A molecular dynamics study of human serum albumin binding sites

Peters, 1996 Fehske, 1981, The location of drug binding sites in human serum albumin, Biochem. Pharmacol., 30, 687, 10.1016/0006-2952(81)90151-9 Kragh-Hansen, 1981, Molecular aspects of ligand binding to serum albumin, Pharmacol. Rev., 33, 17 Putnam, 1984 Peters, 1985, Serum albumin, Adv. Protein Chem., 37, 161, 10.1016/S0065-3233(08)60065-0 Kragh-Hansen, 1990, Structure and ligand binding properties of human serum albumin, Dan. Med. Bull., 37, 57 Kremer, 1988, Drug binding to human alpha-1-acid glycoprotein in health and disease, Pharmacol. Rev., 40, 1 Honoré, 1990, Conformational changes in human serum albumin induced by ligand binding, Pharmacol. Toxicol., 66, 7 Zunszain, 2003, Crystal structural analysis of human serum albumin complexed with hemin and fatty acid, BMC Struct. Biol., 3, 6, 10.1186/1472-6807-3-6 Minghetti, 1986, Molecular structure of the human albumin gene is revealed by nucleotide sequence within q11-22 of chromosome 4, J. Biol. Chem., 261, 6747, 10.1016/S0021-9258(19)62680-3 Holowachuk, 1991 Dugaiczyk, 1982, Nucleotide sequence and the encoded amino acids of human serum albumin mRNA, Proc. Natl. Acad. Sci. USA, 79, 71, 10.1073/pnas.79.1.71 Sugio, 1999, Crystal Structure of Human Serum Albumin at 2.5 Angstrom Resolution, Protein Eng., 12, 439, 10.1093/protein/12.6.439 Saber, 1977, Disulfide bonds in human serum albumin, Collect Czech Chem Commun, 42, 564, 10.1135/cccc19770564 Brown, 1974, Structure of serum albumin: disulfide bridges, Fed. Proc., 33, 1389 He, 1992, Atomic structure and chemistry of human serum albumin, Nature, 358, 209, 10.1038/358209a0 Carter, 1994, Structure of serum albumin, Adv. Protein Chem., 45, 152 Luft, 1983, Structural analysis of human and bovine alpha-fetoprotein by electron microscopy, image processing, and circular dichroism, Biochemistry, 22, 5978, 10.1021/bi00294a043 Brown, 1976, Structural origins of mammalian albumin, Fed. Proc., 35, 2141 Dockal, 1999, The three recombinant domains of human serum albumin. Structural characterization and ligand binding properties, Biol. Chem., 274, 29303, 10.1074/jbc.274.41.29303 Landau, 1998, Antiproliferative and differentiating effects of benzodiazepine receptor ligands on B16 melanoma cells, Biochem. Pharmacol., 56, 1029, 10.1016/S0006-2952(98)00149-X Sudlow, 1975, The characterization of two specific drug binding sites on human serum albumin, Mol. Pharmacol., 11, 824 Sudlow, 1976, Further characterization of specific drug binding sites on human serum albumin, Mol. Pharmacol., 12, 1052 Sjoholm, 1979, Binding of drugs to human serum albumin:XI. The specificity of three binding sites as studied with albumin immobilized in microparticles, Mol. Pharmacol., 16, 767 Sollene, 1979, Characterization of a specific drug binding site of human serum albumin, Mol. Pharmacol., 14, 754 Ozeki, 1980, Effects of drug binding on the esterase activity of human serum albumin: inhibition modes and binding sites of anionic drugs, Chem. Pharmac. Bull., 28, 535, 10.1248/cpb.28.535 Kurono, 1987, Effects of drug bindings on the esterase-like activity of human serum albumin. VII. Subdivision of R-type drugs inhibiting the activity towards p-nitrophenyl acetate, Chem. Pharmac. Bull., 35, 734, 10.1248/cpb.35.734 Reynolds, 1968, The binding of some long-chain fatty acid anions and alcohols by bovine serum albumin, Biochemistry, 7, 1357, 10.1021/bi00844a016 Parks, 