The third leg: Molecular dynamics simulations of lipid binding proteins

Molecular and Cellular Biochemistry

Volumn 192, Issue 1-2, 1999, Pages 143-156

  Woolf, Thomas B ^a   Tychko, Michael ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

FABP; LBP; Molecular dynamics; Protein lipid interactions; Rational drug design; Structure function

Indexed keywords

FATTY ACID BINDING PROTEIN; LIPID; LIPID BINDING PROTEIN;

COMPUTER SIMULATION; CONFERENCE PAPER; MOLECULAR DYNAMICS; PROTEIN LIPID INTERACTION; PROTEIN STRUCTURE; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

EID: 0032931049     PISSN: 03008177     EISSN: None     Source Type: Journal    
DOI: 10.1007/978-1-4615-4929-1_17     Document Type: Conference Paper

References (42)

1. Allen MP, Tildesley DJ: Computer Simulation of Liquids. Clarendon Press, Oxford, 1987
2. Brooks CLI, Karplus M, Pettitt BM: Proteins: A theoretical perspecitive of dynamics, structure, and thermodynamics. John Wiley and Sons, New York, 1988
3. McCammon JA, Gelin BR, Karplus M: Dynamics of folded proteins. Nature 267: 585-590, 1977
4. Brunger AT, Huber R, Karplus M: Trypsinogen-Trypsin transition: A molecular dynamics study of induced conformational change in the activation domain. Biochem 26: 5153-5162, 1987
5. Steinbach PJ, Brooks BR: New spherical-cutoff methods for long-range forces in macromolecular simulation. J Comp Chem 15: 667-683, 1994
6. Asp in aqueous solution with counterions. J Am Chem Soc 117: 6720-6726, 1995
7. Asp: Structuring effects of C-H--O hydrogen bonds and of long-range hydration forces. J Am Chem Soc 118: 1181-1189, 1996
8. Darden T, York D, Pedersen L: Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092, 1993
9. Kollman P: Free energy calculations: Applications to chemical and biochemical phenomena. Chem Rev 93: 2395-2417, 1993
10. Young ACM, Scapin G, Kromminga A, Patel S13, Veerkamp JH, Sacchettini JC: Structural studies on human muscle fatty acid binding protein at 1.4 Å resolution: Binding interactions with three C18 fatty acids. Structure 2: 523-534, 1994
11. The 3rd International Conference on Lipid-Binding Proteins. Minneapolis, Minnesota. 1997
12. Woolf TB: Simulations of fatty acid binding proteins suggest sites important for function I: stearic acid. Biophys J 74: 681-693, 1998
13. Woolf TB, Tychko M: Simulations of fatty acid binding proteins II: Sites for discrimination of monounsaturated ligands. Biophys J 74: 694-707, 1998
14. Woolf TB, Grossfield A, Tychko M: Differences between apo and three holo intestinal lipid binding proteins seen by molecular dynamics computer calculations. Submitted (1998)
15. Banaszak L, Winter N, Xu Z, Bernlohr DA, Cowan S, Jones TA: Lipid-binding proteins: A family of fatty acid and retinoid transport proteins. Adv Protein Chem 45: 89-151, 1994
16. Eads J, Sacchettini JC, Kromminga A, Cordon JI: Escherichia coli-derived rat intestinal fatty acid binding protein with bound myristate at 1.5 Å resolution and I-FABP Arg106--->Gln with bound oleate at 1.74 Å resolution. J Biol Chem 268: 26375-26785, 1993
17. LaLonde JM, Bernlohr DA, Banaszak Q: X-ray crystallographic structures of adipocyte lipid-binding protein complexed with palmitate and hexadecanesulfonic acid. Properties of cavity binding sites. Biochemistry 33: 4885-4895, 1994
18. Sacchettini JC, Gordon JI, Banaszak LJ: Crystal structure of rat intestinal fatty-acid-binding protein: Refinement and analysis of the Escherichia coli-derived protein with bound palmitate. J Mol Biol 208: 327-3391, 1989
19. Sacchettini JC, Gordon JI: 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, 1993
