PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Sarkar, Anita ^a,b   Pérez, Serge ^a,b,c  

^a CNRS   (France)

^b UNIV GRENOBLE ALPES   (France)

^c EUROPEAN SYNCHROTRON RADIATION FACILITY   (France)

Author keywords

Atomic coordinates; Carbohydrates; Graphical user interface (GUI); Information portal; Polysaccharides; Three dimensional (3D) database

Indexed keywords

3 DIMENSIONAL STRUCTURE; 3D REPRESENTATIONS; 3D STRUCTURE; ANNOTATED DATABASE; ATOMIC COORDINATE; BIO-ETHANOLS; BIOMACROMOLECULES; DRUG DESIGN; EXTERNAL LINKS; GLYCOSIDIC LINKAGES; GRAPHICAL USER INTERFACES (GUI); HOST-PATHOGEN INTERACTIONS; INFORMATION PORTALS; INTERACTIVE DISPLAY; MATERIAL SCIENCE; POLYSACCHARIDE STRUCTURE; PRODUCTION OF; REPEAT UNITS; SCIENTIFIC LITERATURE; SPACE GROUPS; STRUCTURAL INFORMATION; STRUCTURAL STABILIZATION; STRUCTURE-RELATED; TECHNOLOGICAL PROCESS; THREE DIMENSIONAL (3D) STRUCTURES; UNIT-CELL DIMENSIONS; VACCINE DEVELOPMENT; WEB INTERFACE;

CARBOHYDRATES; DATABASE SYSTEMS; GRAPHICAL USER INTERFACES; MOLECULAR RECOGNITION; ORGANIC COMPOUNDS; POLYSACCHARIDES; SEARCH ENGINES; SUGARS; THREE DIMENSIONAL;

THREE DIMENSIONAL COMPUTER GRAPHICS;

POLYSACCHARIDE;

ARTICLE; CARBOHYDRATE ANALYSIS; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; FACTUAL DATABASE; INTERNET; MOLECULAR GENETICS;

CARBOHYDRATE SEQUENCE; DATABASES, FACTUAL; INTERNET; MOLECULAR SEQUENCE ANNOTATION; POLYSACCHARIDES; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84868678244     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-302     Document Type: Article

References (100)

