Modeling polysaccharides: Present status and challenges

Journal of Molecular Graphics - Tập 14 - Trang 307-321 - 1996
Serge Pérez1, Milou Kouwijzer1, Karim Mazeau1, Søren Balling Engelsen2
1Centre de Recherches sur les Macromolécules Végétales, CNRS, Grenoble, France
2The Royal Veterinary and Agricultural University, Food Technology, Frederiksberg, Denmark

Tài liệu tham khảo

Dwek, 1996, Glycobiology: Toward understanding the function of sugars, Chem. Rev., 96, 683, 10.1021/cr940283b Laine, 1994, A calculation of all possible oligosaccharide isomers both branch and linear yields 1.05 × 1012 structures for a reducing hexasaccharide: The isomer barrier to development of single-method saccharide sequencing or synthesis systems, Glycobiology, 4, 759, 10.1093/glycob/4.6.759 Engelsen, 1996, A molecular builder for carbohydrates: Application to polysaccharides and complex carbohydrates, Biopolymers, 39, 417, 10.1002/(SICI)1097-0282(199609)39:3<417::AID-BIP13>3.3.CO;2-R Cremer, 1975, General definition of ring puckering coordinates, J. Am. Chem. Soc., 97, 1354, 10.1021/ja00839a011 Levitt, 1978, Extreme conformational flexibility of the furanose ring in DNA and RNA, J. Am. Chem. Soc., 100, 2607, 10.1021/ja00477a004 French, 1990, Analysis of fructofuranose conformations by molecular mechanics, Biopolymers, 29, 1599, 10.1002/bip.360291210 Cros, 1993, Modelling of arabinofuranose and arabinan. 1. Conformational flexibility of the arabinofuranose ring, Carbohydr. Res., 248, 81, 10.1016/0008-6215(93)84117-O Pérez, 1991, A data base of three-dimensional structures of monosaccharides from molecular-mechanics calculations, Carbohydr. Res., 212, 253, 10.1016/0008-6215(91)84062-J Tvaroska, 1989, Anomeric and exo-anomeric effects in carbohydrate chemistry, Adv. Carbohydr. Chem. Biochem., 47, 45, 10.1016/S0065-2318(08)60412-6 van Gunsteren, 1987 Allinger, 1977, Conformational analysis. 130 MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms, J. Am. Chem. Soc., 99, 8127, 10.1021/ja00467a001 Allinger, 1989, Molecular Mechanics. The MM3 force field for hydrocarbons. 1, J. Am. Chem. Soc., 111, 8551, 10.1021/ja00205a001 Tvaroska, 1986, Conformational-energy calculations for oligosaccharides: A comparison of methods and a strategy of calculation, Carbohydr. Res., 149, 389, 10.1016/S0008-6215(00)90060-0 Brooks, 1983, CHARMM: A program for macromolecular energy, minimization, and dynamics calculation, J. Comput. Chem., 4, 187, 10.1002/jcc.540040211 Ha, 1988, A revised potential-energy surface for molecular mechanics studies of carbohydrates, Carbohydr. Res., 180, 207, 10.1016/0008-6215(88)80078-8 Grootenhuis, 1993, A CHARMm based force field for carbohydrates using the CHEAT approach: Carbohydrate Hydroxyl groups represented by Extended Atoms, Mol. Simul., 10, 75, 10.1080/08927029308022160 Kouwijzer, 1995, Parametrization and application of CHEAT95, an extended atom force field for hydrated (oligo)saccharides, J. Phys. Chem., 99, 13426, 10.1021/j100036a017 Weiner, 1986, An all atom force field for simulations of proteins and nucleic acids, J. Comput. Chem., 7, 230, 10.1002/jcc.540070216 Homans, 1990, A molecular mechanics force field for the conformational analysis of oligosaccharides: Comparison of theoretical and crystal structures of Manα1-3Manβ1-4GlcNAc, Biochemistry, 29, 9110, 10.1021/bi00491a003 Glennon, 1994, J. Comput. Chem., 15, 1019, 10.1002/jcc.540150910 Woods, 1995, Molecular mechanical and molecular dynamical simulations of glycoproteins and oligosaccharides. 1. GLYCAM 93 parameter development, J. Phys. Chem., 99, 3832, 10.1021/j100011a061 Lifson, 1968, Consistent force field for calculations of conformation, vibrational spectra, and enthalpies of cycloalkane and n-alkane molecules, J. Chem. Phys., 49, 5116, 10.1063/1.1670007 Kildeby, 1977, Conformations of α- and β-d-glucopyranose from and empirical force field, Acta Chem. Scand., A31, 1, 10.3891/acta.chem.scand.31a-0001 Engelsen, 1993, Conformations of disaccharides by empirical force field calculations. V. Conformational maps of β-gentiobiose in an optimized consistent force field, Int. J. Biol. Macromol., 15, 56, 10.1016/S0141-8130(05)80089-3 Clark, 1989, Validation of the general purpose Tripos 5.2 force field, J. Comput. Chem., 10, 982, 10.1002/jcc.540100804 Imberty, 1991, Molecular modelling of protein-carbohydrate interactions. Docking of monosaccharides in the binding site of concanavalin A, Glycobiology, 1, 631, 10.1093/glycob/1.6.631 Mayo, 1990, DREIDING: A generic force field for molecular simulations, J. Phys. Chem., 94, 8897, 10.1021/j100389a010 Halgren, 1996, Merck Molecular Force Field, J. Comput. Chem., 17, 490, 10.1002/(SICI)1096-987X(199604)17:6<490::AID-JCC1>3.3.CO;2-V French, 1988, Rigid- and relaxed-residue conformational analyses of cellobiose using the computer program MM2, Biopolymers, 27, 1519, 10.1002/bip.360270914 Kozár, 1990, RAMM—a new procedure