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For: Rundlöf T, Venable RM, Pastor RW, Kowalewski J, Widmalm G. Distinguishing Anisotropy and Flexibility of the Pentasaccharide LNF-1 in Solution by Carbon-13 NMR Relaxation and Hydrodynamic Modeling. J Am Chem Soc 1999. [DOI: 10.1021/ja992675b] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Ruda A, Aytenfisu AH, Angles d’Ortoli T, MacKerell AD, Widmalm G. Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields. Phys Chem Chem Phys 2023;25:3042-3060. [PMID: 36607620 PMCID: PMC9890503 DOI: 10.1039/d2cp05203b] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
2
Lalithamaheswari B, Anu Radha C. Structural and conformational dynamics of human milk oligosaccharides, lacto-N-fucopentaose I and II, through molecular dynamics simulation. J Carbohydr Chem 2022. [DOI: 10.1080/07328303.2022.2150203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
3
Rönnols J, Engström O, Schnupf U, Säwén E, Brady JW, Widmalm G. Inter-residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations. Chembiochem 2019;20:2519-2528. [PMID: 31066963 DOI: 10.1002/cbic.201900301] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Indexed: 12/15/2022]
4
Zerbetto M, Angles d'Ortoli T, Polimeno A, Widmalm G. Differential Dynamics at Glycosidic Linkages of an Oligosaccharide as Revealed by 13C NMR Spin Relaxation and Stochastic Modeling. J Phys Chem B 2018;122:2287-2294. [PMID: 29385337 DOI: 10.1021/acs.jpcb.7b12478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
5
Pendrill R, Engström O, Volpato A, Zerbetto M, Polimeno A, Widmalm G. Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and (13)C NMR spin relaxation: conformational preferences of α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe in water and dimethyl sulfoxide solutions. Phys Chem Chem Phys 2016;18:3086-96. [PMID: 26741055 DOI: 10.1039/c5cp06288h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
6
Kang Y, Gohlke U, Engström O, Hamark C, Scheidt T, Kunstmann S, Heinemann U, Widmalm G, Santer M, Barbirz S. Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein–Polysaccharide Interactions. J Am Chem Soc 2016;138:9109-18. [DOI: 10.1021/jacs.6b00240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
7
Pendrill R, Säwén E, Widmalm G. Conformation and dynamics at a flexible glycosidic linkage revealed by NMR spectroscopy and molecular dynamics simulations: analysis of β-L-Fucp-(1→6)-α-D-Glcp-OMe in water solution. J Phys Chem B 2013;117:14709-22. [PMID: 24175957 DOI: 10.1021/jp409985h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
8
Widmalm G. A perspective on the primary and three-dimensional structures of carbohydrates. Carbohydr Res 2013;378:123-32. [PMID: 23522728 DOI: 10.1016/j.carres.2013.02.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 02/13/2013] [Indexed: 10/27/2022]
9
Kotsyubynskyy D, Zerbetto M, Soltesova M, Engström O, Pendrill R, Kowalewski J, Widmalm G, Polimeno A. Stochastic modeling of flexible biomolecules applied to NMR relaxation. 2. Interpretation of complex dynamics in linear oligosaccharides. J Phys Chem B 2012. [PMID: 23185964 DOI: 10.1021/jp306627q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
10
Säwén E, Hinterholzinger F, Landersjö C, Widmalm G. Conformational flexibility of the pentasaccharide LNF-2 deduced from NMR spectroscopy and molecular dynamics simulations. Org Biomol Chem 2012;10:4577-85. [PMID: 22572908 DOI: 10.1039/c2ob25189b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
11
Xia J, Case DA. Sucrose in aqueous solution revisited, Part 2: adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation. Biopolymers 2011;97:289-302. [PMID: 22058066 DOI: 10.1002/bip.22004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/21/2011] [Accepted: 10/26/2011] [Indexed: 11/07/2022]
12
Xia J, Margulis CJ, Case DA. Searching and optimizing structure ensembles for complex flexible sugars. J Am Chem Soc 2011;133:15252-5. [PMID: 21863822 DOI: 10.1021/ja205251j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