1. Gabius H-J. Biological Information Transfer Beyond the Genetic Code: The Sugar Code. " The Codes of Life" , Biosemiotics 2008, 223-246. Springer, The Netherlands, Barbiori M, Hoffmeyer J.
2. Gabius HJ. Cell surface glycans: The why and how of their functionality as biochemical signals in lectin-mediated information transfer. Crit Rev Immunol 2006, 26(1):43-79. 10.1615/CritRevImmunol.v26.i1.30, 16472068.
3. Iozzo RV. Matrix Proteoglycans: From molecular design to cellular function. Annu Rev Biochem 1998, 67(1):609-652. 10.1146/annurev.biochem.67.1.609, 9759499.
4. Pérez S, Imberty A, Scaringe Raymond P. Modeling of Interactions of Polysaccharide Chains. Computer Modeling of Carbohydrate Molecules. ACS Symposium Series 430 1990, 281-299. American Chemical Society, French AD, Brady JW.
5. Berman H, Henrick K, Nakamura H. Announcing the worldwide Protein Data Bank. Nat Struct Biol 2003, 10(12):980. 10.1038/nsb1203-980, 14634627.
6. Allen F. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr B 2002, 58(3 Part 1):380-388.
7. Chandrasekaran R. Molecular architecture of polysaccharide helices in oriented fibers. Adv Carbohydr Chem Biochem 1997, 52:311-439.
8. Zugenmaier P. Crystalline Cellulose and Derivatives: Characterization and Structures 2008, Springer, Berlin Heidelberg.
9. Apache Web Server http://www.apache.org/.
10. PHP Hypertext Preprocessor http://www.php.net/, PHP.
11. Vaswani V. MySQL: The Complete Reference 2003, McGraw-Hill Osborne Media, Emeryville, Cal., USA, 1.
12. TRIPOS SYBYL-X 1.3, Tripos International, 1699 South Hanley Rd., St. Louis, Missouri, 63144, USA TRIPOS.
13. DeLano WL. The PyMol Molecular Vizualization System on an open source foundation and Shrodinger LLC www.pymol.org.
14. Engelsen SB, Cros S, Mackie W, Pérez S. A molecular builder for carbohydrates: Application to polysaccharides and complex carbohydrates. Biopolymers 1996, 39(3):417-433. 10.1002/(SICI)1097-0282(199609)39:3<417::AID-BIP13>3.3.CO;2-R, 8756520.
15. Macrae CF, Bruno IJ, Chisholm JA, Edgington PR, McCabe P, Pidcock E, Rodriguez-Monge L, Taylor R, Van de Streek J, Wood PA. Mercury CSD 2.0 - new features for the visualization and investigation of crystal structures. J Appl Crystallogr 2008, 41(2):466-470.
16. Foord SA, Atkins EDY. New X-ray diffraction results from agarose: Extended single helix structures and implications for gelation mechanism. Biopolymers 1989, 28(8):1345-1365.
17. Arnott S, Fulmer A, Scott WE, Dea IC, Moorhouse R, Rees DA. The agarose double helix and its function in agarose gel structure. J Mol Biol 1974, 90(2):269-284. 10.1016/0022-2836(74)90372-6, 4453017.
18. Kouwijzer M, Pérez S. Molecular modeling of agarose helices, leading to the prediction of crystalline allomorphs. Biopolymers 1998, 46(1):11-29.
19. Atkins EDT, Nieduszynski IA, Mackie W, Parker KD, Smolko EE. Structural components of alginic acid. II. The crystalline structure of poly-α-L-guluronic acid. Results of X-ray diffraction and polarized infrared studies. Biopolymers 1973, 12(8):1879-1887. 10.1002/bip.1973.360120814, 4733713.
20. Atkins EDT, Nieduszynski IA, Mackie W, Parker KD, Smolko EE. Structural components of alginic acid. I. The crystalline structure of poly-β-D-mannuronic acid. Results of X-ray diffraction and polarized infrared studies. Biopolymers 1973, 12(8):1865-1878. 10.1002/bip.1973.360120813, 4733712.
21. Braccini I, Grasso RP, Pérez S. Conformational and configurational features of acidic polysaccharides and their interactions with calcium ions: a molecular modeling investigation. Carbohydr Res 1999, 317(1-4):119-130.
