Literature DB >> 32363727

Accurate Backbone 13 C and 15 N Chemical Shift Tensors in Galectin-3 Determined by MAS NMR and QM/MM: Details of Structure and Environment Matter.

Jodi Kraus1,2, Rupal Gupta1,3, Manman Lu1,2,4, Angela M Gronenborn2,4, Mikael Akke5, Tatyana Polenova1,2.   

Abstract

Chemical shift tensors obtained from solid-state NMR spectroscopy are very sensitive reporters of structure and dynamics in proteins. While accurate 13 C and 15 N chemical shift tensors are accessible by magic angle spinning (MAS) NMR, their quantum mechanical calculations remain challenging, particularly for 15 N atoms. Here we compare experimentally determined backbone 13 Cα and 15 NH chemical shift tensors by MAS NMR with hybrid quantum mechanics/molecular mechanics/molecular dynamics (MD-QM/MM) calculations for the carbohydrate-binding domain of galectin-3. Excellent agreement between experimental and computed 15 NH chemical shift anisotropy values was obtained using the Amber ff15ipq force field when solvent dynamics was taken into account in the calculation. Our results establish important benchmark conditions for improving the accuracy of chemical shift calculations in proteins and may aid in the validation of protein structure models derived by MAS NMR.
© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  Chemical shift anisotropy; QM/MM; microcrystalline protein; recoupling; solid-state NMR

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Year:  2020        PMID: 32363727      PMCID: PMC8080305          DOI: 10.1002/cphc.202000249

Source DB:  PubMed          Journal:  Chemphyschem        ISSN: 1439-4235            Impact factor:   3.102


  34 in total

1.  Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals.

Authors:  Joshua D Hartman; Ryan A Kudla; Graeme M Day; Leonard J Mueller; Gregory J O Beran
Journal:  Phys Chem Chem Phys       Date:  2016-07-19       Impact factor: 3.676

2.  Assignment of 1H, 15N and 13C resonances of the carbohydrate recognition domain of human galectin-3.

Authors:  K Umemoto; H Leffler
Journal:  J Biomol NMR       Date:  2001-05       Impact factor: 2.835

3.  Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment.

Authors:  K V Jovan Jose; Krishnan Raghavachari
Journal:  J Chem Theory Comput       Date:  2017-02-14       Impact factor: 6.006

4.  Perspective: Quantum mechanical methods in biochemistry and biophysics.

Authors:  Qiang Cui
Journal:  J Chem Phys       Date:  2016-10-14       Impact factor: 3.488

5.  Calculation of chemical shift anisotropy in proteins.

Authors:  Sishi Tang; David A Case
Journal:  J Biomol NMR       Date:  2011-08-26       Impact factor: 2.835

6.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

7.  Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy.

Authors:  Guangjin Hou; In-Ja L Byeon; Jinwoo Ahn; Angela M Gronenborn; Tatyana Polenova
Journal:  J Chem Phys       Date:  2012-10-07       Impact factor: 3.488

8.  Investigation into the feasibility of thioditaloside as a novel scaffold for galectin-3-specific inhibitors.

Authors:  Khuchtumur Bum-Erdene; Ivan A Gagarinov; Patrick M Collins; Moritz Winger; Andrew G Pearson; Jennifer C Wilson; Hakon Leffler; Ulf J Nilsson; I Darren Grice; Helen Blanchard
Journal:  Chembiochem       Date:  2013-07-22       Impact factor: 3.164

9.  Dynamics of reassembled thioredoxin studied by magic angle spinning NMR: snapshots from different time scales.

Authors:  Jun Yang; Maria Luisa Tasayco; Tatyana Polenova
Journal:  J Am Chem Soc       Date:  2009-09-30       Impact factor: 15.419

10.  Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model.

Authors:  Karl T Debiec; David S Cerutti; Lewis R Baker; Angela M Gronenborn; David A Case; Lillian T Chong
Journal:  J Chem Theory Comput       Date:  2016-07-22       Impact factor: 6.006

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  2 in total

1.  Polymorphic Forms of Valinomycin Investigated by NMR Crystallography.

Authors:  Jiří Czernek; Jiří Brus
Journal:  Int J Mol Sci       Date:  2020-07-11       Impact factor: 5.923

2.  Scaled recoupling of chemical shift anisotropies at high magnetic fields under MAS with interspersed C-elements.

Authors:  Keith J Fritzsching; Eric G Keeler; Chengming He; Ann E McDermott
Journal:  J Chem Phys       Date:  2020-09-14       Impact factor: 4.304

  2 in total

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