Post-translational methylation of lysine side chains is of great importance for protein regulation, including epigenetic control. Here, we present specific CHD labeling of dimethylated lysines as a sensitive probe of the structure, interactions, and dynamics of these groups, and outline a theoretical and experimental framework for analyzing their conformational dynamics using H and C CPMG relaxation dispersion experiments. Dimethylated lysine side chains in calcium-loaded calmodulin show a marked pH dependence of their Carr-Purcell-Meiboom-Gill (CPMG) dispersion profiles, indicating complex exchange behavior. Combined analysis of H and C CPMG relaxation dispersions requires consideration of 12-state correlated exchange of the two methyl groups due to circular three-state rotamer jumps around the Cε-Nζ axis combined with proton exchange and amine inversion. Taking into account a number of fundamental constraints, the exchange model can be reduced to include only three fitted parameters, namely, the geometric average of the rotamer-jump rate constants, the rate constant of deprotonation of Nζ, and the chemical shift difference between the trans and gauge positions of the C or H nuclei. The pH dependence indicates that protonation of the end group dramatically slows down rotamer exchange for some lysine residues, whereas deprotonation leads to rapid amine inversion coupled with rotamer scrambling. The observed variation among residues in their exchange behavior appears to depend on the structural environment of the side chain. Understanding this type of exchange process is critical to correctly interpreting NMR spectra of methylated lysine side chains. The exchange model presented here forms the basis for studying the structure and dynamics of epigenetically modified lysine side chains and perturbations caused by changes in pH or interactions with target proteins.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/acs.jpcb.9b06408 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
PEGylation of Dipeptide Linker Improves Therapeutic Index and Pharmacokinetics of Antibody-Drug Conjugates.
Bioconjug Chem
January 2025
Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
Hydrophobic payloads incorporated into antibody-drug conjugates (ADCs) typically are superior to hydrophilic ones in tumor penetration and "bystander killing" upon release from ADCs. However, they are prone to aggregation and accelerated plasma clearance, which lead to reduced efficacies and increased toxicities of ADC molecules. Shielding the hydrophobicity of payloads by incorporating polyethylene glycol (PEG) elements or sugar groups into the ADC linkers has emerged as a viable alternative to directly adopting hydrophilic payloads.
View Article and Find Full Text PDFMany protein bioconjugation strategies focus on the modification of lysine residues owing to the nucleophilicity of their amine side-chain, the generally high abundance of lysine residues on a protein's surface and the ability to form robustly stable amide-based bioconjugates. However, the plethora of solvent accessible lysine residues, which often have similar reactivity, is a key inherent issue when searching for regioselectivity and/or controlled loading of an entity. A relevant example is the modification of antibodies and/or antibody fragments, whose conjugates offer potential for a wide variety of applications.
View Article and Find Full Text PDFRiboflavin-mediated ultraviolet photosensitive oxidation of beef myofibrillar proteins with different storage times.
Food Chem
January 2025
Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Product Processing, Ministry of Agriculture, Beijing 100193, China; Zibo Institute for Digital Agriculture and Rural Research, Zibo 255051, China. Electronic address:
The study was designed to investigate the mechanism of Riboflavin (RF)-mediated UVA photosensitive oxidation on beef myofibrillar proteins (MP) oxidized at different storage times. To elucidate the direct relationship between RF and protein oxidation, the mechanism of action was analyzed in terms of amino acid and side chain residues, protein structure, and protein oxidative metabolism. Oxidation of MP resulted in significant changes in the levels of carbonyls, sulfhydryls, Lysine, Arginine, Threonin, and Histidine.
View Article and Find Full Text PDFAlginate Heterografted Copolymer Thermo-Induced Hydrogel Reinforced by PAA-g-P(boc-L-Lysine): Effects on Hydrogel Thermoresponsiveness.
Polymers (Basel)
December 2024
Department of Chemical Engineering, University of Patras, 26500 Patras, Greece.
In this article, we report on the alginate heterografted by Poly(N-isopropyl acrylamide-co-N-tert-butyl acrylamide) and Poly(N-isopropyl acrylamide) (ALG-g-P(NIPAM86-co-NtBAM14)-g-PNIPAM) copolymer thermoresponsive hydrogel, reinforced by substituting part of the 5 wt% aqueous formulation by small amounts of Poly(acrylic acid)-g-P(boc-L-Lysine) (PAA-g-P(b-LL)) graft copolymer (up to 1 wt%). The resulting complex hydrogels were explored by oscillatory and steady-state shear rheology. The thermoresponsive profile of the formulations were affected remarkably by increasing the PAA-g-P(b-LL) component of the polymer blend.
View Article and Find Full Text PDFSynthesis of Temporin-SHa Retro Analogs with Lysine Addition/Substitution and Antibiotic Conjugation to Enhance Antibacterial, Antifungal, and Anticancer Activities.
Antibiotics (Basel)
December 2024
Third World Center for Science and Technology, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
In the face of rising the threat of resistant pathogens, antimicrobial peptides (AMPs) offer a viable alternative to the current challenge due to their broad-spectrum activity. This study focuses on enhancing the efficacy of temporin-SHa derived NST-2 peptide (), which is known for its antimicrobial and anticancer activities. We synthesized new analogs of using three strategies, i.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!