22. Braccini I, Pérez S. Molecular basis of Ca2+-induced gelation in alginates and pectins: the egg-box model revisited. Biomacromolecules 2001, 2(4):1089-1096. 10.1021/bm010008g, 11777378.
23. Imberty A, Chanzy H, Pérez S, Buleon A, Tran V. The double-helical nature of the crystalline part of A-starch. J Mol Biol 1988, 201(2):365-378. 10.1016/0022-2836(88)90144-1, 3418703.
24. Popov D, Buleon A, Burghammer M, Chanzy H, Montesanti N, Putaux JL, Potocki-Veronese G, Riekel C. Crystal Structure of A-amylose: A Revisit from Synchrotron Microdiffraction Analysis of Single Crystals. Macromolecules 2009, 42(4):1167-1174.
25. Pérez S, Bertoft E. The molecular structures of starch components and their contribution to the architecture of starch granules: A comprehensive review. Starch-Starke 2010, 62(8):389-420.
26. O'Sullivan AC, Pérez S. The relationship between internal chain length of amylopectin and crystallinity in starch. Biopolymers 1999, 50(4):381-390. 10.1002/(SICI)1097-0282(19991005)50:4<381::AID-BIP4>3.0.CO;2-W, 10423547.
27. Imberty A, Pérez S. A revisit to the three-dimensional structure of B-type starch. Biopolymers 1988, 27(8):1205-1221.
28. Winter WT, Sarko A. Crystal and molecular structure of the amylose-DMSO complex. Biopolymers 1974, 13(7):1461-1482.
29. Sarko A, Biloski A. Crystal structure of the KOH-amylose complex. Carbohydr Res 1980, 79(1):11-21.
30. Sarko A, Marchessault RH. Crystalline structure of amylose triacetate I. Stereochemical approach. J Am Chem Soc 1967, 89(25):6454-6462.
31. Bluhm TL, Zugenmaier P. The crystal and molecular structure of tri-o-ethylamylose (TEA 3). Carbohydr Res 1979, 68(1):15-21.
32. Winter WT, Sarko A. Crystal and molecular structure of V-anhydrous amylose. Biopolymers 1974, 13(7):1447-1460.
33. Nishiyama Y, Mazeau K, Morin M, Cardoso MB, Chanzy H, Putaux J-L. Molecular and crystal structure of 7-fold V-amylose complexed with 2-propanol. Macromolecules 2010, 43(20):8628-8636.
34. Guizard C, Chanzy H, Sarko A. Molecular and crystal structure of dextrans: a combined electron and X-ray diffraction study. 1. The anhydrous, high-temperature polymorph. Macromolecules 1984, 17(1):100-107.
35. Guizard C, Chanzy H, Sarko A. The molecular and crystal structure of dextrans: a combined electron and X-ray diffraction study. II. A low temperature, hydrated polymorph. J Mol Biol 1985, 183(3):397-408. 10.1016/0022-2836(85)90010-5, 2410620.
36. Strino F, Nahmany A, Rosen J, Kemp GJL, Sá-correia I, Nyholm P-G. Conformation of the exopolysaccharide of Burkholderia cepacia predicted with molecular mechanics (MM3) using genetic algorithm search. Carbohydr Res 2005, 340(5):1019-1024. 10.1016/j.carres.2004.12.031, 15780266.
37. Brisson JR, Baumann H, Imberty A, Pérez S, Jennings HJ. Helical epitope of the group B meningococcal alpha(2-8)-linked sialic acid polysaccharide. Biochemistry 1992, 31(21):4996-5004. 10.1021/bi00136a012, 1376145.
38. Moorhouse R, Winter WT, Arnott S, Bayer ME. Conformation and molecular organization in fibers of the capsular polysaccharide from Escherichia coli M41 mutant. J Mol Biol 1977, 109(3):373-391. 10.1016/S0022-2836(77)80018-1, 319241.
39. Lee EJ, Chandrasekaran R. The " pseudo double-helical" structure of the gel-forming capsular polysaccharide from Rhizobium trifolii. Carbohydr Res 1992, 231:171-183.
40. Chandrasekaran R, Radha A, Thailambal VG. Roles of potassium ions, acetyl and L-glyceryl groups in native gellan double helix: an X-ray study. Carbohydr Res 1992, 224:1-17.
41. Chandrasekaran R, Puigjaner LC, Joyce KL, Arnott S. Cation interactions in gellan: An x-ray study of the potassium salt. Carbohydr Res 1988, 181:23-40.
