Modelling and Simulations of Extracellular Glycoproteins.
Glycoproteins
Glycosylation
Molecular dynamics
Molecular modelling
Posttranslational modifications
Web portal CHARMM-GUI
doGlycans
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2023
2023
Historique:
entrez:
20
1
2023
pubmed:
21
1
2023
medline:
25
1
2023
Statut:
ppublish
Résumé
While the knowledge of protein structure and function has seen vast advances in previous decades, the understanding of how their posttranslational modifications, such as glycosylations, influence their structure and function remains poor. However, advances in in silico methodologies to study glycosylations in recent past have enabled us to study this and understand the role of glycosylations in protein structure and function in ways that would not be possible by conventional experimental methods. In this chapter, we will demonstrate how to leverage these methodologies to study glycoproteins and their structural and dynamic properties using molecular modelling techniques.
Identifiants
pubmed: 36662478
doi: 10.1007/978-1-0716-2946-8_21
doi:
Substances chimiques
Glycoproteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
293-313Informations de copyright
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Rao RM, Dauchez M, Baud S (2022) How molecular modelling can better broaden the understanding of glycosylations. Opinion in Structural Biology 75:102393. https://doi.org/10.1016/j.sbi.2022.102393
doi: 10.1016/j.sbi.2022.102393
Jo S, Kim T, Iyer VG, Im W (2008) CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem 29(11):1859–1865. https://doi.org/10.1002/jcc.20945
doi: 10.1002/jcc.20945
Jo S, Song KC, Desaire H, MacKerell AD, Im W (2011) Glycan reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. J Comput Chem 32(14):3135–3141. https://doi.org/10.1002/jcc.21886
doi: 10.1002/jcc.21886
Liu H, Nowak C, Andrien B, Shao M, Ponniah G, Neill A (2017) Impact of IgG fc-oligosaccharides on recombinant monoclonal antibody structure, stability, safety, and efficacy. Biotechnol Prog 33(5):1173–1181. https://doi.org/10.1002/btpr.2498
doi: 10.1002/btpr.2498
Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, MacKerell AD (2017) CHARMM36m: an improved force field for folded and intrinsically disordered proteins. Nat Methods 14(1):71–73. https://doi.org/10.1038/nmeth.4067
doi: 10.1038/nmeth.4067
Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. https://doi.org/10.1016/0010-4655(95)00042-E
doi: 10.1016/0010-4655(95)00042-E
Kutzner C, Páll S, Fechner M, Esztermann A, de Groot BL, Grubmüller H (2019) More bang for your buck: improved use of GPU nodes for GROMACS 2018. J Comput Chem 40(27):2418–2431. https://doi.org/10.1002/jcc.26011
doi: 10.1002/jcc.26011
Danne R, Poojari C, Martinez-Seara H, Rissanen S, Lolicato F, Róg T, Vattulainen I (2017) doGlycans –tools for preparing carbohydrate structures for atomistic simulations of glycoproteins, glycolipids, and carbohydrate polymers for GROMACS. J Chem Inf Model 57(10):2401–2406. https://doi.org/10.1021/acs.jcim.7b00237
doi: 10.1021/acs.jcim.7b00237
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera—a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612. https://doi.org/10.1002/jcc.20084
doi: 10.1002/jcc.20084
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38. https://doi.org/10.1016/0263-7855(96)00018-5
doi: 10.1016/0263-7855(96)00018-5
Lütteke T, Bohne-Lang A, Loss A, Goetz T, Frank M (2006) GLYCOSCIENCES.de: an internet portal to support glycomics and glycobiology research. Glycobiology 16(5). https://doi.org/10.1093/glycob/cwj049
Bohne-Lang A, Lieth C (2005) GlyProt: in silico glycosylation of proteins. Nucleic Acids Res 33:W214. https://doi.org/10.1093/nar/gki385
doi: 10.1093/nar/gki385
Bohne A, Lang E, Lieth C (1998) W3-SWEET: carbohydrate modeling by internet. J Mol Med 4:33–43. https://doi.org/10.1007/s008940050068
doi: 10.1007/s008940050068
Bohne A, Lang E, Lieth C (1999) SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides. Bioinformatics 15(9):767. https://doi.org/10.1093/bioinformatics/15.9.767
doi: 10.1093/bioinformatics/15.9.767
Daura X, Gademann K, Jaun B, Seebach D, Van Gunsteren WF, Mark AE (1999) Peptide folding: when simulation meets experiment. Angew Chem Int Ed 38(1–2):236–240
doi: 10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M
Mercadante D, Gräter F, Daday C (2018) CONAN: a tool to decode dynamical information from molecular interaction maps. Biophys J 114(6):1267–1273. https://doi.org/10.1016/j.bpj.2018.01.033
doi: 10.1016/j.bpj.2018.01.033
Hubbard SJ, Thornton JM (1993) Naccess. Computer program, Department of Biochemistry and Molecular Biology, University College London 2(1)
Miller S, Janin J, Lesk AM, Chothia C (1987) Interior and surface of monomeric proteins 196:641. https://doi.org/10.1016/0022-2836(87)90038-6
doi: 10.1016/0022-2836(87)90038-6
Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M (1995) The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J Comput Chem 16(3):273–284. https://doi.org/10.1002/jcc.540160303
doi: 10.1002/jcc.540160303