HSEA calculations, conformation

Gentiobiose octaacetate was analyzed by NMR spectroscopy and HSEA calculations [98]. The calculations were performed with the conformations of the hydro-... 

HSEA calculation and NMR data [191]. Interestingly, GM3 contains a different conformation of the neuramic acid compared to G, and GM1, whereas the terminal neuramic acid in GDlh is expected to show the same

differing from all other neuramic acid conformations studied here. The different shapes of the molecules are discussed in terms of their specific binding of cholera and tetanus toxins. 

A study of the conformation of Salmonella O-antigens of serogroups A, B, and Dx by HSEA calculations and NMR has been described [198,199]. As can be seen from... 

Fig. 30. Conformation of acarbose in comparison to maltotetraose as obtained from HSEA calculations...

Bock K, Meldal M, Bundle DR, Iversen T, Garegg PJ, Norbeig T, Lindberg AA, Svenson SB (1984) The conformation of Salmonella O-antigenic polysaccharide chains of serogroup A, B and D1 predicted by semi-empirical hard-sphere (HSEA) calculations. Carbohydr Res 130 23-34... 

HSEA method has been found to generate conformations that are frequently consistent with the NMR dataA Early HSEA-based predictions of the conformations of the blood group antigenic determinants remain examples of the success of the HSEA method when applied to molecules that appear to exist predominantly in one conformation in solution. In contrast, based on somewhat limited data from nuclear Overhauser effect (NOE) intensities, HSEA calculations predicted that sucrose preferred a single rigid conformation in solution. More recent experimental data demonstrated that sucrose is more flexible than had been believed. This example clearly illustrates the pitfalls associated with fitting structures to insufficient and insensitive experimental data. 

R. U. Lemieux and K. Bock, Arch. Biochem. Biophys., 221, 125 (1983). The Conformational Analysis of Oligosaccharides by H-NMR and HSEA Calculation. 

Calculation of the Minimum-Energy Conformers by the HSEA Algorithm ... 

Analysis by H-NMR techniques and different calculation methods by Bush et al. [118] showed that the minimum energy conformation obtained by the Hopfinger potential as well as the HSEA potential described the experimental data for the terminal A-blood group tetrasaccharide very well, whereas the modified Scheraga potential did not reproduce the experimental data — NOE and longitudinal relaxation times — adequately. The glycosidic bond of fucose showed calculated and experimental values of cp = 60° and i — 10° and that of iV-acetyl-galactosamine showed cp = —70° and J/ = -40°. 

Fig. 21 a, b. Conformation of globoside calculated by the HSEA program a without and b with constraint imposed via a potential function to account for the observed NOEs. Stereo plots with the reducing end to the right... 

Fig. 23. Calculated minimum energy conformation of the GMrganglioside using the HSEA program. Stereo plot with the reducing ends to the top...

A study on the macrolide antibiotic Idjaniniycin, whidi contains the tetrasaccharide residue 41, by antr. spectrosot uid HSEA fi)rce fidd calculations on the caibol drate nKxety, showed that the a-(1 3)4inlred d oxose residues are severdy restricted in their confi>rniationai fieedom. The predominant solution conformation of the synthetic intermediates, such as macrocyde 42, of IS-membered azalides have been established by similar tedmiques. Molecular dynamics studies on calidiean ns are r rred to in Chapto 19. 

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