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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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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., et al. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998003254 · Cited by 15,715
MolProbity : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115
Enzymatic assembly of DNA molecules up to several hundred kilobases
Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009) · Nature Methods · doi:10.1038/nmeth.1318 · Cited by 9,996
ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391
Accurate prediction of protein structures and interactions using a 3-track network
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,549
AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
Laskowski, R., Rullmann, J. A., MacArthur, M., Kaptein, R., & Thornton, J. (1996) · Journal of Biomolecular NMR · doi:10.1007/bf00228148 · Cited by 5,502
Scoring function for automated assessment of protein structure template quality
Zhang, Y., & Skolnick, J. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20264 · Cited by 2,392
Ulrich, E. L., Akutsu, H., Doreleijers, J. F., Harano, Y., Ioannidis, Y., Lin, J. C., Livny, M., Mading, S., Maziuk, D., Miller, Z., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm957 · Cited by 1,472
Automated NMR Structure Calculation With CYANA
Güntert, P. (2004) · Protein NMR Techniques · doi:10.1385/1-59259-809-9:353 · Cited by 1,351
Shen, Y., & Bax, A. (2013) · Journal of Biomolecular NMR · doi:10.1007/s10858-013-9741-y · Cited by 1,119
Measurement ofJand Dipolar Couplings from Simplified Two-Dimensional NMR Spectra
Ottiger, M., Delaglio, F., & Bax, A. (1998) · Journal of Magnetic Resonance · doi:10.1006/jmre.1998.1361 · Cited by 967
Cornilescu, G., Marquardt, J. L., Ottiger, M., & Bax, A. (1998) · Journal of the American Chemical Society · doi:10.1021/ja9812610 · Cited by 909
Wüthrich, K., Billeter, M., & Braun, W. A. (1984) · Journal of Molecular Biology · doi:10.1016/0022-2836(84)90034-2 · Cited by 765
Evaluating protein structures determined by structural genomics consortia
Bhattacharya, A., Tejero, R., & Montelione, G. T. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21165 · Cited by 729
Protein flexibility predictions using graph theory
Jacobs, D. J., Rader, A. J., Kuhn, L. A., & Thorpe, M. F. (2001) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.1081 · Cited by 727
Zweckstetter, M., & Bax, A. (2000) · Journal of the American Chemical Society · doi:10.1021/ja0000908 · Cited by 706
Aurora, R., & Rose, G. D. (1998) · Protein Science · doi:10.1002/pro.5560070103 · Cited by 697
SHIFTX2: significantly improved protein chemical shift prediction
Han, B., Liu, Y., Ginzinger, S. W., & Wishart, D. S. (2011) · Journal of Biomolecular NMR · doi:10.1007/s10858-011-9478-4 · Cited by 671
Williamson, M. P., Havel, T. F., & Wüthrich, K. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90347-x · Cited by 629
Self-citationRefinement of protein structures in explicit solvent
Linge, J. P., Williams, M. A., Spronk, C. A. E. M., Bonvin, A. M. J. J., & Nilges, M. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10299 · Cited by 606
Temperature dependence of 1H chemical shifts in proteins
Baxter, N. J., & Williamson, M. P. (1997) · Journal of Biomolecular NMR · doi:10.1023/a:1018334207887 · Cited by 497
Self-citationDirect Observation of Hydrogen Bonds in Proteins by Interresidue 3hJNC‘ Scalar Couplings
Cordier, F., & Grzesiek, S. (1999) · Journal of the American Chemical Society · doi:10.1021/ja983945d · Cited by 412
Combined automated NOE assignment and structure calculation with CYANA
Güntert, P., & Buchner, L. (2015) · Journal of Biomolecular NMR · doi:10.1007/s10858-015-9924-9 · Cited by 402
WAGNER, G., KUMAR, A., & WÜTHRICH, K. (1981) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1981.tb05157.x · Cited by 284
Dana, J. M., Gutmanas, A., Tyagi, N., Qi, G., O’Donovan, C., Martin, M. J., & Velankar, S. S. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1114 · Cited by 268
Chou, J. J., Gaemers, S., Howder, B., Louis, J. M., & Bax, A. (2001) · Journal of Biomolecular NMR · doi:10.1023/a:1013336502594 · Cited by 242
