Determining the Binding Constant of LANA Protein Fragment with Nucleosome

Novikov, R. V.; Bondarenko, Elena; Malyuchenko, N. V.; Feofanov, Аlexey V.; Studitsky, Vasily M.; Shaytan, Alexey K.

doi:10.3103/s0096392520040070

Cited by 1 publication

(2 citation statements)

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“…For the most studied nucleosome-binding peptide-the LANA peptide-conflicting binding affinity estimates have been reported. Studies based on fluorescence polarization and thermophoresis assays have reported Kd values around 200 nM, while studies using gel electrophoresis to detect and quantify LANA-bound nucleosome reported estimates in the range of 1-10 µM [16,27,33]. We revisited this question in this work using a fluorescence polarization assay and reported a binding constant of around 400 nM ± 0.1 nM or lower, suggesting that the LANA nucleosome-binding constant may indeed be in the submicromolar range, at least for the binding buffer used in this study.…”

Section: Discussionmentioning

confidence: 99%

“…Ideally, nucleosome-binding peptides should have high (yet tunable) affinity and high specificity. The reported data currently suggests that the LANA 1-23 peptide may bind nucleosomes with an affinity as high as 160 nM [31], although some studies report lower affinity values (~180 nM [32], 250 nM [26], 8 µM [27], 1-9 µM [33]). The CENP-C motif peptides have been reported to bind canonical nucleosomes with an affinity of ~1-6 µM [25], and CTD-IE1 with an affinity of 420 nM [26].…”

Section: Introductionmentioning

confidence: 99%

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Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study

Oleinikov,

Fedulova,

Armeev

et al. 2023

IJMS

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In eukaryotic organisms, genomic DNA associates with histone proteins to form nucleosomes. Nucleosomes provide a basis for genome compaction, epigenetic markup, and mediate interactions of nuclear proteins with their target DNA loci. A negatively charged (acidic) patch located on the H2A-H2B histone dimer is a characteristic feature of the nucleosomal surface. The acidic patch is a common site in the attachment of various chromatin proteins, including viral ones. Acidic patch-binding peptides present perspective compounds that can be used to modulate chromatin functioning by disrupting interactions of nucleosomes with natural proteins or alternatively targeting artificial moieties to the nucleosomes, which may be beneficial for the development of new therapeutics. In this work, we used several computational and experimental techniques to improve our understanding of how peptides may bind to the acidic patch and what are the consequences of their binding. Through extensive analysis of the PDB database, histone sequence analysis, and molecular dynamic simulations, we elucidated common binding patterns and key interactions that stabilize peptide–nucleosome complexes. Through MD simulations and FRET measurements, we characterized changes in nucleosome dynamics conferred by peptide binding. Using fluorescence polarization and gel electrophoresis, we evaluated the affinity and specificity of the LANA1-22 peptide to DNA and nucleosomes. Taken together, our study provides new insights into the different patterns of intermolecular interactions that can be employed by natural and designed peptides to bind to nucleosomes, and the effects of peptide binding on nucleosome dynamics and stability.

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Section: Discussionmentioning

confidence: 99%