A molecular dynamics investigation of N-glycosylation effects on T-cell receptor kinetics

Rollins, Zachary; Harris, Bradley; George, Steven; Faller, Roland

doi:10.1080/07391102.2022.2091660

A molecular dynamics investigation of N-glycosylation effects on T-cell receptor kinetics

Journal Article · 28 June 2022 · Journal of Biomolecular Structure and Dynamics

DOI:https://doi.org/10.1080/07391102.2022.2091660· OSTI ID:2424271

Rollins, Zachary ^[1]; Harris, Bradley ^[1]; George, Steven ^[2]; Faller, Roland ^[1]

Department of Chemical Engineering, University of California, Davis, Davis, CA, USA
Department of Biomedical Engineering, University of California, Davis, Davis, CA, USA

Not provided.

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC52-07NA27344

OSTI ID:: 2424271

Journal Information:: Journal of Biomolecular Structure and Dynamics, Journal Name: Journal of Biomolecular Structure and Dynamics Journal Issue: 12 Vol. 41; ISSN 0739-1102

Publisher:: Taylor & Francis

Country of Publication:: United States

Language:: English

References (47)

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations Michaud-Agrawal, Naveen; Denning, Elizabeth J.; Woolf, Thomas B. Journal of Computational Chemistry, Vol. 32, Issue 10 https://doi.org/10.1002/jcc.21787	journal	April 2011
Relevance of glycans in the interaction between T lymphocyte and the antigen presenting cell Gómez-Henao, Wilton; Tenorio, Eda Patricia; Sanchez, Francisco Raúl Chávez International Reviews of Immunology, Vol. 40, Issue 4 https://doi.org/10.1080/08830185.2020.1845331	journal	November 2020
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
GLYCAM06: A generalizable biomolecular force field. Carbohydrates: GLYCAM06 Kirschner, Karl N.; Yongye, Austin B.; Tschampel, Sarah M. Journal of Computational Chemistry, Vol. 29, Issue 4 https://doi.org/10.1002/jcc.20820	journal	September 2007
Array programming with NumPy Harris, Charles R.; Millman, K. Jarrod; van der Walt, Stéfan J. Nature, Vol. 585, Issue 7825 https://doi.org/10.1038/s41586-020-2649-2	journal	September 2020
Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding Sibener, Leah V.; Fernandes, Ricardo A.; Kolawole, Elizabeth M. Cell, Vol. 174, Issue 3 https://doi.org/10.1016/j.cell.2018.06.017	journal	July 2018
A statistical analysis of N- and O-glycan linkage conformations from crystallographic data Petrescu, A. J.; Petrescu, S. M.; Dwek, R. A. Glycobiology, Vol. 9, Issue 4 https://doi.org/10.1093/glycob/9.4.343	journal	April 1999
Human T cell glycosylation and implications on immune therapy for cancer De Bousser, Elien; Meuris, Leander; Callewaert, Nico Human Vaccines & Immunotherapeutics, Vol. 16, Issue 10 https://doi.org/10.1080/21645515.2020.1730658	journal	March 2020
Structural requirements of N-glycosylation of proteins. Studies with proline peptides as conformational probes Bause, E. Biochemical Journal, Vol. 209, Issue 2 https://doi.org/10.1042/bj2090331	journal	February 1983
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations Gowers, Richard; Linke, Max; Barnoud, Jonathan Proceedings of the Python in Science Conference https://doi.org/10.25080/Majora-629e541a-00e	conference	January 2016
The missing term in effective pair potentials Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The Journal of Physical Chemistry, Vol. 91, Issue 24 https://doi.org/10.1021/j100308a038	journal	November 1987
Glycans Instructing Immunity: The Emerging Role of Altered Glycosylation in Clinical Immunology Lyons, Jonathan J.; Milner, Joshua D.; Rosenzweig, Sergio D. Frontiers in Pediatrics, Vol. 3 https://doi.org/10.3389/FPED.2015.00054	journal	June 2015
An atomistic perspective on antibody-dependent cellular cytotoxicity quenching by core-fucosylation of IgG1 Fc N-glycans from enhanced sampling molecular dynamics Harbison, Aoife; Fadda, Elisa Glycobiology, Vol. 30, Issue 6 https://doi.org/10.1093/glycob/cwz101	journal	December 2019
ACPYPE - AnteChamber PYthon Parser interfacE Sousa da Silva, Alan W.; Vranken, Wim F. BMC Research Notes, Vol. 5, Issue 1 https://doi.org/10.1186/1756-0500-5-367	journal	January 2012
Using molecular dynamics simulations to interrogate T cell receptor non-equilibrium kinetics Rollins, Zachary A.; Faller, Roland; George, Steven C. Computational and Structural Biotechnology Journal, Vol. 20 https://doi.org/10.1016/j.csbj.2022.04.018	journal	January 2022
ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS Bernardi, Austen; Faller, Roland; Reith, Dirk SoftwareX, Vol. 10 https://doi.org/10.1016/j.softx.2019.100241	journal	July 2019
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
Polymorphic transitions in single crystals: A new molecular dynamics method Parrinello, M.; Rahman, A. Journal of Applied Physics, Vol. 52, Issue 12 https://doi.org/10.1063/1.328693	journal	December 1981
T cells modulate glycans on CD43 and CD45 during development and activation, signal regulation, and survival Clark, Mary C.; Baum, Linda G. Annals of the New York Academy of Sciences, Vol. 1253, Issue 1 https://doi.org/10.1111/j.1749-6632.2011.06304.x	journal	January 2012
