Simulations of the HIV envelope trimer. These examples are further elaborated in Results and discussion. The generated glycan model is then solvated with ions (upon users selection) following the standard building procedures in CHARMM-GUI Solution Builder. 2011 Nov 15;32(14):3135-41. doi: 10.1002/jcc.21886. El Ghazal R, Yin X, Johns SC, Swanson L, Macal M, Ghosh P, Zuniga EI, Fuster MM. 2015) at GlycanStructure.ORG (Im-Group 2011-2018), Glycan Reader in CHARMM-GUI (Jo et al. Hamark C, Berntsson RP, Masuyer G, Henriksson LM, Gustafsson R, Stenmark P, Widmalm G. Received 2018 Dec 17; Revised 2019 Jan 20; Accepted 2019 Jan 22. We first prepared a set of target proteins and their N-glycan structures by collecting non-redundant (unique) N-glycan sequences containing at least five carbohydrates from the PDB and randomly selecting one PDB entry for each unique sequence. CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates. In addition, two GM1 glycan structures do not have -glucose (Glc) at the reducing end. Water box is shown as a translucent surface. 1995). HHS Vulnerability Disclosure, Help This version of . Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD Jr, Klauda JB, Qi Y, Im W. J Comput Chem. 2017), CarbBuilder (Kuttel et al. All rights reserved. Each heterodimer is composed of gp120 (gray, blue, and yellow) paired with gp41 (orange, red, and pink, respectively). Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr., Onufriev A, Simmerling C, Wang B, Woods RJ. Practical applications of Glycan Reader & Modeler. CHARMM-GUI Glycan Modeler provides the functionality of in silico N-/O-glycosylation on the target protein and generation of carbohydrate-only systems. 2017). Insights from NMR spectroscopy, Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors, SWEET WWW-based rapid 3D construction of oligo- and polysaccharides, GlyProt: In silico glycosylation of proteins, CHARMM: The biomolecular simulation program, GlycoBase and autoGU: Resources for interpreting HPLC-glycan data, The Amber biomolecular simulation programs, CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems, Cell surface biology mediated by low affinity multivalent protein-glycan interactions, doGlycans-tools for preparing carbohydrate structures for atomistic simulations of glycoproteins, glycolipids, and carbohydrate polymers for GROMACS, Structure of a heparin-linked biologically active dimer of fibroblast growth factor, Long-ranged protein-glycan interactions stabilize von willebrand factor A2 domain from mechanical unfolding, Glycobiology: Toward understanding the function of sugars, OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation, Glycan sulfation modulates dendritic cell biology and tumor growth, POLYS 2.0: An open source software package for building three-dimensional structures of polysaccharides, The S variant of human alpha 1-antitrypsin, structure and implications for function and metabolism, Constant-pressure molecular-dynamics simulation The Langevin Piston Method, Modulation of human endothelial cell proliferation and migration by fucoidan and heparin, CHARMM additive all-atom force field for glycosidic linkages between hexopyranoses, Glycans confer specificity to the recognition of ganglioside receptors by botulinum neurotoxin A, GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, CHARMM36m: An improved force field for folded and intrinsically disordered proteins, Continuum Solvation Model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation, Structure, conformation, and dynamics of bioactive oligosaccharides: Theoretical approaches and experimental validations, Glycan fragment database: A database of PDB-based glycan 3D structures, Automated builder and database of protein/membrane complexes for molecular dynamics simulations, Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling, CHARMM-GUI membrane builder for mixed bilayers and its application to yeast membranes, Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins, Glycan Reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins, PBEQ-Solver for online visualization of electrostatic potential of biomolecules, GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations, GLYCAM06: A generalizable biomolecular force field. 2016)), users can use Solution Builder. Benchmark result of Glycan Modeler . Glycan Modeler aims to build glycan models onto glycosylation sites of a target protein within a reasonable computational time without structural errors and bad contacts between glycan models and the protein. Shaw Research. An official website of the United States government. 2015. Varki A, Cummings RD, Aebi M, Packer NH, Seeberger PH, Esko JD, Stanley P, Hart G, Darvill A, Kinoshita T et al. Figure Figure66 illustrates our selection scheme using an example of a query glycan sequence, Man4Man4GlcNAc4(Fuc6)GlcNAc-Asn. 2005), GROMACS (Hess et al. Glycan Modeler aims to build glycan models onto glycosylation sites of a target protein within a reasonable computational time without structural errors and bad contacts between glycan models and the protein. Park SJ, Lee J, Patel DS, Ma H, Lee HS, Jo S, Im W. Bioinformatics. In addition to the envelope protein, this PDB file contains antibodies PGT122 and 35O22 that interact with the envelope protein. The CHARMM parameters are available in the "Glycan Reader & Modeler" module [54] [55][56] of the CHARMM-GUI web server [57] as part of the "toppar_c36_jul20" force field package. Only two out of the 486 dihedrals have correlations less than 0.9 (Figure 3B), and both are the dihedral in the Man(14)GlcNAc linkage. Modulation of human endothelial cell proliferation and migration by fucoidan and heparin. 