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Proteinoids - thermal proteins - are produced by heating amino acids to their melting point and initiation of polymerisation to produce polymeric chains. Proteinoids swell in aqueous solution into hollow microspheres. The proteinoid microspheres produce endogenous burst of electrical potential spikes and change patterns of their electrical activity in response to illumination. The microspheres can interconnect by pores and tubes and form networks with a programmable growth. We speculate on how ensembles of the proteinoid microspheres can be developed into unconventional computing devices., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Microfluidic chip electrophoresis has been widely employed for separation of various biochemical species owing to its advantages of low sample consumption, low cost, fast analysis, high throughput, and integration capability. In this article, we reviewed the development of four different modes of microfluidics-based electrophoresis technologies including capillary electrophoresis, gel electrophoresis, dielectrophoresis, and field (electric) flow fractionation. Coupling detection schemes on microfluidic electrophoresis platform were also reviewed such as optical, electrochemical, and mass spectrometry method. We further discussed the innovative applications of microfluidic electrophoresis for biomacromolecules (nucleic acids and proteins), biochemical small molecules (amino acids, metabolites, ions, etc.), and bioparticles (cells and pathogens) analysis. The future direction of microfluidic chip electrophoresis was predicted., (© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Here we report two phase modulated NMR experiments: PM-2D HN(CACBHB) and PM-2D HN(HB), that use 1 H β chemical shifts to rapidly identify amino acid type in proteins. The magnetization on the 1 H β spins during the experiments is allowed to evolve for a fixed evolution period that results in phase modulation (positive or negative) of the cross peaks corresponding to various amino acid residues on their 2D HN projections, resembling a typical 2D [ 1 H- 15 N]-HSQC spectrum. All amino acids except glycine can be categorized into three discernible groups based on their 1 H β chemical shifts, resulting in unique phase patterns at different fixed evolution periods for 1 H β , thus facilitating their identification. Remarkably, the PM-2D HN(HB) stands out among all amino acid type identification NMR techniques for its applicability with cost-effective and most routinely employed 15 N-labeled protein samples for NMR studies. Furthermore, when combined effectively with the 13 C β chemical shift-based phase modulated NMR method (PM-2D HN(CACB)), these methods resolved the identification of large groups of amino acids into relatively smaller groups. Moreover, these techniques can accelerate the sequence-specific sequential resonance assignment (SSRA) process and would help in fast tracking of assigned NMR signals exhibiting chemical shift perturbation on the 2D [ 1 H- 15 N]-HSQC spectrum of proteins during various experiments (e.g., temperature change, pH change, and protein or ligand or cofactor binding) as well as in site-directed mutagenesis., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Amino acid scales are crucial for protein prediction tasks, many of them being curated in the AAindex database. Despite various clustering attempts to organize them and to better understand their relationships, these approaches lack the fine-grained classification necessary for satisfactory interpretability in many protein prediction problems. To address this issue, we developed AAontology-a two-level classification for 586 amino acid scales (mainly from AAindex) together with an in-depth analysis of their relations-using bag-of-word-based classification, clustering, and manual refinement over multiple iterations. AAontology organizes physicochemical scales into 8 categories and 67 subcategories, enhancing the interpretability of scale-based machine learning methods in protein bioinformatics. Thereby it enables researchers to gain a deeper biological insight. We anticipate that AAontology will be a building block to link amino acid properties with protein function and dysfunctions as well as aid informed decision-making in mutation analysis or protein drug design., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Amino acid propensities for protein secondary structures are vital for protein structure prediction, understanding folding, and design, and have been studied using various theoretical and experimental methods. Traditional assessments of average propensities using statistical methods have been done on relatively smaller dataset for only a few secondary structures. They also involve averaging out the environmental factors and lack insights into consistency of preferences across diverse protein structures. While a few studies have explored variations in propensities across protein structural classes and folds, exploration of such variations across protein structures remains to be carried out. In this work, we have revised the average propensities for all six different secondary structures, namely α-helix, β-strand, 3 10 -helix, π-helix, turn and coil, analyzing the most exhaustive dataset available till date using two robust secondary structure assignment algorithms, DSSP and STRIDE. The propensities evaluated here can serve as a standard reference. Moreover, we present here, for the first time, the propensities within individual protein structures and investigated how the preferences of residues and more interestingly, of their groups formed based on their structural features, vary across different unique structures. We devised a novel approach- the minimal set analysis, based on the propensity distribution of residues, which along with the group propensities led us to the conclusion that a residue's preference for a specific secondary structure is primarily dictated by its side chain's structural features. The findings in this study provide a more insightful picture of residues propensities and can be useful in protein folding and design studies., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Solid-phase fluorescence excitation-emission matrix (SPF-EEM) spectroscopy has potential for non-extractive, non-destructive, and non-contact analytical measurements of powder and solid-state samples, as well as front-face EEM spectroscopy for suspensions of high optical density. However, as there is no unified measurement method for SPF spectroscopy, comparing samples measured in different research fields is difficult. Therefore, this study designs a cell that can be created by a 3D printer and examines reproducibility on measuring fluorescent powders. The developed cell is applied to proteins (ovalbumin, BSA, gliadin, gluten, powdered collagen, casein), amino acids (tryptophan, tyrosine, and phenylalanine), soybean ingredients (daidzein, and genistein), and fluorescent chemicals (rhodamine B, fluorescein sodium salt, pyrene, and quinine sulfate dihydrate) and their spectra are compared with those in the solution states. When samples are refilled into the cell three times, the cell exhibits high reproducibility in terms of fluorescence peak wavelength and intensity. The solid proteins exhibit peaks attributed to the fluorescent amino acid residues, and broad peaks which are not detected for the proteins in the solution states. Powdered rhodamine B and fluorescein sodium salt do not exhibit fluorescence, possibly due to the inner-filter effect (IFE). Some non-colored molecules also exhibit loss of fluorescence or a remarkable difference between the solid and solution states, possibly due to the interaction of the fluorescent structure with the surrounding local environment, similar to the solvent effect, which is possibly affected by the molecular proximity, three-dimensional structure, and moisture absorption capacity., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The chalcogen elements oxygen, sulfur, and selenium are essential constituents of side chain functions of natural amino acids. Conversely, no structural and biological function has been discovered so far for the heavier and more metallic tellurium element. In the methionine series, only the sulfur-containing methionine is a proteinogenic amino acid, while selenomethionine and telluromethionine are natural amino acids that are incorporated into proteins most probably because of the tolerance of the methionyl-tRNA synthetase; so far, methoxinine the oxygen analogue has not been discovered in natural compounds. Similarly, the chalcogen analogues of tryptophan and phenylalanine in which the benzene ring has been replaced by the largely isosteric thiophene, selenophene, and more recently, even tellurophene are fully synthetic mimics that are incorporated with more or less efficiency into proteins via the related tryptophanyl- and phenylalanyl-tRNA synthetases, respectively. In the serine/cysteine series, also selenocysteine is a proteinogenic amino acid that is inserted into proteins by a special translation mechanism, while the tellurocysteine is again most probably incorporated into proteins by the tolerance of the cysteinyl-tRNA synthetase. For research purposes, all of these natural and synthetic chalcogen amino acids have been extensively applied in peptide and protein research to exploit their different physicochemical properties for modulating structural and functional properties in synthetic peptides and rDNA expressed proteins as discussed in the following review., (© 2019 The Authors. Journal of Peptide Science published by European Peptide Society and John Wiley & Sons Ltd.)

