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A single amino acid in a peptide sequence can play an important role to tune the self‐assembly and hydrogelation behaviour. Here, a C‐terminal cysteine‐containing ultrashort peptide hydrogelator forms hydrogel through non‐covalent and covalent interactions. Interestingly, the hydrogel is insoluble in water and buffer solutions at different pH values (1‐13) and is thixotropic and injectable. In recent years, removing dyes from contaminated water has become a significant concern because of the shortage of freshwater resources. Therefore, the adsorption of dyes through a reliable, straightforward, nontoxic, cheap, and environmentally friendly adsorbent has become a popular topic. Hence, the hydrogelator was exploited to remove organic dyes from wastewater, harnessing its applicability in the gel phase and solid supports (filter paper and cotton). [ABSTRACT FROM AUTHOR]

The aim of this work is to offer an alternative or complementary analytical tool to the time‐consuming and expensive methods commonly used for the recognition of animal species according to their hair. The paper introduces a simple and fast way for species differentiation of animal hairs called in‐sample digestion. A total of 10 European animal species, including cat, cow, common degu, dog, fallow deer, goat, horse, sika deer, rabbit, roe deer, and 17 different breeds of dogs were examined using specific tryptic cleavage directly in hair followed by matrix‐assisted laser desorption/ionization–time of flight mass spectrometry and liquid chromatography‐electrospray ionization quadrupole time of flight. Principal component analysis was used for the subsequent mass spectrometric data evaluation. This novel approach demonstrates the ability to distinguish among individual animal species, which is supported by finding characteristic m/z values obtained by the mass spectrometry for each animal species. The approach was successfully tested on two "blind" samples. On the other hand, the attempt to distinguish among hairs of different dog breeds has not been successful due to the very similar protein composition and their amino acid sequences. [ABSTRACT FROM AUTHOR]

As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label‐free and high‐throughput protein sequencing. In recent years, nanopore‐based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing. [ABSTRACT FROM AUTHOR]

While autoregulative adaptation is a common feature of living tissues, only a few feedback-controlled adaptive biomaterials are available so far. This paper herein reports a new polymer hydrogel platform designed to release anti-inflammatory molecules in response to the inflammatory activation of human blood. In this system, anti-inflammatory peptide drugs, targeting either the complement cascade, a complement receptor, or cyclophilin A, are conjugated to the hydrogel by a peptide sequence that is cleaved by elastase released from activated granulocytes. As a proof of concept, the adaptive drug delivery from the gel triggered by activated granulocytes and the effect of the released drug on the respective inflammatory pathways are demonstrated. Adjusting the gel functionalization degree is shown to allow for tuning the drug release profiles to effective doses within a micromolar range. Feedback-controlled delivery of covalently conjugated drugs from a hydrogel matrix is concluded to provide valuable safety features suitable to equip medical devices with highly active anti-inflammatory agents without suppressing the general immunosurveillance. [ABSTRACT FROM AUTHOR]

This paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein–protein interactions. The descriptors can be used to predict various properties of interest, such as protein–protein binding affinities, or inhibitory concentrations (IC50), using approaches that range from simple regression to more complex machine learning models. The software is highly modular. It supports different protocols for generating structures, and 95 descriptors can be currently computed. More protocols and descriptors can be easily added. The implementation is highly parallel and can fully exploit the available cores in a single workstation, or multiple nodes on a supercomputer, allowing many systems to be analyzed simultaneously. As an illustrative application, ppdx is used to parametrize a model that predicts the IC50 of a set of antigens and a class of antibodies directed to the influenza hemagglutinin stalk. [ABSTRACT FROM AUTHOR]