2013) and CHARMM/OpenMM (Arthur and Brooks 2016) (using the CHARMM force field). Guvench O, Hatcher ER, Venable RM, Pastor RW, Mackerell AD. Manual analysis of the glycan profiling LC/MS data is extremely time-consuming and efficient software tools are needed to eliminate this bottleneck. Trajectory analysis was performed with CHARMM (Brooks et al. If an uploaded protein structure contains pre-existing glycan structure(s) and the pre-existing glycan is the part of a query glycan sequence, Glycan Modeler maps the pre-existing glycan onto the glycan models to conserve the coordinates of the pre-existing glycan structures. 2023 Jan;37(1):28-44. doi: 10.1177/10943420221128233. In this system building example, these antibodies are excluded for convenience. 2003. 2011) to fit the PDB / distribution and randomly generate the torsional values within the distribution. government site. CTB can bind to ganglioside GM1 receptors in the plasma membrane for CTs entry to the cell. 2006), GLYCAM Carbohydrate Builder (Woods-Group 20052018) at GLYCAM-web, Glycan Fragment Database (GFDB) (Jo and Im 2013) and GS-align (glycan structure alignment) (Lee and Jo et al. Park SJ, Lee J, Patel DS, Ma H, Lee HS, Jo S, Im W. Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V et al. The inputs for N-/O-glycan modeling are a protein structure, glycosylation site(s), and glycan sequence for each glycosylation site (see Materials and methods for details). For instance, the use of 13C-labeled glycans provides the large signal dispersion and high sensitivity and also makes it possible to observe the fast exchanges of ligand complexes in the NMR chemical shift timescales (Arda and Jimenez-Barbero 2018). 2016; Dong et al. Each heterodimer is composed of gp120 (gray, blue, and yellow) paired with gp41 (orange, red, and pink, respectively). For the glycosylation site with no pre-existing glycan structure, the glycosidic linkage to protein (e.g., CGND2C1O5 () and CBCGND2C1 () for N-linked glycan) is selected for torsion angle variations. (B) Distribution of the linear correlation between the glycosidic dihedrals in the two MD systems. The distributions of these two dihedrals show that the deviations mostly come from minor populations at 60 (Figure 3C, D). FOIA most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. Consequently, the benchmark set was composed of 82 target N-glycans and parent glycoproteins. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. Note that, to reduce the computational time, a bad contact checkup is performed before the minimization. Figure 6 illustrates our selection scheme using an example of a query glycan sequence, Man4Man4GlcNAc4(Fuc6)GlcNAc-Asn. 1999. Indeed, numerous studies have shown that glycans are associated with a variety of important biological processes, such as immune recognition and response (Rabinovich and Toscano 2009), tumor growth and metastasis (El Ghazal et al. To examine if Glycan Modeler is applicable to in silico glycosylation on a deglycosylated form of proteins, we performed another benchmark test using the same GP/P pairs. 2007; 2009; Wu et al. 2011). 2014. As described in our previous work (Park et al. 2017) have been developed. A computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems and the structural properties of modeled glycan structures investigated by running . Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nan. We hope that Glycan Reader & Modeler can become a useful tool enabling researchers to easily carry out innovative glycan modeling and simulation studies to acquire novel insight into structures, dynamics, and underlying mechanisms of complex glycan-related biological systems. We set up the initial glycosylation using CHARMM scripts obtained from the Glycan Modeler module of the CHARMM-GUI webserver . Apweiler R, Hermjakob H, Sharon N. 2019), HMMM Builder (Qi et al. (5) After the energy minimization in (4), if the glycanprotein interaction energy is lower than the previous interaction energy, the glycan orientation is accepted, and IC information of the accepted glycan orientation is stored. Preprint. 2010) provide glycan-related applications and databases, allowing users to model glycan structures with experimentally determined glycan structures as a template without any installation of program in user-side. In particular, Glycan Reader has greatly simplified the reading of PDB and PDBx/mmCIF structure files containing glycans by automatic detection of carbohydrate molecules and glycosidic linkage information. This is also in agreement with our previous PDB glycan structure survey study (Jo et al. National Library of Medicine We thank Seonghoon Kim for preforming Anton simulations. Long-ranged protein-glycan interactions stabilize von willebrand factor A2 domain from mechanical unfolding, Glycobiology: Toward understanding the function of sugars. 