A novel helical N-capping motif has been considered. It occurs in the βα-arches of right-handed βαβ-units and contains an N-cap residue in a sterically strained conformation. Moreover, this amino acid position contains almost no glycines, that could relieve strain. It was shown that the N-cap adopts this conformation as a result of the unusual convergence between the second and third amino acid positions of the α-helix (counting from the N-cap) and the second position of the preceding β-strand. This is achieved by the presence of glycines in the specified positions (i.e. positions i - 2, i + 2 and i + 3, if N-cap is i). The N-cap conformation is stabilized by a hydrogen bond between the backbone amide group in the second position of the α-helix and the carbonyl group in the first position of the β-strand. The occurrence of similar N-capping motifs in different types of βαβ-units was compared and their structural differences caused by the influence of the environment were described. Study results may be useful for protein design and ab initio prediction of the 3D protein structure., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Physical compartments are essential for the origin of life. While lipid vesicles are commonly regarded as precursors of cell membranes, we propose a simpler and more primitive model based on proteinoids. Proteinoids are macromolecules formed by the thermal polymerization of amino acids, mimicking primitive proteins. They self-assemble into spherical microspheres in water. Under a temperature gradient, proteinoid microspheres (PM) dissolve and flow, forming microcapsules with thin shells. The mechanism of this process has not yet been elucidated. We hypothesize that it involves the interplay between the dissolution and flow of PM. We tested our hypothesis by applying forced flow to the PM and observing capsule formation. We found that neither heat nor flow alone can produce capsules, confirming our hypothesis. We conclude that flow-induced capsule formation is a general phenomenon and a plausible model for the origin of physical compartments in early life., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

A circular paper chromatographic method was developed for the separation of the amino acids in proteins into 7 subgroups. Butanol-acetic acid water (4+1+1) was used as the developing solvent. Eluted ninhydrin-stained aminograms gave rise to graphic profiles or numerical indexes based on absorbance percentages. The profiles can be used to compare protein-containing samples. Twenty different samples were studied through 190 comparisons of graphic profiles and coefficients of correlation, with only 4% misleading results. The method showed excellent reproducibility for the identification or differentiation of proteins and has the advantage of being performed with low-priced apparatus and reagents.

The NH(2)-terminal amino acid composition of the soluble and ribosomal proteins from Neurospora crassa mycelia and conidia was determined by the dinitrophenyl method. A nonrandom distribution of NH(2)-terminal amino acids was observed in the complex protein mixtures. Glycine, alanine, and serine accounted for 75% of the NH(2)-terminal amino acids, and glycine appeared most frequently in mature proteins of mycelia. The appearance of phenylalanine as one of the major NH(2)-termini in crude conidial fraction suggests that the composition of proteins may vary in different developmental stages.