42. Chandrasekaran R, Millane RP, Arnott S, Atkins EDT. The crystal structure of gellan. Carbohydr Res 1988, 175(1):1-15.
43. Bian W, Chandrasekaran R, Rinaudo M. Molecular structure of the rhamsan-like exocellular polysaccharide RMDP17 from Sphingomonas paucimobilis. Carbohydr Res 2002, 337(1):45-56. 10.1016/S0008-6215(01)00277-4, 11755911.
44. Chandrasekaran R, Radha A, Lee EJ. Structural roles of calcium ions and side chains in welan: an X-ray study. Carbohydr Res 1994, 252:183-207.
45. Moorhouse R, Walkinshaw MD, Arnott S. Xanthan Gum - Molecular Conformation and Interactions. Extracellular Microbial Polysaccharides 1977, 90-102. American Chemical Society, WASHINGTON, D. C..
46. Arnott S, Scott WE, Rees DA, McNab CG. Iota-carrageenan: molecular structure and packing of polysaccharide double helices in oriented fibres of divalent cation salts. J Mol Biol 1974, 90(2):253-267. 10.1016/0022-2836(74)90371-4, 4453016.
47. Janaswamy S, Chandrasekaran R. Three-dimensional structure of the sodium salt of iota-carrageenan. Carbohydr Res 2001, 335(3):181-194. 10.1016/S0008-6215(01)00219-1, 11578634.
48. Millane RP, Chandrasekaran R, Arnott S, Dea ICM. The molecular structure of kappa-carrageenan and comparison with iota-carrageenan. Carbohydr Res 1988, 182(1):1-17.
49. Nishiyama Y, Sugiyama J, Chanzy H, Langan P. Crystal Structure and Hydrogen Bonding System in Cellulose Iα from Synchrotron X-ray and Neutron Fiber Diffraction. J Am Chem Soc 2003, 125(47):14300-14306. 10.1021/ja037055w, 14624578.
50. Nishiyama Y, Langan P, Chanzy H. Crystal Structure and Hydrogen-Bonding System in Cellulose Iβ from Synchrotron X-ray and Neutron Fiber Diffraction. J Am Chem Soc 2002, 124(31):9074-9082. 10.1021/ja0257319, 12149011.
51. Stipanovic AJ, Sarko A. Molecular and crystal structure of cellulose triacetate I: A parallel chain structure. Polymer 1978, 19(1):3-8.
52. Langan P, Nishiyama Y, Chanzy H. X-ray structure of mercerized cellulose II at 1 Å resolution. Biomacromolecules 2001, 2(2):410-416. 10.1021/bm005612q, 11749200.
53. David ML, John B. Structure of cellulose II hydrate. Biopolymers 1981, 20(10):2165-2179.
54. David ML, John B, Litt MH. Structure of a cellulose II-hydrazine complex. Biopolymers 1983, 22(5):1383-1399.
55. Roche E, Chanzy H, Boudeulle M, Marchessault RH, Sundararajan P. Three-dimensional crystalline structure of cellulose triacetate II. Macromolecules 1978, 11(1):86-94.
56. Wada M, Chanzy H, Nishiyama Y, Langan P. Cellulose III1 Crystal Structure and Hydrogen Bonding by Synchrotron X-ray and Neutron Fiber Diffraction. Macromolecules 2004, 37(23):8548-8555.
57. Gardiner ES, Sarko A. Packing analysis of carbohydrates and polysaccharides .16. The crystal structures of cellulose-IVI and cellulose-IVII. Canadian Journal of Chemistry-Revue Canadienne De Chimie 1985, 63(1):173-180.
58. Pérez S, Samain D. Structure and Engineering of Celluloses. Advances in carbohydrate chemistry and biochemistry 2010, 25-116. Academic Press, Derek H, 64.
59. Gardner KH, Blackwell J. Refinement of the structure of beta-chitin. Biopolymers 1975, 14(8):1581-1595. 10.1002/bip.1975.360140804, 1156656.
60. Carlstrom D. The Crystal Structure of alpha-chitin (Poly-N-Acetyl-D-Glucosamine). J Cell Biol 1957, 3(5):669-683.
61. Yui T, Imada K, Okuyama K, Obata Y, Suzuki K, Ogawa K. Molecular and Crystal-Structure of the Anhydrous Form of Chitosan. Macromolecules 1994, 27(26):7601-7605.
62. Mazeau K, Winter WT, Chanzy H. Molecular and crystal structure of a high-temperature polymorph of chitosan from electron diffraction data. Macromolecules 1994, 27(26):7606-7612.
