We have developed, implemented, and assessed an efficient protocol for the prediction of NMR chemical shifts of large nucleic acids using our molecules-in-molecules (MIM) fragment-based quantum chemical approach. To assess the performance of our approach, MIM-NMR calculations are calibrated on a test set of three nucleic acids, where the structure is derived from solution-phase NMR studies. For DNA systems with multiple conformers, the one-layer MIM method with trimer fragments (MIM1(trimer)) is...
[NMR paper] Accurate and cost-effective NMR chemical shift predictions for proteins using a molecules-in-molecules fragmentation-based method.
Accurate and cost-effective NMR chemical shift predictions for proteins using a molecules-in-molecules fragmentation-based method.
Related Articles Accurate and cost-effective NMR chemical shift predictions for proteins using a molecules-in-molecules fragmentation-based method.
Phys Chem Chem Phys. 2020 Nov 27;:
Authors: Chandy SK, Thapa B, Raghavachari K
Abstract
We have developed an efficient protocol using our two-layer Molecules-in-Molecules (MIM2) fragmentation-based quantum chemical method for the prediction of NMR chemical...
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11-29-2020 08:12 AM
Concentration-dependent changes to diffusion and chemical shift of internal standard molecules in aqueous and micellar solutions
Concentration-dependent changes to diffusion and chemical shift of internal standard molecules in aqueous and micellar solutions
Abstract
Sodium 4,4-dimethyl-4-silapentane-1-sulfonate (DSS) is the most widely accepted internal standard for protein NMR studies in aqueous conditions. Since its introduction as a reference standard, however, concerns have been raised surrounding its propensity to interact with biological molecules through electrostatic and hydrophobic interactions. While DSS has been shown to interact with certain proteins, membrane...
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06-06-2018 01:42 PM
[NMR paper] Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.
Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.
Related Articles Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions.
J Chem Theory Comput. 2016 Dec 19;
Authors: Steinmann C, Bratholm LA, Olsen JM, Kongsted J
Abstract
Full-protein NMR shielding constants based on ab initio calculations are desirable since they can assist in...
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12-21-2016 07:20 AM
[NMR paper] Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes.
Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes.
Related Articles Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes.
Nucleic Acids Res. 2014 Nov 17;
Authors: Victora A, Möller HM, Exner TE
Abstract
NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis,...
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11-19-2014 04:32 PM
[NMR paper] Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Related Articles Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.
Adv Exp Med Biol. 2015;827:49-70
Authors: Zhu T, Zhang JZ, He X
Abstract
The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the...
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11-14-2014 08:33 AM
[NMR paper] Cost-effective method for the preparation of uniformly labeled myristoylated proteins for NMR measurements.
Cost-effective method for the preparation of uniformly labeled myristoylated proteins for NMR measurements.
Related Articles Cost-effective method for the preparation of uniformly labeled myristoylated proteins for NMR measurements.
Protein Expr Purif. 2014 Mar 21;
Authors: Kroupa T, Prchal J, Doležal M, Ruml T, Hrabal R
Abstract
Nuclear magnetic resonance (NMR) is a powerful technique for solving protein structures orstudying their interactions. However, it requires molecules labeled with NMR sensitive isotopes like carbon(13)C and...
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03-26-2014 12:44 PM
Cost-effective method for the preparation of uniformly labeled myristoylated proteins for NMR measurements
Cost-effective method for the preparation of uniformly labeled myristoylated proteins for NMR measurements
Publication date: Available online 21 March 2014
Source:Protein Expression and Purification</br>
Author(s): Tomáš Kroupa , Jan Prchal , Michal Doležal , Tomáš Ruml , Richard Hrabal</br>
Nuclear magnetic resonance (NMR) is a powerful technique for solving protein structures orstudying their interactions. However, it requires molecules labeled with NMR sensitive isotopes like carbon13C and nitrogen15N. The recombinant expression of labeled proteins is simple...
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03-22-2014 01:28 AM
[NMR paper] Ab initio NMR chemical-shift calculations based on the combined fragmentation method.
Ab initio NMR chemical-shift calculations based on the combined fragmentation method.
Related Articles Ab initio NMR chemical-shift calculations based on the combined fragmentation method.
Phys Chem Chem Phys. 2013 Apr 12;
Authors: Tan HJ, Bettens RP
Abstract
NMR chemical shift is a molecular property that can be computed from first principles. In this work we show that by utilizing our combined fragmentation method (CFM), one is able to accurately compute this property for small proteins. Without nonbonded interactions, the root mean...
Accurate and Cost-Effective NMR Chemical Shift Predictions for Nucleic Acids Using a Molecules-in-Molecules Fragmentation-Based Method
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