Shaping up for structural glycomics: a predictive protocol for oligosaccharide conformational analysis applied to N-linked glycans

Sattelle, Benedict M.; Almond, Andrew

doi:10.1016/j.carres.2013.10.011

Cited by 23 publications

(53 citation statements)

References 58 publications

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“…However, the data suggest that 100 ns MD simulation is far too short to sample the conformational space of the glycosidic linkage sufficiently when an oligomer is simulated by such a canonical MD, while the microsecond‐scale MD simulation succeeded in sampling the minima obtained by the PMF calculations. This is in agreement with the previous observations about the timescales for rigorous sampling of oligosaccharides by the MD approach . The minima of the PMFs determined by umbrella‐sampling simulations agree well with the data obtained for heparin in microsecond‐scale MD simulations and from the experiment (PDB ID: 1HPN) .…”

Section: Resultssupporting

confidence: 91%

“…This is in agreement with the previous observations about the timescales for rigorous sampling of oligosaccharides by the MD approach. [41,42] The minima of the PMFs determined by umbrella-sampling simulations agree well with the data obtained for heparin in microsecond-scale MD simulations [16] and from the experiment (PDB ID: 1HPN). [43] For GlcNS(6S)-IdoA(2S), two minima corresponding to (ϕ, ψ) values near (−70, −120) and (−100, 60), respectively, were obtained.…”

Section: Contact Potentials From the Pdbsupporting

confidence: 72%

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Local and long range potentials for heparin‐protein systems for coarse‐grained simulations

et al. 2019

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Heparin belongs to glycosaminoglycans (GAGs), a class of periodic linear anionic polysaccharides, which are functionally important components of the extracellular matrix owing to their interactions with various protein targets. Heparin is known to be involved in many cell signaling processes, while the experimental data available for heparin are significantly more abundant than for other GAGs. At the same time, the length and conformational flexibility of the heparin represent major challenges for its theoretical analysis. Coarse‐grained (CG) approaches, which enable us to extend the size‐ and time‐scale by orders of magnitude owing to reduction of system representation, appear, therefore, to be useful in simulating these systems. In this work, by using umbrella‐sampling molecular dynamics simulations, we derived and parameterized the CG backbone‐local potentials of heparin chains and the orientational potentials for the interactions of heparin with amino acid side chains to be further included in the physics‐based Unified Coarse‐Grained Model of biological macromolecules. With these potentials, simulations of extracellular matrix processes where both heparin and multiple proteins participate will be possible.

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Section: Resultssupporting

confidence: 91%

Section: Contact Potentials From the Pdbsupporting

confidence: 72%

Local and long range potentials for heparin‐protein systems for coarse‐grained simulations

et al. 2019

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“…Polysaccharides are found throughout the biosphere, alone and also conjugated to other biopolymers such as proteins, in the form of glycoproteins, or to lipids in the form of glycolipids [140,141]. In comparison to nucleic acids and proteins, carbohydrates have larger capacity of complexity through the presence of numerous chiral centers within the sugar/ monosacchride subunits, the greater possible combinations of glycosidic linkages between different carbons within the sugar subunits resulting in branching, and to modifications to individual sugar subunits such as acetylation, methylation, oxidation, and sulfation [139,142].…”

Section: Imaging Of Biopolymersmentioning

confidence: 99%

Application of helium ion microscopy to nanostructured polymer materials

Bliznyuk

LaJeunesse

Boseman

2014

Nanotechnology Reviews

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Helium ion microscopy (HIM) is a relatively new high-resolution nanotechnology imaging and nanofabrication tool. HIM offers a near-molecular resolution (approaching that of TEM) combined with a simplicity of sample preparation and high depth of field similar to SEM. Simultaneously, the technique is not limited by the surface roughness as scanning probe microscopy (SPM) techniques or by the surface charging or radiation damage like SEM. In our review, we consider general principles, advantages, and prospects of HIM application in polymer science. Examples of high-resolution imaging of polymer-based nanocomposites, polymer nanoparticles, nanofibers, nanoporous materials, polymer nanocrystals, biopolymers, and polymer-based photovoltaic and sensor devices are presented. We compare the HIM's applicability with other modern imaging techniques: SPM and SEM.

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“…Also on the topic of bacterial membranes, Kong et al [50] studied the multi-microsecond dynamics of export through the Wza transporter of K30 oligosaccharides (part of bacteria's protective layer) of various lengths. Sattelle et al [51] used multi-microsecond simulations to study the dynamics of oligosaccharides in water, modeled in the GLYCAM force field [52].…”

Section: Conformational Rearrangements and Unstructured Proteinsmentioning

confidence: 99%

“…It is thanks to extensive and detailed refinements in force fields conducted in the last decades, and still ongoing, that we can extract kinetic information and extrapolate timescales even for conformations outside of the typical "stability basins" of backbones and side chains. Force-fields are still ongoing refinements, and this is especially important because they are now covering nonprotein macromolecules, as we have seen in the review: small molecules [59], lipids [58], and proteoglycans [51], ions, etc.…”

Section: Past Present and Future Challenges Of MDmentioning

confidence: 99%

Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale

Martínez-Rosell

Giorgino

Harvey

et al. 2017

CTMC

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Bio-molecular dynamics (MD) simulations based on graphical processing units (GPUs) were first released to the public in the early 2009 with the code ACEMD. Almost 8 years after, applications now encompass a broad range of molecular studies, while throughput improvements have opened the way to millisecond sampling timescales. Based on an extrapolation of the amount of sampling in published literature, the second timescale will be reached by the year 2022, and therefore we predict that molecular dynamics is going to become one of the main tools in drug discovery in both academia and industry. Here, we review successful applications in the drug discovery domain developed over these recent years of GPU-based MD. We also retrospectively analyse limitations that have been overcome over the years and give a perspective on challenges that remain to be addressed.

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Shaping up for structural glycomics: a predictive protocol for oligosaccharide conformational analysis applied to N-linked glycans

Abstract: Graphical abstract

Cited by 23 publications

References 58 publications

Local and long range potentials for heparin‐protein systems for coarse‐grained simulations

Local and long range potentials for heparin‐protein systems for coarse‐grained simulations

Application of helium ion microscopy to nanostructured polymer materials

Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale

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