63. Okuyama K, Otsubo A, Fukuzawa Y, Ozawa M, Harada T, Kasai N. Single-helical structure of native curdlan and its aggregation state. J Carbohydr Chem 1991, 10(4):645-656.
64. Chuah CT, Sarko A, Deslandes Y, Marchessault RH. Packing analysis of carbohydrates and polysaccharides. Part 14. Triple-helical crystalline structure of curdlan and paramylon hydrates. Macromolecules 1983, 16(8):1375-1382.
65. Deslandes Y, Marchessault RH, Sarko A. Triple-helical Structure of (1,3)-β-D-glucan. Macromolecules 1980, 13(6):1466-1471.
66. Sattelle BM, Shakeri J, Roberts IS, Almond A. A 3D-structural model of unsulfated chondroitin from high-field NMR: 4-sulfation has little effect on backbone conformation. Carbohydr Res 2010, 345(2):291-302. 10.1016/j.carres.2009.11.013, 3098369, 20022001.
67. Cael JJ, Winter WT, Arnott S. Calcium chondroitin 4-sulfate: molecular conformation and organization of polysaccharide chains in a proteoglycan. J Mol Biol 1978, 125(1):21-42. 10.1016/0022-2836(78)90252-8, 712856.
68. Millane RP, Mitra AK, Arnott S. Chondroitin 4-sulfate: Comparison of the structures of the potassium and sodium salts. J Mol Biol 1983, 169(4):903-920. 10.1016/S0022-2836(83)80142-9, 6415288.
69. Winter WT, Arnott S, Isaac DH, Atkins ED. Chondroitin 4-sulfate: the structure of a sulfated glycosaminoglycan. J Mol Biol 1978, 125(1):1-19. 10.1016/0022-2836(78)90251-6, 712855.
70. Mitra AK, Arnott S, Atkins ED, Isaac DH. Dermatan sulfate: molecular conformations and interactions in the condensed state. J Mol Biol 1983, 169(4):873-901. 10.1016/S0022-2836(83)80141-7, 6631956.
71. Guss JM, Hukins DW, Smith PJ, Winter WT, Arnott S. Hyaluronic acid: molecular conformations and interactions in two sodium salts. J Mol Biol 1975, 95(3):359-384. 10.1016/0022-2836(75)90196-5, 1152059.
72. Winter WT, Smith PJ, Arnott S. Hyaluronic acid: structure of a fully extended 3-fold helical sodium salt and comparison with the less extended 4-fold helical forms. J Mol Biol 1975, 99(2):219-235. 10.1016/S0022-2836(75)80142-2, 1206703.
73. Mitra AK, Raghunathan S, Sheehan JK, Arnott S. Hyaluronic acid: molecular conformations and interactions in the orthorhombic and tetragonal forms containing sinuous chains. J Mol Biol 1983, 169(4):829-859. 10.1016/S0022-2836(83)80139-9, 6631954.
74. Mitra AK, Arnott S, Sheehan JK. Hyaluronic acid: molecular conformation and interactions in the tetragonal form of the potassium salt containing extended chains. J Mol Biol 1983, 169(4):813-827. 10.1016/S0022-2836(83)80138-7, 6631953.
75. Arnott S, Mitra AK, Raghunathan S. Hyaluronic acid double helix. J Mol Biol 1983, 169(4):861-872. 10.1016/S0022-2836(83)80140-5, 6631955.
76. Winter WT, Arnott S. Hyaluronic acid: the role of divalent cations in conformation and packing. J Mol Biol 1977, 117(3):761-784. 10.1016/0022-2836(77)90068-7, 609101.
77. Haxaire K, Braccini I, Milas M, Rinaudo M, Pérez S. Conformational behavior of hyaluronan in relation to its physical properties as probed by molecular modeling. Glycobiology 2000, 10(6):587-594. 10.1093/glycob/10.6.587, 10814700.
78. Khan S, Gor J, Mulloy B, Perkins SJ. Semi-rigid solution structures of heparin by constrained X-ray scattering modelling: new insight into heparin-protein complexes. J Mol Biol 2010, 395(3):504-521. 10.1016/j.jmb.2009.10.064, 19895822.
79. Mulloy B, Forster MJ, Jones C, Davies DB. N.M.R. and molecular-modelling studies of the solution conformation of heparin. Biochem J 1993, 293(Pt 3):849-858. 1134446, 8352752.
