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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]

Abstract: Protein ORIGAMI ( http://ibg.kit.edu/protein_origami) is a browser‐based web application that allows the user to create straightforward 3D paper models of folded peptides for research, teaching and presentations. An amino acid sequence can be turned into α‐helices, β‐strands and random coils that can be printed out and folded into properly scaled models, with a color code denoting the biophysical characteristics of each amino acid residue (hydrophobicity, charge, etc.). These models provide an intuitive visual and tactile understanding of peptide interactions with other partners, such as helix‐helix assembly, oligomerization, membrane binding, or pore formation. Helices can also be displayed as a helical wheel or helical mesh in 2D graphics, to be used in publications or presentations. The highly versatile programme Protein ORIGAMI is also suited to create less conventional helices with arbitrary pitch (e.g., 310‐helix, π‐helix, or left‐handed helices). Noncanonical amino acids, labels and different terminal modifications can be defined and displayed at will, and different protonation states can be shown. In addition to the web application, the program source code can be downloaded and installed locally on a PC. The printed paper models can be readily used for daily research and discussions, just as for educational purposes and teaching. © 2018 by The International Union of Biochemistry and Molecular Biology, 46:403–409, 2018. [ABSTRACT FROM AUTHOR]

Most of the current nonclassical proteins prediction methods involve manual feature selection, such as constructing features of samples based on the physicochemical properties of proteins and position‐specific scoring matrix (PSSM). However, these tasks require researchers to perform some tedious search work to obtain the physicochemical properties of proteins. This paper proposes an end‐to‐end nonclassical secreted protein prediction model based on deep learning, named DeepNCSPP, which employs the protein sequence information and sequence statistics information as input to predict whether it is a nonclassical secreted protein. The protein sequence information and sequence statistics information are extracted using bidirectional long‐ and short‐term memory and convolutional neural networks, respectively. Among the experiments conducted on the independent test dataset, DeepNCSPP achieved excellent results with an accuracy of 88.24%, Matthews coefficient (MCC) of 77.01%, and F1‐score of 87.50%. Independent test dataset testing and 10‐fold cross‐validation show that DeepNCSPP achieves competitive performance with state‐of‐the‐art methods and can be used as a reliable nonclassical secreted protein prediction model. A web server has been constructed for the convenience of researchers. The web link is https://www.deepncspp.top/. The source code of DeepNCSPP has been hosted on GitHub and is available online (https://github.com/xiaoliu166370/DEEPNCSPP). This paper proposes an end‐to‐end nonclassical secreted protein prediction model DeepNCSPP based on deep learning, which employs the protein sequence information and sequence statistics information as input to predict whether it is a nonclassical secreted protein. The protein sequence information and sequence statistics information are extracted using bidirectional long‐ and short‐term memory and convolutional neural networks, respectively. [ABSTRACT FROM AUTHOR]

The purification and the amino acid sequence of the peptide containing the essential sulphydryl group of arginine kinase from Homarus vulgaris muscle is described. The fractionation of the tryptic digest of arginine kinase labelled with N-[1-14C]ethylmaleimide has been caused out using gel filtration, ion-exchange chromatography and paper chromatography. The composition of the radioactive peptide, isolated from the digest, is reported together with its amino acid sequence. A structural comparison is made between the peptide of arginine kinase and the corresponding active-cysteine containing peptide isolated from rabbit muscle creatine kinase. [ABSTRACT FROM AUTHOR]

The article presents a list of articles related to biochemistry. The articles include "The Reaction of Hemin With H2O2," by M. L. Kremer, "Amino Acid Sequence of the Monomer Subunit of the Giant Multisubunit Hemoglobin From the Earthworm Pheretima sieboldi," by T. Suzuki, "Purification and Properties of Saccharomyces cerevisiae Acetolactate Synthase From Recombinant Escherichia coli," by C. Poulsen and P. Stougaard, "The Mitochondrial Inner-Membrane Anion Channel Possesses Two Mercurial-Reactive Regulatory Sites," by A. D. Beavis.

