-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathpaper.bib
103 lines (96 loc) · 8.62 KB
/
paper.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
@article {addomer,
author = {Vragniau, Charles and Bufton, Joshua C. and Garzoni, Fr{\'e}d{\'e}ric and Stermann, Emilie and Rabi, Fruzsina and Terrat, C{\'e}line and Guidetti, M{\'e}lanie and Josserand, V{\'e}ronique and Williams, Matt and Woods, Christopher J. and Viedma, Gerardo and Bates, Phil and Verrier, Bernard and Chaperot, Laurence and Schaffitzel, Christiane and Berger, Imre and Fender, Pascal},
title = {Synthetic self-assembling ADDomer platform for highly efficient vaccination by genetically encoded multiepitope display},
volume = {5},
number = {9},
elocation-id = {eaaw2853},
year = {2019},
doi = {10.1126/sciadv.aaw2853},
publisher = {American Association for the Advancement of Science},
abstract = {Self-assembling virus-like particles represent highly attractive tools for developing next-generation vaccines and protein therapeutics. We created ADDomer, an adenovirus-derived multimeric protein-based self-assembling nanoparticle scaffold engineered to facilitate plug-and-play display of multiple immunogenic epitopes from pathogens. We used cryo{\textendash}electron microscopy at near-atomic resolution and implemented novel, cost-effective, high-performance cloud computing to reveal architectural features in unprecedented detail. We analyzed ADDomer interaction with components of the immune system and developed a promising first-in-kind ADDomer-based vaccine candidate to combat emerging Chikungunya infectious disease, exemplifying the potential of our approach.},
URL = {https://advances.sciencemag.org/content/5/9/eaaw2853},
eprint = {https://advances.sciencemag.org/content/5/9/eaaw2853.full.pdf},
journal = {Science Advances}
}
@article{nicotinic_receptor,
author = {Oliveira, Ana Sofia F. and Edsall, Christopher J. and Woods, Christopher J. and Bates, Phil and Nunez, Gerardo Viedma and Wonnacott, Susan and Bermudez, Isabel and Ciccotti, Giovanni and Gallagher, Timothy and Sessions, Richard B. and Mulholland, Adrian J.},
title = {A General Mechanism for Signal Propagation in the Nicotinic Acetylcholine Receptor Family},
journal = {Journal of the American Chemical Society},
volume = {141},
number = {51},
pages = {19953-19958},
year = {2019},
doi = {10.1021/jacs.9b09055},
note ={PMID: 31805762},
URL = {https://doi.org/10.1021/jacs.9b09055},
eprint = {https://doi.org/10.1021/jacs.9b09055}
}
@ARTICLE{radiotherapy,
author={L. {Beck} and J. J. {Velthuis} and R. F. {Page} and R. P. {Hugtenburg} and C. {De Sio} and J. {Pritchard}},
journal={IEEE Transactions on Radiation and Plasma Medical Sciences},
title={A Novel Approach to Contamination Suppression in Transmission Detectors for Radiotherapy},
year={2020},
volume={},
number={},
pages={1-1},
doi = {10.1109/trpms.2020.2995059},
}
@inproceedings{carbon_seq,
month = {December},
author = {Ryan. L. Payton and Sun. Yizhuo and Andrew Kingdon and Saswata Hier-Majumder},
booktitle = {AGU Fall Meeting 2019},
address = {San Francisco, Ca, USA},
title = {Pore Scale Modelling of Carbon Capture and Sequestration},
publisher = {American Geophysical Union},
pages = {0--2},
year = {2019},
url = {http://nora.nerc.ac.uk/id/eprint/526317/},
}
@article{nicotinic_sars_cov,
author = {F. Oliveira, A. Sofia and Ibarra, Amaurys Avila and Bermudez, Isabel and Casalino, Lorenzo and Gaieb, Zied and Shoemark, Deborah K. and Gallagher, Timothy and Sessions, Richard B. and Amaro, Rommie E. and Mulholland, Adrian J.},
title = {Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors},
elocation-id = {2020.07.16.206680},
year = {2020},
doi = {10.1101/2020.07.16.206680},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Changeux et al. recently suggested that the SARS-CoV-2 spike (S) protein may interact with nicotinic acetylcholine receptors (nAChRs). Such interactions may be involved in pathology and infectivity. Here, we use molecular simulations of validated atomically detailed structures of nAChRs, and of the S protein, to investigate this {\textquoteleft}nicotinic hypothesis{\textquoteright}. We examine the binding of the Y674-R685 loop of the S protein to three nAChRs, namely the human α4β2 and α7 subtypes and the muscle-like αβγd receptor from Tetronarce californica. Our results indicate that Y674-R685 has