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Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: the SH2 domain of SH2B1
Open accessPreprint — published as 10.1016/j.str.2023.05.012
Abstract
Protein structures calculated using NMR data are less accurate and less well defined than they could be. Here we use the program ANSURR to show that this deficiency is at least in part due to a lack of hydrogen bond restraints. We then describe a protocol to introduce hydrogen bond restraints into the structure calculation of the SH2 domain from SH2B1 in a systematic and transparent way, and show that the structures generated are more accurate and better defined as a result. We also show that ANSURR can be used as a guide to know when the structure calculation is good enough to stop.
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Research works printed but not linked: 2
- Neuhaus, D. ; Williamson, M. P. , The nuclear Overhauser effect in structural and conformational analysis. 2nd ed.; Wiley-VCH: New York, 2000
- 10.1126/science.abj8754 · DOI · Paper page
Metadata
- Authors
- Fowler, N. J., Albalwi, M. F., Lee, S., Hounslow, A. M., & Williamson, M. P.
- Affiliations
- University of Sheffield (GB)
- Corresponding author
- Williamson, Mike P.
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2022-08-29
- OpenAlex
- W4293538895
- Cited by
- 0
- References
- 50
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (submittedVersion)
- Funders
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council (BB/P020038/1, BB/R000727/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Spectroscopy › Advanced NMR Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- SH2 domain, SH2B1, structural validation, structure refinement
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- The paper
- Fowler, N. J., Albalwi, M. F., Lee, S., Hounslow, A. M., & Williamson, M. P. (2022). Improved methodology for protein NMR structure calculation using hydrogen bond restraints and ANSURR validation: the SH2 domain of SH2B1. bioRxiv (Cold Spring Harbor Laboratory). https://doi.org/10.1101/2022.08.29.505644
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