13
Säwén E, Stevensson B, Ostervall J, Maliniak A, Widmalm G. Molecular conformations in the pentasaccharide LNF-1 derived from NMR spectroscopy and molecular dynamics simulations. J Phys Chem B 2011;115:7109-21. [PMID: 21545157 DOI: 10.1021/jp2017105] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
14
Ganguly S, Xia J, Margulis C, Stanwyck L, Bush CA. Measuring the magnitude of internal motion in a complex hexasaccharide. Biopolymers 2010;95:39-50. [DOI: 10.1002/bip.21532] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
15
Venable RM, Hatcher E, Guvench O, MacKerell AD, Pastor RW. Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling. J Phys Chem B 2010;114:12501-7. [PMID: 20831149 PMCID: PMC3040444 DOI: 10.1021/jp105549s] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
16
Woodcock HL, Brooks BR, Pastor RW. Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran. J Am Chem Soc 2008;130:6345-7. [PMID: 18444612 PMCID: PMC2935315 DOI: 10.1021/ja077633z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
17
Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy. Biophys J 2008;95:1590-9. [PMID: 18456821 DOI: 10.1529/biophysj.108.133025] [Citation(s) in RCA: 321] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
18
Mobli M, Nilsson M, Almond A. The structural plasticity of heparan sulfate NA-domains and hence their role in mediating multivalent interactions is confirmed by high-accuracy (15)N-NMR relaxation studies. Glycoconj J 2007;25:401-14. [PMID: 18080183 PMCID: PMC2413117 DOI: 10.1007/s10719-007-9081-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Revised: 10/16/2007] [Accepted: 10/18/2007] [Indexed: 10/29/2022]
19
Eklund R, Lycknert K, Söderman P, Widmalm G. A conformational dynamics study of alpha-l-Rhap-(1-->2)[alpha-l-Rhap-(1-->3)]-alpha-l-Rhap-OMe in solution by NMR experiments and molecular simulations. J Phys Chem B 2007;109:19936-45. [PMID: 16853578 DOI: 10.1021/jp053198o] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
20
Landersjö C, Jansson JLM, Maliniak A, Widmalm G. Conformational analysis of a tetrasaccharide based on NMR spectroscopy and molecular dynamics simulations. J Phys Chem B 2007;109:17320-6. [PMID: 16853211 DOI: 10.1021/jp052206y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
21
Angulo J, Hricovíni M, Gairi M, Guerrini M, de Paz JL, Ojeda R, Martín-Lomas M, Nieto PM. Dynamic properties of biologically active synthetic heparin-like hexasaccharides. Glycobiology 2005;15:1008-15. [PMID: 15958415 DOI: 10.1093/glycob/cwi091] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
22
Andersson A, Ahl A, Eklund R, Widmalm G, Mäler L. Dynamics in the cyclic Enterobacterial common antigen as studied by 13C NMR relaxation. JOURNAL OF BIOMOLECULAR NMR 2005;31:311-20. [PMID: 15928997 DOI: 10.1007/s10858-005-1605-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Accepted: 01/21/2005] [Indexed: 05/02/2023]
23
Venable RM, Delaglio F, Norris SE, Freedberg DI. The utility of residual dipolar couplings in detecting motion in carbohydrates: application to sucrose. Carbohydr Res 2005;340:863-74. [PMID: 15780252 DOI: 10.1016/j.carres.2005.01.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Accepted: 01/18/2005] [Indexed: 11/17/2022]
24
Almond A, Petersen BO, Duus JØ. Oligosaccharides Implicated in Recognition Are Predicted to Have Relatively Ordered Structures. Biochemistry 2004;43:5853-63. [PMID: 15134459 DOI: 10.1021/bi0354886] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
25
Lycknert K, Widmalm G. Dynamics of the Escherichia coli O91 O-Antigen Polysaccharide in Solution as Studied by Carbon-13 NMR Relaxation. Biomacromolecules 2004;5:1015-20. [PMID: 15132695 DOI: 10.1021/bm0345108] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Dixon AM, Venable R, Widmalm G, Bull TE, Pastor RW. Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides. Biopolymers 2003;69:448-60. [PMID: 12879491 DOI: 10.1002/bip.10421] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
