Literature DB >> 29577158

Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM.

Matthew Fritz1, Caitlin M Quinn, Mingzhang Wang, Guangjin Hou, Xingyu Lu, Leonardus M I Koharudin, Jochem Struppe, David A Case, Tatyana Polenova, Angela M Gronenborn.   

Abstract

Chemical shifts are highly sensitive probes of local conformation and overall structure. Both isotropic shifts and chemical shift tensors are readily accessible from NMR experiments but their quantum mechanical calculations remain challenging. In this work, we report and compare accurately measured and calculated 15NH and 13Cα chemical shift tensors in proteins, using the microcrystalline agglutinin from Oscillatoria agardhii (OAA). Experimental 13Cα and 15NH chemical tensors were obtained by solid-state NMR spectroscopy, employing tailored recoupling sequences, and for their quantum mechanics/molecular mechanics (QM/MM) calculations different sets of functionals were evaluated. We show that 13Cα chemical shift tensors are primarily determined by backbone dihedral angles and dynamics, while 15NH tensors mainly depend on local electrostatic contributions from solvation and hydrogen bonding. In addition, the influence of including crystallographic waters, the molecular mechanics geometry optimization protocol, and the level of theory on the accuracy of the calculated chemical shift tensors is discussed. Specifically, the power of QM/MM calculations in accurately predicting the unusually upfield shifted 1HN G26 and G93 resonances is highlighted. Our integrated approach is expected to benefit structure refinement of proteins and protein assemblies.

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Year:  2018        PMID: 29577158      PMCID: PMC5892194          DOI: 10.1039/c8cp00647d

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  31 in total

1.  Density functional investigation of intermolecular effects on 13C NMR chemical-shielding tensors modeled with molecular clusters.

Authors:  Sean T Holmes; Robbie J Iuliucci; Karl T Mueller; Cecil Dybowski
Journal:  J Chem Phys       Date:  2014-10-28       Impact factor: 3.488

2.  SIMPSON: a general simulation program for solid-state NMR spectroscopy. 2000.

Authors:  Mads Bak; Jimmy T Rasmussen; Niels Chr Nielsen
Journal:  J Magn Reson       Date:  2011-12       Impact factor: 2.229

3.  Novel fold and carbohydrate specificity of the potent anti-HIV cyanobacterial lectin from Oscillatoria agardhii.

Authors:  Leonardus M I Koharudin; William Furey; Angela M Gronenborn
Journal:  J Biol Chem       Date:  2010-10-19       Impact factor: 5.157

4.  Structural basis of the anti-HIV activity of the cyanobacterial Oscillatoria Agardhii agglutinin.

Authors:  Leonardus M I Koharudin; Angela M Gronenborn
Journal:  Structure       Date:  2011-08-10       Impact factor: 5.006

5.  Critical Analysis of Cluster Models and Exchange-Correlation Functionals for Calculating Magnetic Shielding in Molecular Solids.

Authors:  Sean T Holmes; Robbie J Iuliucci; Karl T Mueller; Cecil Dybowski
Journal:  J Chem Theory Comput       Date:  2015-11-10       Impact factor: 6.006

6.  (1)H, (13)C and (15)N resonance assignment of the anti-HIV lectin from Oscillatoria agardhii.

Authors:  Marta G Carneiro; Leonardus M I Koharudin; Christian Griesinger; Angela M Gronenborn; Donghan Lee
Journal:  Biomol NMR Assign       Date:  2015-02-14       Impact factor: 0.746

7.  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

8.  Structural insights into the anti-HIV activity of the Oscillatoria agardhii agglutinin homolog lectin family.

Authors:  Leonardus M I Koharudin; Sireesha Kollipara; Christopher Aiken; Angela M Gronenborn
Journal:  J Biol Chem       Date:  2012-08-04       Impact factor: 5.157

Review 9.  Chemical shifts and three-dimensional protein structures.

Authors:  E Oldfield
Journal:  J Biomol NMR       Date:  1995-04       Impact factor: 2.835

10.  A software framework for analysing solid-state MAS NMR data.

Authors:  Tim J Stevens; Rasmus H Fogh; Wayne Boucher; Victoria A Higman; Frank Eisenmenger; Benjamin Bardiaux; Barth-Jan van Rossum; Hartmut Oschkinat; Ernest D Laue
Journal:  J Biomol NMR       Date:  2011-09-28       Impact factor: 2.835

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  4 in total

1.  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.

Authors:  Jodi Kraus; Rupal Gupta; Manman Lu; Angela M Gronenborn; Mikael Akke; Tatyana Polenova
Journal:  Chemphyschem       Date:  2020-06-04       Impact factor: 3.102

Review 2.  Using quantum chemistry to estimate chemical shifts in biomolecules.

Authors:  David A Case
Journal:  Biophys Chem       Date:  2020-09-16       Impact factor: 2.352

3.  Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR.

Authors:  Manman Lu; Ryan W Russell; Alexander J Bryer; Caitlin M Quinn; Guangjin Hou; Huilan Zhang; Charles D Schwieters; Juan R Perilla; Angela M Gronenborn; Tatyana Polenova
Journal:  Nat Struct Mol Biol       Date:  2020-09-08       Impact factor: 15.369

4.  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

  4 in total

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