SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged due to glycan interaction

Huang, Yihan; Harris, Bradley S.; Minami, Shiaki A.; Jung, Seongwon; Shah, Priya S.; Nandi, Somen; McDonald, Karen A.; Faller, Roland

doi:10.1016/j.bpj.2021.12.002

Title: SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged due to glycan interaction

Journal Article · 01 January 2022 · Biophysical Journal

DOI: https://doi.org/10.1016/j.bpj.2021.12.002 · OSTI ID:1834646

Huang, Yihan; Harris, Bradley S.;

; Jung, Seongwon;

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Sponsoring Organization:: USDOE

OSTI ID:: 1834646

Journal Information:: Biophysical Journal, Journal Name: Biophysical Journal Journal Issue: 1 Vol. 121; ISSN 0006-3495

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (54)

LINCS: A linear constraint solver for molecular simulations Hess, Berk; Bekker, Henk; Berendsen, Herman J. C. Journal of Computational Chemistry, Vol. 18, Issue 12 https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H	journal	September 1997
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models Miyamoto, Shuichi; Kollman, Peter A. Journal of Computational Chemistry, Vol. 13, Issue 8 https://doi.org/10.1002/jcc.540130805	journal	October 1992
Composition and divergence of coronavirus spike proteins and host ACE2 receptors predict potential intermediate hosts of SARS‐CoV‐2 Liu, Zhixin; Xiao, Xiao; Wei, Xiuli Journal of Medical Virology, Vol. 92, Issue 6 https://doi.org/10.1002/jmv.25726	journal	March 2020
Viral glycoproteins: biological role and application in diagnosis Banerjee, Nilotpal; Mukhopadhyay, Sumi VirusDisease, Vol. 27, Issue 1 https://doi.org/10.1007/s13337-015-0293-5	journal	January 2016
Force Fields for Protein Simulations Ponder, Jay W.; Case, David A. Protein Simulations https://doi.org/10.1016/S0065-3233(03)66002-X	book	January 2003
Determining kinetics and affinities of protein interactions using a parallel real-time label-free biosensor, the Octet Abdiche, Yasmina; Malashock, Dan; Pinkerton, Alanna Analytical Biochemistry, Vol. 377, Issue 2 https://doi.org/10.1016/j.ab.2008.03.035	journal	June 2008
Exploitation of glycosylation in enveloped virus pathobiology Watanabe, Yasunori; Bowden, Thomas A.; Wilson, Ian A. Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1863, Issue 10 https://doi.org/10.1016/j.bbagen.2019.05.012	journal	October 2019
Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interaction Cao, Wenpeng; Dong, Chuqiao; Kim, Seonghan Biophysical Journal, Vol. 120, Issue 6 https://doi.org/10.1016/j.bpj.2021.02.007	journal	March 2021
Glycosylation in Cellular Mechanisms of Health and Disease Ohtsubo, Kazuaki; Marth, Jamey D. Cell, Vol. 126, Issue 5 https://doi.org/10.1016/j.cell.2006.08.019	journal	September 2006
Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein Walls, Alexandra C.; Park, Young-Jun; Tortorici, M. Alejandra Cell, Vol. 181, Issue 2 https://doi.org/10.1016/j.cell.2020.02.058	journal	April 2020
Virus recognition of glycan receptors Thompson, Andrew J.; de Vries, Robert P.; Paulson, James C. Current Opinion in Virology, Vol. 34 https://doi.org/10.1016/j.coviro.2019.01.004	journal	February 2019
GROMACS implementation of free energy calculations with non-pairwise Variationally derived Intermediates Reinhardt, Martin; Grubmüller, Helmut Computer Physics Communications, Vol. 264 https://doi.org/10.1016/j.cpc.2021.107931	journal	July 2021
The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization Bayarri-Olmos, Rafael; Rosbjerg, Anne; Johnsen, Laust Bruun Journal of Biological Chemistry, Vol. 296 https://doi.org/10.1016/j.jbc.2021.100536	journal	January 2021
Structural zinc binding sites shaped for greater works: Structure-function relations in classical zinc finger, hook and clasp domains Padjasek, Michał; Kocyła, Anna; Kluska, Katarzyna Journal of Inorganic Biochemistry, Vol. 204 https://doi.org/10.1016/j.jinorgbio.2019.110955	journal	March 2020
Subtle Influence of ACE2 Glycan Processing on SARS-CoV-2 Recognition Allen, Joel D.; Watanabe, Yasunori; Chawla, Himanshi Journal of Molecular Biology, Vol. 433, Issue 4 https://doi.org/10.1016/j.jmb.2020.166762	journal	February 2021