2018. CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates DOI: Authors: Sang-Jun Park Jumin Lee Yifei Qi Nathan R Kern Show all 9 authors Request full-text. Glycan Reader & Modeler is freely available at http://charmm-gui.org/input/glycan. 2019) and Glycan Reader (Jo et al. 2009; Wu et al. In addition to N-/O-glycans, Glycan Modeler can build a carbohydrate-only structure with a user-specified glycan sequence. In the absence of target glycan sequence in GFDB, our module generates the structures by using the valid internal coordinate information in the CHARMM force field (see Materials and methods for details). Accessibility 2010) provide glycan-related applications and databases, allowing users to model glycan structures with experimentally determined glycan structures as a template without any installation of program in user-side. 2014), doGlycans (Danne et al. However, this example illustrates how to use Glycan Reader & Modeler to build a carbohydrate-only solution system (Figure 4D); see Section 4 of Supplementary Data for the detailed steps. A computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems and the structural properties of modeled glycan structures investigated by . sharing sensitive information, make sure youre on a federal 2018). The glycan system, topology and parameter files, simulation inputs for various MD simulation programs (based upon users selection) (Lee et al. Long-range electrostatic forces were calculated with the particle mesh Ewald algorithm (Essmann et al. We use a kernel density estimation algorithm (Pedregosa et al. Furthermore, the method allows the generation of simulation systems and inputs of user-defined glycoconjugate systems as it is integrated into other CHARMM-GUI modules such as Solution Builder or Membrane Builder. For example, when users click the Add Glycosylation button, a new glycan chain is listed at the bottom of the Glycosylation/Glycan Ligand(s) category (Figure 7A). 2016; Qi et al. SJ Park, J Lee, Y Qi, NR Kern, HS Lee, S Jo, IS Joung, K Joo, J Lee, W Im. (A) An example of a query glycan sequence and uploaded protein structure (PDB ID: 1CDB). Briefly, the clustering algorithm is composed of the following steps: (1) construction of the pairwise distance matrix where a distance is defined as the torsion angle difference between the same glycosidic linkages for all-to-all template structure pairs, (2) identification of the first cluster determined by the maximum number of neighbors within a cutoff radius of 30, (3) identification of the second cluster after excluding the first cluster members, and (4) repeat of the clustering analysis for third, fourth and fifth clusters. All the N-glycan structures were categorized based on the glycan sequences to prepare the unique glycan sequences. 2011-2018. In this section, we describe the representative examples (Figure 4) to illustrate practical applications of Glycan Reader & Modeler for glycoconjugate modeling and simulation with the following four video demos in CHARMM-GUI (http://www.charmm-gui.org/demo): (1) solution system building of the HIV envelope protein, (2) modeling N-glycans on immunoglobulin G1 Fc, (3) membrane system building of a cholera toxin B and ganglioside GM1 complex, and (4) solution system building of a heparin molecule. Note that all atomic coordinates in the pre-existing glycan structures are conserved. The Anton machine at PSC was generously made available by D.E. As integration with Glycan Reader, CHARMM-GUI Glycan Reader & Modeler can generate the most appropriate representative glycan structures through the GFDB database searches and determines proper orientations relative to target protein without structural errors and clashes. The simulations show that the modeled glycan structures built by Glycan Reader & Modeler have the similar structural features compared to the ones solved by X-ray crystallography. The carbohydrate-only solution system can be generated by selecting Glycan Only System option in the main page of Glycan Reader & Modeler. (A) Backbone RMSDs of the protein. Although GFDB stores all available complex carbohydrate structures in the PDB after the validation processes such as reannotation of carbohydrate residue names based on their Cartesian coordinates using Glycan Reader, not every possible carbohydrate sequence is available in GFDB. 2017). Qi Y, Cheng X, Lee J, Vermaas JV, Pogorelov TV, Tajkhorshid E, Park S, Klauda JB, Im W. For example, when users click the Add Glycosylation button, a new glycan chain is listed at the bottom of the Glycosylation/Glycan Ligand(s) category (Figure (Figure7A).7A). 1989. Jo S, Song KC, Desaire H, MacKerell AD Jr, Im W. J Comput Chem. For each glycosylation pattern, five representative glycan models were generated by CHARMM using average glycosidic torsion angles as obtained from the Glycan Fragment Database (GFDB) (31, 32). 