How Hydrophobicity and the Glycosylation Site of Glycans Affect Protein Folding and Stability: A Molecular Dynamics Simulation Lu, Diannan; Yang, Cheng; Liu, Zheng The Journal of Physical Chemistry B, Vol. 116, Issue 1 https://doi.org/10.1021/jp203926r	journal	December 2011
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
Mechano-regulation of Peptide-MHC Class I Conformations Determines TCR Antigen Recognition Wu, Peng; Zhang, Tongtong; Liu, Baoyu Molecular Cell, Vol. 73, Issue 5 https://doi.org/10.1016/j.molcel.2018.12.018	journal	March 2019
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
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
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
GROMACS: Fast, flexible, and free Van Der Spoel, David; Lindahl, Erik; Hess, Berk Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20291	journal	January 2005
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
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical p K _a Predictions Olsson, Mats H. M.; Søndergaard, Chresten R.; Rostkowski, Michal Journal of Chemical Theory and Computation, Vol. 7, Issue 2 https://doi.org/10.1021/ct100578z	journal	December 2010
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB Maier, James A.; Martinez, Carmenza; Kasavajhala, Koushik Journal of Chemical Theory and Computation, Vol. 11, Issue 8 https://doi.org/10.1021/acs.jctc.5b00255	journal	July 2015
Preferred conformations ofN-glycan core pentasaccharide in solution and in glycoproteins Jo, Sunhwan; Qi, Yifei; Im, Wonpil Glycobiology https://doi.org/10.1093/glycob/cwv083	journal	September 2015
The Nose–Hoover thermostat Evans, D. J.; Holian, B. L. The Journal of Chemical Physics, Vol. 83, Issue 8 https://doi.org/10.1063/1.449071	journal	October 1985
SciPy 1.0: fundamental algorithms for scientific computing in Python Virtanen, Pauli; Gommers, Ralf; Oliphant, Travis E. Nature Methods https://doi.org/10.1038/s41592-019-0686-2	journal	February 2020
Mammalian glycosylation in immunity Marth, Jamey D.; Grewal, Prabhjit K. Nature Reviews Immunology, Vol. 8, Issue 11 https://doi.org/10.1038/nri2417	journal	November 2008
Roles for major histocompatibility complex glycosylation in immune function Ryan, Sean O.; Cobb, Brian A. Seminars in Immunopathology, Vol. 34, Issue 3 https://doi.org/10.1007/s00281-012-0309-9	journal	March 2012
Dynamic Views of the Fc Region of Immunoglobulin G Provided by Experimental and Computational Observations Yanaka, Saeko; Yogo, Rina; Inoue, Rintaro Antibodies, Vol. 8, Issue 3 https://doi.org/10.3390/antib8030039	journal	July 2019
TCRs Used in Cancer Gene Therapy Cross-React with MART-1/Melan-A Tumor Antigens via Distinct Mechanisms Borbulevych, Oleg Y.; Santhanagopolan, Sujatha M.; Hossain, Moushumi The Journal of Immunology, Vol. 187, Issue 5 https://doi.org/10.4049/jimmunol.1101268	journal	July 2011
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
Blockade of N-Glycosylation Promotes Antitumor Immune Response of T Cells Sasawatari, Shigemi; Okamoto, Yuki; Kumanogoh, Atsushi The Journal of Immunology, Vol. 204, Issue 5 https://doi.org/10.4049/jimmunol.1900937	journal	March 2020
Turning 'sweet' on immunity: galectin–glycan interactions in immune tolerance and inflammation Rabinovich, Gabriel A.; Toscano, Marta A. Nature Reviews Immunology, Vol. 9, Issue 5 https://doi.org/10.1038/nri2536	journal	May 2009
A Stochastic Algorithm for the Isobaric–Isothermal Ensemble with Ewald Summations for All Long Range Forces Di Pierro, Michele; Elber, Ron; Leimkuhler, Benedict Journal of Chemical Theory and Computation, Vol. 11, Issue 12 https://doi.org/10.1021/acs.jctc.5b00648	journal	November 2015
Molecular dynamics with coupling to an external bath Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F. The Journal of Chemical Physics, Vol. 81, Issue 8 https://doi.org/10.1063/1.448118	journal	October 1984
Pingouin: statistics in Python Vallat, Raphael Journal of Open Source Software, Vol. 3, Issue 31 https://doi.org/10.21105/joss.01026	journal	November 2018
Global view of human protein glycosylation pathways and functions Schjoldager, Katrine T.; Narimatsu, Yoshiki; Joshi, Hiren J. Nature Reviews Molecular Cell Biology, Vol. 21, Issue 12 https://doi.org/10.1038/s41580-020-00294-x	journal	October 2020
Die Berechnung optischer und elektrostatischer Gitterpotentiale Ewald, P. P. Annalen der Physik, Vol. 369, Issue 3 https://doi.org/10.1002/andp.19213690304	journal	January 1921
Expression and characterization of soluble epitope-defined major histocompatibility complex (MHC) from stable eukaryotic cell lines Wooster, Amanda L.; Anderson, Trevor S.; Lowe, Devin B. Journal of Immunological Methods, Vol. 464 https://doi.org/10.1016/j.jim.2018.10.006	journal	January 2019
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K _a Values Søndergaard, Chresten R.; Olsson, Mats H. M.; Rostkowski, Michał Journal of Chemical Theory and Computation, Vol. 7, Issue 7 https://doi.org/10.1021/ct200133y	journal	June 2011
Data Structures for Statistical Computing in Python McKinney, Wes Proceedings of the Python in Science Conference https://doi.org/10.25080/Majora-92bf1922-00a	conference	January 2010

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