Virtual screening and molecular dynamics study of approved drugs as inhibitors of spike protein S1 domain and ACE2 interaction in SARS-CoV-2 Prajapat, Manisha; Shekhar, Nishant; Sarma, Phulen Journal of Molecular Graphics and Modelling, Vol. 101 https://doi.org/10.1016/j.jmgm.2020.107716	journal	December 2020
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
Sticky fingers: zinc-fingers as protein-recognition motifs Gamsjaeger, R.; Liew, C.; Loughlin, F. Trends in Biochemical Sciences, Vol. 32, Issue 2 https://doi.org/10.1016/j.tibs.2006.12.007	journal	February 2007
Biopharmaceutical production in plants: problems, solutions and opportunities Gomord, Véronique; Chamberlain, Paul; Jefferis, Roy Trends in Biotechnology, Vol. 23, Issue 11 https://doi.org/10.1016/j.tibtech.2005.09.003	journal	November 2005
Virus glycosylation: role in virulence and immune interactions Vigerust, David J.; Shepherd, Virginia L. Trends in Microbiology, Vol. 15, Issue 5 https://doi.org/10.1016/j.tim.2007.03.003	journal	May 2007
Smoothing and Differentiation of Data by Simplified Least Squares Procedures. Savitzky, Abraham.; Golay, M. J. E. Analytical Chemistry, Vol. 36, Issue 8 https://doi.org/10.1021/ac60214a047	journal	July 1964
N- and O-Glycosylation of the SARS-CoV-2 Spike Protein Sanda, Miloslav; Morrison, Lindsay; Goldman, Radoslav Analytical Chemistry, Vol. 93, Issue 4 https://doi.org/10.1021/acs.analchem.0c03173	journal	January 2021
Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane Choi, Yeol Kyo; Cao, Yiwei; Frank, Martin Journal of Chemical Theory and Computation, Vol. 17, Issue 4 https://doi.org/10.1021/acs.jctc.0c01144	journal	March 2021
Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane Woo, Hyeonuk; Park, Sang-Jun; Choi, Yeol Kyo The Journal of Physical Chemistry B, Vol. 124, Issue 33 https://doi.org/10.1021/acs.jpcb.0c04553	journal	June 2020
Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein Casalino, Lorenzo; Gaieb, Zied; Goldsmith, Jory A. ACS Central Science, Vol. 6, Issue 10 https://doi.org/10.1021/acscentsci.0c01056	journal	September 2020
Glycosylation of SARS-CoV-2 Steers Evolutionary Outcomes in the Postvaccination Phase Fernández, Ariel ACS Pharmacology & Translational Science, Vol. 4, Issue 1 https://doi.org/10.1021/acsptsci.1c00015	journal	January 2021
The basis of a more contagious 501Y.V1 variant of SARS-CoV-2 Liu, Haolin; Zhang, Qianqian; Wei, Pengcheng Cell Research, Vol. 31, Issue 6 https://doi.org/10.1038/s41422-021-00496-8	journal	April 2021
Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor Yang, Jinsung; Petitjean, Simon J. L.; Koehler, Melanie Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-18319-6	journal	September 2020
SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity Ozono, Seiya; Zhang, Yanzhao; Ode, Hirotaka Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21118-2	journal	February 2021
Structural basis of receptor recognition by SARS-CoV-2 Shang, Jian; Ye, Gang; Shi, Ke Nature, Vol. 581, Issue 7807 https://doi.org/10.1038/s41586-020-2179-y	journal	March 2020
The proximal origin of SARS-CoV-2 Andersen, Kristian G.; Rambaut, Andrew; Lipkin, W. Ian Nature Medicine, Vol. 26, Issue 4 https://doi.org/10.1038/s41591-020-0820-9	journal	March 2020
N-Glycosylation can selectively block or foster different receptor–ligand binding modes Vuorio, Joni; Škerlová, Jana; Fábry, Milan Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-021-84569-z	journal	March 2021
Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study Lee, Hui Sun; Qi, Yifei; Im, Wonpil Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep08926	journal	March 2015
Canonical sampling through velocity rescaling Bussi, Giovanni; Donadio, Davide; Parrinello, Michele The Journal of Chemical Physics, Vol. 126, Issue 1 https://doi.org/10.1063/1.2408420	journal	January 2007
Strain fluctuations and elastic constants Parrinello, M.; Rahman, A. The Journal of Chemical Physics, Vol. 76, Issue 5 https://doi.org/10.1063/1.443248	journal	March 1982
A unified formulation of the constant temperature molecular dynamics methods Nosé, Shuichi The Journal of Chemical Physics, Vol. 81, Issue 1 https://doi.org/10.1063/1.447334	journal	July 1984
