Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank

Kumaran Baskaran; Eliza Ploskon; Roberto Tejero; Masashi Yokochi; Deborah Harrus; Yuhe Liang; Ezra Peisach; Irina Persikova; Theresa A Ramelot; Monica Sekharan; James Tolchard; John D Westbrook; Benjamin Bardiaux; Charles D Schwieters; Ardan Patwardhan; Sameer Velankar; Stephen K Burley; Genji Kurisu; Jeffrey C Hoch; Gaetano T Montelione; Geerten W Vuister; Jasmine Y Young

doi:10.1016/j.str.2024.02.011

Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank

Structure. 2024 Mar 7:S0969-2126(24)00050-9. doi: 10.1016/j.str.2024.02.011. Online ahead of print.

Authors

Kumaran Baskaran¹, Eliza Ploskon², Roberto Tejero³, Masashi Yokochi⁴, Deborah Harrus⁵, Yuhe Liang⁶, Ezra Peisach⁶, Irina Persikova⁶, Theresa A Ramelot⁷, Monica Sekharan⁶, James Tolchard⁵, John D Westbrook⁶, Benjamin Bardiaux⁸, Charles D Schwieters⁹, Ardan Patwardhan¹⁰, Sameer Velankar⁵, Stephen K Burley¹¹, Genji Kurisu⁴, Jeffrey C Hoch¹², Gaetano T Montelione¹³, Geerten W Vuister¹⁴, Jasmine Y Young¹⁵

Affiliations

¹ Biological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA. Electronic address: baskaran@uchc.edu.
² Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, UK.
³ Departamento de Quίmica Fίsica, Universidad de Valencia, Dr. Moliner, 50 46100 Burjassot, Valencia, Spain.
⁴ Protein Data Bank Japan, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan; Protein Data Bank Japan, Protein Research Foundation, Minoh, Osaka 562-8686, Japan.
⁵ Protein Data Bank in Europe, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
⁶ Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
⁷ Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
⁸ Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3528, 75015 Paris, France.
⁹ Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
¹⁰ The Electron Microscopy Data Bank, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
¹¹ Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, La Jolla, La Jolla, CA, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
¹² Biological Magnetic Resonance Data Bank, Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030-3305, USA.
¹³ Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA. Electronic address: monteg3@rpi.edu.
¹⁴ Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, UK. Electronic address: gv29@leicester.ac.uk.
¹⁵ Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA. Electronic address: jasmin@rcsb.rutgers.edu.

PMID: 38490206
DOI: 10.1016/j.str.2024.02.011

Abstract

Biomolecular structure analysis from experimental NMR studies generally relies on restraints derived from a combination of experimental and knowledge-based data. A challenge for the structural biology community has been a lack of standards for representing these restraints, preventing the establishment of uniform methods of model-vs-data structure validation against restraints and limiting interoperability between restraint-based structure modeling programs. The NEF and NMR-STAR formats provide a standardized approach for representing commonly used NMR restraints. Using these restraint formats, a standardized validation system for assessing structural models of biopolymers against restraints has been developed and implemented in the wwPDB OneDep data deposition-validation-biocuration system. The resulting wwPDB restraint violation report provides a model vs. data assessment of biomolecule structures determined using distance and dihedral restraints, with extensions to other restraint types currently being implemented. These tools are useful for assessing NMR models, as well as for assessing biomolecular structure predictions based on distance restraints.

Keywords: NMR; NMR exchange format; NMR-STAR; Protein Data Bank; biomolecular structures; data standard; dihedral-angle restraints; distance restraints; restraint violation; validation.