Computational and experimental approaches for assessing the interactions between the model calycin β-lactoglobulin and two antibacterial fluoroquinolones

Proteins: Structure, Function and Genetics

Volumn 65, Issue 3, 2006, Pages 555-567

  Eberini, Ivano ^a   Fantucci, Piercarlo ^b   Rocco, Alessandro Guerini ^a   Gianazza, Elisabetta ^a   Galluccio, Lara ^a   Maggioni, Daniela ^a   Dal Ben, Ilaria ^a   Galliano, Monica ^c   Mazzitello, Rosalba ^b   Gaiji, Noura ^b   Beringhelli, Tiziana ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF MILANO BICOCCA   (Italy)

^c UNIVERSITY OF PAVIA   (Italy)

Author keywords

Binding free energy; Denaturant gradient gel electrophoresis; Genetic algorithm; Molecular docking; Molecular dynamics; Monte Carlo; Nuclear magnetic resonance

Indexed keywords

BETA LACTOGLOBULIN; LEVOFLOXACIN; LIPOCALIN; NORFLOXACIN; OFLOXACIN; PALMITIC ACID; QUINOLINE DERIVED ANTIINFECTIVE AGENT; RETINOIC ACID;

ARTICLE; CRYSTAL STRUCTURE; DENATURING GRADIENT GEL ELECTROPHORESIS; DRUG BINDING SITE; DRUG PROTEIN BINDING; DRUG STRUCTURE; HYDROPHOBICITY; LIGAND BINDING; LIPOPHILICITY; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PH; PRIORITY JOURNAL; THERMODYNAMICS;

ANIMALS; ANTI-BACTERIAL AGENTS; BINDING SITES; CATTLE; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; HYDROGEN-ION CONCENTRATION; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; HYDROPHOBICITY; LACTOGLOBULINS; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NORFLOXACIN; OFLOXACIN; THERMODYNAMICS;

BOS TAURUS;

EID: 33750066955     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21109     Document Type: Article

References (58)

1. Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nat Rev Drug Discov 2004;3:935-949.
2. Kellenberger E, Rodrigo J, Muller P, Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 2004;57:225-242.
3. Cole JC, Murray CW, Nissink JW, Taylor RD, Taylor R. Comparing protein-ligand docking programs is difficult. Proteins 2005;60:325-332.
4. Sawyer L, Kontopidis G. The core lipocalin, bovine β-lactoglobulin. Biochim Biophys Acta 2000;1482:136-148.
5. Flower DR, North ACT, Sansom CE. The lipocalin protein family: structural and sequence overview. Biochym Biophys Acta 2000;1482:9-24.
6. Åkerstrom B, Flower DR, Salier J-P. Lipocalins: unity in diversity. Biochim Biophys Acta 2000;1482:1-8.
7. Smith PC, Firestein S, Hunt JF. The crystal structure of the olfactory marker protein at 2.3 Å resolution. J Mol Biol 2002;319:807-821.
8. Wogulis M, Morgan T, Ishida Y, Leal WS, Wilson DK. The crystal structure of an odorant binding protein from Anopheles gambiae: evidence for a common ligand release mechanism. Biochem Biophys Res Commun 2006;339:157-164.
9. Capaldi S, Guariento M, Perduca M, Di Pietro SM, Santome JA, Monaco HL. Crystal structure of axolotl (Ambystoma mexicanum) liver bile acid-binding protein bound to cholic and oleic acid. Proteins 2006;64:79-88.
10. Monaco HL. Three-dimensional structure of the transthyretinretinol- binding protein complex. Clin Chem Lab Med 2002;40:1229-1236.
11. Perez DM, Diaz de Villegras C, Sanchez L, Aranda P, Ena JM, Calvo M. Interaction of fatty acids with β-lactoglobulin and albumin from ruminant milk. J Biochem (Tokio) 1989;106:1094-1097.
12. Dodin G, Andrieux M, al Kabbani H. Binding of ellipticine to β-lactoglobulin. A physico-chemical study of the specific interaction of an antitumor drug with a transport protein. Eur J Biochem 1990;193:697-700.
13. Dufour E, Marden MC, Haertle T. β-Lactoglobulin binds retinol and protoporphyrin IX at two different binding sites. FEBS Lett 1990;277:223-226.
14. Dufour E, Haertle T. Binding of retinoids and β-carotene to β-lactoglobulin: influence of protein modifications. Biochim Biophys Acta 1991;1079:316-320.
15. Marden MC, Dufour E, Christova P, Huang Y, Leclerc-L'Hostis E, Haertle T. Binding of heme-CO to bovine and porcine β-lactoglobulins. Arch Biochem Biophys 1994;311:258-262.
16. Wang Q, Allen JC, Swaisgood HE. Binding of vitamin D and cholesterol to β-lactoglobulin. J Dairy Sci 1997;80:1054-1059.
17. D'Alfonso L, Collini M, Baldini G. Evidence of heterogeneous 1-anilinonaphthalene-8-sulfonate binding to β-lactoglobulin from fluorescence spectroscopy. Biochim Biophys Acta 1999;1432:194-202.
18. Monaco HL, Zanotti G, Spadon P, Bolognesi M, Sawyer L, Eliopoulos EE. Crystal structure of the trigonal form of bovine β-lactoglobulin and of its complex with retinol at 2.5 Å resolution. J Mol Biol 1987;197:695-706.
19. Narayan M, Berliner LJ. Fatty acids and retinoids bind independently and simultaneously to β-lactoglobulin. Biochemistry 1997;36:1906-1911.
20. Leach AR. Molecular modeling: principles and applications. Harlow: Prentice Hall; 2001.
21. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998;19:1639-1662.
22. Clamp ME, Baker PG, Stirling CJ, Brass A. Hybrid Monte Carlo: an efficient algorithm for condensed matter simulation. J Comput Chem 1994;15:838-846.
23. Senderowitz H, Guarnieri F, Still WC. A Smart Monte Carlo technique for free energy simulations of multiconformational molecules: direct calculations of the conformational populations of organic molecules. J Amer Chem Soc 1995;117:8211-8219.
24. Eldridge MD, Murray CW, Auton TR, Paoliniand GV, Mee RP. Empirical scoring funtions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. JCAMD 1997;11:425-445.
25. Murray CW, Auton TR, Eldridge MD. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model. JCAMD 1998;12:503-519.
26. Cistola DP, Hall KB. Probing internal water molecules in proteins using two-dimensional 19F-1H NMR. J Biomol NMR 1995;5:415-419.
27. 19F-NMR studies of retinol transfer between cellular retinol binding proteins and phospholipid vesicles. FEBS Lett 1997;402:116-120.
28. 19F NMR studies of tryptophan/serum albumin binding. Bioorg Med Chem 2003;11:69-75.