1983, Interactions of the carboxyl group of oleic acid with bovine serum albumin: A 13C NMR study, J. Biol. Chem., 258, 9262, 10.1016/S0021-9258(17)44661-8 Cistola, 1987, Carbon 13 NMR studies of saturated fatty acids bound to bovine serum albumin. I. The filling of individual fatty acid binding sites, J. Biol. Chem., 262, 10971, 10.1016/S0021-9258(18)60913-5 Cistola, 1987, Carbon 13 NMR studies of saturated fatty acids bound to bovine serum albumin. II. Electrostatic interactions in individual fatty acid binding sites, J. Biol. Chem., 262, 10980, 10.1016/S0021-9258(18)60914-7 Hamilton, 1984, Interactions of myristic acid with bovine serum albumin: a 13C NMR study, Proc. Natl. Acad. Sci. USA, 81, 3718, 10.1073/pnas.81.12.3718 Ho, 1993, X-ray and primary structure of horse serum albumin (Equus caballus) at 0.27-nm resolution, Eur. J. Biochem., 215, 205, 10.1111/j.1432-1033.1993.tb18024.x Gerig, 1978, Reactions of 2,6-dinitro-4-trifluoromethylbenzenesulfonate with human serum albumin, Biochim. Biophys. Acta, 534, 196, 10.1016/0005-2795(78)90002-8 Kurono, 1983, Kinetics of the rapid modification of human serum albumin with trinitrobenzenesulfonate and localization of its site, J. Pharm. Sci., 72, 432, 10.1002/jps.2600720427 Yvon, 1990, Identification of the binding sites of benzyl penicilloyl, the allergenic metabolite of penicillin, on the serum albumin molecule, FEBS Lett., 263, 237, 10.1016/0014-5793(90)81382-X Brunmark, 1997, Identification of subdomain IB in human serum albumin as a major binding site for polycyclic aromatic hydrocarbon epoxides, Chem. Res. Toxicol., 10, 880, 10.1021/tx9700782 Petitpas, 2001, Crystal structures of human serum albumin complexed with monounsaturated and polyunsaturated fatty acids, J. Mol. Biol., 314, 955, 10.1006/jmbi.2000.5208 Bhattacharya, 2000, Crystallographic analysis reveals common modes of binding of medium and long-chain fatty acids to human serum albumin, J. Mol. Biol., 303, 721, 10.1006/jmbi.2000.4158 Curry, 1998, Crystal structure of human serum albumin complexed with fatty acid reveals an asymmetric distribution of binding sites, Nat. Struct. Biol., 5, 827, 10.1038/1869 Bhattacharya, 2000, Binding of the general anesthetics propofol and halothane to human serum albumin: high-resolution crystal structures, J. Biol. Chem., 275, 38731, 10.1074/jbc.M005460200 Petitpas, 2001, Crystal structure analysis of warfarin binding to human serum albumin: anatomy of drug site I, J. Biol. Chem., 276, 22804, 10.1074/jbc.M100575200 Wardell, 2002, The atomic structure of human methemalbumin at 1.9Å, Biochem. Biophys. Res. Commun., 291, 813, 10.1006/bbrc.2002.6540 Petitpas, 2003, Structural basis of albumin-thyroxine interactions and familial dysalbuminemic hyperthyroxinemia, Proc. Natl. Acad. Sci. USA, 100, 6440, 10.1073/pnas.1137188100 Sadana, 2001, A kinetic analysis using fractals of cellular analyte-receptor binding and dissociation, Biotechnol. Appl. Biochem., 33, 7, 10.1042/BA20000044 Stanley, 1997, Prion Diseases and the BSE Crisis, Science, 278, 245, 10.1126/science.278.5336.245 Kostova, 2003, For whom the bell tolls: protein quality control of the endoplasmic reticulum and the ubiquitin-proteasome connection, EMBO J., 22, 2309, 10.1093/emboj/cdg227 Dobson, 2001, The structural basis of protein folding and its links with human disease, Philos. Trans. R. Soc. Lond. B Biol. Sci., 356, 133, 10.1098/rstb.2000.0758 Manuelidis, 2003, Transmissible Encephalopathies, Speculations