Protein structure prediction (PSP) is the prediction of the three‐dimensional (3D) folding of a protein (its tertiary structure) starting from its amino acid sequence (its primary structure). The state of the art in PSP is achieved by deep learning pipelines that require several input features extracted from amino acid sequences. It has been demonstrated that features that grasp the relative orientation of amino acids positively impact the prediction accuracy of the 3D coordinates of atoms in the protein backbone. In this paper, we demonstrate the relevance of geometric algebra (GA) in instantiating orientational features for PSP problems. We do so by proposing two novel GA‐based metrics which contain information on relative orientations of amino acid residues. We then employ these metrics as additional input features to a graph transformer (GT) architecture to aid the prediction of the 3D coordinates of a protein, and compare them to classical angle‐based metrics. We show how our GA features yield comparable results to angle maps in terms of accuracy of the predicted coordinates. This is despite being constructed from less initial information about the protein backbone. The features are also fewer and more informative and can be (i) closely associated to protein secondary structures and (ii) more easily predicted compared to angle maps. We hence deduce that GA can be employed as a tool to simplify the modeling of protein structures and pack orientational information in a more natural and meaningful way. [ABSTRACT FROM AUTHOR]

This document is a corrigendum to an article published in the New Phytologist journal. The authors of the original article have identified errors in their work. Specifically, the equation used for carotenoid quantification in the Materials and Methods section was incorrect, resulting in incorrect graphs. The corrected equation and graphs are provided in the corrigendum. The errors do not change the conclusions of the paper. The authors apologize for the mistakes. [Extracted from the article]

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]

Finding new protein sources and processes comprising targeted functional properties is crucial for the increasing global food demand. In the current paper, a new protein isolate is introduced with potential benefits based on the seeds of Persian everlasting pea (Lathyrus rotundifolius L.). Conventional aqueous extraction for the preparation of protein isolates (CPEP) was compared with pre‐ultrasonic (PUPEP) and ultrasound‐assisted (UAPEP) extractions, and the physicochemical and functional properties of the proteins were investigated. By the implication of ultrasound trials, protein recovery was increased from 49.88% for CPEP to 55.02% and 56.11%, for PUPEP and UAPEP, respectively. According to gel electrophoresis, no major distinction in molecular weight between protein fractions of different samples was perceived and sonication practice did not convert the primary structures of proteins. FTIR results uncovered changes in different extraction modes, implying that ultrasound could transform the secondary structures of the protein. Thermal properties and surface tension were decreased during sonication due to the conformational changes. The results of this study indicated that Persian everlasting pea protein isolate could be considered as a novel source of valuable protein and functional ingredient in the food industry. Practical applications: The utilization of plant‐based protein products as sustainable alternatives to animal proteins has been increasing recently. However, compared with animal proteins, plant‐based proteins reveal relatively weak functional properties such as water‐holding capacity and gelation. Therefore, they need to be modified before being incorporated into food products. Ultrasonic treatment is an emerging technology that has many applications in food science and technology, such as increasing the extraction efficiency and improving the physicochemical and functional properties of food ingredients. Lathyrus rotundifolius seeds contain high amounts of protein and can be used as a source of plant‐based protein. The effect of ultrasonic treatment in the study was investigated and confirmed to improve the extraction efficiency and functional properties of Persian everlasting pea protein, which can be used in the food industry. [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]

Presents several research papers related to biochemistry. "Effect of Thiol Reagents on the Proton Conductivity of the H+ATPase of Mitochondria," by F. Guerrieri and S. Papa; "Purification of Penicillin-Binding Protein 3 from Streptococcus pneumoniae," by R. Hakenbeck and M. Kohiyama; "Reutilization of Preformed Pyrimidines for the Synthesis of DNA in Rat Liver and Kidney," by J. Seifert; "Human Progastriesin: Analysis of Intermediates during Activation in Gastriesin and Determination of the Amino Acid Sequence of the Propart," by B. Foltmann and A. L. Jensen; Others.

