Conformational analyses of  -4, -6-branching tri- -glucopyranosides; influence of  -4 linked residues on solution conformations about C5C6 bonds at (1–6)-linkages

Nishida, Yoshihiro; Hori, Hiroshi; Ohrui, Hiroshi; Meguro, Hiroshi; Uzawa, Jun; Reimer, D.; Sinnwell, Volker; Paulsen, Hans

doi:10.1016/s0040-4039(00)80522-5

Cited by 27 publications

(20 citation statements)

References 19 publications

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“…In general, ϕ/ψ and ψ/ω free energy maps for 1 – 9 qualitatively agree with the prior theoretical and experimental observations. 37 , 60 , 64 , 74 , 129 , 130 For instance, Wormald et al 10 reported the crystallographic average of 64.7 ± 10.4°/–178.4° ± 10.0°/–60.3 ± 14.0° ( gg rotamer) and 67.0 ± 10.5°/178.5 ± 13.7°/66.0 ± 13.8° ( gt rotamer) for the ϕ/ψ/ω torsion angles in α- d -Man p -(1→6)- d -Man p . Detailed analysis of the ϕ/ψ and ψ/ω energy maps also provided conformational preferences of ω when ψ deviates from the antiperiplanar conformation.…”

Section: Resultsmentioning

confidence: 99%

Conformational Properties of α- or β-(1→6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments

et al. 2014

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Conformational sampling for a set of ten α- or β-(1→6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian Replica Exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J-coupling constants and proton-proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with > 3 Hz deviation of the calculated 3J(H5,H6R) values from the experimental data, prompting optimization of the ω torsion angle parameters associated with (1→6)-linkages. The resulting force field is in overall good agreement (i.e. within ~ 0.5 Hz deviation) from experimental 3J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6· · ·HO2′ hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the ω torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1→6)-linkage as compared to the O6' atom in the non-reducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of ω torsion angles in oligosaccharides is also explored.

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Section: Resultsmentioning

confidence: 99%

Conformational Properties of α- or β-(1→6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments

et al. 2014

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“…The calculated heteronuclear coupling constants for the α(1→4) linkage show good agreement with experiments (Table II) and together these observations confirm that α‐forkose ( 5 ) is not significantly affected by the hydration. In the case of α‐forkose, experimental evidence has indicated that for the beta anomer the ω dihedral exhibit an equal distribution of ω = 60° and ω = 300° rotamers, just like in unsubstituted glucose 26, 27…”

Section: Resultsmentioning

confidence: 99%

Structure and hydration of the amylopectin trisaccharide building blocks—Synthesis, NMR, and molecular dynamics

Larsen

Motawia

et al. 2008

Biopolymers

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To gain insight into the molecular details and hydration of amylopectin, the five constituting trisaccharides have been chemically synthesized as their methyl alpha-glycosides. All five trisaccharides were subjected to 950 MHz NMR spectroscopy for complete assignment and nanosecond molecular dynamics trajectories were calculated to study the structure and dynamics of the trisaccharides in aqueous solution. Systematic analysis of the simulation data revealed several examples of bridging water molecules playing an important role in the stabilization of specific amylopectin conformations, which was also supported by the experimental NMR data such as interresidue NOE's and heteronuclear scalar couplings between nuclei from neighboring residues. Although alpha-maltotriose, alpha-iso-maltotriose, alpha-panose and alpha-isopanose are relatively well characterized structures, the study also includes one less characterized trisaccharide with the structure alphaGlcp(1-->4)alphaGlcp(1-->6)alphaGlcp. This trisaccharide, tentatively labelled alpha-forkose, is located at the branch point of amylopectin, forking the amylopectin into two strands that align into double-helical segments. The results show that the conformation of alpha-forkose takes a natural bend form which fits well into the structure of the double-helical segment of amylopectin. As the only trisaccharide in this study the structure of alpha-forkose is not significantly influenced by the hydration. In contrast, alpha-isopanose takes a restricted, but rather extended form due to an exceptionally strong localized water density. The two homo-linkage oligomers, alpha-maltotriose and alpha-iso-maltotriose, showed to be the most extended and the most flexible trimers, respectively, providing regular structure for crystalline domains and maximum linker flexibility for amorphous domains.

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“…The H‐6proR signal of a (1–6) linked mannose residue, such as Man‐ 4 ′, shifts to a lower field compared with the corresponding H‐6proS signal. In contrast, the H‐6proR signals of mannose residues without this (1–6) linkage, such as Man‐ A , ‐ B , ‐ D 2 , and ‐ D 3 , shift to a higher field compared with the corresponding H‐6proS signals …”

Section: Resultsmentioning

confidence: 92%

“…NOEs between H‐1 and H‐3/H‐4 have been widely used to study the conformations of 1–3 and 1–4 glycosidic bonds in the oligosaccharides. In the late 1980s, studies of the 1–6 glycosidic bond up to mannose trisaccharides led to the development of an empirical rule according to sugar type . However, assignment of NMR signals derived from pentasaccharides or larger oligosaccharides is usually hampered by overlapping signals.…”

Section: Introductionmentioning

confidence: 99%

Structural analyses of mannose pentasaccharide of high mannose type oligosaccharides by 1D and 2D NMR spectroscopy

Kubota

Hori

Sawa

et al. 2012

Magnetic Reson in Chemistry

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NMR spectroscopy is a very important and useful method for the structural analysis of oligosaccharides, despite its low sensitivity. We first applied conventional measuring methods, 2D DQF COSY, (1)H-(13)C HSQC, and (1)H-(13)C HMBC, and also the Double Pulsed Field Gradient Spin Echo (DPFGSE)-TOCSY and DPFGSE-NOESY/ROESY techniques to analyze a branched mannose pentasaccharide as a model of high mannose type N-glycans in natural abundance. The NMR spectra of the model compound are very complex and difficult to analyze owing to overlapping signals. The superior selective irradiation capability of the DPFGSE technique is useful for fine structural and conformational analyses of such complex oligosaccharides. We here introduce a novel technique called DPFGSE-Double-Selective Population Transfer (SPT)-Difference and DPFGSE-NOE/ROE-SPT-Difference spectroscopy. The DPFGSE-Double-SPT-Difference method involves irradiation of two peaks from one proton and the subtraction of higher and lower peaks from each spectrum. The DPFGSE-NOE/ROE-SPT-Difference method involves the transfer of the magnetization polarized by NOE/ROE from the nuclei to the spin-coupled nuclei through scalar spin-spin interaction using the SPT method. Even if the signals in the NMR spectra overlap, each signal can be accurately assigned. In particular, DPFGSE-NOE/ROE-SPT-Difference is very useful for identifying sugar connectivity.

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Conformational analyses of -4, -6-branching tri- -glucopyranosides; influence of -4 linked residues on solution conformations about C5C6 bonds at (1–6)-linkages

Cited by 27 publications

References 19 publications

Conformational Properties of α- or β-(1→6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments

Conformational Properties of α- or β-(1→6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments

Structure and hydration of the amylopectin trisaccharide building blocks—Synthesis, NMR, and molecular dynamics

Structural analyses of mannose pentasaccharide of high mannose type oligosaccharides by 1D and 2D NMR spectroscopy

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