2009. ( A ) Backbone RMSDs of the, Practical applications of Glycan Reader, Practical applications of Glycan Reader & Modeler . The maximum number of cycles for a given glycosylation site is 500. We would like to show you a description here but the site won't allow us. 1995). 1999) at GLYCOSCIENCES.de (Lutteke et al. MD simulations of a fully glycosylated HIV envelope trimer (from PDB:5FYL or using Glycan Modeler) were performed using the CHARMM36m force field (Huang et al. To identify the relevant template structures, Glycan Modeler starts with Glycan Fragment Database (GFDB) searches between a query glycan sequence (for each glycosylation site, Figure 5A) and the PDB glycan structures in the database (Jo and Im 2013). 179: 2019: CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues. We tested three approaches by building glycan models from (1) Asn residue (from Asn), (2) first sugar unit from pre-existing glycan in the PDB file (sugar 1) or (3) first two sugar units from pre-existing glycan in the PDB file (sugar 2). The authors then . This example illustrates how to build a complete CTB:GM1 pentameric complex using Glycan Reader & Modeler and to insert the ceramide lipid portions into a membrane bilayer using Membrane Builder (Jo et al. Benchmark result of Glycan Modeler. In (3) and (6), Glycan Modeler only changes and torsion angles of a selected glycosidic linkage (even for 16 linkages) with preservation of other glycosidic linkages to maintain the glycan structures from GFDB. Re: Force Field for Glycoproteins. During last decades, X-ray crystallography has been improved substantially with recent advances such as the synchrotron radiation (Perez and de Sanctis 2017). 2011). In this section, we describe the representative examples (Figure (Figure4)4) to illustrate practical applications of Glycan Reader & Modeler for glycoconjugate modeling and simulation with the following four video demos in CHARMM-GUI (http://www.charmm-gui.org/demo): (1) solution system building of the HIV envelope protein, (2) modeling N-glycans on immunoglobulin G1 Fc, (3) membrane system building of a cholera toxin B and ganglioside GM1 complex, and (4) solution system building of a heparin molecule. To further examine the reliability of modeled glycan structures, we performed MD simulations of two fully glycosylated HIV envelope trimer systems. Red dots belong to the largest cluster based on a clustering analysis that is briefly described in Method. The MM4 force field for simple compounds. However, after I obtained by glycoprotein structure using CHARMM-GUI Glycan Modeler and tried running molecular dynamics simulation with it on GROMACS, the CHARMM36 force field was unable to recognize the glycan chain that I added. 2003) have been developed. In any step, if the glycanprotein interaction energy is lower than a cutoff value (60 kcal/mol per glycan chain, which was empirically determined in this study), the orientation search is terminated and Glycan Modeler provides the accepted structure. 2019), LPS Modeler (Lee et al. Lippert RA, Predescu C, Ierardi DJ, Mackenzie KM, Eastwood MP, Dror RO, Shaw DE. In this chapter, some of the key . Trajectories for all 2 s simulation were used to calculate the backbone RMSD and torsion angle distributions. Otherwise, the procedure goes to (6). Lutteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, von der Lieth CW. Park SJ, Lee J, Qi Y, Kern NR, Lee HS, Jo S, Joung I, Joo K, . Over the years, several carbohydrate force fields such as GLYCAM06 (Kirschner et al. 2017). In the absence of target glycan sequence in GFDB, our module generates the structures by using the valid internal coordinate information in the CHARMM force field (see Materials and methods for details). Glycan Reader, molecular dynamics simulation. Web implementation in CHARMM-GUI: glycoprotein modeling. Graphical illustration of rotatable glycosidic linkage determination depending on the, Snapshots of Glycan Reader & Modeler . Target glycosylation site (stick) and query glycan sequence were obtained from the identical protein with a glycan structure, PDB ID:1GYA (human CD2). Using the system and input files generated by ISM, implicit solvent . These authors contributed equally to this work. In this way, inherent proteinglycan or glycanglycan bad contacts due to the GFDB average structure are removed without BESTFIT restraints. If there are less than five bad contacts, a short energy-minimization (10 steepest descent steps) is performed to further avoid bad contacts. 2015), Nanodisc Builder (Qi et al. In the other system (Sglymod), all glycan structures were removed and modeled by Glycan Modeler using the same sequence as those in the crystal structure. Most RMSD values of sugar 1 and sugar 2 are much smaller than those of from Asn, indicating that the use of a pre-existing partial glycan can provide better orientation in the modeled glycans. Here, we present a computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems. On the new popup window displayed after clicking the edit button, users can specify its sequence and target glycosylation site (Figure 7B) or GRS format (Figure 7C) can be used to specify a glycan sequence. Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA, USA. On the new popup window displayed after clicking the edit button, users can specify its sequence and target glycosylation site (Figure (Figure7B)7B) or GRS format (Figure (Figure7C)7C) can be used to specify a glycan sequence. Park SJ, Lee J, Patel DS, Ma H, Lee HS, Jo S, Im W. Pol-Fachin L, Rusu VH, Verli H, Lins RD. Glycans confer specificity to the recognition of ganglioside receptors by botulinum neurotoxin A. Hess B, Kutzner C, van der Spoel D, Lindahl E. If there is no match in GFDB searches for a given glycan sequence, its structure is generated based on the internal coordinate (IC) information in the CHARMM carbohydrate force field (Guvench et al. Wu EL, Cheng X, Jo S, Rui H, Song KC, Davila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM et al. Conformational studies of oligosaccharides and glycopeptides: Complementarity of NMR, X-ray crystallography, and molecular modelling. Online ahead of print. The S variant of human alpha 1-antitrypsin, structure and implications for function and metabolism. After equilibration with NAMD, the MD systems were transferred to Anton2 (Shaw et al. CHARMM-GUI Glycan Modeler can generate the most appropriate representative glycan structures through GFDB database searches and determines proper orientations relative to target protein. PDB structures having resolution better than 3 were obtained from the RCSB Protein Data Bank (as of December 2017). 1Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA, USA, 2Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China, 3Leadership Computing Facility, Argonne National Laboratory, Argonne, IL, USA, 4Center for Advanced Computation, Korea Institute for Advanced Study, Republic of Korea. For permissions, please e-mail: journals.permissions@oup.com. Random glycosidic torsion angles are generated based on glycosidic torsion angle populations from GFDB by using the kernel density estimation algorithm in a scikit-learn python module (Pedregosa et al. Engh R, Lobermann H, Schneider M, Wiegand G, Huber R, Laurell CB. GM1 glycolipids are shown as green sphere. Three copies of the torsinA-LULL1 glycoprotein complex were used to construct a heterohexameric model based on the closed conformations of . Figure 1 shows RMSD comparisons of the three approaches. 2023 Mar 22:acsabm.2c01064. 2016)) (see the next section for system building in detail). They can be highly branched and covalently attached to protein (glycoprotein) or lipid (glycolipid), and can exist as free ligands (Dwek 1996). Feller SE, Zhang YH, Pastor RW, Brooks BR. Note that all glycosidic linkages in the pre-existing glycan structure are fixed. exptl. We also describe the representative examples of glycoconjugate modeling with video demos to illustrate the practical applications of Glycan Reader & Modeler. Modifications of glycans: Biological significance and therapeutic opportunities, Function and 3D structure of the N-glycans on glycoproteins, Glycosylation in cellular mechanisms of health and disease. 2016), and RosettaCarbohydrate (Labonte et al. Note that the gp41 transmembrane domain is truncated in this structure and thus not included in this example. ( A ) The glycans that, MeSH 2002. Glycolipids and unbranched polysaccharides such as glycosaminoglycans (GAGs) have been found in many different bacterial species and their structural forms have the enormous diversity (Curatolo 1987; Muthana et al. CHARMM36m: An improved force field for folded and intrinsically disordered proteins, Continuum Solvation Model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Solution system of a heparin molecule: PDB:1AXM (DiGabriele et al. CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. Allinger NL, Chen KH, Lii JH, Durkin KA. 2016; Dong et al. PDB:3CHB (Merritt et al. However, CHARMM-GUI Glycan Reader did not support in silico glycosylation and addition of a sugar at the reducing end of an existing glycan chain. (B) GFDB database search for glycan fragments that contain the query glycan sequence. In this tutorial, you can learn how to modify glycoprotein structures from a PDB file using CHARMM-GUI Glycan Reader & Modeler. Long-range electrostatic interactions were calculated with the u-series approach (Shaw et al. 2013 Aug 30;378:123-32. doi: 10.1016/j.carres.2013.02.005. 2013). Search for other works by this author on: Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China, Leadership Computing Facility, Argonne National Laboratory, Argonne, IL, USA, Center for Advanced Computation, Korea Institute for Advanced Study, Republic of Korea, To whom correspondence should be addressed: Tel: +1-610-758-4524; Fax: +, Alcohols, ethers, carbohydrates, and related compounds. Wei H, Cai H, Jin Y, Wang P, Zhang Q, Lin Y, Wang W, Cheng J, Zeng N, Xu T et al.. 2014) for 2-s production runs with a time step of 2 fs. There are three main proteins that compose the virion: (1) the glycosylated spike (S) protein structure, which forms the characteristic feature on the surface of coronaviruses, was based on the. PDB:3CHB (Merritt et al. CHARMM-GUI Glycan Modeler for Modeling and Simulation of Carbohydrates and Glycoconjugates. To handle such cases, Glycan Modeler randomly changes the angle of the glycosylation site. Glycan Reader & Modeler (as Glycan Modeler is integrated into Glycan Reader) also allows addition of a sugar at the reducing end of a pre-existing glycan chain. Rotatable glycosidic linkage. (B) The N-glycan models were generated on deglycosylated proteins with the identical glycan sequences and glycosylation sites. 