27
Höög C, Rotondo A, Johnston BD, Pinto BM. Synthesis and conformational analysis of a pentasaccharide corresponding to the cell-wall polysaccharide of the Group A Streptococcus. Carbohydr Res 2002;337:2023-36. [PMID: 12433468 DOI: 10.1016/s0008-6215(02)00218-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
28
Dixon AM, Venable RM, Pastor RW, Bull TE. Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study. Biopolymers 2002;65:284-98. [PMID: 12382289 DOI: 10.1002/bip.10249] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
29
Kowalewski J, Effemey M, Jokisaari J. Dipole-dipole coupling constant for a directly bonded CH pair--a carbon-13 relaxation study. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002;157:171-177. [PMID: 12323134 DOI: 10.1006/jmre.2002.2590] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
30
Freedberg DI. An alternative method for pucker determination in carbohydrates from residual dipolar couplings: a solution NMR study of the fructofuranosyl ring of sucrose. J Am Chem Soc 2002;124:2358-62. [PMID: 11878992 DOI: 10.1021/ja010981v] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
31
Wormald MR, Petrescu AJ, Pao YL, Glithero A, Elliott T, Dwek RA. Conformational studies of oligosaccharides and glycopeptides: complementarity of NMR, X-ray crystallography, and molecular modelling. Chem Rev 2002;102:371-86. [PMID: 11841247 DOI: 10.1021/cr990368i] [Citation(s) in RCA: 322] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
32
Engelsen SB, Monteiro C, Hervé de Penhoat C, Pérez S. The diluted aqueous solvation of carbohydrates as inferred from molecular dynamics simulations and NMR spectroscopy. Biophys Chem 2001;93:103-27. [PMID: 11804720 DOI: 10.1016/s0301-4622(01)00215-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
33
Monteiro C, Hervé du Penhoat C. Translational Diffusion of Dilute Aqueous Solutions of Sugars as Probed by NMR and Hydrodynamic Theory. J Phys Chem A 2001. [DOI: 10.1021/jp0113836] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
34
Bogusz S, Venable RM, Pastor RW. Molecular Dynamics Simulations of Octyl Glucoside Micelles:  Dynamic Properties. J Phys Chem B 2001. [DOI: 10.1021/jp004475o] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
35
Höög C, Landersjö C, Widmalm G. Oligosaccharides display both rigidity and high flexibility in water as determined by 13C NMR relaxation and 1H,1H NOE spectroscopy: evidence of anti-phi and anti-psi torsions in the same glycosidic linkage. Chemistry 2001;7:3069-77. [PMID: 11495434 DOI: 10.1002/1521-3765(20010716)7:14<3069::aid-chem3069>3.0.co;2-a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
36
Almond A, Bunkenborg J, Franch T, Gotfredsen CH, Duus JO. Comparison of aqueous molecular dynamics with NMR relaxation and residual dipolar couplings favors internal motion in a mannose oligosaccharide. J Am Chem Soc 2001;123:4792-802. [PMID: 11457289 DOI: 10.1021/ja0025696] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
37
Tian F, Al-Hashimi HM, Craighead JL, Prestegard JH. Conformational analysis of a flexible oligosaccharide using residual dipolar couplings. J Am Chem Soc 2001;123:485-92. [PMID: 11456551 DOI: 10.1021/ja002900l] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
38
Duus J, Gotfredsen CH, Bock K. Carbohydrate structural determination by NMR spectroscopy: modern methods and limitations. Chem Rev 2000;100:4589-614. [PMID: 11749359 DOI: 10.1021/cr990302n] [Citation(s) in RCA: 509] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
39
Höög C, Widmalm G. Conformational Flexibility of the Disaccharide α-d-Manp-(1→3)-β-d-Glcp-OMe Employing Molecular Dynamics Simulations and trans-Glycosidic 3JC,H from NMR Experiment. J Phys Chem A 2000. [DOI: 10.1021/jp0018697] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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