دورية أكاديمية
أعرض في EDS

Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints.

التفاصيل البيبلوغرافية
العنوان: Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints.
المؤلفون: Kuenze G; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA. Electronic address: georg.kuenze@gmail.com., Bonneau R; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Department of Computer Science, New York University, New York, NY 10012, USA., Leman JK; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA. Electronic address: julia.koehler.leman@gmail.com., Meiler J; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA. Electronic address: jens@meilerlab.org.
المصدر: Structure (London, England : 1993) [Structure] 2019 Nov 05; Vol. 27 (11), pp. 1721-1734.e5. Date of Electronic Publication: 2019 Sep 12.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Cell Press Country of Publication: United States NLM ID: 101087697 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1878-4186 (Electronic) Linking ISSN: 09692126 NLM ISO Abbreviation: Structure Subsets: MEDLINE
أسماء مطبوعة: Publication: 2000- : Cambridge, Mass. : Cell Press
Original Publication: London : Current Biology, c1993-
مواضيع طبية MeSH: Molecular Dynamics Simulation* , Software*, Molecular Docking Simulation/*methods , Nuclear Magnetic Resonance, Biomolecular/*methods, Animals ; Humans ; Protein Conformation
مستخلص: Computational methods to predict protein structure from nuclear magnetic resonance (NMR) restraints that only require assignment of backbone signals, hold great potential to study larger proteins. Ideally, computational methods designed to work with sparse data need to add atomic detail that is missing in the experimental restraints. We introduce a comprehensive framework into the Rosetta suite that uses NMR restraints derived from paramagnetic labeling. Specifically, RosettaNMR incorporates pseudocontact shifts, residual dipolar couplings, and paramagnetic relaxation enhancements. It continues to use backbone chemical shifts and nuclear Overhauser effect distance restraints. We assess RosettaNMR for protein structure prediction by folding 28 monomeric proteins and 8 homo-oligomeric proteins. Furthermore, the general applicability of RosettaNMR is demonstrated on two protein-protein and three protein-ligand docking examples. Paramagnetic restraints generated more accurate models for 85% of the benchmark proteins and, when combined with chemical shifts, sampled high-accuracy models (≤2Å) in 50% of the cases.
(Copyright © 2019 Elsevier Ltd. All rights reserved.)
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معلومات مُعتمدة: 18POST34080422 United States AHA American Heart Association-American Stroke Association; R01 DA046138 United States DA NIDA NIH HHS; R01 GM080403 United States GM NIGMS NIH HHS; S10 OD023680 United States OD NIH HHS
فهرسة مساهمة: Keywords: NMR spectroscopy; Rosetta; integrative modeling; paramagnetic NMR; protein structure prediction; sparse experimental restraints
تواريخ الأحداث: Date Created: 20190917 Date Completed: 20200623 Latest Revision: 20220129
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC6834914
DOI: 10.1016/j.str.2019.08.012
PMID: 31522945
قاعدة البيانات: MEDLINE
الوصف
تدمد:1878-4186
DOI:10.1016/j.str.2019.08.012