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]

SARS-CoV-2 is a newly discovered beta coronavirus at the end of 2019, which is highly pathogenic and poses a serious threat to human health. In this paper, 1875 SARS-CoV-2 whole genome sequences and the sequence coding spike protein (S gene) sampled from the United States were used for bioinformatics analysis to study the molecular evolutionary characteristics of its genome and spike protein. The MCMC method was used to calculate the evolution rate of the whole genome sequence and the nucleotide mutation rate of the S gene. The results showed that the nucleotide mutation rate of the whole genome was 6.677 × 10-4 substitution per site per year, and the nucleotide mutation rate of the S gene was 8.066 × 10-4 substitution per site per year, which was at a medium level compared with other RNA viruses. Our findings confirmed the scientific hypothesis that the rate of evolution of the virus gradually decreases over time. We also found 13 statistically significant positive selection sites in the SARS-CoV-2 genome. In addition, the results showed that there were 101 nonsynonymous mutation sites in the amino acid sequence of S protein, including seven putative harmful mutation sites. This paper has preliminarily clarified the evolutionary characteristics of SARS-CoV-2 in the United States, providing a scientific basis for future surveillance and prevention of virus variants. [ABSTRACT FROM AUTHOR]

Molecular replacement (MR) is a well established computational method for phasing in macromolecular crystallography. In MR searches, spaces of motions are explored for determining the appropriate placement of rigid models of macromolecules in crystallographic asymmetric units. In the first paper of this series, it was shown that this space of motions, when endowed with an appropriate composition operator, forms an algebraic structure called a quasigroup. In this second paper, the geometric properties of these MR search spaces are explored and analyzed. This analysis includes the local differential geometry, global geometry and symmetry properties of these spaces. [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]

Presents a list of studies that will be published in the "European Journal of Biochemistry." "Peroxisomal Oxidation of L-2-Hydroxyphytanic Acid in Rat Kidney Cortex," by J.-P. Draye, F. van Hoof, E. de Hoffmann and J. Vamecq; "Probing the Heparin-Binding Domain of Human Antithrombin III With V8 Protease," by C.-S. Liu and J.-Y. Chang; "Protein Phosphatases of the Guinea-Pig Parotid Gland," by G. Mieskes and H.-D. Söling; "Amino Acid Sequence of Endothiapepsin--Complete Primary Structure of the Aspartic Protease From Endothia Parasitica," by V. Barkholt.

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]

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]

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 amino acid sequence of the light chain of a human monoclonal IgA1 (Mem) was established, in part by analogy with already known sequences. By homology its variable part was shown to belong to the VλI subgroup while the isotype-associated amino acid residues characterized it as Mcg+, Kern+ and Oz-. The normal primary structure of this chain was in contrast to its abnormal physical and antigenic properties: (a) its apparent molecular mass estimated by SDS/polyacrylamide gel electrophoresis, by gel filtration chromatography and by gradient ultracentrifugation was found to be lower by &assymp; 10% than the values (23.5 kDa) of ‘normal’ light chain used as controls; (b) the λI chain Mem, when tested in native state was not antigenically reactive. These abnormalities were reverted when the chain was treated with 8 M urea. These data suggest that the abnormal behaviour of λI chain Mere is at a conformational level. [ABSTRACT FROM AUTHOR]

After CNBr cleavage of p-hydroxybenzoate hydroxylase from Pseudornonas fluorescens, five peptides and free homoserine were isolated (see preceding paper in this journal). The amino acid sequences of the three smallest peptides, viz. CB3, CB4 and CB5, were determined by automated Edman degradation and analysis of enzymatic subdigests. These peptides form a continuous stretch of 110 residues from the N terminus: [This equation can not be represent in ASCII.TXT]. [ABSTRACT FROM AUTHOR]

Tryptic digestion of peptide A, the C-terminal fragment of thioredoxin, obtained by cyanogen bromide cleavage, resulted in the isolation of nine peptides. The complete amino acid sequence of each was determined, and the N-terminal and C-terminal fragments of peptide A were identified. Together the nine tryptic peptides accounted for all 71 residues of peptide A. Hydrazinolysis and studies with carboxypeptidase A established -Asn-Leu-Ala to be the C-terminal sequence of peptide A and of thioredoxin. [ABSTRACT FROM AUTHOR]

