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Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field
2009
Journal of Computational Chemistry
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The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension ...
For each linkage, we compare and contrast the oligosaccharide and respective disaccharide carb-Rama plots, validate the simulations and the Glycam06 force field through comparison to experimental data, ...
Acknowledgments Acknowledgment is made to NSF, NIH and to Hamilton College for support of this work. ...
doi:10.1002/jcc.21099
pmid:18785152
fatcat:pity4npz2feazhy7hrek2pn7de
In-Depth Molecular Dynamics Study of All Possible Chondroitin Sulfate Disaccharides Reveals Key Insight into Structural Heterogeneity and Dynamism
2022
Biomolecules
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In the present study, we used the all-atom GLYCAM06 force field for the first time to explore the conformational space of all possible CS building blocks. ...
molecular dynamics (MD). ...
Acknowledgments: We also thank the computing resources made available through the S10RR027411 grant from the National Center for Research Resources to VCU. ...
doi:10.3390/biom12010077
pmid:35053225
pmcid:PMC8773825
fatcat:4s3irih7fbesvee3vteddmw5wq
Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces
2008
Glycobiology
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Here, we employ all-atom explicit solvent molecular dynamics (MD) simulations, using the GLYCAM06 force field, to model the conformation and dynamics of ganglioside G M3 (α-Neu5Ac-(2-3)-β-Gal-(1-4)-β-Glc-ceramide ...
The accuracy of data from the MD simulations was determined by comparison to NMR and crystallographic data for the head group in solution and for G M3 in membrane-mimicking environments. ...
Using all structures deposited in the PDB that contained carbohydrates with α-Neu5Ac-(2-3)-β-Gal or β-Gal-(1-4)-β-Glc sequences, Ramachandran-style plots of the glycosidic linkages were generated ( Figure ...
doi:10.1093/glycob/cwn137
pmid:19056784
pmcid:PMC2733776
fatcat:vypzee3r75befh6forqyqmyyf4
Three-Dimensional Structures of Carbohydrates and Where to Find Them
2020
International Journal of Molecular Sciences
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Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed. ...
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. ...
; (c) conformational space of a two-torsion glycosidic linkage (Ramachandran plot); (d) transitions of glycosidic dihedrals. ...
doi:10.3390/ijms21207702
pmid:33081008
fatcat:sympabhcbzd47k4ll4h2gqiwkq
Carbohydrates in Cyberspace
2015
Frontiers in Immunology
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The GLYCAM-Web server (5) and the GLYCAM force field (7) were used for the investigation of recognition specificity of ABO blood group antigens by antibodies (8). Such circulating antibodies ...
derivatives, and other biomolecules; self-containment and transferability to many quadratic force fields; ability to treat both αand β-anomers without specific atom types. ...
Acknowledgments The authors gratefully acknowledge the contribution toward this study from the Victorian Operational Infrastructure Support Program received by the Burnet Institute. ...
doi:10.3389/fimmu.2015.00300
pmid:26113848
pmcid:PMC4462093
fatcat:uqzdrt3k25gp7i7d24hkq5nwuq
Characterization of the interaction of interleukin-8 with hyaluronan, chondroitin sulfate, dermatan sulfate and their sulfated derivatives by spectroscopy and molecular modeling
2011
Glycobiology
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Our results highlight the importance of combining experimental and theoretical approaches to obtain a better understanding of the molecular recognition properties of GAG-protein systems. ...
We analyze the effects of GAG length and sulfation patterns in binding strength and specificity, and the influence of GAG binding on IL-8 dimer formation. ...
Acknowledgements We are grateful to Ralf Gey for his invaluable technical support and to Clemens Horn for help with the assignment of the NOESY and TOCSY spectra of IL-8. ...
doi:10.1093/glycob/cwr120
pmid:21873605
pmcid:PMC3230280
fatcat:7zzqha5trrb63acjgtsztvu7ci
Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
2021
Biomolecules
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Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. ...
In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms ...
The parameters were derived from microsecond all-atom simulations using the GLYCAM06 force field [188] . ...
doi:10.3390/biom11091347
pmid:34572559
pmcid:PMC8465211
fatcat:baazxyytureapcq7p7hlhrqf54
Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Acα2-6Galβ1-4GlcNAc human-type influenza receptor
2011
Glycobiology
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Here, we report a crystallographic and molecular dynamics (MD) analysis of a lectin from Polyporus squamosus (PSL) that is specific for glycans terminating with the sequence Neu5Acα2-6Galβ. ...
Carbohydrate-binding proteins (lectins) with specificity for Neu5Ac are particularly useful in the detection and isolation of sialylated glycoconjugates, such as those associated with pathogen adhesion ...
Acknowledgements We thank the Advanced Photon Source, Argonne, IL, USA, and the staff at the IMCA-CAT beamline 17 for synchrotron time and assistance during data collection. ...
doi:10.1093/glycob/cwr030
pmid:21436237
pmcid:PMC3110490
fatcat:pd4zcnqtuzfuvfyitdnphpffpy
Immunoglobulin G1 Fc Domain Motions: Implications for Fc Engineering
2014
Journal of Molecular Biology
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This observation motivated an extensive molecular dynamics investigation of polypeptide and glycan motions that revealed greater amplitude of motion for the N-terminal Cγ2 domains and N-glycan than previously ...
