Starting structures and NMR and simulation relaxation data for the structural ensembles of Dengue protease NS2B/NS3pro
SND-ID: 2023-244. Version: 1. DOI: https://doi.org/10.5878/5wea-fk76
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amber_input_simulation_parameters.in (1.43 KB)
S135A_G2_Methyl_Fig3.tsv (20.49 KB)
S135A_NS2B_NOE_Fig2.tsv (3.96 KB)
S135A_NS2B_R1_Fig2.tsv (4.96 KB)
S135A_NS2B_R2_Fig2.tsv (5.31 KB)
S135A_NS3_NOE_Fig2.tsv (14 KB)
... Show more..amber_input_simulation_parameters.in (1.43 KB)
S135A_G2_Methyl_Fig3.tsv (20.49 KB)
S135A_NS2B_NOE_Fig2.tsv (3.96 KB)
S135A_NS2B_R1_Fig2.tsv (4.96 KB)
S135A_NS2B_R2_Fig2.tsv (5.31 KB)
S135A_NS3_NOE_Fig2.tsv (14 KB)
S135A_NS3_R1_Fig2.tsv (14.11 KB)
S135A_NS3_R2_Fig2.tsv (15.23 KB)
S135A_R1_Methyl_Fig3.tsv (12.72 KB)
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Citation
Creator/Principal investigator(s)
Peter Agback
- Swedish University of Agricultural Sciences, Department of Molecular Sciences
Tatiana Agback - Swedish University of Agricultural Sciences, Department of Molecular Sciences
Dmitry Lesovoy - Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Department of Structural Biology
Xiao Han - Karolinska Institute, Department of Medicine
Alexander Lomzov - Institute of Chemical Biology and Fundamental Medicine SB RAS, Laboratory for Structural Biology
... Show more..
Peter Agback
- Swedish University of Agricultural Sciences, Department of Molecular Sciences
Tatiana Agback - Swedish University of Agricultural Sciences, Department of Molecular Sciences
Dmitry Lesovoy - Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Department of Structural Biology
Xiao Han - Karolinska Institute, Department of Medicine
Alexander Lomzov - Institute of Chemical Biology and Fundamental Medicine SB RAS, Laboratory for Structural Biology
Renhua Sun - Karolinska Institute, Department of Medicine
Tatyana Sandalova - Karolinska Institute, Department of Medicine
Vladislav Orekhov - Gothenburg University, Swedish NMR Centre
Adnane Achour - Karolinska Institute, Department of Medicine
Show less..Research principal
Swedish University of Agricultural Sciences
- Department of Molecular Sciences
Principal's reference number
SLU.molsci.2023.4.4..IÄ-12
Description
The dengue protease NS2B/NS3pro has been reported to adopt either an ‘open’ or a ‘closed’ conformation. We have developed a conformational filter that combines nuclear magnetic resonance (NMR) with molecular dynamics (MD) simulations to identify conformational ensembles that dominate in solution. Experimental values derived from relaxation parameters for the backbone and methyl side chains were compared with the corresponding back-calculated relaxation parameters of different conformational ensembles obtained from free MD simulations. Our results demonstrate a high prevalence for the ‘closed’ conformational ensemble while the ‘open’ conformation is absent, indicating that the latter conformation is most probably due to crystal contacts. Conversely, conformational ensembles in which the positioning of the co-factor NS2B results in a ‘partially’ open conformation, previously described in both MD simulations and X-ray studies, were identified by our conformational filter. Altogether, we believe that our approach allows for unambiguous identification of true conformational ensembles, an essential
... Show more..Data contains personal data
No
Language
Time period(s) investigated
2018-01-01 – 2022-12-31
Species and taxons
Responsible department/unit
Department of Molecular Sciences
Other research principals
Funding 1
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Funding agency:
Swedish Foundation for Strategic Research
- Funding agency's reference number: ITM17-0218
- Project name on the application: Innovative experimental modelling of dynamic protein states.
Funding 2
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Funding agency:
Swedish Research Council
- Funding agency's reference number: 2021-05061
Funding 3
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Funding agency:
Swedish Cancer Society
- Funding agency's reference number: 21 1605 Pj01H
Funding 4
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Funding agency:
Swedish Research Council
- Funding agency's reference number: 2019-03561
Research area
Bioinformatics (computational biology) (Standard för svensk indelning av forskningsämnen 2011)
Other physics topics (Standard för svensk indelning av forskningsämnen 2011)
Structural biology (Standard för svensk indelning av forskningsämnen 2011)
Agback, T., Lesovoy, D., Han, X., Lomzov, A., Sun, R., Sandalova, T., Yu, V., Adnane Achour, O., Agback, P. (2023). Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro. Communications Biology 6:1193.
DOI:
https://doi.org/10.1038/s42003-023-05584-6
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