Angiotensin‐I‐converting enzyme (ACE) inhibitory peptides are able to inhibit the activity of ACE, which is the key enzymatic factor mediating systemic hypertension. ACE‐inhibitory peptides can be obtained from edible proteins and have the function of antihypertension. The amino acid sequences and the secondary structures of ACE‐inhibitory peptides determine the inhibitory activities and stability. The resistance of ACE‐inhibitory peptides to digestive enzymes and peptidase affect their antihypertensive bioactivity in vivo. In this paper, the mechanism of ACE‐inhibition, sources of the inhibitory peptides, structure–activity relationships, stability during digestion, absorption and transportation of ACE‐inhibitory peptides, and consumption of ACE‐inhibitory peptides are reviewed, which provide guidance to the development of new functional foods and production of antihypertensive nutraceuticals and pharmaceuticals. [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]

Neural precursor cells (NPC) are primary cells intensively used in the context of research on adult neurogenesis and modeling of neuronal development in health and diseased states. Substrates that can facilitate NPC adhesion will be very useful for culturing these cells. Due to the presence of laminin in basal lamina as well as their involvement in differentiation, migration, and adhesion of many types of cells, surfaces modified with laminin-derived peptides are focused upon and compared with the widely used fibronectin-derived Arg-Gly-Asp (RGD) peptides. An array of 46 peptides is synthesized on cellulose paper (SPOT) to identify laminin-derived peptides that promote short-term adhesion of murine NPC and human primary endothelial cells. Various previously reported peptide sequences are re-evaluated in this work. Initial adhesion experiments show NPC preferred several laminin-derived peptides by up to 5-time higher cell numbers, compared to the well-known promiscuous integrin binding RGD peptide. Importantly, screening of cell adhesion has revealed a synergetic effect of filamentous matrix, peptide sequence, surface property, ligand density, and the dynamic process of NPC adhesion. [ABSTRACT FROM AUTHOR]

Transcription can be regulated by controlling the provision of transcriptional factors (TFs), because TFs determine the transcription process by specifying the binding of RNA polymerase holoenzyme on promoters. Manipulations, such as replacing endogenous TFs with mutants obtained through directed evolution (or rational design), and introducing compatible heterogeneous TFs, are effective ways to regulate transcription. Designing artificial TFs with desired properties by following the principles of protein design and reconstructing ancestral TFs with the information gained from a perspective of evolution by multiple sequence alignments of the related TFs, are feasible alternative options. The engineered TFs can be used to create inducible protein expression systems that respond to a specific stimulus. Moreover, the engineered TFs could lead to a transcriptional profile different from that of the wild‐type strains. Accordingly, these engineered TFs could be utilized to construct strains resistant to adverse conditions, since the emergence of resistance generally requires global transcriptional changes at the transcriptomic scale. Meanwhile, these engineered TFs can also be employed in the construction of sophisticatedly designed genetic circuits for diverse purposes. In this paper, we reviewed the advances in the above‐mentioned aspects. © 2020 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Non-crystallographic symmetry (NCS) averaging is a well known method for improving the quality of an electron-density map and thus aiding structure determination. Prior methods of NCS-operator determination based on estimated heavy-atom positions are prone to errors arising from inaccuracies in these coordinates or differences in the relative orientations of domains between molecules. In this paper, two real-space methods to determine NCS relationships from initial electron-density maps are presented. A brute-force method identifies matching regions in a map by local density correlation. A feature-based algorithm uses rotation-invariant features to reduce the computational time taken by the brute-force algorithm by filtering out regions that are likely to have dissimilar density patterns. This makes the feature-based algorithm faster and as accurate as the brute-force approach. Neither method requires the positions of heavy atoms or any information regarding the protein sequence. Both methods have been tested on a diverse range of experimentally phased maps and the correct NCS relationships were accurately identified for almost all of the test cases. The NCS operators obtained by the feature-based algorithm were used to perform NCS averaging and an improvement in map correlation was observed for some cases. [ABSTRACT FROM AUTHOR]

