Identification of Possible Binding Modes of SARS-CoV-2 Spike -terminal Domain for Ganglioside GM1

Overview

Journal Chem Phys Lett

Date 2022 Dec 19

PMID 36532818

Authors

Tanushree Das

Chaitali Mukhopadhyay

Affiliations

Soon will be listed here.

Abstract

Coarse-grained molecular dynamics simulations of the lipid bilayer mixture of POPC and cholesterol were carried out in the presence and absence of ganglioside monosialo 1 (GM1) with N - terminal domain (NTD) of SARS-CoV-2 spike glycoprotein. The interactions of GM1 with two different NTD orientations were compared. NTD orientation I compactly bind GM1 predominantly through the sialic acid and the external galactose moieties providing more restriction to GM1 mobility whereas orientation II is more distributed on the lipid surface and due to the relaxed mobility of GM1 there, presumably, the NTD receptor penetrates more through the membrane.

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References

Monticelli L, Kandasamy S, Periole X, Larson R, Tieleman D, Marrink S . The MARTINI Coarse-Grained Force Field: Extension to Proteins. J Chem Theory Comput. 2015; 4(5):819-34. DOI: 10.1021/ct700324x. View

de Fatima Martins M, Honorio-Ferreira A, Martins P, Goncalves C . Presence of sialic acids in bronchioloalveolar cells and identification and quantification of N-acetylneuraminic and N-glycolylneuraminic acids in the lung. Acta Histochem. 2019; 121(6):712-717. DOI: 10.1016/j.acthis.2019.06.004. View

Loschwitz J, Olubiyi O, Hub J, Strodel B, Poojari C . Computer simulations of protein-membrane systems. Prog Mol Biol Transl Sci. 2020; 170:273-403. PMC: 7109768. DOI: 10.1016/bs.pmbts.2020.01.001. View

Torgersen M, Skretting G, van Deurs B, Sandvig K . Internalization of cholera toxin by different endocytic mechanisms. J Cell Sci. 2001; 114(Pt 20):3737-47. DOI: 10.1242/jcs.114.20.3737. View

Klinakis A, Cournia Z, Rampias T . N-terminal domain mutations of the spike protein are structurally implicated in epitope recognition in emerging SARS-CoV-2 strains. Comput Struct Biotechnol J. 2021; 19:5556-5567. PMC: 8489513. DOI: 10.1016/j.csbj.2021.10.004. View

Fantini J, Chahinian H, Yahi N . Synergistic antiviral effect of hydroxychloroquine and azithromycin in combination against SARS-CoV-2: What molecular dynamics studies of virus-host interactions reveal. Int J Antimicrob Agents. 2020; 56(2):106020. DOI: 10.1016/j.ijantimicag.2020.106020. View

Peters M, Barber K, Grant C . Lateral distribution of gangliosides in bilayer membranes: lipid and ionic effects. J Neurosci Res. 1984; 12(2-3):343-53. DOI: 10.1002/jnr.490120221. View

de Jong D, Lopez C, Marrink S . Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors. Faraday Discuss. 2013; 161:347-63. DOI: 10.1039/c2fd20086d. View

Villanueva R, Rouille Y, Dubuisson J . Interactions between virus proteins and host cell membranes during the viral life cycle. Int Rev Cytol. 2005; 245:171-244. PMC: 7112339. DOI: 10.1016/S0074-7696(05)45006-8. View

10.

Lopez C, Sovova Z, van Eerden F, De Vries A, Marrink S . Martini Force Field Parameters for Glycolipids. J Chem Theory Comput. 2015; 9(3):1694-708. DOI: 10.1021/ct3009655. View

11.

Bussi G, Donadio D, Parrinello M . Canonical sampling through velocity rescaling. J Chem Phys. 2007; 126(1):014101. DOI: 10.1063/1.2408420. View

12.

Marrink S, Tieleman D . Perspective on the Martini model. Chem Soc Rev. 2013; 42(16):6801-22. DOI: 10.1039/c3cs60093a. View

13.

van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark A, Berendsen H . GROMACS: fast, flexible, and free. J Comput Chem. 2005; 26(16):1701-18. DOI: 10.1002/jcc.20291. View

14.

Rawat S, Viard M, Gallo S, Blumenthal R, Puri A . Sphingolipids, cholesterol, and HIV-1: a paradigm in viral fusion. Glycoconj J. 2006; 23(3-4):189-97. DOI: 10.1007/s10719-006-7924-4. View

15.

Humphrey W, Dalke A, Schulten K . VMD: visual molecular dynamics. J Mol Graph. 1996; 14(1):33-8, 27-8. DOI: 10.1016/0263-7855(96)00018-5. View

16.

Neu U, Woellner K, Gauglitz G, Stehle T . Structural basis of GM1 ganglioside recognition by simian virus 40. Proc Natl Acad Sci U S A. 2008; 105(13):5219-24. PMC: 2278218. DOI: 10.1073/pnas.0710301105. View

17.

Lopez P, Schnaar R . Gangliosides in cell recognition and membrane protein regulation. Curr Opin Struct Biol. 2009; 19(5):549-57. PMC: 2763983. DOI: 10.1016/j.sbi.2009.06.001. View

18.

Ramstedt B, Peter Slotte J . Sphingolipids and the formation of sterol-enriched ordered membrane domains. Biochim Biophys Acta. 2006; 1758(12):1945-56. DOI: 10.1016/j.bbamem.2006.05.020. View

19.

Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang C, Pettersen E . UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol. 2011; 179(3):269-78. PMC: 3410985. DOI: 10.1016/j.jsb.2011.09.006. View

20.

Fantini J, Di Scala C, Chahinian H, Yahi N . Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection. Int J Antimicrob Agents. 2020; 55(5):105960. PMC: 7128678. DOI: 10.1016/j.ijantimicag.2020.105960. View