20. Scapin G, Gordon JI, Sacchettini JC: Refinement of the structure of recombinant rat intestinal fatty acid-binding apoprotein at 1.2 Å resolution. J Biol Chem 267: 4253-4269, 1992
21. Cistola DP, Sacchettini JC, Banaszak LJ, Walsh MT, Gordon JI: Fatty acid interactions with rat intestinal and liver fatty acid-binding proteins expressed in Escherichia coli. J Biol Chem 264: 2700-2710, 1989
22. Antosiewicz J, McCammon JA, Cilson MK: Prediction of pH-dependent properties of proteins. J Mol Biol 238: 415-436, 1994
23. Sharp KA, Honig B: Electrostatic interactions in macromolecules: Theory and applications. Annu Rev Biophys Chem 19: 301-332, 1990
24. Richieri CV, Ogata RT, Kleinfeld AM: Equilibrium constants for the binding of fatty acids with fatty acid-binding proteins from adipocyte, intenstine, heart, and liver measured with the fluorescent probe ADIFAB. J Biol Chem 269: 23918-23930, 1994
25. Richieri CV, Ogata RT, Kleinfeld AM: 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, 1995
26. Richieri CV, Ogata RT, Kleinfeld AM: Kinetics of fatty acid interactions with fatty acid binding proteins from adipocyte, heart, and intestine. J Biol Chem 271: 11291-11300, 1996
27. Richieri CV, Low PJ, Ogata RT, Kleinfeld AM: Mutants of rat intestinal fatty acid binding protein illustrate the critical role played by enthalphy-entropy compensation in ligand binding. J Biol Chem 272: 16737-16740, 1997
28. Woolf TB, Tychko M: In preparation
29. Lau FTK, Karplus M: Molecular recognition in proteins: Simulation analysis of substrate binding by a TyrosyPtRNA synthetase mutant. J Mol Biol 236: 1049-1066, 1994
30. Aqvist J, Medina C, Samuelsson JE: A new method for predicting binding affinity in computer-aided drug design. Protein Eng 7: 385-391, 1994
31. Aqvist J, Mowbray SL: Sugar recognition by a glucose/galactose receptor. J Biol Chem 270: 9978-9981, 1995
32. Aqvist J, Hansson T: On the validity of electrostatic linear response in polar solvents. J Phys Chem 100: 9512-9521, 1996
33. King C, Barford RA: Calculation of electrostatic free energy differences with a time-saving approximate method. J Phys Chem 97: 8798-8802, 1993
34. Levy RM, Belhadj M, Kitchen DB: Gaussian fluctuation formula for electrostatic free-energy changes in solution. J Chem Phys 95: 3627-3633, 1991
35. Jakoby MG, Miller KR, Toner JJ, Bauman A, Cheng L, Li E, Cistola DR: Ligand-protein electrostatic interactions govern the specificity of retinol- and fatty acid-binding proteins. Biochemistry 32: 872-878, 1993
36. Amadei A, Linssen BM, Berendsen HJC: Essential dynamics of proteins. Proteins 17: 412-425, 1993
37. Kuntz ID, Meng EC, Schoichet BK: Structure-Based Molecular Design-Acc Chem Res 27: 117-123, 1994
38. Roux B, Karplus M: Ion transport in a model gramicidin channel. Structure and Thermodynamics. Biophys J 59: 961-981, 1991
39. Pastor RW, Venable RM: Molecular and stochastic dynamics simulation of lipid membranes. Computer Simulation of Biomolecular Systems Vol 2. Leiden, 1993
40. Herr FM, Matarese V, Bernlohr DA, Storch J: Surface lysine residues modulate the collisional transfer of fatty acid from adipocyte fatty acid binding protein to membranes. Biochemistry 34: 11840-11845, 1995
41. Herr FM, Aronson J, Storch J: Role of portal region lysine residues in electrostatic interactions between heart fatty acid binding protein and phospholipid membranes. Biochemistry 35: 1296-1303, 1996
42. Ben-Tal N, Honig B, Peitzach R, Denisov G, McLaughlin S: Binding of small basic peptides to membranes containing acidic lipids: Theoretical models and experimental results. Biophys J 71: 561-575, 1996