80. Arnott S, Gus JM, Hukins DW, Dea IC, Rees DA. Conformation of keratan sulphate. J Mol Biol 1974, 88(1):175-184. 10.1016/0022-2836(74)90303-9, 4280446.
81. Chandrasekaran R, Lee EJ, Thailambal VG, Zevenhuizen LPTM. Molecular architecture of a galactoglucan from Rhizobium meliloti. Carbohydr Res 1994, 261(2):279-295. 10.1016/0008-6215(94)84024-5, 7954516.
82. Chandrasekaran R, Radha A, Okuyama K. Morphology of galactomannans: an X-ray structure analysis of guaran. Carbohydr Res 1998, 306(1-2):243-255.
83. Yui T, Ogawa K, Sarko A. Molecular and crystal structure of konjac glucomannan in the mannan II polymorphic form. Carbohydr Res 1992, 229(1):41-55. 10.1016/S0008-6215(00)90479-8, 1516105.
84. Chanzy H, Pérez S, Miller DP, Paradossi G, Winter WT. An electron diffraction study of the mannan I crystal and molecular structure. Macromolecules 1987, 20(10):2407-2413.
85. Millane RP, Hendrixson TL. Crystal structures of mannan and glucomannans. Carbohydr Polym 1994, 25(4):245-251.
86. Yui T, Ogawa K, Sarko A. Molecular and crystal structure of the regenerated form of (1 → 3)-α-D-mannan. Carbohydr Res 1992, 229(1):57-74. 10.1016/S0008-6215(00)90480-4, 1516106.
87. Ogawa K, Miyanishi T, Yui T, Hara C, Kiho T, Ukai S, Sarko A. X-Ray diffraction study on (1 → 3)-α-D-mannan dihydrate. Carbohydr Res 1986, 148(1):115-120.
88. Walkinshaw MD, Arnott S. Conformation and interactions of pectins. I. X-ray diffraction analyses of sodium pectate in neutral and acidified forms. J Mol Biol 1981, 153(4):1055-1073. 10.1016/0022-2836(81)90467-8, 7343679.
89. Walkinshaw MD, Arnott S. Conformations and interactions of pectins. II. Models for junction zones in pectinic acid and calcium pectate gels. J Mol Biol 1981, 153(4):1075-1085. 10.1016/0022-2836(81)90468-X, 7343680.
90. Engelsen SB, Cros S, Mackie W, Pérez S. A molecular builder for carbohydrates: Application to polysaccharides and complex carbohydrates. Biopolymers 1996, 39(3):417-433. 10.1002/(SICI)1097-0282(199609)39:3<417::AID-BIP13>3.3.CO;2-R, 8756520.
91. Pérez S, Rodríguez-Carvajal MA, Doco T. A complex plant cell wall polysaccharide: rhamnogalacturonan II. A structure in quest of a function. Biochimie 2003, 85(1-2):109-121. 10.1016/S0300-9084(03)00053-1, 12765781.
92. Bluhm TL, Deslandes Y, Marchessault RH, Pérez S, Rinaudo M. Solid-state and solution conformation of scleroglucan. Carbohydr Res 1982, 100(1):117-130.
93. Atkins EDT, Parker KD. The helical structure of a β-D-1,3-xylan. Journal of Polymer Science Part C: Polymer Symposia 1969, 28(1):69-81.
94. Nieduszynski I, Marchessault RH. Structure of β-D-(1,4')-Xylan Hydrate. Nature 1971, 232(5305):46-47. 10.1038/232046a0, 16062821.
95. Nieduszynski IA, Marchessault RH. Structure of β-D-(1,4')-xylan hydrate. Biopolymers 1972, 11(7):1335-1344.
96. Pérez S, Roux M, Revol JF, Marchessault RH. Dehydration of nigeran crystals: crystal structure and morphological aspects. J Mol Biol 1979, 129(1):113-133. 10.1016/0022-2836(79)90063-9, 448733.
97. André I, Mazeau K, Tvaroska I, Putaux JL, Winter WT, Taravel FR, Chanzy H. Molecular and crystal structures of inulin from electron diffraction data. Macromolecules 1996, 29(13):4626-4635.
98. Ogawa K, Okamura K, Sarko A. Molecular and crystal structure of the regenerated form of (1 → 3)-α-D-glucan. Int J Biol Macromol 1981, 3(1):31-36.
99. Yui T, Sarko A. Molecular and crystal structure of (1,3)-α-D-glucan triacetate. Int J Biol Macromol 1992, 14(2):87-96. 10.1016/0141-8130(92)90004-R, 1515405.
100. Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ 2006, 34(4):255-261. 10.1002/bmb.2006.494034042644, 21638687.