Unique carbohydrate-carbohydrate interactions are required for high affinity binding between Fc RIII and antibodies lacking core fucose Ferrara, C.; Grau, S.; Jager, C. Proceedings of the National Academy of Sciences, Vol. 108, Issue 31 https://doi.org/10.1073/pnas.1108455108	journal	July 2011
Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike Mehdipour, Ahmad Reza; Hummer, Gerhard Proceedings of the National Academy of Sciences, Vol. 118, Issue 19 https://doi.org/10.1073/pnas.2100425118	journal	April 2021
ACE2 X-Ray Structures Reveal a Large Hinge-bending Motion Important for Inhibitor Binding and Catalysis Towler, Paul; Staker, Bart; Prasad, Sridhar G. Journal of Biological Chemistry, Vol. 279, Issue 17 https://doi.org/10.1074/jbc.M311191200	journal	January 2004
Global aspects of viral glycosylation Bagdonaite, Ieva; Wandall, Hans H. Glycobiology, Vol. 28, Issue 7 https://doi.org/10.1093/glycob/cwy021	journal	March 2018
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
Glycosylation in immune cell trafficking Sperandio, Markus; Gleissner, Christian A.; Ley, Klaus Immunological Reviews, Vol. 230, Issue 1 https://doi.org/10.1111/j.1600-065X.2009.00795.x	journal	July 2009
ELAM-1 mediates cell adhesion by recognition of a carbohydrate ligand, sialyl-Lex Phillips, M.; Nudelman, E.; Gaeta, F. Science, Vol. 250, Issue 4984 https://doi.org/10.1126/science.1701274	journal	November 1990
Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 Yan, Renhong; Zhang, Yuanyuan; Li, Yaning Science, Vol. 367, Issue 6485 https://doi.org/10.1126/science.abb2762	journal	March 2020
Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2 Chan, Kui K.; Dorosky, Danielle; Sharma, Preeti Science, Vol. 369, Issue 6508 https://doi.org/10.1126/science.abc0870	journal	August 2020
Kinetic Rates of Antibody Binding Correlate with Neutralization Sensitivity of Variant Simian Immunodeficiency Virus Strains Steckbeck, Jonathan D.; Orlov, Irina; Chow, Andrew Journal of Virology, Vol. 79, Issue 19 https://doi.org/10.1128/JVI.79.19.12311-12320.2005	journal	October 2005
Interaction of SARS-CoV-2 and Other Coronavirus With ACE (Angiotensin-Converting Enzyme)-2 as Their Main Receptor: Therapeutic Implications Davidson, Anne M.; Wysocki, Jan; Batlle, Daniel Hypertension, Vol. 76, Issue 5 https://doi.org/10.1161/HYPERTENSIONAHA.120.15256	journal	November 2020
Atomistic fingerprint of hyaluronan–CD44 binding Vuorio, Joni; Vattulainen, Ilpo; Martinez-Seara, Hector PLOS Computational Biology, Vol. 13, Issue 7 https://doi.org/10.1371/journal.pcbi.1005663	journal	July 2017
Generation of Biologically Active Multi-Sialylated Recombinant Human EPOFc in Plants Castilho, Alexandra; Neumann, Laura; Gattinger, Pia PLoS ONE, Vol. 8, Issue 1 https://doi.org/10.1371/journal.pone.0054836	journal	January 2013
Structural analysis of human glycoprotein butyrylcholinesterase using atomistic molecular dynamics: The importance of glycosylation site ASN241 Bernardi, Austen; Kirschner, Karl N.; Faller, Roland PLOS ONE, Vol. 12, Issue 11 https://doi.org/10.1371/journal.pone.0187994	journal	November 2017
Development and simulation of fully glycosylated molecular models of ACE2-Fc fusion proteins and their interaction with the SARS-CoV-2 spike protein binding domain Bernardi, Austen; Huang, Yihan; Harris, Bradley PLOS ONE, Vol. 15, Issue 8 https://doi.org/10.1371/journal.pone.0237295	journal	August 2020
Trafficking of endoplasmic reticulum-retained recombinant proteins is unpredictable in Arabidopsis thaliana De Meyer, Thomas; Depicker, Ann Frontiers in Plant Science, Vol. 5 https://doi.org/10.3389/fpls.2014.00473	journal	September 2014
Effects of N-Glycosylation on the Structure, Function, and Stability of a Plant-Made Fc-Fusion Anthrax Decoy Protein Xiong, Yongao; Karuppanan, Kalimuthu; Bernardi, Austen Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00768	journal	June 2019
Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2 Nguyen, Kien; Chakraborty, Srirupa; Mansbach, Rachael A. Viruses, Vol. 13, Issue 5 https://doi.org/10.3390/v13050927	journal	May 2021

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