NMR chemical shifts provide a sensitive probe of protein structure and dynamics but remain challenging to predict and interpret. We examine the effect of protein conformational distributions on ^(15)N chemical shifts for dihydrofolate reductase (DHFR), comparing QM/MM predicted shifts with experimental shifts in solution as well as frozen distributions. Representative snapshots from MD trajectories exhibit variation in predicted ^(15)N chemical shifts of up to 25 ppm. The average over the...
[NMR paper] Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics
Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics
NMR chemical shifts provide a sensitive probe of protein structure and dynamics. Prediction of shifts, and therefore interpretation of shifts, particularly for the frequently measured amidic ^(15) N sites, remains a tall challenge. We demonstrate that protein ^(15) N chemical shift prediction from QM/MM predictions can be improved if conformational variation is included via MD sampling, focusing on the antibiotic target, E. coli Dihydrofolate reductase (DHFR). Variations...
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[NMR paper] Efficient Screening of Target-Specific Selected Compounds in Mixtures by 19F NMR Binding Assay with Predicted 19F NMR Chemical Shifts
Efficient Screening of Target-Specific Selected Compounds in Mixtures by 19F NMR Binding Assay with Predicted 19F NMR Chemical Shifts
Ligand-based 19 F NMR screening is a highly effective and well-established hit-finding approach. The high sensitivity to protein binding makes it particularly suitable for fragment screening. Different criteria can be considered for generating fluorinated fragment libraries. One common strategy is to assemble a large, diverse, well-designed and characterized fragment library which is screened in mixtures, generated based on experimental 19 F NMR chemical...
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04-28-2022 12:02 AM
[NMR paper] Predicting 19 F NMR chemical shifts: A combined computational and experimental study of a trypasonomal oxidoreductase-inhibitor complex.
Predicting 19 F NMR chemical shifts: A combined computational and experimental study of a trypasonomal oxidoreductase-inhibitor complex.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7388-69-wiley-full-text.png Related Articles Predicting 19 F NMR chemical shifts: A combined computational and experimental study of a trypasonomal oxidoreductase-inhibitor complex.
Angew Chem Int Ed Engl. 2020 Apr 02;:
Authors: Dietschreit J, Wagner A, Le TA, Klein P, Schindelin H, Opatz T, Engels B, Hellmich U,...
Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins
Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins
Abstract
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not...
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11-21-2014 09:04 PM
[NMR paper] NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding.
NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding.
Related Articles NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding.
Phys Chem Chem Phys. 2014 Mar 7;
Authors: Cembran A, Kim J, Gao J, Veglia G
Abstract
Proteins exist as an ensemble of conformers that are distributed on free energy landscapes resembling folding funnels. While the most stable conformers populate low energy basins, protein function is often...
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03-10-2014 10:35 AM
[NMR paper] Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
Related Articles Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
J Biomol NMR. 2013 Jun 2;
Authors: Shen Y, Bax A
Abstract
A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+....
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06-04-2013 06:31 PM
[NMR paper] Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its us
Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.
Related Articles Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements.
J Biomol NMR. 2005 May;32(1):71-81
Authors: Eghbalnia HR, Wang L, Bahrami A, Assadi A, Markley JL
We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low...
Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics
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