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An automated iterative approach for protein structure refinement using pseudocontact shifts
Aug 02, 2021 - 5:20 PM - by nmrlearner
nmrlearner's Avatar An automated iterative approach for protein structure refinement using pseudocontact shifts

Abstract

NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing.



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Engineering Biologics toward Challenging Membrane Protein Targets - Genetic Engineering & Biotechnology News
Aug 02, 2021 - 5:20 PM - by nmrlearner
nmrlearner's Avatar Engineering Biologics toward Challenging Membrane Protein Targets Genetic Engineering & Biotechnology News
Engineering Biologics toward Challenging Membrane Protein Targets - Genetic Engineering & Biotechnology News
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0 Replies | 6 Views
Researchers discover titanium oxide nanoparticle that recognizes SARS-CoV-2ís non-structural protein 1 - News-Medical.Net
Aug 02, 2021 - 5:20 PM - by nmrlearner
nmrlearner's Avatar Researchers discover titanium oxide nanoparticle that recognizes SARS-CoV-2ís non-structural protein 1 - News-Medical.Net

Researchers discover titanium oxide nanoparticle that recognizes SARS-CoV-2ís non-structural protein 1 News-Medical.Net Read here
0 Replies | 6 Views
Protein Crystallization & Crystallography Market Research Report by Technology, by Product & Service, by End User - GlobeNewswire
Aug 02, 2021 - 5:20 PM - by nmrlearner
nmrlearner's Avatar Protein Crystallization & Crystallography Market Research Report by Technology, by Product & Service, by End User - GlobeNewswire

Protein Crystallization & Crystallography Market Research Report by Technology, by Product & Service, by End User GlobeNewswire Read here
0 Replies | 6 Views
[NMR paper] Structure and Dynamics Perturbations in Ubiquitin Adsorbed or Entrapped in Silica Materials Are Related to Disparate Surface Chemistries Resolved by Solid-State NMR Spectroscopy
Aug 02, 2021 - 5:20 PM - by nmrlearner
nmrlearner's Avatar Structure and Dynamics Perturbations in Ubiquitin Adsorbed or Entrapped in Silica Materials Are Related to Disparate Surface Chemistries Resolved by Solid-State NMR Spectroscopy

Protein immobilization on material surfaces is emerging as a powerful tool in the design of devices and active materials for biomedical and pharmaceutical applications as well as for catalysis. Preservation of the protein's biological functionality is crucial to the design process and is dependent on the ability to maintain its structural and dynamical integrity while removed from the natural surroundings. The scientific techniques to validate the structure of immobilized proteins are scarce and...

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0 Replies | 11 Views
[NMR paper] The accuracy of NMR protein structures in the Protein Data Bank
Aug 01, 2021 - 4:02 PM - by nmrlearner
nmrlearner's Avatar The accuracy of NMR protein structures in the Protein Data Bank

The program ANSURR measures the accuracy of NMR structures by comparing rigidity obtained from experimental backbone chemical shifts and from structures. We report on ANSURR analysis of 7,000 PDB NMR ensembles within the Protein Data Bank, which can be found at ansurr.com. The accuracy of NMR structures progressively improved up until 2005, but since then, it has plateaued. Most structures have accurate secondary structure, but are generally too floppy, particularly in loops. Thus, there is a...

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[NMR paper] GlycA measured by NMR spectroscopy is associated with disease activity and cardiovascular disease risk in chronic inflammatory diseases
Jul 31, 2021 - 7:13 AM - by nmrlearner
nmrlearner's Avatar GlycA measured by NMR spectroscopy is associated with disease activity and cardiovascular disease risk in chronic inflammatory diseases

GlycA is a biomarker of systemic inflammation, quantifying both the protein concentrations and glycosylation states of several acute phase proteins. GlycA has been shown to be associated with both subclinical atherosclerosis and with cardiovascular disease (CVD). GlycA levels are higher in acute and chronic inflammation. During ongoing systemic inflammatory processes, GlycA specific acute phase reactants and proteins undergo circulating concentration and glycosylation pattern changes, and these...

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