution structure of human intestinal fatty acid binding protein: implications for ligand entry and exit. J. Biomol. NMR. 9:213-228.
41. Zhu, L., M. D. Kemple, E. Kurian, and F. G. Prendergast. 1997. Backbone dynamics of the rat intestinal fatty acid binding protein by 15N NMR. Biophys. J. 72:A107.