A fundamental aspect of evolutionary biology is natural selection on trait variation. Classically, selection has been estimated primarily on external morphological traits such as beak size and coloration, or on easily assayable physiological traits such as heat‐tolerance. As technologies and methods improved, evolutionary biologists began examining selection on molecular traits such as protein sequences and cellular processes. In a From the Cover paper in this issue of Molecular Ecology, Ahmad et al. continue this trend by estimating parasite‐driven selection on the molecular trait of transcript abundance in a wild population of brown trout (Salmo trutta) by uniquely combining a mark–recapture experimental design with noninvasive RNA sampling. Using transcript abundance to estimate selection allows for many different traits (each unique gene's transcript counts) to be tested in a single experiment, providing the opportunity to examine trends in selection. Ahmad et al. find directional selection strength on transcript counts is generally low and normally distributed. Surprisingly, transcripts under nonlinear selection showed a disruptive selection bias, contradicting previous comparative studies and theoretical work. This highlights the importance of within‐generation selection studies, where mechanisms may differ from longer time frames. Their paper also highlights the benefits of a cost‐effective 3′ RNA sequencing technique to measure gene expression. [ABSTRACT FROM AUTHOR]

Milk proteins are recognized as the main source of biologically active peptides. Casein's primary structure contains several bioactive amino acid sequences on its latent inactive form. These potential active sequences can be released during cheese manufacture and ripening, giving rise to peptides with biological activity such as antihypertensive, antidiabetic, antioxidant, immunomodulatory, and mineral‐binding properties. However, the presence of biopeptides in cheese does not imply actual biological activity in vivo because these peptides can be further hydrolyzed during gastrointestinal transit. This paper reviews the recent advances in biopeptide formation in ripened cheeses production, focusing on the influence of technological parameters affecting proteolysis and the consequent release of peptides. The main discoveries in the field of cheese peptide digestion through recent in vivo and in vitro model studies are also reviewed. © 2021 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Since the large‐scale protein sequence data is available, applying deep neural networks to mine better features from the sequences becomes possible. Eukaryotic protein subcellular localization prediction which makes a contribution in many biology process, has used protein sequences in many automatic predicting methods. Moreover, gene ontology (GO) annotation has been shown to be helpful in improving the prediction accuracy of subcellular localization. However, experimentally annotated proteins are not always available. On the other hand, experimentally annotated proteins are available for certain species such as human, mouse, Arabidopsis thaliana, etc. It is highly motivated to perform deep learning of GO annotations on the available experimentally annotated proteins and to transfer it to subcellular localization prediction on other species. In this paper, we propose a deep protein subcellular localization predictor, consisting of a linear classifier and a deep feature extractor of convolution neural network (CNN). The deep CNN feature extractor is first shared and pre‐trained in a deep GO annotation predictor, and then is transferred to the subcellular localization predictor with fine‐tuning using protein localization samples. In this way, we have a deep protein subcellular localization predictor enhanced with transfer learning of GO annotation. The proposed method has good performances on the Swiss‐Prot datasets, when transfer learning using the protein samples both within and out species. Moreover, it outperforms the state‐of‐the‐art traditional methods on benchmark datasets. © 2021 Institute of Electrical Engineers of Japan. Published by Wiley Periodicals LLC. [ABSTRACT FROM AUTHOR]

The alteration of amino acid register in peptides could affect their folding properties and thus functions. The effect of sequence in metal ion induced folding of peptide/protein is important in the design of new functional protein structures, such as biomimetics. In this paper, a set of hairpin peptides with identical composition but different histidine locations have been designed to exploit the metal ion‐mediated peptide intramolecular folding transformation through the adjustment of histidine and lysine residue locations. The results demonstrated that the histidine positions in peptide sequence could dramatically affect the coordination modes between peptides and Cu(II) ion. The Cu(II) coordination could affect the secondary structure transformation and self‐assembly along with electrostatic interaction and hydrogen bonding synergistically. Three molecules with VHVH sequence at each side of the turn segment (VDPPT) were apt to coordinate with Cu(II) ion with three or four histidines. The closer the VHVH motifs were to the turn segment, the more easier the molecules were to form β sheet structure with the promotion of Cu(II) ions. These results demonstrated that the purposeful location of key amino acids in peptides could achieve the controllable conformation transformation of hairpin peptides, which provides useful strategies for biomimetic design, such as metalloenzymes. [ABSTRACT FROM AUTHOR]

