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Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field

Amanda M. Salisburg, Ashley L. Deline, Katrina W. Lexa, George C. Shields, Karl N. Kirschner
2009 Journal of Computational Chemistry  
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

Balaji Nagarajan, Nehru Viji Sankaranarayanan, Umesh R. Desai
2022 Biomolecules  
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

M. L DeMarco, R. J Woods
2008 Glycobiology  
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

Sofya I. Scherbinina, Philip V. Toukach
2020 International Journal of Molecular Sciences  
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

Elizabeth Yuriev, Paul A. Ramsland
2015 Frontiers in Immunology  
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

Annelie Pichert, Sergey A Samsonov, Stephan Theisgen, Lars Thomas, Lars Baumann, Jürgen Schiller, Annette G Beck-Sickinger, Daniel Huster, M Teresa Pisabarro
2011 Glycobiology  
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

Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, Agnieszka G. Lipska, Sergey A. Samsonov, Rajesh K. Murarka
2021 Biomolecules  
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

Renuka Kadirvelraj, Oliver C Grant, Irwin J Goldstein, Harry C Winter, Hiroaki Tateno, Elisa Fadda, Robert J Woods
2011 Glycobiology  
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

Martin Frank, Ross C. Walker, William N. Lanzilotta, James H. Prestegard, Adam W. Barb
2014 Journal of Molecular Biology  
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

Eleonora Macchi, Timothy R. Rudd, Rahul Raman, Ram Sasisekharan, Edwin A. Yates, Annamaria Naggi, Marco Guerrini, Stefano Elli
2016 Biochemistry  
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

Javier Iglesias-Fernández, Susan M Hancock, Seung Seo Lee, Maola Khan, Jo Kirkpatrick, Neil J Oldham, Katherine McAuley, Anthony Fordham-Skelton, Carme Rovira, Benjamin G Davis
2017 Nature Chemical Biology  
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

Renuka Kadirvelraj, B. Lachele Foley, Jane D. Dyekjær, Robert J. Woods
2008 Journal of the American Chemical Society  
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

Matilde de las Rivas, Erandi Lira-Navarrete, Earnest James Paul Daniel, Ismael Compañón, Helena Coelho, Ana Diniz, Jesús Jiménez-Barbero, Jesús M. Peregrina, Henrik Clausen, Francisco Corzana, Filipa Marcelo, Gonzalo Jiménez-Osés (+2 others)
2017 Nature Communications  
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]

Linda J. Olson, Sandeep Misra, Mayumi Ishihara, Kevin Battaile, Oliver Grant, Amika Sood, Robert J Woods, Jung-Ja P. Kim, Michael Tiemeyer, Gang Ren, Joshua Sharp, Nancy M. Dahms
2020 biorxiv/medrxiv   pre-print
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

Linda J. Olson, Sandeep K. Misra, Mayumi Ishihara, Kevin P. Battaile, Oliver C. Grant, Amika Sood, Robert J. Woods, Jung-Ja P. Kim, Michael Tiemeyer, Gang Ren, Joshua S. Sharp, Nancy M. Dahms
2020 Communications Biology  
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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