Nuclear magnetic resonance analysis of protein–DNA interactions

Campagne, Sébastien; Gervais, Virginie; Milon, Alain

doi:10.1098/rsif.2010.0543

Cited by 35 publications

(39 citation statements)

References 126 publications

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“…Nevertheless, if during the complex formation, the protein undergoes significant structural modification, chemical shift perturbations can also occur in residues outside the direct interaction site. Since chemical shift perturbations are highly sensitive to binding events, it is a commonly used method to map the binding surfaces of protein-protein, protein-nucleic acid, and protein-small molecule interactions [25–27]. …”

Section: Resultsmentioning

confidence: 99%

Chemical shift perturbation mapping of the Ubc9-CRMP2 interface identifies a pocket in CRMP2 amenable for allosteric modulation of Nav1.7 channels

et al. 2018

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Drug discovery campaigns directly targeting the voltage-gated sodium channel NaV1.7, a highly prized target in chronic pain, have not yet been clinically successful. In a differentiated approach, we demonstrated allosteric control of trafficking and activity of NaV1.7 by prevention of SUMOylation of collapsin response mediator protein 2 (CRMP2). Spinal administration of a SUMOylation incompetent CRMP2 (CRMP2 K374A) significantly attenuated pain behavior in the spared nerve injury (SNI) model of neuropathic pain, underscoring the importance of SUMOylation of CRMP2 as a pathologic event in chronic pain. Using a rational design strategy, we identified a heptamer peptide harboring CRMP2’s SUMO motif that disrupted the CRMP2-Ubc9 interaction, inhibited CRMP2 SUMOylation, inhibited NaV1.7 membrane trafficking, and specifically inhibited NaV1.7 sodium influx in sensory neurons. Importantly, this peptide reversed nerve injury-induced thermal and mechanical hypersensitivity in the SNI model, supporting the practicality of discovering pain drugs by indirectly targeting NaV1.7 via prevention of CRMP2 SUMOylation. Here, our goal was to map the unique interface between CRMP2 and Ubc9, the E2 SUMO conjugating enzyme. Using computational and biophysical approaches, we demonstrate the enzyme/substrate nature of Ubc9/CRMP2 binding and identify hot spots on CRMP2 that may form the basis of future drug discovery campaigns disrupting the CRMP2-Ubc9 interaction to recapitulate allosteric regulation of NaV1.7 for pain relief.

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Section: Resultsmentioning

confidence: 99%

Chemical shift perturbation mapping of the Ubc9-CRMP2 interface identifies a pocket in CRMP2 amenable for allosteric modulation of Nav1.7 channels

et al. 2018

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“…DNA-binding residues should be much more in DNA-binding proteins in comparison to nonbinding proteins. The structural distribution of DNA-binding residues also has some regular pattern, such as DNA-binding residues which tend to gather together spatially on the surface of DNA-binding protein [38]. Two components of BP feature revealed the character of DNA-binding proteins for sequence level and spatial level, respectively.…”

Section: Resultsmentioning

confidence: 99%

Identification of DNA-Binding Proteins Using Support Vector Machine with Sequence Information

Xue

2013

Computational and Mathematical Methods in Medicine

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DNA-binding proteins are fundamentally important in understanding cellular processes. Thus, the identification of DNA-binding proteins has the particularly important practical application in various fields, such as drug design. We have proposed a novel approach method for predicting DNA-binding proteins using only sequence information. The prediction model developed in this study is constructed by support vector machine-sequential minimal optimization (SVM-SMO) algorithm in conjunction with a hybrid feature. The hybrid feature is incorporating evolutionary information feature, physicochemical property feature, and two novel attributes. These two attributes use DNA-binding residues and nonbinding residues in a query protein to obtain DNA-binding propensity and nonbinding propensity. The results demonstrate that our SVM-SMO model achieves 0.67 Matthew's correlation coefficient (MCC) and 89.6% overall accuracy with 88.4% sensitivity and 90.8% specificity, respectively. Performance comparisons on various features indicate that two novel attributes contribute to the performance improvement. In addition, our SVM-SMO model achieves the best performance than state-of-the-art methods on independent test dataset.

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“…To gain insight in the molecular basis of complex formation with SELEX-DNA we utilized NMR spectroscopy [41][42][43][44]. The complex was initially examined through chemical shift perturbation (CSP) experiments.…”

Section: Chemical Shift Mapping Reveals a Unique Binding Mode To Selementioning

confidence: 99%

The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain

Sanchez

Zhang

Evoli

et al. 2019

Preprint

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AbstractThe ATP-dependent BAF chromatin remodeling complex plays a critical role in gene regulation by modulating chromatin architecture, and is frequently mutated in cancer. Indeed, subunits of the BAF complex are found to be mutated in >20% of human tumors. The mechanism by which BAF properly navigates chromatin is not fully understood, but is thought to involve a multivalent network of histone and DNA contacts. We previously identified a composite domain in the BRG1 ATPase subunit that is capable of associating with both histones and DNA in a multivalent manner. Mapping the DNA binding pocket revealed that it contains several cancer mutations. Here, we utilize SELEX-seq to identify the DNA specificity of this composite domain and NMR spectroscopy and molecular modelling to determine the structural basis of DNA binding. Finally, we demonstrate that cancer mutations in this domain alter the mode of DNA association.

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Nuclear magnetic resonance analysis of protein–DNA interactions

Cited by 35 publications

References 126 publications

Chemical shift perturbation mapping of the Ubc9-CRMP2 interface identifies a pocket in CRMP2 amenable for allosteric modulation of Nav1.7 channels

Chemical shift perturbation mapping of the Ubc9-CRMP2 interface identifies a pocket in CRMP2 amenable for allosteric modulation of Nav1.7 channels

Identification of DNA-Binding Proteins Using Support Vector Machine with Sequence Information

The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain

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