In solution NMR, chemical shift perturbation (CSP) experiments are widely employed to study intermolecular interactions. However, excluding the nonsignificant peak shift is difficult because little is known about errors in CSP. Here, to address this issue, we introduce a method for estimating errors in CSP based on the noise level. First, we developed a technique that involves line shape fitting to estimate errors in peak position via Monte Carlo simulations. Second, this technique was applied...
[NMR paper] pH Effects Can Dominate Chemical Shift Perturbations in 1H,15N-HSQC NMR Spectroscopy for Studies of Small Molecule/?-Synuclein Interactions
pH Effects Can Dominate Chemical Shift Perturbations in 1H,15N-HSQC NMR Spectroscopy for Studies of Small Molecule/?-Synuclein Interactions
¹H,^(15)N-Heteronuclear Single Quantum Coherence (HSQC) NMR is a powerful technique that has been employed to characterize small-molecule interactions with intrinsically disordered monomeric ?-Synuclein (aSyn). We report how solution pH can impact the interpretation of aSyn HSQC NMR spectra and demonstrate that small-molecule formulations (e.g., complexation with acidic salts) can lower sample pH and confound interpretation of drug binding and...
nmrlearner
Journal club
0
02-08-2023 10:25 PM
[NMR paper] Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori.
Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori.
Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori.
J Biomol NMR. 2016 Mar 10;
Authors: Gardiennet C, Wiegand T, Bazin A, Cadalbert R, Kunert B, Lacabanne D, Gutsche I, Terradot L, Meier BH, Böckmann A
Abstract
We here investigate the interactions between the DnaB helicase and the C-terminal domain of the...
nmrlearner
Journal club
0
03-11-2016 12:00 PM
Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori
Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori
Abstract
We here investigate the interactions between the DnaB helicase and the C-terminal domain of the corresponding DnaG primase of Helicobacter pylori using solid-state NMR. The difficult crystallization of this 387Â*kDa complex, where the two proteins interact in a six to three ratio, is circumvented by simple co-sedimentation of the two proteins directly into the MAS-NMR rotor. While the amount of information...
nmrlearner
Journal club
0
03-10-2016 10:40 PM
CSI 2.0: a significantly improved version of the Chemical Shift Index
CSI 2.0: a significantly improved version of the Chemical Shift Index
Abstract
Protein chemical shifts have long been used by NMR spectroscopists to assist with secondary structure assignment and to provide useful distance and torsion angle constraint data for structure determination. One of the most widely used methods for secondary structure identification is called the Chemical Shift Index (CSI). The CSI method uses a simple digital chemical shift filter to locate secondary structures along the protein chain using backbone 13C and 1H chemical...
nmrlearner
Journal club
0
10-02-2014 06:36 AM
Proteinâ??ligand structure guided by backbone and side-chain proton chemical shift perturbations
Proteinâ??ligand structure guided by backbone and side-chain proton chemical shift perturbations
Abstract
The fragment-based drug design approach consists of screening libraries of fragment-like ligands, to identify hits that typically bind the protein target with weak affinity ( \(100\,\upmu \hbox {M}\) â??5Â*mM). The determination of the proteinâ??fragment complex 3D structure constitutes a crucial step for uncovering the key interactions responsible for...
nmrlearner
Journal club
0
09-26-2014 01:03 PM
[NMR paper] Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations.
Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations.
Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations.
J Am Chem Soc. 2013 Oct 14;
Authors: Kukic P, Farrell D, McIntosh LP, Garcia-Moreno E B, Jensen KS, Toleikis Z, Teilum K, Nielsen JE
Abstract
Understanding the connection between protein structure and function requires a quantitative understanding of electrostatic effects. Structure-based electrostatics calculations are essential for this purpose, but their use have been limited by a...
nmrlearner
Journal club
0
10-16-2013 11:22 AM
Improved chemical shift prediction by Rosetta conformational sampling
Improved chemical shift prediction by Rosetta conformational sampling
Abstract Chemical shift frequencies represent a time-average of all the conformational states populated by a protein. Thus, chemical shift prediction programs based on sequence and database analysis yield higher accuracy for rigid rather than flexible protein segments. Here we show that the prediction accuracy can be significantly improved by averaging over an ensemble of structures, predicted solely from amino acid sequence with the Rosetta program. This approach to chemical shift and structure prediction has the...
Improved analysis of NMR chemical shift perturbations through an error estimation method
Linear Mode