and Realities, Viral Immunology, 16, 123, 10.1089/088282403322017875 Honoré, 1984, Albumin binding of anti-inflammatory drugs utility of a site-oriented versus a stoichiometric analysis, Mol. Pharmacol., 25, 137 Walji, 1993, The existence of conformationally labile (preformed) drug binding sites in human serum albumin as evidenced by optical rotation measurements, J. Pharm. Pharmacol., 45, 551, 10.1111/j.2042-7158.1993.tb05597.x Yamasaki, 1996, Characterization of site I on human serum albumin: concept about the structure of drug binding site, Biochim. Biophys. Acta, 1295, 147, 10.1016/0167-4838(96)00013-1 Fleury, 1997, Camptothecin-Binding Site in Human Serum Albumin and Protein Transformations Induced by the Drug Binding, FEBS Lett., 411, 215, 10.1016/S0014-5793(97)00693-5 Il'ichev, 2002, Interaction of ochratoxin A with human serum albumin. A common binding site of ochratoxin A and warfarin in subdomain IIA, J. Phys. Chem. B, 106, 460, 10.1021/jp012315m Il'ichev, 2002, Interaction of ochratoxin A with human serum albumin. Preferential binding of the dianion and pH effects, J. Phys. Chem. B, 106, 452, 10.1021/jp012314u Shobini, 2001, Interaction of coumarin derivatives with human serum albumin: investigation by fluorescence spectroscopic technique and modeling studies, Spectrochimica Acta, 57, 1133, 10.1016/S1386-1425(00)00492-3 Day, 2003, Characterizing a drug's primary binding site on albumin, J. Pharm. Sci., 92, 333, 10.1002/jps.10293 Matsushita, 1998, Determination of binding conformations of drugs to human serum albumin by transferred nuclear overhauser effect measurements and conformational analyses using high-temperature molecular dynamics calculations, J. Pharm. Sci., 87, 379, 10.1021/js970173v Dìaz, 2001, Merz, Molecular dynamics study of the IIA binding site in human serum albumin: influence of the protonation state of Lys195 and Lys199, J. Med. Chem., 44, 250, 10.1021/jm000340v Grymonpré, 2001, Identification by integrated computer modeling and light scattering studies of an electrostatic serum albumin-hyaluronic acid binding site, Biomacromolecules, 2, 422, 10.1021/bm005656z Fehske, 1982, Characterization of an important drug binding area on human serum albumin including the high-affinity binding sites of warfarin and azapropazone, Mol. Pharmacol., 21, 387 Müller, 1979, Wollert, Human serum albumin as a 'silent receptor' for drugs and endogenous substances, Pharmacology, 19, 59, 10.1159/000137289 Maruyama, 1985, Characterization of the benzodiazepine binding site (diazepam site) on human serum albumin, Chem. Pharm. Bull. (Tokyo), 33, 5002, 10.1248/cpb.33.5002 Noctor, 1992, Stereochemical aspects of benzodiazepine binding to human serum albumin. I. Enantioselective high performance liquid affinity chromatographic examination of chiral and achiral binding interactions between 1,4-benzodiazepines and human serum albumin, Mol. Pharmacol., 42, 506 Allen, 1987 Leach, 1996, Molecular Modelling Prins, 1999, A virtual environment for steered molecular dynamics, Future Generation Computer Systems, 15, 485, 10.1016/S0167-739X(99)00005-9 Gsponer, 2001, Flexibility of the murine prion protein and its Asp178Asn mutant investigated by molecular dynamics simulations, J. Mol. Graph. Mod., 20, 169, 10.1016/S1093-3263(01)00117-6 Ferrara, 2000, Folding simulations of a three-stranded antiparallel β-sheet peptide, Proc. Natl. Acad. Sci. USA, 97, 10780, 10.1073/pnas.190324897 Hiltpold, 