affinity for nAChRs and the region responsible for binding contains the PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses. In particular, R682 has a key role in the stabilisation of the complexes as it forms interactions with loops A, B and C in the receptor{\textquoteright}s binding pocket. The conformational behaviour of the bound Y674-R685 region is highly dependent on the receptor subtype, adopting extended conformations in the α4β2 and α7 complexes and more compact ones when bound to the muscle-like receptor. In the α4β2 and αβγd complexes, the interaction of Y674-R685 with the receptors forces the loop C region to adopt an open conformation similar to other known nAChR antagonists. In contrast, in the α7 complex, Y674-R685 penetrates deeply into the binding pocket where it forms interactions with the residues lining the aromatic box, namely with TrpB, TyrC1 and TyrC2. Estimates of binding energy suggest that Y674-R685 forms stable complexes with all three nAChR subtypes. Analyses of the simulations of the full-length S protein show that the Y674-R685 region is accessible for binding, and suggest a potential binding orientation of the S protein with nAChRs.Competing Interest StatementThe authors have declared no competing interest.},
URL = {https://www.biorxiv.org/content/early/2020/09/14/2020.07.16.206680},
eprint = {https://www.biorxiv.org/content/early/2020/09/14/2020.07.16.206680.full.pdf},
journal = {bioRxiv}
}
@article {fatty_acid_sars_cov,
author = {Toelzer, Christine and Gupta, Kapil and Yadav, Sathish K. N. and Borucu, Ufuk and Davidson, Andrew D. and Kavanagh Williamson, Maia and Shoemark, Deborah K. and Garzoni, Frederic and Staufer, Oskar and Milligan, Rachel and Capin, Julien and Mulholland, Adrian J. and Spatz, Joachim and Fitzgerald, Daniel and Berger, Imre and Schaffitzel, Christiane},
title = {Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein},
elocation-id = {eabd3255},
year = {2020},
doi = {10.1126/science.abd3255},
publisher = {American Association for the Advancement of Science},
abstract = {COVID-19, caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), represents a global crisis. Key to SARS-CoV-2 therapeutic development is unraveling the mechanisms driving high infectivity, broad tissue tropism and severe pathology. Our 2.85 {\r A} cryo-EM structure of SARS-CoV-2 spike (S) glycoprotein reveals that the receptor binding domains (RBDs) tightly bind the essential free fatty acid (FFA) linoleic acid (LA) in three composite binding pockets. The pocket also appears to be present in the highly pathogenic coronaviruses SARS-CoV and MERS-CoV. LA binding stabilizes a locked S conformation giving rise to reduced ACE2 interaction in vitro. In human cells, LA supplementation synergizes with the COVID-19 drug remdesivir, suppressing SARS-CoV-2 replication. Our structure directly links LA and S, setting the stage for intervention strategies targeting LA binding by SARS-CoV-2.},
issn = {0036-8075},
URL = {https://science.sciencemag.org/content/early/2020/09/18/science.abd3255},
eprint = {https://science.sciencemag.org/content/early/2020/09/18/science.abd3255.full.pdf},
journal = {Science}
}
@inproceedings{performance_yellow_brick_road_exascale,
author={Deakin, Tom and Poenaru, Andrei and Lin, Tom and McIntosh-Smith, Simon},
booktitle={2020 IEEE/ACM International Workshop on Performance, Portability and Productivity in HPC (P3HPC)},
title={Tracking Performance Portability on the Yellow Brick Road to Exascale},
year={2020},
volume={},
number={},
pages={1-13},
doi={10.1109/P3HPC51967.2020.00006}
}
@article{https://doi.org/10.1002/cpz1.55,
author = {Sari-Ak, Duygu and Bufton, Joshua and Gupta, Kapil and Garzoni, Frederic and Fitzgerald, Daniel and Schaffitzel, Christiane and Berger, Imre},
title = {VLP-factory™ and ADDomer©: Self-assembling Virus-Like Particle (VLP) Technologies for Multiple Protein and Peptide Epitope Display},
journal = {Current Protocols},
volume = {1},
number = {3},
pages = {e55},
keywords = {antigenic epitope, baculovirus expression vector system (BEVS), immunization, MultiBac, protein and peptide display, vaccine, virus-like particle (VLP)},
doi = {https://doi.org/10.1002/cpz1.55},
url = {https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.55},
eprint = {https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cpz1.55},
year = {2021}
}