[NMR paper] Systematic QM/MM Study for Predicting (31)P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment
Systematic QM/MM Study for Predicting (31)P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment
NMR (nuclear magnetic resonance) spectroscopy allows for important atomistic insights into the structure and dynamics of biological macromolecules; however, reliable assignments of experimental spectra are often difficult. Herein, quantum mechanical/molecular mechanical (QM/MM) calculations can provide crucial support. A major problem for the simulations is that experimental NMR signals are time-averaged over much longer time scales, and since computed chemical shifts are highly sensitive to...
[NMR paper] Ligand 1 H NMR Chemical Shifts as Accurate Reporters for Protein-Ligand Binding Interfaces in Solution
Ligand 1 H NMR Chemical Shifts as Accurate Reporters for Protein-Ligand Binding Interfaces in Solution
The availability of high-resolution 3D structural information is crucial for investigating guest-host systems across a wide range of fields. In the context of drug discovery, the information is routinely used to establish and validate structure-activity relationships, grow initial hits from screening campaigns, and to guide molecular docking. For the generation of protein-ligand complex structural information, X-ray crystallography is the experimental method of choice, however, with...
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11-13-2023 06:35 PM
[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,...
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04-03-2020 09:41 PM
[NMR paper] Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment.
Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment.
Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment.
J Chem Theory Comput. 2017 Feb 14;:
Authors: Jose KV, Raghavachari K
Abstract
We present an efficient implementation of the molecules-in-molecules (MIM) fragment-based quantum chemical method for the evaluation of NMR chemical shifts of large...
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02-15-2017 03:40 PM
Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts
Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts
Abstract
A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine \({}^{13}{\text{C}}^{'}\) , 13Cα, 13Cβ, 1Hα, 1HN, and 15NH chemical shifts was...
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09-22-2016 06:26 AM
Metabolite release and protein hydrolysis during the in vitro digestion of cooked sea bass fillets. A study by 1H NMR
Metabolite release and protein hydrolysis during the in vitro digestion of cooked sea bass fillets. A study by 1H NMR
Publication date: Available online 18 January 2016
Source:Food Research International</br>
Author(s): Natalia P. Vidal, Gianfranco Picone, Encarnacion Goicoechea, Luca Laghi, María J. Manzanos, Francesca Danesi, Alessandra Bordoni, Francesco Capozzi, María D. Guillén</br>
Proton Nuclear Magnetic Resonance (1H NMR) was used to study micro-wave cooked European sea bass (Dicentrarchus labrax) fillets, along five different points of...
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01-19-2016 07:18 AM
[NMR paper] A systematic approach to obtain validated partial least square models for predicting lipoprotein subclasses from serum NMR spectra.
A systematic approach to obtain validated partial least square models for predicting lipoprotein subclasses from serum NMR spectra.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles A systematic approach to obtain validated partial least square models for predicting lipoprotein subclasses from serum NMR spectra.
Anal Chem. 2014 Jan 7;86(1):543-50
Authors: Mihaleva VV, van Schalkwijk DB, de Graaf AA, van Duynhoven J, van Dorsten FA, Vervoort J, Smilde A, Westerhuis JA,...
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07-16-2014 10:46 AM
RCI - Random Coil Index for predicting protein flexibility from chemical shifts
RCI website
RCI method predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts and predicting values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index.
The key advantages of this protocol over existing methods of studying protein flexibility are (i) it does not require prior knowledge of a protein's tertiary structure, (ii) it is not sensitive to the protein's overall tumbling and (iii) it does not require additional NMR measurements beyond the standard experiments for backbone...
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02-02-2012 11:36 PM
[NMR paper] The NMR solution structure and characterization of pH dependent chemical shifts of th
The NMR solution structure and characterization of pH dependent chemical shifts of the beta-elicitin, cryptogein.
Related Articles The NMR solution structure and characterization of pH dependent chemical shifts of the beta-elicitin, cryptogein.
J Biomol NMR. 1998 Nov;12(4):523-34
Authors: Gooley PR, Keniry MA, Dimitrov RA, Marsh DE, Keizer DW, Gayler KR, Grant BR
The NMR structure of the 98 residue beta-elicitin, cryptogein, which induces a defence response in tobacco, was determined using 15N and 13C/15N labelled protein samples. In aqueous...
Systematic QM/MM Study for Predicting (31)P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment
Linear Mode
