Related ArticlesQuantitative Protein Disorder Assessment Using NMR Chemical Shifts.
Methods Mol Biol. 2020;2141:303-317
Authors: Nielsen JT, Mulder FAA
Abstract
Disorder is vital for the biological function of many proteins. The huge diversity found in disorder composition and amplitude reflects the complexity and pluripotency of intrinsically disordered proteins (IDPs). The first step toward a better understanding of IDPs is a quantitative and position-specific experimental characterization, and nuclear magnetic resonance (NMR) spectroscopy has emerged as the method of first choice. Here, we describe how to quantitatively assess the local balance between order and disorder in proteins by utilizing the Chemical shift Z-score for assessing Order/Disorder (CheZOD Z-score). This order/disorder metric is computed from the difference between experimentally determined NMR chemical shifts and computed random coil reference values. We explain in detail how CheZOD Z-scores are calculated fast and easily, either by using a python executable or by data submission to a server.
Non-uniform sampling in quantitative assessment of heterogeneous solid-state NMR line shapes
Non-uniform sampling in quantitative assessment of heterogeneous solid-state NMR line shapes
Abstract
Non-uniform sampling has been successfully used for solution and solid-state NMR of homogeneous samples. In the solid state, protein samples are often dominated by inhomogeneous contributions to the homogeneous line widths. In spite of different technical strategies for peak reconstruction by different methods, we validate that NUS can generally be used also for such situations where spectra are made up of complex peak shapes rather than Lorentian...
[NMR paper] Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.
Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.
Related Articles Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.
Comput Theor Chem. 2017 Jan 01;1099:152-166
Authors: Koes DR, Vries JK
Abstract
Accurate chemical shifts for the atoms in molecular mechanics (MD) trajectories can be obtained from quantum mechanical (QM) calculations that depend solely on the coordinates of the atoms in the localized regions surrounding atoms of interest. If these...
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[NMR paper] Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
J Phys Chem B. 2013 Feb 1;
Authors: Camilloni C, Cavalli A, Vendruscolo M
Abstract
It has been recently...
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02-03-2013 10:19 AM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
January 2012
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
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The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction...
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12-01-2012 06:10 PM
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
Abstract The combination of the wide availability of protein backbone and side-chain NMR chemical shifts with advances in understanding of their relationship to protein structure makes these parameters useful for the assessment of structural-dynamic protein models. A new chemical shift predictor (PPM) is introduced, which is solely based on physicalâ??chemical contributions to the chemical shifts for both the protein backbone and methyl-bearing amino-acid side chains. To...
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09-15-2012 09:04 AM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
Jakob T. Nielsen, Hamid R. Eghbalnia, Niels Chr. Nielsen</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise,...
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03-09-2012 09:16 AM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Publication year: 2011
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 23 May 2011</br>
Jakob T., Nielsen , Hamid R., Eghbalnia , Niels Chr., Nielsen</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we...
Quantitative Protein Disorder Assessment Using NMR Chemical Shifts.
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