Front cover: Kagami‐mochi (mirror rice cake) is a representative of Japanese New Year decorations. It usually consists of a couple of stacked large round‐shaped mochi that resemble ancient bronze mirrors with one daidai (Japanese bitter orange) on top. This year, however, our kagami‐mochi is somewhat different from the usual; it is a so‐called ribosome‐like kagami‐mochi. Two stacked mochi likened the ribosome's large and small subunits bind to a gohei (a folded ribbon of paper) that resembles an mRNA encoding (DAIDAI)n amino acid sequence, and a chain of daidais extends upward from the mochi likened the large subunit. It looks like a polypeptide chain itself. Designed by TRAIS Co., Ltd. (Kobe, Japan). [ABSTRACT FROM AUTHOR]

In this paper, a plasma membrane engineering approach is reported for tumor targeting drug delivery and contact-cell-enhanced photodynamic therapy ('CONCEPT') by anchoring functionalized conjugates to cell vehicles. The membrane anchoring conjugates are comprised of a positively charged tetra-arginine peptide sequence, a palmitic-acid-based membrane insertion moiety, and a lysine linker whose ε-amine is modified with camptothecin (CPT), protoporphyrin IX (PpIX), or fluorescein (FAM). The amphipathic CPT, PpIX, or FAM conjugates (short as aCPT, aPpIX, or aFAM, respectively) can easily and steadily anchor or coanchor on the cell membrane of RAW264.7 cells (short as RCs), red blood cells, or mesenchymal stem cells. After anchoring aPpIX in RC cells, the tumor targeting ability and therapeutic effect of aPpIX-anchored RC cells (short as aPRCs) is demonstrated in vitro and in vivo. Importantly, aPRCs exhibit the 'CONCEPT' effect, which can enhance the therapeutic efficacy and reduce side effects at the single cell level. Due to the good tumor-targeting ability, aPRCs can efficiently inhibit the tumor growth with no systemic toxicity after photoirradiation by photodynamic therapy. [ABSTRACT FROM AUTHOR]

In this paper, we experimentally address the debate about why functional transfer of mitochondrial genes to the nucleus has been halted in some organismal groups and why cytosolic expression of mitochondrial proteins has proven remarkably difficult. By expressing all 13 human mitochondrial-encoded genes with strong mitochondrial-targeting sequences in the cytosol of human cells, we show that all proteins, except ATP8, are transported to the endoplasmic reticulum (ER). These results confirm and extend previous findings based on three mitochondrial genes lacking mitochondrial-targeting sequences that also were relocated to the ER during cytosolic expression. We conclude that subcellular protein targeting constitutes a major barrier to functional transfer of mitochondrial genes to the nuclear genome. [ABSTRACT FROM AUTHOR]

Rationale The electron capture dissociation (ECD) of proteins/peptides is affected by the nature and sequence of amino acid residues. Electron capture/transfer with no dissociation is an intriguing phenomenon that has occasionally been observed. We have previously identified that diarginated peptides enriched with glutamic acid residues were found to show suppression of backbone fragmentation. In this paper, we report the effect of geometrical parameters of a peptide, including chain length, conformation and amide hydrogen, on the suppression of ECD fragmentation using synthetic model peptides. Methods Glycine containing model polypeptides were used to probe the mechanism. Molecular-mechanics was used to obtain the conformation of the precursor ions. The ECD experiments were performed on a Bruker APEX III 4.7 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Results Significant decreases in the intensities of the fragment ions were observed for the 23-mer polypeptide with only one E residue. This implied that the E:R ratio was no longer the sole determining factor for the occurrence of suppression effects. Results of conformational searches showed that there was a hydrogen-bonding 'ladder' formed in the 23-mer polypeptide, which was not found in the 15-mer peptide. Substituting the normal amino acid residues by the corresponding N-methylated amino acid residues in the model peptide, the suppression effect disappeared. Conclusions Our results indicate that survival of the intact reduced peptide ion after electron capture depends also on the length of the peptide. The amide hydrogen was critical in forming the resonance structure that suppressed the ECD fragmentation. Copyright © 2015 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

