NMR spectroscopy is an important tool for the measurement of the electrostatic properties of biomolecules. To this point, paramagnetic relaxation enhancements (PREs) of ¹H nuclei arising from nitroxide cosolutes in biomolecular solutions have been used to measure effective near-surface electrostatic potentials (?(ENS)) of proteins and nucleic acids. Here, we present a gadolinium (Gd)-based NMR method, exploiting Gd chelates with different net charges, for measuring ?(ENS) values and demonstrate...
[NMR paper] Influence of an Intrinsically Disordered Region on Protein Domains Revealed by NMR-Based Electrostatic Potential Measurements
Influence of an Intrinsically Disordered Region on Protein Domains Revealed by NMR-Based Electrostatic Potential Measurements
Many human proteins possess intrinsically disordered regions containing consecutive aspartate or glutamate residues ("D/E repeats"). Approximately half of them are DNA/RNA-binding proteins. In this study, using nuclear magnetic resonance (NMR) spectroscopy, we investigated the electrostatic properties of D/E repeats and their influence on folded domains within the same protein. Local electrostatic potentials were directly measured for the HMGB1 protein, its isolated...
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05-22-2024 02:25 AM
[NMR paper] NMR screening method based on 19F spin-spin relaxation time for analyses of fluorinated compound bound to proteins
NMR screening method based on 19F spin-spin relaxation time for analyses of fluorinated compound bound to proteins
NMR screening methods based on ^(19)F spin-spin relaxation time (^(19)F-T(2)) were applied to fluorinated compounds bound to human serum albumin. Diflunisal and fleroxacin (the fluorinated compounds) contain two and three fluorine atoms per molecule, respectively, and are suitable as the model system for ^(19)F NMR analysis. It was shown that ^(19)F-T(2) was more sensitive in monitoring the binding affinity to the target protein than ^(19)F spin-lattice relaxation time...
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10-17-2023 03:24 AM
[NMR paper] De novo determination of near-surface electrostatic potentials by NMR
De novo determination of near-surface electrostatic potentials by NMR
Electrostatic potentials computed from three-dimensional structures of biomolecules by solving the Poisson-Boltzmann equation are widely used in molecular biophysics, structural biology, and medicinal chemistry. Despite the approximate nature of the Poisson-Boltzmann theory, validation of the computed electrostatic potentials around biological macromolecules is rare and methodologically limited. Here, we present a unique and powerful NMR method that allows for straightforward and extensive...
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07-03-2021 08:12 PM
[NMR paper] NMR Spin Relaxation Theory of Biomolecules Undergoing Highly Asymmetric Exchange with Large Interaction Partners
NMR Spin Relaxation Theory of Biomolecules Undergoing Highly Asymmetric Exchange with Large Interaction Partners
The transient interactions of proteins and other molecules with much larger structures, such as synthetic or biological nanoparticles, lead to certain types of enhanced nuclear magnetic resonance (NMR) spin relaxation effects, which can be accurately measured by multidimensional solution NMR techniques. These relaxation effects provide new information about the nanostructures and the protein, their interactions, internal dynamics, and associated kinetic and thermodynamic...
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03-23-2021 07:56 PM
Gadolinium based endohedral metallofullerene Gd2@C79N as a relaxation boosting agent for dissolution DNP at high fields
From The DNP-NMR Blog:
Gadolinium based endohedral metallofullerene Gd2@C79N as a relaxation boosting agent for dissolution DNP at high fields
Wang, X., et al., Gadolinium based endohedral metallofullerene Gd2@C79N as a relaxation boosting agent for dissolution DNP at high fields. Chem Commun (Camb), 2018. 54(19): p. 2425-2428.
https://www.ncbi.nlm.nih.gov/pubmed/29457159
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05-08-2018 02:39 AM
[NMR paper] Electrostatic Energetics of Bacillus subtilis Ribonuclease P Protein by NMR-based Histidine pKa Measurements.
Electrostatic Energetics of Bacillus subtilis Ribonuclease P Protein by NMR-based Histidine pKa Measurements.
Electrostatic Energetics of Bacillus subtilis Ribonuclease P Protein by NMR-based Histidine pKa Measurements.
Biochemistry. 2015 Aug 12;
Authors: Mosley PL, Daniels KG, Oas TG
Abstract
The pKa values of ionizable groups in proteins report the free energy of site-specific proton binding and provide a direct means of studying pH-dependent stability. We measured histidine pKa values (H3, H22, and H105) in the unfolded...
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08-13-2015 02:00 PM
Mapping Membrane Protein Backbone Dynamics: A Comparison of Site-Directed Spin Labeling with NMR 15N-Relaxation Measurements
Mapping Membrane Protein Backbone Dynamics: A Comparison of Site-Directed Spin Labeling with NMR 15N-Relaxation Measurements
Publication date: 7 October 2014
Source:Biophysical Journal, Volume 107, Issue 7</br>
Author(s): Ryan*H. Lo , Brett*M. Kroncke , Tsega*L. Solomon , Linda Columbus</br>
The ability to detect nanosecond backbone dynamics with site-directed spin labeling (SDSL) in soluble proteins has been well established. However, for membrane proteins, the nitroxide appears to have more interactions with the protein surface, potentially hindering the...
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10-08-2014 04:17 AM
[KPWU blog] [PyMOL] side-by-side comparison of 3 electrostatic surface potentials
side-by-side comparison of 3 electrostatic surface potentials
Here is an example using “grid mode” provided in PyMOL to show the charged states of a protein (PDB entry: 1Z66) at pH 4 (left), 7 (center) and 11 (right). *PyMOL script is attached after the figure. First, *the potential maps at three pH states have to be generated. I used APBS web http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=798&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
Gadolinium-Based NMR Spin Relaxation Measurements of Near-Surface Electrostatic Potentials of Biomolecules
Linear Mode