Residues in the Cγ2/Cγ3 interface and disulfide-bonded hinge were identified as influencing the Cγ2 motion. Our results are consistent with a model of Fc that is structurally dynamic. ...
The AMBER ff99SB [45] force field was used for the protein, and carbohydrate parameters were taken from the GLYCAM06 force field [46] . ...
doi:10.1016/j.jmb.2014.01.011
pmid:24522230
pmcid:PMC4041121
fatcat:ckvwvp2wdfd7fjk32rkmglacyy
Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors
2016
Biochemistry
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Two complementary techniques, 1 H saturation transfer difference ( 1 H STD) nuclear magnetic resonance and molecular dynamics (MD) simulation, were applied to analyze the interaction of the new H7 (A/Anhui ...
Molecular details and dynamics of glycan-HA interactions are of interest, both in predicting the pandemic potential of a new emerging strain and in searching for new antiviral drugs. ...
Part of the MD simulations was performed by the "High Performance Computing ...
doi:10.1021/acs.biochem.6b00693
pmid:27933797
pmcid:PMC5559875
fatcat:hyams35i75gmbgxtynbvt2y7uq
A front-face 'SNi synthase' engineered from a retaining 'double-SN2' hydrolase
2017
Nature Chemical Biology
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Destruction of the first S N 2 nucleophile through E387Y mutation created a b-stereoselective catalyst for glycoside synthesis from activated substrates, despite lacking a nucleophile. ...
and reveal a quantum mechanics-molecular mechanics (QM/MM) free-energy landscape for the substitution reaction that is similar to those of natural, S N i-like glycosyltransferases. ...
(wild type) or other (for example, endogenously expressed host Escherichia coli) glycosidases that use nucleophilic catalysis. ...
doi:10.1038/nchembio.2394
pmid:28604696
fatcat:6pgm7lghxfhgxixsaayfroz5by
Involvement of Water in Carbohydrate−Protein Binding: Concanavalin A Revisited
2008
Journal of the American Chemical Society
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This new structural data provides a firm basis for molecular dynamics simulations and thermodynamic integration calculations whose results indicate that differences in van der Waals contacts (insertion ...
When combined with the new crystallographic data, this study provides a straightforward interpretation for the lower affinity of the synthetic analog; specifically, that it arises primarily from weaker ...
JDD thanks the Carlsberg Foundation for a postdoctoral fellowship. ...
doi:10.1021/ja8039663
pmid:19053475
pmcid:PMC2626182
fatcat:7ebikpxp55hqvkvbg3s4w3mvle
The interdomain flexible linker of the polypeptide GalNAc transferases dictates their long-range glycosylation preferences
2017
Nature Communications
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Kinetics and molecular dynamics simulations on several GalNAc-T2 flexible linker constructs show altered remote prior glycosylation preferences, confirming that the flexible linker dictates the rotation ...
This work for the first time provides the structural basis for the different remote prior glycosylation preferences of the GalNAc-Ts. ...
Force field parameters for the substrates were generated with the antechamber module of Amber14 using a combination of GLYCAM06 35 parameters for the GalNAc unit and the general Amber force field (GAFF ...
doi:10.1038/s41467-017-02006-0
pmid:29208955
pmcid:PMC5716993
fatcat:5im2l7darfgkhnwsse2e5zvb6i
Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor
[article]
2020
biorxiv/medrxiv
pre-print
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cell types. ...
These data, coupled with surface plasmon resonance studies and molecular modeling, allow us to propose a bi-dentate oligosaccharide binding model, which could explain how high affinity carbohydrate binding ...
mannose 6-phosphate receptor (CI-MPR) from SEC-SAXS), SASDHN4 (N-terminal 5 domains of the cation-independent mannose-6-phosphate receptor (CI-MPR) bound to mannose 6-phosphate (M6P)), SASDHP4 (palmitoylprotein ...
doi:10.1101/2020.02.21.959957
fatcat:x2m5t2xctjexxk5ke5etsdof54
Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor
2020
Communications Biology
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These data, coupled with X-ray crystallography, surface plasmon resonance and molecular modeling, allow us to propose a model explaining how high-affinity carbohydrate binding is achieved through allosteric ...
The cation-independent mannose 6-phosphate receptor (CI-MPR, IGF2 receptor or CD222), is a multifunctional glycoprotein required for normal development. ...
mannose 6-phosphate receptor (CI-MPR) from SEC-SAXS), SASDHN4 (N-terminal 5 domains of the cation-independent mannose-6-phosphate receptor (CI-MPR) bound to mannose 6-phosphate (M6P)), SASDHP4 (palmitoylprotein ...
doi:10.1038/s42003-020-01211-w
pmid:32908216
fatcat:igkgfkyywrberlewsmgjubz7ju
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