Fluorescence lifetime imaging microscopy (FLIM) opens new dimensions for highly multiplexed imaging in live cells and organisms using differences in fluorescence lifetime to distinguish spectrally identical fluorescent probes. Here, a set of fluorescence‐activating and absorption‐shifting tags (FASTs) capable of modulating the fluorescence lifetime of embedded fluorogenic 4‐hydroxybenzylidene rhodanine (HBR) derivatives is described. It is shown that changes in the FAST protein sequence can vary the local environment of the chromophore and lead to significant changes in fluorescence lifetime. These fluorescence lifetime‐modulating tags enable multiplexed imaging of up to three targets in one spectral channel using a single HBR derivative in live cells and live zebrafish larvae. The combination of fluorescence lifetime multiplexing with spectral multiplexing allows to successfully image six targets in live cells, opening great prospects for multicolor fluorescence lifetime multiplexing. [ABSTRACT FROM AUTHOR]

The silicifying peptide R5 (H‐SSKKSGSYSGSKGSKRRIL‐OH) derived from diatoms is extensively investigated, but the mechanism underlying silica synthesis by R5 or R5‐alike peptides is still poorly understood, limiting the design of silicifying peptides Herein, machine learning techniques are used to design peptides with silicifying functionality. Utilizing a comprehensive dataset of peptides and their corresponding silicification outcomes, a deep learning model based on antimicrobial peptide migration learning is created. This model exhibits the remarkable capability to accurately predict peptide sequences with a high potential for facilitating silica formation. A selection of artificially designed peptides can catalyze the biomimetic synthesis of nanosilica, some of which demonstrate better catalytic activity with a wider pH range and faster reaction rate compared with the peptide R5. Additionally, the designed peptide is used to wrap the model diatom Phaeodactylum tricornutum with nanosilica coatings, resulting in a significant enhancement in the UV resistance of cells. The new silicified peptides are highly significant for advancing the understanding of the silica synthesis mechanism in diatoms, and the encapsulation of P. tricornutum has potential benefits in the development of new biosensors. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: The legume crop cowpea is grown worldwide, but 90% of the world's total share is produced in Africa. It is a promising species due to its resilience properties, balance of macro and micronutrients and presence of health‐promoting bioactive compounds. In African countries, cowpea has a crucial role in guaranteeing food security as a subsistence crop for families and commercial income for small farmers. The discovery of compounds with high nutraceutical value and bioactive properties supports socio‐economic policies to improve health and nutrition, especially in low‐ and middle‐income countries. In turn, this encourages biodiversity protection and crop enhancement programmes. Summary: Bowman–Birk protease inhibitors (BBIs) are a restricted group of small proteins in plants mainly involved in defence mechanisms against pests. BBIs are demonstrated to be active components capable of reducing the viabilities of different cancer cell lines. BBI bioactivity is directly linked to the inhibition capacity, but the variability and the efficiency against the physiological targets of different BBI isoforms remain still unexplored.We analysed the natural genetic diversity of two main genes encoding BBI trypsin‐trypsin (BBI‐TT) and trypsin‐chymotrypsin (BBI‐TC) in wild and domesticated cowpea samples mainly spread in Sub‐Saharan Africa. We analysed DNA sequences and respective amino acidic isoforms/isoproteins to explore signs of natural selection and haplotype relationships. Moreover, we calculated the binding energy between BBIs and their biological targets to identify which are the most efficient inhibitors and their geographical locations.We found a high level of haplotype diversity for both genes, almost exclusively in wild accessions and detected positive and negative selection signals in the amino acid sequences. Furthermore, in the wild diversity pool, some BBI‐TT and BBI‐TC mature proteins were potentially better interactors with the physiological targets.The long interaction between plant‐pathogen has selected new and useful isoforms in wild lineages that have allowed the chances of survival of the species to improve. On the other hand, the domestication process has produced an intense bottleneck leaving only poorly efficient BBI variants. In addition to providing information on the natural diversity and evolution of BBIs, our work discusses the potential applications in agriculture and human health. [ABSTRACT FROM AUTHOR]