29. Creighton TE. Electrophoretic analysis of the unfolding of proteins by urea. J Mol Biol 1979;129:235-264.
30. Gianazza E, Eberini I, Santi O, Vignati M. Denaturant-gradient gel electrophoresis: technical aspects and practical applications. Anal Chim Acta 1998;372:99-120.
31. McAlpine AS, Sawyer L. β-lactoglobulin: a protein drug carrier? Biochem Soc Trans 1990;18:879.
32. Kontopidis G, Holt C, Sawyer L. The ligand-binding site of bovine β-lactoglobulin: evidence for a function. J Mol Biol 2002;318:1043-1055.
33. Wu SY, Perez MD, Puyol P, Sawyer L. β-lactoglobulin binds palmitate within its central cavity. J Biol Chem 1999;274:170-174.
34. Qin BY, Bewley MC, Creamer LK, Baker HM, Baker EN, Jameson GB. Structural basis of the Tanford transition of bovine β-lactoglobulin. Biochemistry 1998;37:14014-14023.
35. Mehler EL, Solmajer T. Electrostatic effects in proteins: comparison of dielectric and charge models. Protein Eng 1991;4:903-910.
36. Fugate RD, Song PS. Spectroscopic characterization of β-lactoglobulin-retinol complex. Biochim Biophys Acta 1980;625:28-42.
37. Cho Y, Batt CA, Sawyer L. Probing the retinol-binding site of bovine β-lactoglobulin. J Biol Chem 1994;269:11102-11107.
38. Piez KA, Davie EW, Folk JE, Gladner JA. β-lactoglobulins A and B: I. Chromatografic separation and amino acid composition. J Biol Chem 1961;263:2912-2916.
39. Halgren TA. The Merck force field, J Comp Chem 1996;17:490-512, 520-522, 553-586, 587-615, 616-641.
40. van Gunsteren WF, Billeter SR, Eising AA, Hünenberger PH, Krüger P, Mark AE, Scott WRP, Tironi IG. Biomolecular simulation: the GROMOS96 manual and user guide. Zürich: Vdf Hochschulverlag AG an der ETH Zürich; 1996.
41. Villoutreix BO, Spassov VZ, Atanasov BP, Herve G, Ladjimi MM. Structural modeling and electrostatic properties of aspartate transcarbamylase from Saccharomyces cerevisiae. Proteins 1994;19:230-243.
42. Böhm HJ. The development of a simple empirical scoring function to estimete the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Design 1994;8:243-256.
43. Creighton TE. Detection of folding intermediates using urea-gradient electrophoresis. Methods Enzymol 1986;131:156-172.
44. Beringhelli T, Eberini I, Galliano M, Pedoto A, Perduca M, Sportiello A, Fontana E, Monaco HL, Gianazza E. pH and ionic strength dependence of protein (un)folding and ligand binding to bovine β-lactoglobulins A and B. Biochemistry 2002;41:15415-15422.
45. Gianazza E, Calabresi L, Santi O, Sirtori CR, Franceschini G. Denaturation and self-association of apolipoprotein A-I investigated by electrophoretic techniques. Biochemistry 1997;36:7898-7905.
46. Goldenberg DP. Analysis of protein conformation by gel electrophoresis. In: Creighton TE, editor. Protein structure: a practical approach. Oxford: IRL Press; 1989. p 225-250.
47. Creighton TE. Kinetic study of protein unfolding and refolding using urea gradient electrophoresis. J Mol Biol 1980;137:61-80.
48. Mazuel C. Analytical profiles of drug substances. Vol. 20. New York: Academic Press; 1991. p 557-600.
49. Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Prot Eng 1995;8:127-134.
50. Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins 1998;33:1-17.
51. Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci 1998;7:1884-1897.
52. Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins 1998;33:18-29.
53. Qin BY, Creamer LK, Baker EN, Jameson GB. 12-Bromododecanoic acid binds inside the calyx of bovine β-lactoglobulin. FEBS Lett 1998;438:272-278.
54. Ragona L, Fogolari F, Zetta L, Perez DM, Puyol P, De Kruif K, Lohr F, Ruterjans H, Molinari H. Bovine β-lactoglobulin: interaction studies with palmitic acid. Protein Sci 2000;9:1347-1356.
55. Ragona L, Fogolari F, Catalano M, Ugolini R, Zetta L, Molinari H. EF loop conformational change triggers ligand binding in β-lactoglobulins. J Biol Chem 2003;278:38840-38846.
56. Insight II - Ludi. San Diego: MSI - Molecular Simulations; 2000.
57. Böhm HJ. LUDI: rule based automatic design of new sobstituents for enzyme inhibitor leads. J Comput Aided Mol Des 1992;6:593-606.
58. Böhm HJ. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from the de novo design or 3D database search programs. J Comput Aided Mol Des 1998;12:309-323.