I also thank the contributors, each a luminary in the field, who participated in interviews about the past and future of GnRH research for the article ending this Special Issue. Guillemin and Schally for the discovery that led to the wide array of research covered in this Special Issue, and hope that they enjoy reading it as the latest fruition of their work. It was 50 years ago last summer that Roger Guillemin and Andrew Schally published their breakthrough papers reporting the isolation and discovery of the peptide sequence of gonadotropin-releasing hormone (GnRH), for which they were later awarded the Nobel Prize. [Extracted from the article]

Dr Mischak: "Re-analysis of peptidomic analysis of cartilage and subchondral bone in OA patients" In May 2019 issue of European Journal of Clinical Investigations, we in our paper I Peptidomic analysis of cartilage and subchondral bone in OA patients i 1 reported a pilot study which primarily is a protocol for endogenous peptide extraction from cartilage and subchondral bone from OA patients. Peptidomic analysis of cartilage and subchondral bone in OA patients. [Extracted from the article]

Protein prenylation, a well‐defined protein consensus motifs direct modification by one of three prenyl‐transferases, has been an area of fairly settled science for 20 or 30 years. Protein prenylation, the specific prenyl modification (farnesyl or geranylgeranyl), as well as the prenyl‐transferases involved can be inferred by protein sequence. Two new papers now upset this settled wisdom with the discovery of a fourth prenyl‐transferase, namely geranylgeranyl‐transferase‐III (GGTase‐III) (Kuchay et al, 2019; Shirakawa et al, 2020). [ABSTRACT FROM AUTHOR]

Anti-Prelog stereoselectivity, biocatalysis, ketoreductase, multi-factorial screening, substrate scope In their Full Paper, M. Voss, R. Küng et al. present the multi-faceted set-up of a diverse ketoreductase library and demonstrate the use of 51 enzymes for the synthesis of valuable building blocks. Keywords: anti-Prelog stereoselectivity; biocatalysis; ketoreductase; multi-factorial screening; substrate scope EN anti-Prelog stereoselectivity biocatalysis ketoreductase multi-factorial screening substrate scope 1413 1413 1 03/24/21 20210319 NES 210319 B The Cover Feature b highlights the synthetic potential of a diverse, off-the-shelf ketoreductase library for the selective reduction of small molecule ketones. [Extracted from the article]

Invited for this month's cover picture is the group of Professor Enrica Bordignon at the Ruhr University Bochum. The cover picture shows an artistic view of E. coli cells and two spin‐labeled recombinantly produced proteins, which can be inserted into the cells for EPR studies. The primary sequence of the proteins is schematically shown with the one‐letter amino acid code, and cysteine residues are functionalized with the two new gem diethyl nitroxide spin labels designed to better sustain the reducing cellular environment. Read the full text of their Full Paper at 10.1002/open.201900119. [ABSTRACT FROM AUTHOR]

2 ‐ Methoxy ‐ 4 ‐ methylsulfinylbenzyl (Mmsb) is a new backbone amide ‐ protecting group based on the safety ‐ catch concept. Mmsb is stable during the elongation of the peptide sequence and to trifluoroacetic acid cleavage from the resin. The presence of Mmsb reduces intra ‐ and inter ‐ chain interactions and thereby improves the synthetic process, as well as the properties of the quasi ‐ unprotected peptide. Mmsb offers the possibility to purify and characterize complex peptide sequences before the final cleavage that renders the target peptide. For more details, see the Full Paper by F. Albericio, J. Tulla ‐ Puche, and Paradís ‐ Bas on page 15031 ff. [ABSTRACT FROM AUTHOR]