Chemical shift transfer (CST) is a well-established technique in NMR spectroscopy that utilizes the chemical shift assignment of one protein (source) to identify chemical shifts of another (target). Given similarity between source and target systems (e.g., using homologs), CST allows the chemical shifts of the target system to be assigned using a limited amount of experimental data. In this study, we propose a deep-learning based workflow, ARTINA-CST, that automates this procedure, allowing CST...
[NMR paper] 1H, 15N, and 13C chemical shift backbone resonance NMR assignment of the accumulation-associated protein (Aap) lectin domain from Staphylococcus epidermidis
1H, 15N, and 13C chemical shift backbone resonance NMR assignment of the accumulation-associated protein (Aap) lectin domain from Staphylococcus epidermidis
Staphylococcus epidermidis is the leading causative agent for hospital-acquired infections, especially device-related infections, due to its ability to form biofilms. The accumulation-associated protein (Aap) of S. epidermidis is primarily responsible for biofilm formation and consists of two domains, A and B. It was found that the A domain is responsible for the attachment to the abiotic/biotic surface, whereas the B domain is...
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04-06-2023 05:43 PM
[NMR paper] Accurate and Cost-Effective NMR Chemical Shift Predictions for Nucleic Acids Using a Molecules-in-Molecules Fragmentation-Based Method
Accurate and Cost-Effective NMR Chemical Shift Predictions for Nucleic Acids Using a Molecules-in-Molecules Fragmentation-Based Method
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...
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01-12-2023 02:17 PM
[NMR paper] ssPINE: Probabilistic Algorithm for Automated Chemical Shift Assignment of Solid-State NMR Data from Complex Protein Systems
ssPINE: Probabilistic Algorithm for Automated Chemical Shift Assignment of Solid-State NMR Data from Complex Protein Systems
The heightened dipolar interactions in solids render solid-state NMR (ssNMR) spectra more difficult to interpret than solution NMR spectra. On the other hand, ssNMR does not suffer from severe molecular weight limitations like solution NMR. In recent years, ssNMR has undergone rapid technological developments that have enabled structure-function studies of increasingly larger biomolecules, including membrane proteins. Current methodology includes stable isotope...
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09-23-2022 06:24 AM
[NMR paper] Solid state NMR chemical shift assignment of the non-structural single-stranded DNA binding protein gVp from fd bacteriophage
Solid state NMR chemical shift assignment of the non-structural single-stranded DNA binding protein gVp from fd bacteriophage
The non-structural gene V protein (pV, gVp) from fd virus is a non-specific single-stranded DNA binding protein. The role of gVp is to sequester the single-stranded DNA thus reducing the generation of the replicative DNA form and leading to the formation of progeny phage. In this study, we assigned the ^(13)C and ^(15)N resonances of the crystalline unbound protein by magic-angle spinning solid-state NMR. The secondary structure predicted by the NMR shifts is in...
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04-25-2022 09:37 PM
[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
[NMR paper] Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
J Biomol NMR. 2013 Apr 28;
Authors: Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M
Abstract
We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic...
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04-30-2013 10:21 PM
[NMR paper] Four-dimensional NMR spectroscopy of a 723-residue protein: chemical shift assignment
Four-dimensional NMR spectroscopy of a 723-residue protein: chemical shift assignments and secondary structure of malate synthase g.
Related Articles Four-dimensional NMR spectroscopy of a 723-residue protein: chemical shift assignments and secondary structure of malate synthase g.
J Am Chem Soc. 2002 Aug 28;124(34):10025-35
Authors: Tugarinov V, Muhandiram R, Ayed A, Kay LE
A four-dimensional (4-D) NMR study of Escherichia coli malate synthase G (MSG), a 723-residue monomeric enzyme (81.4 kDa), is described. Virtually complete backbone (1)HN,...
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11-24-2010 08:58 PM
[NMR paper] The chemical shift index: a fast and simple method for the assignment of protein seco
The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy.
Related Articles The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy.
Biochemistry. 1992 Feb 18;31(6):1647-51
Authors: Wishart DS, Sykes BD, Richards FM
Previous studies by Wishart et al. have demonstrated that 1H NMR chemical shifts are strongly dependent on the character and nature of protein secondary structure. In particular, it has been...
Chemical shift transfer: an effective strategy for protein NMR assignment with ARTINA
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