New methods of structure refinement for macromolecular structure determination by NMR
Clore, G. M., & Gronenborn, A. M. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.11.5891 · Cited by 227
Recommendations of the wwPDB NMR Validation Task Force
Montelione, G. T., Nilges, M., Bax, A., Güntert, P., Herrmann, T., Richardson, J. S., Schwieters, C. D., Vranken, W., Vuister, G. W., Wishart, D. S., et al. (2013) · Structure · doi:10.1016/j.str.2013.07.021 · Cited by 165
Automated Protein Structure Determination from NMR Spectra
Mendez, B. L., & Güntert, P. (2006) · Journal of the American Chemical Society · doi:10.1021/ja061136l · Cited by 164
The relationship between amide proton chemical shifts and secondary structure in proteins
Asakura, T., Taoka, K., Demura, M., & Williamson, M. P. (1995) · Journal of Biomolecular NMR · doi:10.1007/bf00197804 · Cited by 142
Self-citationApplication of the random coil index to studying protein flexibility
Berjanskii, M. V., & Wishart, D. S. (2007) · Journal of Biomolecular NMR · doi:10.1007/s10858-007-9208-0 · Cited by 134
SH2B1 (SH2-B) and JAK2: a multifunctional adaptor protein and kinase made for each other
Maures, T. J., Kurzer, J. H., & Carter‐Su, C. (2006) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2006.11.007 · Cited by 126
Andrec, M., Snyder, D. A., Zhou, Z., Young, J. Y., Montelione, G. T., & Levy, R. M. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21507 · Cited by 117
Li, Z., Zhou, Y., Carter‐Su, C., Myers, M. G., & Rui, L. (2007) · Molecular Endocrinology · doi:10.1210/me.2007-0111 · Cited by 111
Morris, D. L., Cho, K. W., Zhou, Y., & Rui, L. (2009) · Diabetes · doi:10.2337/db08-1388 · Cited by 94
Differential Binding to and Regulation of JAK2 by the SH2 Domain and N-Terminal Region of SH2-Bβ
Rui, L., Gunter, D. R., Herrington, J. B., & Carter‐Su, C. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.9.3168-3177.2000 · Cited by 63
A method for validating the accuracy of NMR protein structures
Fowler, N., Sljoka, A., & Williamson, M. P. (2020) · Nature Communications · doi:10.1038/s41467-020-20177-1 · Cited by 63
Self-citationAutomated protein structure calculation from NMR data
Williamson, M. P., & Craven, C. J. (2009) · Journal of Biomolecular NMR · doi:10.1007/s10858-008-9295-6 · Cited by 61
Self-citationRobertson, A. J., Courtney, J. M., Shen, Y., Ying, J., & Bax, A. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c10588 · Cited by 59
Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems
Chiliveri, S. C., Robertson, A. J., Shen, Y., Torchia, D. A., & Bax, A. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00730 · Cited by 55
Huang, Y. J., Zhang, N., Bersch, B., Fidelis, K., Inouye, M., Ishida, Y., Kryshtafovych, A., Kobayashi, N., Kuroda, Y., Liu, G., et al. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26246 · Cited by 49
X‐ray vs. NMR structures as templates for computational protein design
Schneider, M., Fu, X., & Keating, A. E. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22421 · Cited by 48
Effects of Domain Dissection on the Folding and Stability of the 43 kDa Protein PGK Probed by NMR
Reed, M. A. C., Hounslow, A. M., Sze, K. H., Barsukov, I. G., Hosszu, L. L. P., Clarke, A. R., Craven, C. J., & Waltho, J. P. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00625-9 · Cited by 47
Self-citationAmide temperature coefficients in the protein G B1 domain
Tomlinson, J. H., & Williamson, M. P. (2011) · Journal of Biomolecular NMR · doi:10.1007/s10858-011-9583-4 · Cited by 42
Self-citationBuchner, L., & Güntert, P. (2015) · Structure · doi:10.1016/j.str.2014.11.014 · Cited by 29
Schwieters, C. D., Bermejo, G. A., & Clore, G. M. (2019) · Protein Science · doi:10.1002/pro.3745 · Cited by 22
Hermann, R. R. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(19970115)18:1<139::aid-jcc13>3.0.co;2-h · Cited by 20
The accuracy of NMR protein structures in the Protein Data Bank
Fowler, N. J., Sljoka, A., & Williamson, M. P. (2021) · Structure · doi:10.1016/j.str.2021.07.001 · Cited by 14
Self-citation
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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