Folding of poly-amino acids and intrinsically disordered proteins in overcrowded milieu induced by pH change

pH-induced structural changes of the synthetic homopolypeptides poly-E, poly-K, poly-R, and intrinsically disordered proteins (IDPs) prothymosin alpha (ProT alpha) and linker histone H1, in concentrated PEG solutions simulating macromolecular crowding conditions within the membrane-less organelles, were characterized. The conformational transitions of the studied poly-amino acids in the concentrated PEG solutions depend on the polymerization degree of these homopolypeptides, the size of their side chains, the charge distribution of the side chains, and the crowding agent concentration. The results obtained for poly-amino acids are valid for IDPs having a significant total charge. The overcrowded conditions promote a significant increase in the cooperativity of the pH-induced coil-alpha-helix transition of ProTa and provoke histone H1 aggregation. The most favorable conditions for the pH-induced structural transitions in concentrated PEG solutions are realized when the charged residues are grouped in blocks, and when the distance between the end of the side group carrying charge and the backbone is small. Therefore, the block-wise distribution of charged residues within the IDPs not only plays an important role in the liquid-liquid phase transitions, but may also define the expressivity of structural transitions of these proteins in the overcrowded conditions of the membrane-less organelles. (C) 2018 Elsevier B.V. All rights reserved.Peer reviewe

C-terminal domain of nonhistone protein HMGB1 as a modulator of HMGB1–DNA structural interactions

The HMGB1 protein (High Mobility Group protein 1) participates in the formation of functionally significant DNA-protein complexes. HMGB1 protein contains two DNA-binding domains and negatively charged C-terminal region. The latter consists of continuous sequence of dicarboxylic amino acids residues. Structural changes in DNA-protein complexes were studied by circular dichroism spectroscopy (CD) and atomic force microscopy (AFM). Natural HMGB1 and recombinant protein HMGB1(A + B) lacked negatively charged C-terminal region were used. The DNA–HMGB1(A + B) complexes demonstrate an unusually high optical activity in 150 mM NaCl solutions. AFM of the latter complexes shows, that at the low concentration of HMGB1 in the complex the protein is distributed along DNA in a random way. Increase of HMGB1 content leads to cooperative interaction and a redistribution of the bound protein molecules on DNA is observed. Based on the data obtained we conclude that protein–protein interactions play a key role in the formation of highly ordered DNA–HMGB1 complexes. It was shown that C-terminal domain modulate the interactions of DNA with HMGB1 protein. We suggest that the C-terminal domain of HMGB1 also modulates the “packing” of HMGB1 molecules on the DNA.Peer Reviewe

New age data on kimberlites from the Yakutian diamondiferous province

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Fluorescent silver clusters on protein templates: understanding their structure

Luminescent metal nanoclusters (NCs) stabilized by natural proteins are of special interest in bioimaging applications. However, the detailed structure of the protein-templated NCs and the nature of their emissive states remain poorly understood. A fair amount of nonluminescent metal ions and clusters complexed to the proteins hinders probing of the structure of the emitting clusters using mass spectroscopy, infrared, or other conventional spectroscopy methods. In this respect, only luminescent excitation spectra distinguish the emitting NCs. In this experimental and theoretical joint study, we modeled the fluorescent excitation and excitation anisotropy spectra of protein-based silver (Ag) NCs. We varied the synthesis conditions and studied the spectral properties of Ag clusters on bovine serum albumin (BSA) and lysozyme, which had already been used as templates, as well as on HMG box (HMGB1) and histone H1 (H1) proteins. We also calculated the electronic spectra of quantum mechanics-optimized Ag–thiolate, Ag–semiquinone, and Ag–formaldehyde complexes with two confined electrons using second-order algebraic diagrammatic construction [ADC(2)] and resolution-of-identity approximate coupled-cluster singles-and-doubles (RI-CC2) methods and compared them with the experimental spectra. We propose a model for the fluorescent Ag–protein complexes in which two reduced Ag atoms are sufficient to form the fluorescent core of the complex. The proposed structural model of the luminescent centers in the Ag–protein complexes differs from the common view that the fluorescent metal NCs in proteins contain about 10 or more metal atoms. The fluorescent Ag clusters formed on the four investigated natural protein matrices exhibited two different spectral and structural patterns. Deprotonated free cysteine residues stabilized the fluorescent Ag3+1 core formed in the BSA matrix. The second type of fluorescent center was realized in the H1, HMGB1, and lysozyme protein matrixes. In this case, tyrosine residues probably stabilize the fluorescent Ag2 centers