Pyranose ring puckering in aldopentoses, ketohexoses and deoxyaldohexoses. A molecular dynamics study

Panczyk, Karina; Płaziński, Wojciech

doi:10.1016/j.carres.2017.11.011

Cited by 12 publications

(11 citation statements)

References 45 publications

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“…αXyl has the 4 C 1 chair conformation as its global minimum and a secondary Δ G (α 1 , α 2 ) minimum corresponding to the 1 C 4 chair and with a value of 2.17 kcal/mol. This compares favorably to the value of 1.65 kcal/mol computed with the GROMOS 56a6CARBO force field (Table 1 in [ 48 ]), which is also exactly the value from Angyal’s scheme for determining ring puckering free energies [ 70 ]. We note that data from Angyal’s scheme have been used for quantitative comparison in other force field evaluations for a wide variety of pyranoses.…”

Section: Resultssupporting

confidence: 69%

“…A logical means to address this issue is to apply a bias to θ during a simulation and either to reweight the sampling distribution to get unbiased conformational probabilities or to directly compute Δ G from the bias. Such an approach employing metadynamics [ 57 , 58 ] has enabled a number of studies to this end [ 29 , 32 , 33 , 45 , 48 , 59 ]. As demonstrated in these studies, this approach allows one to obtain a good estimate for Δ G with much less computation time than through standard (non-biased) molecular dynamics.…”

Section: Resultsmentioning

confidence: 99%

“…It is possible to tune ring puckering thermodynamics by selectively refining specific force field parameters and by using ring puckering thermodynamics as target data in the parametrization process. In the case of the GROMOS force field, such an approach was taken as a force field revision [ 31 , 32 , 47 ], and has yielded excellent results for ring puckering across a wide variety of pyranoses [ 32 , 33 , 45 , 48 ]. In the case of CHARMM, ring puckering thermodynamics in solution were not used as target data for CHARMM parametrization, and both bonded and nonbonded force field parameters, which built upon quantum mechanical gas phase puckering energetics for tetrahydropyran [ 36 , 49 ], are conserved across all of the different monosaccharides considered here.…”

Section: Introductionmentioning

confidence: 99%

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Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins

Guvench

Martin

Greene

2021

IJMS

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The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the quality of the force field parametrization used in the simulations. A key determinant of the conformational properties of carbohydrates is ring puckering. Here, we applied extended system adaptive biasing force (eABF) all-atom explicit-solvent molecular dynamics simulations to characterize the ring puckering thermodynamics of the ten common pyranose monosaccharides found in vertebrate biology (as represented by the CHARMM carbohydrate force field). The results, along with those for idose, demonstrate that the CHARMM force field reliably models ring puckering across this diverse set of molecules, including accurately capturing the subtle balance between 4C1 and 1C4 chair conformations in the cases of iduronate and of idose. This suggests the broad applicability of the force field for accurate modeling of carbohydrate-containing vertebrate biomolecules such as glycoproteins, proteoglycans, and glycolipids.

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Section: Resultssupporting

confidence: 69%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins

Guvench

Martin

Greene

2021

IJMS

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“…The glucose adopts an O,3 B conformation, which is ∼4 to 6 kcal/mol higher in energy than the 4 C 1 conformation (57,58). Though this conformation is likely stabilized by van der Waals interactions (A342 and F435) and hydrogen bonding (K347 and N343), this probably contributes to the low-affinity binding of ADPG.…”

Section: Discussionmentioning

confidence: 99%

ADP-ribose and analogues bound to the deMARylating macrodomain from the bat coronavirus HKU4

Hammond

Schormann

McPherson

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Macrodomains are proteins that recognize and hydrolyze ADP ribose (ADPR) modifications of intracellular proteins. Macrodomains are implicated in viral genome replication and interference with host cell immune responses. They are important to the infectious cycle of Coronaviridae and Togaviridae viruses. We describe crystal structures of the conserved macrodomain from the bat coronavirus (CoV) HKU4 in complex with ligands. The structures reveal a binding cavity that accommodates ADPR and analogs via local structural changes within the pocket. Using a radioactive assay, we present evidence of mono-ADPR (MAR) hydrolase activity. In silico analysis presents further evidence on recognition of the ADPR modification for hydrolysis. Mutational analysis of residues within the binding pocket resulted in diminished enzymatic activity and binding affinity. We conclude that the common structural features observed in the macrodomain in a bat CoV contribute to a conserved function that can be extended to other known macrodomains.

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“…In turn, the nonplanarity of self-associates opens the possibility for the conformational mobility, that is, various wavelike motions within the hydrogen bond rings without the bond breakage. Below, while discussing such conformational motions, we will refer to them as “twists” or “puckerings”, following the terminology used to describe conformations of sugars. − …”

Section: Discussionmentioning

confidence: 99%

Conformational Mobility and Proton Transfer in Hydrogen-Bonded Dimers and Trimers of Phosphinic and Phosphoric Acids

et al. 2019

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The monomers, H-bonded cyclic dimers, and trimers of five acids were studied by density functional theory calculations, such as hypophosphorous acid (H2POOH, 1), dimethylphosphinic acid (Me2POOH, 2), phenylphosphinic acid (PhHPOOH, 3), dimethylphosphoric acid ((MeO)2POOH, 4), and diphenylphosphoric acid ((PhO)2POOH, 5). Particular attention was paid to the conformational manifold existing due to the internal degrees of freedom: proton transfer (PT), puckering (“twist”) within the ring of H-bonds, and mobility of the substituents (namely, −Ph, −OMe, and −OPh rotations). For acid 3, the number of conformers is additionally increased because of the varying relative orientation of nonequivalent substituents in cyclic complexes. We show that 31P NMR chemical shifts (δP) are very sensitive to the details of the conformation, spanning ranges from ca. 1 ppm (for trimers of acids 1 and 2) to ca. 12 ppm (for trimers of 4). The energy barriers for the transitions between conformers are rather low (<6 kcal/mol for PTs, <2.5 kcal/mol for puckerings, and ca. <3 kcal/mol for rotations of substituents), such that the fast exchange regime in the NMR timescale and subsequent δP averaging are expected. Correlations are proposed linking the change of average δP with the H-bond energy, showing the slope of ca. 4 ppm per kcal/mol. The sensitivity of δP to the OPO angle and the OPOH dihedral angle and the geometries of both H-bonds formed by the POOH moiety are analyzed.

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Pyranose ring puckering in aldopentoses, ketohexoses and deoxyaldohexoses. A molecular dynamics study

Cited by 12 publications

References 45 publications

Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins

Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins

ADP-ribose and analogues bound to the deMARylating macrodomain from the bat coronavirus HKU4

Conformational Mobility and Proton Transfer in Hydrogen-Bonded Dimers and Trimers of Phosphinic and Phosphoric Acids

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