Literature DB >> 21557322

Toward the quantum chemical calculation of nuclear magnetic resonance chemical shifts of proteins.

Andrea Frank1, Ionut Onila, Heiko M Möller, Thomas E Exner.   

Abstract

Despite the many protein structures solved successfully by nuclear magnetic resonance (NMR) spectroscopy, quality control of NMR structures is still by far not as well established and standardized as in crystallography. Therefore, there is still the need for new, independent, and unbiased evaluation tools to identify problematic parts and in the best case also to give guidelines that how to fix them. We present here, quantum chemical calculations of NMR chemical shifts for many proteins based on our fragment-based quantum chemical method: the adjustable density matrix assembler (ADMA). These results show that (13)C chemical shifts of reasonable accuracy can be obtained that can already provide a powerful measure for the structure validation. (1)H and even more (15)N chemical shifts deviate more strongly from experiment due to the insufficient treatment of solvent effects and conformational averaging.
Copyright © 2011 Wiley-Liss, Inc.

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Year:  2011        PMID: 21557322     DOI: 10.1002/prot.23041

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  11 in total

1.  Converging nuclear magnetic shielding calculations with respect to basis and system size in protein systems.

Authors:  Joshua D Hartman; Thomas J Neubauer; Bethany G Caulkins; Leonard J Mueller; Gregory J O Beran
Journal:  J Biomol NMR       Date:  2015-05-21       Impact factor: 2.835

2.  Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

Authors:  Matthias Trautwein; Kai Fredriksson; Heiko M Möller; Thomas E Exner
Journal:  J Biomol NMR       Date:  2016-08-02       Impact factor: 2.835

Review 3.  Using quantum chemistry to estimate chemical shifts in biomolecules.

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

4.  Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes.

Authors:  Andrea Victora; Heiko M Möller; Thomas E Exner
Journal:  Nucleic Acids Res       Date:  2014-11-17       Impact factor: 16.971

Review 5.  Chemical shifts in biomolecules.

Authors:  David A Case
Journal:  Curr Opin Struct Biol       Date:  2013-02-17       Impact factor: 6.809

6.  Cytochrome-P450-cytochrome-b5 interaction in a membrane environment changes 15N chemical shift anisotropy tensors.

Authors:  Manoj Kumar Pandey; Subramanian Vivekanandan; Shivani Ahuja; Rui Huang; Sang-Choul Im; Lucy Waskell; Ayyalusamy Ramamoorthy
Journal:  J Phys Chem B       Date:  2013-10-28       Impact factor: 2.991

7.  AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.

Authors:  Jason Swails; Tong Zhu; Xiao He; David A Case
Journal:  J Biomol NMR       Date:  2015-08-02       Impact factor: 2.835

8.  Quantum chemical calculations of amide-15N chemical shift anisotropy tensors for a membrane-bound cytochrome-b5.

Authors:  Manoj Kumar Pandey; Ayyalusamy Ramamoorthy
Journal:  J Phys Chem B       Date:  2013-01-10       Impact factor: 2.991

9.  Can quantum-chemical NMR chemical shifts be used as criterion for force-field development.

Authors:  Thomas E Exner; Andrea Frank; Heiko M Möller; Martin Dračínský
Journal:  J Cheminform       Date:  2014-03-11       Impact factor: 5.514

10.  NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction.

Authors:  Anna Katharina Dehof; Simon Loew; Hans-Peter Lenhof; Andreas Hildebrandt
Journal:  BMC Bioinformatics       Date:  2013-03-16       Impact factor: 3.169

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