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Evolution in its course has found a variety of solutions to the same optimisation problem. The advent of high-throughput genomic sequencing has made available extensive data from which, in principle, one can infer the underlying structure on which biological functions rely. In this paper, we present a new method aimed at the extraction of sites encoding structural and functional properties from a set of protein primary sequences, namely a multiple sequence alignment. The method, called critical variable selection, is based on the idea that subsets of relevant sites correspond to subsequences that occur with a particularly broad frequency distribution in the dataset. By applying this algorithm to in silico sequences, to the response regulator receiver and to the voltage sensor domain of ion channels, we show that this procedure recovers not only the information encoded in single site statistics and pairwise correlations but also captures dependencies going beyond pairwise correlations. The method proposed here is complementary to statistical coupling analysis, in that the most relevant sites predicted by the two methods differ markedly. We find robust and consistent results for datasets as small as few hundred sequences that reveal a hidden hierarchy of sites that are consistent with the present knowledge on biologically relevant sites and evolutionary dynamics. This suggests that critical variable selection is capable of identifying a core of sites encoding functional and structural information in a multiple sequence alignment.

Protein expression is closely related to many biological processes including cell growth, differentiation and signaling. It is a challenge to selectively monitor newly synthesized proteins under both physiological and pathological conditions due to shortage of efficient analytical methods. Here, we proposed a new strategy to selectively monitor newly synthesized proteins in cells by combining fluorescence correlation spectroscopy (FCS) with bioorthogonal noncanonical amino acid tagging (BONCAT) technique. Firstly, homopropargylglycine (HPG), an alkyne surrogate of methionine, was metabolically incorporated into newly synthesized proteins in living cells, and the proteins containing the alkyne functional group were subsequently labeled with chemoselective fluorescence reporters using the Cu(I)-catalyzed azide–alkyne cycloaddition (CuAAC) reaction. Then, FCS was used to analyze the newly synthesized proteins based on the difference in the characteristic diffusion times of labeled proteins and free fluorescent dyes. We optimized the conditions of HPG metabolic incorporation and the CuAAC click reaction and applied this new method to study autophagic protein degradation and in situ monitor secreted proteins in cells. Compared to current methods, our method is simple, fast, and without separation, and it may become a promising approach for in situ studying protein expression in living cells. [ABSTRACT FROM AUTHOR]

Organometallic complexes have important application in the field of protein staining, with potential for use in proteomic analysis. The rational synthesis of a trinuclear luminescent organometallic complex with two platinum(II) centres appended to the cyclometalated ligand of the iridium(III) centre is reported here. Two di-2-picolylamine groups bonded to the cyclometalated phenyl pyridine moiety provide three coordinating sites to each platinum centre. The replacement of chloride in the fourth coordination site of two square planar platinum metal centres with the imidazole nitrogen or sulphur atom of histidine/cysteine is evident from the change in luminescence intensity upon binding these amino acids. The increase in luminescence emission intensity upon binding of histidine to the organometallic complex allowed it to be used as a protein staining agent. Reversibility of staining upon washing with imidazole enhances the possibility of its application in mass spectrometric analysis. [ABSTRACT FROM AUTHOR]

Microalgae-based bulk production, especially for biofuel, is not yet economically feasible. One way to improve financial performance of such systems is to maximise value through a biorefinery approach (e.g. co-production streams, waste minimisation). This can be implemented via extraction of valuable intracellular compounds upon cell disruption; however both low-cost, energy efficient, and scalable cell disruption techniques, and green chemicals are required. Waste heat is a readily available resource in most production plants, and can be used to power a hydrothermal pre-treatment (HTP) step to disrupt the cells. In this study, we use HTP (120–180 °C, 5–30 min) to disrupt Chlorella sp. cell walls. We perform a subsequent water-miscible solvent and/or urea extraction (UX) to solubilise and recover proteins. The maximum extraction efficiency of 62% was achieved after HTP at 180 °C for 10 min. Regardless of the reaction time, 120 °C was found to be ineffective for protein extraction. The efficiency can be further increased to 84% if a filter-washing step with acetone and urea is implemented. Most of the recovered proteins are between 8 to 14 kDa across all temperature ranges, suggesting that extraction efficiency depended both on partial protein hydrolysis and on accessibility to solvent (i.e. cell wall degradation, solid dispersion, membrane solubilisation). The most significant amino acid losses on a per mole basis were lysine (22%) and arginine (14%). The production of flexible and high-value protein-based products via HTP-UX may enable a circular and sustainable production step for microalgal biorefineries, while improving the downstream fuel processes through nitrogen heteroatom reduction. [ABSTRACT FROM AUTHOR]

Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications. [ABSTRACT FROM AUTHOR]

One of the most attractive areas in inorganic chemistry is the synthesis of polyoxometalates (POMs) exhibiting new properties and applications. Since the impact of POMs in biochemistry and related fields of research has increased in the last few years, there has been a special interest in this topic. Significant progress in biological applications has been made where the interaction of POMs with amino acids, peptides and proteins is relevant. Versatile POMs play a series of different roles in the interaction with these biomolecules as described in this review. Various types of interactions are established, depending on the POM shape and charge, the amino acid side chain, peptide sequence or protein structure. Experimental conditions such as temperature, acidity, solvent, etc. are also important factors that influence the binding/reactivity of POM with biomolecules, as described herein. This understanding allows the adequate design of the POM-biomolecule couple for tailoring and controlling mechanisms of action such as catalysis, inhibition, and aggregation, or the crystallising agent. [ABSTRACT FROM AUTHOR]