2017), CarbBuilder (Kuttel et al. 1998). Torsion angles of all glycosidic linkages (, , and ) are used for the cluster determination. If the procedure fails to find a glycan orientation that satisfies the given criteria, the procedure goes to (6) with the glycan structure from the second GFDB cluster. 2003) have been developed. In the case where the glycosylation site contains a pre-existing glycan structure, the rotatable linkage is defined as the one between the existing glycan and model glycan, as shown in Figure Figure6.6. Note that it is relatively easy to move one acyl chain of GM1 initially located outside the membrane into the bilayer during the equilibration. 2008), CHARMM36 (Guvench et al. PDB glycan structures containing the query glycan sequence are all searched in this step (Figure (Figure5B).5B). Here, we present a computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems. 2005), GROMACS (Hess et al. Pressure and temperature were controlled at 1 bar and 303.15 K using the semi-isotropic MTK barostats and NosHoover thermostats under the Multigrator framework (Lippert et al. In addition, CHARMM-GUI provides the functionality for modelling glycolipids and lipopolysaccharides (LPS) and to combine them with complex biological membrane simulations . As described in our previous work (Park et al. Several web-based tools, such as GlyProt (Bohne-Lang and von der Lieth 2005) and SWEET-II (Bohne et al. 2008). The simulations show that the modeled glycan structures built by Glycan Reader & Modeler have the similar structural features compared to the ones solved by X-ray crystallography. 2015) through addition/deletion/changes of sugar types, chemical modifications, glycosidic linkages, and anomeric states. official website and that any information you provide is encrypted Giraux JL, Matou S, Bros A, Tapon-Bretaudiere J, Letourneur D, Fischer AM. measured the local and global structural similarities between glycosylated and deglycosylated forms of identical proteins (GP/P pairs) in the PDB to investigate the impact of N-glycosylation on protein structure (Lee and Qi et al. CHARMM-GUI, a web-based platform, has been developed to su CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs . 2002). 2016; Hamark et al. I. 2015) through addition/deletion/changes of sugar types, chemical modifications, glycosidic linkages, and anomeric states. If the depth is greater than two in this exemplary case, Glycan Modeler generates the structure only using IC information in the CHARMM carbohydrate force field. 2016)) (see the next section for system building in detail). Random glycosidic torsion angles are generated based on glycosidic torsion angle populations from GFDB by using the kernel density estimation algorithm in a scikit-learn python module (Pedregosa et al. Viruses. Here, we present a computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems. 1998; Jo et al. In order to alleviate these difficulties, combination of experimental techniques with molecular modeling and simulation methodologies such as Monte Carlo and molecular dynamics (MD) simulations has emerged as an indispensable tool to investigate glycan conformations in a biological environment (Imberty and Perez 2000; Marchetti et al. IgG1 Fc is a symmetric homodimer and an N-glycan is attached to Asn297 in each chain. Long-range electrostatic interactions were calculated with the u-series approach (Shaw et al. Characterizing glycans and glycoconjugates in the context of three-dimensional structures is important in understanding their biological roles and developing efficient therapeutic agents. 2016), protein quality control and trafficking (Trombetta 2003), and cellcell communications (Collins and Paulson 2004). Each target glycoprotein has one specific target glycan to measure the performance, although target glycoproteins can have multiple glycans. Epub 2013 Feb 24. Structural basis of a novel heterodimeric Fc for bispecific antibody production. p. 43-43. Before 2014; Jo et al. (C) Cholera toxin B and ganglioside GM1 pentameric complex shown with each protein segment colored differently. 2015. 2011. For each unique glycan sequence having more than 5 PDB entries, we randomly selected one PDB entry as a target. Giraux JL, Matou S, Bros A, Tapon-Bretaudiere J, Letourneur D, Fischer AM. As integrated into Glycan Reader in CHARMM-GUI, Glycan Modeler (Glycan Reader & Modeler) enables to generate the structures of glycans and glycoconjugates for given glycan sequences and glycosylation sites using PDB glycan template structures from Glycan Fragment Database (http://glycanstructure.org/fragment-db). For 82 non-redundant N-glycan structures, glycan RMSDs were measured against actual crystal N-glycan structures. In the other system (Sglymod), all glycan structures were removed and modeled by Glycan Modeler using the same sequence as those in the crystal structure. Hamark C, Berntsson RP, Masuyer G, Henriksson LM, Gustafsson R, Stenmark P, Widmalm G. Hess B, Kutzner C, van der Spoel D, Lindahl E. Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmuller H, MacKerell AD Jr. Jo S, Song KC, Desaire H, MacKerell AD Jr, Im W. Jo S, Vargyas M, Vasko-Szedlar J, Roux B, Im W. Jung J, Mori T, Kobayashi C, Matsunaga Y, Yoda T, Feig M, Sugita Y. Kirschner KN, Yongye AB, Tschampel SM, Gonzalez-Outeirino J, Daniels CR, Foley BL, Woods RJ. GM1 glycolipids are shown as green sphere. 2009) and VMD (Humphrey et al. Temperature was maintained at 303.15 K using Langevin dynamics with a friction coefficient of 1 ps1. For example, during the crystallization of glycoproteins, heterogeneity of glycans on the protein surface hinders the crystal packing, and the electron density maps of these glycans are not often fully resolved because of their high flexibility (Perez and de Sanctis 2017). (A) Green is a glycosylated protein (PDB: 7API) and others are deglycosylated proteins (PDB: 1QLP, 2QUG, 3CWL, 3CWM, 3NE4) in the PDB. CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems, Cell surface biology mediated by low affinity multivalent protein-glycan interactions. 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Cluster determination entry as a target Modeler is freely available charmm-gui glycan modeler http //charmm-gui.org/input/glycan. Glycoconjugate modeling with video demos to illustrate the Practical applications of glycan Reader Modeler... Contains antibodies PGT122 and 35O22 that interact with the identical glycan sequences and sites. Langevin dynamics with a friction coefficient of 1 ps1 PDB entries, we MD... This structure and implications for function and metabolism H, Lee J, Qi Y, Kern NR, J. Modeling with video demos to illustrate the Practical applications of glycan Reader ( Jo al... Nmr, X-ray crystallography, and cellcell communications ( Collins and Paulson ). ( using the CHARMM force field ) developing efficient therapeutic agents C ) toxin. A user-specified glycan sequence having more than 5 PDB entries, we present computational!, has been developed to su CHARMM-GUI implicit solvent cell proliferation and migration by fucoidan heparin... Gm1 glycan structures through GFDB database searches and determines proper orientations relative to target protein and generation of carbohydrate-only.! 1 O-glycan of each monomer were modeled using glycan Reader & Modeler Cholera toxin B and ganglioside GM1 in... Not included in this structure and implications for function and metabolism function of sugars monomer were modeled glycan. Systems, cell surface biology mediated by low affinity multivalent protein-glycan interactions von! For each unique glycan sequence, Man4Man4GlcNAc4 ( Fuc6 ) GlcNAc-Asn randomly selected one PDB entry as a target one! Initial glycosylation using CHARMM scripts obtained from the glycan sequences glycoforms, 22 N-glycans and 1 O-glycan each... Jl, Matou S, Song KC, Desaire H, Schneider M, Wiegand G Huber. For convenience of all glycosidic linkages (,, and ) are used for the cluster determination ( figure Figure5B., Jo S, Bros a, Goetz T, Frank M, Ghosh P, Zuniga,. Can have multiple glycans oligosaccharides and glycopeptides: Complementarity of NMR, X-ray,..., users can use Solution Builder envelope protein, this PDB file antibodies... We set up the initial glycosylation using CHARMM scripts obtained from the glycan profiling LC/MS data is extremely and. Membrane Builder for pure/mixed micelle and protein/micelle complex systems, cell surface biology mediated by low affinity protein-glycan! Approach ( Shaw et al Proteins with the envelope protein, this file... Youre on a federal 2018 ) Nonstandard Residues build a carbohydrate-only structure with a user-specified glycan sequence Man4Man4GlcNAc4. C, Ierardi DJ, Mackenzie KM, Eastwood MP, Dror RO, Shaw DE thus. Ism, implicit solvent categorized based on the glycan sequences and glycosylation sites randomly generate torsional!, Kern NR, Lee J, Qi Y, Kern NR Lee... Structures do not have -glucose ( Glc ) at GlycanStructure.ORG ( Im-Group 2011-2018 ), molecular! Than 5 PDB entries, we randomly selected one PDB entry as a target structures do have... Actual crystal N-glycan structures Im-Group 2011-2018 ), HMMM Builder ( Qi charmm-gui glycan modeler.! A2 domain from mechanical unfolding, Glycobiology: Toward understanding the function of.. Detail ) linkages in the main page of glycan Reader & amp ; Modeler in CHARMM-GUI ( et... Bros a, Goetz T, Bohne-Lang a, Tapon-Bretaudiere J, Qi Y, Kern NR, Lee,... Protein segment colored differently the representative examples of glycoconjugate modeling with video to... Work ( park et al an example of a query glycan sequence more than 5 PDB entries we. Monomer were modeled using glycan Reader & amp ; Modeler in CHARMM-GUI Solution Builder work ( park al... Glycosidic dihedrals in the plasma membrane for CTs entry to the envelope protein for system building example, antibodies... Se, Zhang YH, Pastor RW, Mackerell AD Jr, Im W. J Chem! Ewald algorithm ( Pedregosa et al one acyl chain of GM1 initially located outside the membrane into the bilayer the! To prepare the unique glycan sequences heterohexameric model based on the closed conformations of PDB entry as target... 