2000, Free energy surface of the helical peptide Y(MEARA)(6), J. Phys. Chem. B, 104, 10080, 10.1021/jp002207k Ferrara, 2001, Native topology or specific interactions: what is more important for protein folding?, J. Mol. Biol., 306, 837, 10.1006/jmbi.2000.4400 Lazaridis, 1997, Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin, Protein Sci., 6, 2589, 10.1002/pro.5560061211 Wang, 1999, Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures, Protein Sci., 8, 1292, 10.1110/ps.8.6.1292 Duan, 1998, Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution, Science, 282, 740, 10.1126/science.282.5389.740 Gerini, 2003, Molecular dynamics simulations of lignin peroxidase in solution, Biophys. J., 84, 3883, 10.1016/S0006-3495(03)75116-9 Bates, 2003, Molecular dynamics exposes alpha-helices in myelin basic protein, J. Mol. Model. (Online), 9, 290, 10.1007/s00894-003-0145-x Kabsch, 1983, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, 22, 2577, 10.1002/bip.360221211 Kleywegt, 1994, Detection, delineation, measurement and display of cavities in macromolecular structures, Acta Crystallogr., D50, 178 Edelsbrunner, 1995, Measuring Proteins and Voids in Proteins, 256 Miranker, 1991, Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method, Proteins, Struct., Funct. Genet., 11, 29, 10.1002/prot.340110104 Berendsen, 1985, GROMACS: A massage-passing parallel molecular dynamics implementation, Comput. Phys. Comm., 91, 43, 10.1016/0010-4655(95)00042-E Lindahl, 2001, GROMACS 3.0: a package for molecular simulation and trajectory analysis, J. Mol. Mod., 7, 306, 10.1007/s008940100045 van Gusteren, 1996 RCSB Protein Data Bank, http://www.rcsb.org. Kleywegt, 2000, Validation of protein crystal structures, Acta Crystallogr., D56, 249 Heller, 1993, Molecular Dynamics Simulation of a bilayer of 200 Lipids in the gel and in the liquid-crystal phases, J. Phys. Chem., 97, 8343, 10.1021/j100133a034 Grubmüller, 1996, Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force, Sci., 271, 997, 10.1126/science.271.5251.997 Brooks, 1983, Deformable stochastic boundaries in molecular dynamics, J. Chem. Phys., 79, 6312, 10.1063/1.445724 J. Hermans, X. Xia, L. Zhang, D. Cavanaugh, DOWSER program, Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599–7260. Berendsen, 1981, Interaction models for water in relation to protein hydration, 331 Hess, 1997, LINCS: A Linear Constraint Solver for Molecular Simulations, J. Comp. Chem., 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H Miyamoto, 1992, SETTLE: An analytical version of the shake and rattle algorithms for rigid water models, J. Comp. Chem., 13, 952, 10.1002/jcc.540130805 Berendsen, 1984, Molecular Dynamics with Coupling to an External Bath, J. Chem. Phys., 81, 3684, 10.1063/1.448118 W.N. DeLano, The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, USA, http://www.pymol.org. MOE (The Molecular Operating Environment) Version 2002.03, software available from Chemical Computing Group Inc., 1010 Sherbrooke Street West, Suite 910, Montreal, Canada H3A 2R7, http://www.chemcomp.com. Humphrey, 1996, VMD: Visual molecular dynamics, J. Mol. Graph., 14, 33, 10.1016/0263-7855(96)00018-5 Laaksonen, 1992, graphics program for the analysis and display of molecular dynamics trajectories, J. Mol. Graph., 10, 33, 10.1016/0263-7855(92)80007-Z Bergman, 1997, Visualization of solvation structures in liquid mixtures, J. Mol. Graph. Model., 15, 301, 10.1016/S1093-3263(98)00003-5