Conformation of Carbohydrates

Rao, V. S. R.; Qasba, Pradman K.; Balaji, Petety V.; Chandrasekaran, R.

doi:10.1201/9780367813529

Cited by 50 publications

(61 citation statements)

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“…Here, we modeled a peptidoglycan octamer with a NAG‐NAM(‐L‐Ala‐γ‐D‐Glu‐L‐Dap‐D‐Ala‐D‐Ala) disaccharide repeating unit since λ lysozyme has been shown to be more active for gram‐negative bacterial cell wall lysis . According to theoretical and experimental analysis, the glycosidic dihedral angles of the NAM‐β(1–4)‐NAG unit are similar to a NAG‐β(1–4)‐NAG unit (chitin‐like structure) whereas the conformational map is more restricted in a NAG‐β(1–4)‐NAM unit . Therefore, we used the φ , ψ :−84°, 102° glycosidic angles for the NAM‐NAG disaccharide, which have been previously determined from free‐energy calculations .…”

Section: Resultsmentioning

confidence: 99%

“…Although there have been many studies of the chemical structure of peptidoglycans, there is no consensus on the preferred 3D molecular structure adopted or its arrangement in the cell wall. [33][34][35][36][37] previously determined from free-energy calculations. 16 Glycosidic angles for the NAG-NAM disaccharide were taken from the NMR structure of a peptidoglycan monomer fragment 36…”

Section: Modeling Of the λ Lysozyme-peptidoglycan Complexmentioning

confidence: 99%

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An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra‐ and hexa‐N‐acetylchitohexaose

et al. 2019

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The X‐ray structure of lysozyme from bacteriophage lambda (λ lysozyme) in complex with the inhibitor hexa‐N‐acetylchitohexaose (NAG6) (PDB: 3D3D) has been reported previously showing sugar units from two molecules of NAG6 bound in the active site. One NAG6 is bound with four sugar units in the ABCD sites and the other with two sugar units in the E′F′ sites potentially representing the cleavage reaction products; each NAG6 cross links two neighboring λ lysozyme molecules. Here we use NMR and MD simulations to study the interaction of λ lysozyme with the inhibitors NAG4 and NAG6 in solution. This allows us to study the interactions within the complex prior to cleavage of the polysaccharide. 1HN and 15N chemical shifts of λ lysozyme resonances were followed during NAG4/NAG6 titrations. The chemical shift changes were similar in the two titrations, consistent with sugars binding to the cleft between the upper and lower domains; the NMR data show no evidence for simultaneous binding of a NAG6 to two λ lysozyme molecules. Six 150 ns MD simulations of λ lysozyme in complex with NAG4 or NAG6 were performed starting from different conformations. The simulations with both NAG4 and NAG6 show stable binding of sugars across the D/E active site providing low energy models for the enzyme‐inhibitor complexes. The MD simulations identify different binding subsites for the 5th and 6th sugars consistent with the NMR data. The structural information gained from the NMR experiments and MD simulations have been used to model the enzyme‐peptidoglycan complex.

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Section: Resultsmentioning

confidence: 99%

Section: Modeling Of the λ Lysozyme-peptidoglycan Complexmentioning

confidence: 99%

An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra‐ and hexa‐N‐acetylchitohexaose

et al. 2019

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“…For glycans, the torsion angles

ϕ

and

ψ

are defined differently than in proteins (Figure ). In NMR (as opposed to crystallographic) studies, the torsional angle

ϕ

and

ψ

between two residues are generally given by

ϕ \equiv

(H1 (i‐1) ‐C1 (i‐1) ‐O1 (i‐1) ‐C x(i) ), and

ψ \equiv

(C1 (i‐1) ‐O1 (i‐1) ‐C x(i) ‐H x(i) ). Glycans are usually found in preferred orientations, but typically, have more than one preferred orientation for each linkage .…”

Section: Glycan Solution Structure Determinationmentioning

confidence: 99%

Solution NMR Structural Studies of Glycans

Freedberg

Kwon

2019

Israel Journal of Chemistry

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In this account, we present a summary of our progress in the study of glycan solution conformations by NMR spectroscopy. We begin by comparing the structural biology of glycans to that of proteins. We continue by defining the challenges in solution structural studies of glycans as we see them and show what we have done to help address those challenges. This includes Residual Dipolar Coupling studies and their hurdles, accurate coupling constant measurement in the presence of strong 1 H-1 H coupling, direct detection of hydrogen bonds where the NHs, OHs or CHs are the hydrogen bond donors, and on-cell NMR structural studies. We also suggest some future approaches to glycan structure determination.

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“…In order to classify our linear saccharides, helical parameter, n (number of residues per pitch) and h (advancement per monomer unit) were calculated according to the def-inition in the following references. [113,52,115] According to Rees'[115] classification of perfectly periodic helices our studied sugars fall into the ribbon family n=2-±4 and h=4-6Å…”

Section: Methodsmentioning

confidence: 99%

“…Carbohydrates, unlike their protein counterparts, simply do not have a backbone and as opposed to proteins which are linear polymers, carbohydrates are often branched. Since these molecules are polyalcohols, there are various plausible linkage points such as 1-1, 1-2, 1-3, 1-4 and 1-6 [113](see Figure 1.1) and this is further complicated by the fact that monosaccharide residues exist in two anomeric configurations, namely α (where the OH group at C1 is axial) and β (where the OH group at C1 is equatorial) with respect to the 4 C 1 chair conformation. In the past, our group has put significant effort in understanding the conformational preferences of oligsaccharies by developing and using a fast sugar structure prediction software as well as by carrying out molecular dynamics simulation studies.…”

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confidence: 99%

Carbohydrate-protein interactions

Ramadugu¹

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The current thesis presents work on the structure and dynamics of oligosaccharides and polysaccharides as well as the free energetics of carbohydrate-protein interactions. By applying various computational tools such as molecular dynamics simulations, our in-house fast sugar structure prediction software, replica exchange molecular dynamics, homology modeling, umbrella sampling, steered molecular dynamics as well as the thermodynamic integration formalism, we have been able to study the role of water on the surface of homopolysaccharides as well as complex oligosachharides, we have been able to produce a prediction of the bound structure of triantennary oligosaccride on the asialoglycoprotein receptor, we have been able to estimate the free energy of binding of Manα1→2Man to the HIV-1 inactivating protein, Cyanovirin-N as well as the relative binding free energies of mutants of Cyanovirin-N to the same ligand. Abstract Approved:Thesis Supervisor

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Conformation of Carbohydrates

Cited by 50 publications

References 0 publications

An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra‐ and hexa‐N‐acetylchitohexaose

An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra‐ and hexa‐N‐acetylchitohexaose

Solution NMR Structural Studies of Glycans

Carbohydrate-protein interactions

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