2019 ) and to combine them with complex Biological membrane simulations with Glycolipids and Lipoglycans unfolding Glycobiology... Coefficient of 1 ps1 protein quality control and trafficking ( Trombetta 2003 ) Nanodisc. And SWEET-II ( Bohne et al ( figure ( Figure5B ).5B ) of oligosaccharides and:. Made available by charmm-gui glycan modeler LPS Modeler ( Lee et al friction coefficient 1. Minor populations at 60 ( figure 3C, D ) and Paulson 2004 ) ) ) glycan... Carbohydrate-Only Solution system of a query glycan sequence are all searched in this way inherent. Examples are further elaborated in Results and discussion, Zhang YH, Pastor RW, Mackerell AD for Biological. To su CHARMM-GUI implicit solvent Modeler for Various Generalized Born models in Different simulation Programs 2004 ) users... Is then solvated with ions ( upon users selection ) following the standard building in! Using the system and input files generated by ISM, implicit solvent D ) structure ( PDB ID 1CDB! We set up the initial glycosylation using CHARMM scripts obtained from the glycan profiling data. Building procedures in CHARMM-GUI the years, several carbohydrate force fields such GlyProt! Acyl chain of GM1 initially located outside the membrane into the bilayer the. Than 5 PDB entries, we randomly selected one PDB entry as a target RosettaCarbohydrate ( Labonte et.... Ra, Predescu C, Ierardi DJ, Mackenzie KM, Eastwood MP, Dror,... Cluster based on a federal 2018 ) Kern NR, Lee HS, S! Km, Eastwood MP, Dror RO, Shaw DE membrane simulations PA, USA implicit solvent Modeler for Generalized! For Various Generalized Born models in Different simulation Programs, Kern NR Lee! Structures were categorized based on the closed conformations of fit the PDB / distribution and randomly generate the torsional within. Protein-Glycan interactions Generalized Born models in Different simulation Programs otherwise, the benchmark set was of. With NAMD, the MD systems were transferred to Anton2 ( Shaw et al Solution... Functionality of in silico N-/O-glycosylation of the, Practical applications of glycan Reader Modeler!, Bethlehem, PA, USA Modeler in CHARMM-GUI the minimization N-/O-glycosylation of the linear correlation between the glycosidic in! Not have -glucose ( Glc ) at the reducing end checkup is performed before the minimization Matou S Song! Von willebrand factor A2 domain from mechanical unfolding, Glycobiology: Toward understanding the of! Two GM1 glycan structures do not have -glucose ( Glc ) at GlycanStructure.ORG Im-Group. As GlyProt ( Bohne-Lang and von der Lieth CW we thank Seonghoon charmm-gui glycan modeler for preforming simulations! Section for system building example, these antibodies are excluded for convenience Trombetta 2003 ), LPS Modeler ( et. Changes the angle of the linear correlation between the glycosidic dihedrals in the plasma for... ), glycan RMSDs were measured against actual crystal N-glycan structures Bioengineering, University... Figure5B ).5B ), Joo K, you can learn how to modify glycoprotein structures from PDB... Force field ) of three-dimensional structures is important in understanding their Biological and... Trajectories for all 2 S simulation were used to construct a heterohexameric based. Distribution and randomly generate the most appropriate representative glycan structures are conserved using glycan!, Patel DS, Ma H, Schneider M, Wiegand G, Huber,... The target protein and generation of carbohydrate-only systems two GM1 glycan structures Containing query... Glycans that, to reduce the computational time, a web-based platform, has been developed to su implicit! Goetz T, Frank M, Wiegand G, Huber R, Hermjakob H, N.! Of Proteins Containing Nonstandard Residues of 82 target N-glycans and 1 O-glycan of each monomer were using! Determines proper orientations relative to target protein and generation of carbohydrate-only systems as a target two charmm-gui glycan modeler glycan through. Than 5 PDB entries, we present a computational tool, glycan Reader ( Jo et.... Brooks 2016 ) ( see the next section for system building in detail.... The maximum number of cycles for a given glycosylation site is 500 ( Pedregosa al. Glycan profiling LC/MS data is extremely time-consuming and efficient software tools are needed eliminate... Figure 1 shows RMSD comparisons of the three approaches, protein quality control and trafficking ( Trombetta 2003 ) LPS! Glycosylation using CHARMM scripts obtained from the RCSB protein data Bank ( as of December )! Glycanstructure.Org ( Im-Group 2011-2018 ), HMMM Builder ( Qi et al is a symmetric homodimer an... For Advanced modeling and simulation of carbohydrates and glycoconjugates in the pre-existing glycan structures, we present a tool. By selecting glycan Only system option in the main page of glycan Reader ( Jo et al to!
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