Search Results (4)

Photosensitization of proteins mediated by chromophores is a mechanism commonly employed by nature and mimicked in a broad array of laboratory research and applications. Nature has evolved specialized complexes of proteins and photosensitizers (PS) that assemble to form photoreceptor proteins (PRP). These are used by many organisms in diverse processes, such as energy conversion, protection against photodamage, etc. The same concept has been used in laboratory settings for many applications, such as the stimulation of neurons or the selective depletion of proteins in a signaling pathway. A key issue in laboratory settings has been the relationship between the photooxidation of proteins and conformational changes in host proteins. For several years, we have been interested in creating non-native PRP using porphyrin PS. In this study, we investigated the self-assembled complex between zinc protoporphyrin IX (ZnPPIX) and bovine β-lactoglobulin (BLG) as a model of non-native PRP. Since BLG undergoes a significant conformational transition near physiological pH, the study was carried out at acidic (pH 5) and alkaline (pH 9) conditions where the two conformations are respectively prevalent. We employed a series of steady-state and time-resolved optical spectroscopies as well as gel electrophoresis to experimentally characterize the photosensitization mechanisms and their effect on the host protein. Our results show that ZnPPIX prompts light-dependent modifications of BLG, which appear to be much more significant at alkaline pH. The modifications seem to be driven by photooxidation of amino acid residues that do not lead to the formation of cross-links or protein fragmentation. Full article

The human cathelicidin LL-37 is a multifunctional peptide of the human innate immune system. Among the various functions of LL-37, its antimicrobial activity is important in controlling the microorganisms of the human body. The target molecules of LL-37 in bacteria include membrane lipids, lipopolysaccharides (LPS), lipoteichoic acid (LTA), proteins, DNA and RNA. In this mini-review, we summarize the entity of LL-37 structural data determined over the last 15 years and specifically discuss features implicated in the interactions with lipid-like molecules. For this purpose, we discuss partial and full-length structures of LL-37 determined in the presence of membrane-mimicking detergents. This constantly growing structural database is now composed of monomers, dimers, tetramers, and fiber-like structures. The diversity of these structures underlines an unexpected plasticity and highlights the conformational and oligomeric adaptability of LL-37 necessary to target different molecular scaffolds. The recent co-crystal structures of LL-37 in complex with detergents are particularly useful to understand how these molecules mimic lipids and LPS to induce oligomerization and fibrillation. Defined detergent binding sites provide deep insights into a new class of peptide scaffolds, widening our view on the fascinating world of the LL-37 structural factotum. Together, the new structures in their evolutionary context allow for the assignment of functionally conserved residues in oligomerization and target interactions. Conserved phenylalanine and arginine residues primarily mediate those interactions with lipids and LPS. The interactions with macromolecules such as proteins or DNA remain largely unexplored and open a field for future studies aimed at structures of LL-37 complexes. These complexes will then allow for the structure-based rational design of LL-37-derived peptides with improved antibiotic properties. Full article

Intrinsically disordered proteins exist as highly dynamic conformational ensembles of diverse forms. However, the majority of virtual screening only focuses on proteins with defined structures. This means that computer-aided drug discovery is restricted. As a breakthrough, understanding the structural characteristics of intrinsically disordered proteins and its application can open the gate for unrestricted drug discovery. First, we segmented the target disorder-to-order transition region into a series of overlapping 20-amino-acid-long peptides. Folding prediction generated diverse conformations of these peptides. Next, we applied molecular docking, new evaluation score function, and statistical analysis. This approach successfully distinguished known compounds and their corresponding binding regions. Especially, Myc proto-oncogene protein (MYC) inhibitor 10058F4 was well distinguished from others of the chemical compound library. We also studied differences between the two Methyl-CpG-binding domain protein 2 (MBD2) inhibitors (ABA (2-amino-N-[[(3S)-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-acetamide) and APC ((R)-(3-(2-Amino-acetylamino)-pyrrolidine-1-carboxylic acid tert-butyl ester))). Both compounds bind MBD2 through electrostatic interaction behind its p66α-binding site. ABA is also able to bind p66α through electrostatic interaction behind its MBD2-binding site while APC-p66α binding was nonspecific. Therefore, structural heterogeneity mimicking of the disorder-to-order transition region at the peptide level and utilization of the new docking score function represent a useful approach that can efficiently discriminate compounds for expanded virtual screening toward intrinsically disordered proteins. Full article

Biomaterials are important for cell and tissue engineering. Chitosan is widely used as a scaffold because it is easily modified using its amino groups, can easily form a matrix, is stable under physiological conditions, and is inactive for cell adhesion. Chitosan is an excellent platform for peptide ligands, especially cell adhesive peptides derived from extracellular matrix (ECM) proteins. ECM proteins, such as collagen, fibronectin, and laminin, are multifunctional and have diverse cell attachment sites. Various cell adhesive peptides have been identified from the ECM proteins, and these are useful to design functional biomaterials. The cell attachment activity of peptides is influenced by the solubility, conformation, and coating efficiency to solid materials, whereas immobilization of peptides to a polysaccharide such as chitosan avoids these problems. Peptide–chitosan matrices promote various biological activities depending on the peptide. When the peptides are immobilized to chitosan, the activity of the peptides is significantly enhanced. Further, mixed peptide–chitosan matrices, conjugated with more than one peptide on a chitosan matrix, interact with multiple cellular receptors and promote specific biological responses via receptor cross-talk. Receptor cross-talk is important for mimicking the biological activity of ECM and the proteins. The mixed peptide–chitosan matrix approach is useful to develop biomaterials as a synthetic ECM for cell and tissue engineering. Full article