for theoretical conformational analysis of carbohydrates, Carbohydr. Res., 204, 27, 10.1016/0008-6215(90)84018-P Hooft, 1991, Implementation and use of the method of prudent ascent in conformational analysis using molecular mechanics, J. Comput. Chem., 12, 943, 10.1002/jcc.540120806 Koca, 1995, Conformational analysis and flexibility of carbohydrates using the CICADA approach with MM3, J. Comput. Chem., 16, 296, 10.1002/jcc.540160305 Peters, 1993, A Monte Carlo method for conformational analysis of saccharides, Carbohydr. Res., 238, 49, 10.1016/0008-6215(93)87005-D Weimar, 1993, Conformational analysis of α-d-Fuc-(1 → 4)-β-d-GlcNac-OMe. One-dimensional transient NOE experiments and Metropolis Monte Carlo simulations, J. Biomol. NMR, 3, 399, 10.1007/BF00176007 Levy, 1991, Simulations of the static and dynamic conformation of xyloglucan. The role of fucosylated side chain in surface specific side chain folding, Plant J., 1, 195, 10.1111/j.1365-313X.1991.00195.x Orozco, 1996, Theoretical methods for the representation of solvent, J. Mol. Modeling, 1, 1, 10.1007/s0089460020001 Tvaroska, 1980, Theoretical studies on the conformation of saccharides. 3. Conformational properties of the glycosidic linkage in solution and their relation to the anomeric and exoanomeric effects, J. Am. Chem. Soc., 102, 6929, 10.1021/ja00543a005 Kouwijzer, 1993, Comparison of two force fields by molecular dynamics simulations of glucose crystals: Effect of using Ewald sums, J. Comput. Chem., 14, 1281, 10.1002/jcc.540141104 French, 1993, Exploration of disaccharide conformations by molecular mechanics, J. Mol. Struct. (Theochem.), 286, 183, 10.1016/0166-1280(93)87162-7 Engelsen, 1995, Molecular relaxation of sucrose in aqueous solution: How a nanosecond molecular dynamics simulation helps to reconcile NMR data, J. Phys. Chem., 99, 13334, 10.1021/j100036a005 van Alsenoy, 1994, Ab initio-MIA and molecular mechanics studies of the distorted sucrose linkage of raffinose, J. Am. Chem. Soc., 116, 9590, 10.1021/ja00100a025 Stevens, 1991, Solution conformation of sucrose from optical rotation, J. Am. Chem. Soc., 113, 8622, 10.1021/ja00023a007 Stevens, 1989, Potential energy surfaces of cellobiose and maltose in aqueous solution: A new treatment of disaccharide optical rotation, J. Am. Chem. Soc., 111, 4149, 10.1021/ja00194a001 Schafer, 1995, A reexamination of the double-helix model for agarose gels using optical rotation, Biopolymers, 36, 103, 10.1002/bip.360360109 Brant, 1975, A general treatment of the configurational statistics of polysaccharides, Macromolecules, 8, 522, 10.1021/ma60046a026 Flory, 1969 Jordan, 1978, A Monte Carlo study of the amylosic chain conformation, Biopolymers, 17, 2617, 10.1002/bip.1978.360171110 Gagnaire, 1982, Configurational statistics of single chains of α-linked glucans, Carbohydr. Polym., 2, 171, 10.1016/0144-8617(82)90050-9 Brant, 1990, Realistic conformational modeling of carbohydrates, 42 Burton, 1983, Comparative flexibility, extension, and conformation of some simple polysactharide chains, Biopolymers, 22, 1769, 10.1002/bip.360220712 Urbani, 1991, Solvent effects on the unperturbed chain conformation of polysaccharides, Polymer, 32, 3013, 10.1016/0032-3861(91)90203-U Cros, 1996, Solution conformations of pectin polysaccharides: Determination of chain characteristics by small angle neutron scattering, viscometry, and molecular modeling, Biopolymers, 39, 339, 10.1002/(SICI)1097-0282(199609)39:3<339::AID-BIP6>3.0.CO;2-P Ruggiero, 1995, Conformational features of galacturonans. II. Configurational statistics of pectic polymers, Int. J. Biol. Macromol., 17, 213, 10.1016/0141-8130(95)92688-M Boutherin, 1996, Conformational statistics of pectin substances in solution by a Metropolis Monte Carlo study, Carbohydr. Polym. Millane, 1990, Polysaccharide structures: X-ray fiber diffraction studies, 315 Pérez, 1990, Modeling of interactions of polysaccharide chains, 281 Marchessault, 1983, Vol. 2, 11 Imberty, 1988, New three-dimensional structures for A-type starch, J. Mol. Biol., 201, 365, 10.1016/0022-2836(88)90144-1 Imberty, 1988, A revisit to the three-dimensional structure of B-type starch, Biopolymers, 27, 1205, 10.1002/bip.360270803 Deslandes, 1980, Triple-helical structure of (1 → 3)-β-d-glucan, Macromolecules, 13, 1466, 10.1021/ma60078a020 Foord, 1989, New X-ray diffraction results from agarose: Extended single helix structures and implications for gelations mechanism, Biopolymers, 28, 1345, 10.1002/bip.360280802 Arnott, 1974, The agarose double helix and its function in agarose gel structures, J. Mol. Biol., 90, 269, 10.1016/0022-2836(74)90372-6 Rees, 1982, Shapes and interactions of carbohydrate chains, Vol. 1, 195 Pérez, 1990, A priori crystal structure modeling of polymeric materials, 33 Spek, 1990, Platon, an integrated tool for the analysis of the results of a single crystal determination, Acta Crystallogr, A46, C34