Incubation of calf tens cortex homogenate with [14C]putrescine or dansylcadaverine, followed by two-dimensional gel electrophoresis and fluorography, enabled the identification of three different β-crystallin chains as the endogenous substrates of Ca2+-dependent lens transglutaminase (R-glutaminyl-peptide:amine-γ-glutamylyltransferase, EC 2.3.2.13). One of these is βBp, the predominant subunit of β-crystallin, of which the amino acid sequence is known. The site of amine-labeling in βBp could be located, by limited proteolysis, in the N-terminal domain of this chain. Tryptic digestion of the N-terminal domain and subdigestion with elastase of the N-terminal tryptic peptide identified glutamine-7 as the single residue to which the amines are bound. This is the first example of an endogenous substrate of intracellular transglutaminase in which the site of the acyl-donor glutamine residue has been established. Tryptic digestion of the putrescine-labeled β-crystallin aggregate, followed by high-voltage paper electrophoresis, provided a preliminary characterization of the labeled peptides originating from the other two labeled β subunits. [ABSTRACT FROM AUTHOR]

A purified glycoprotein with blood-group-A specificity, was digested with insoluble pronase to give a serologically active product enriched in peptide-bonded serine and threonine residues; this was degraded with 0.25 M sulphuric in glacial acetic acid for 24 h. The resultant N-acetylgalactosaminyl-peptide were hydrolysed with 0.2 M hydrocholoric acid for 24 h at 110 °C. fractionation of the products on Sephadex G-10, followed by preparative separation on amino-acid analyzer and paper electrophoresis at pH 1.9 yielded the following homogeneous oligopeptides; one tripeptide with the N-terminal sequence Thr-Thr-Ser, three tetrapeptides with the sequences, Thr-Ser-Thr-Ser, Thr-Pro-Thr-Ser and Pro-Thr-Thr-Ser, one pentapeptide with the sequence Thr-Pro-Thr-Ser, one hexapeptide with the sequence Pro-Thr-Thr-Thr-Pro-Ser and one heptapeptide with the sequence Ala-Pro-Thr-Thr-Ser-Gly-Ser. Galactosamine was present in several of these fragments and the hexapeptide and heptapeptide both contained sufficient of this sugar for all the serine and threonine residues to be glycosylated. The following five tetrapeptides sequences were deduced from mixtures of two peptides which differed by the amino-acid substituent at only one position in the chain; Pro-Thr-Ala-ser, Thr-Thr Pro-Ser, thr-Thr-Ala-Ser, Ser-Pro-Thr-Ser, and Ser-Ala-Thr-Ser. A tripeptide mixture which differed only in the nature of the third amino acid yielded the following three tripeptide sequences: Pro-Thr-Ser, Pro-thr-Ala. These peptides do not indicate a clearly defined amino-acid sequence surrounding the glycosylated hydroxy amino acids but establish that in the human blood-group-specific glycoproteins there is close packing of the threonine in the region of the peptide moiety carrying the carbohydrate chains. [ABSTRACT FROM AUTHOR]

Conditions including heating mode, time, temperature, pH, moisture and protein concentration, shear, and the presence of alcohols, chaotropic/reducing agents, enzymes, and/or salt influence amyloid fibril (AF) formation as they can affect the accessibility of amino acid sequences prone to aggregate. As some conditions applied on model protein resemble conditions in food processing unit operations, we here hypothesize that food processing can lead to formation of protein AFs with a compact cross β‐sheet structure. This paper reviews conditions and food constituents that affect amyloid fibrillation of egg and cereal proteins. While egg and cereal proteins often coexist in food products, their impact on each other's fibrillation remains unknown. Hen egg ovalbumin and lysozyme form AFs when subjected to moderate heating at acidic pH separately. AFs can also be formed at higher pH, especially in the presence of alcohols or chaotropic/reducing agents. Tryptic wheat gluten digests can form fibrillar structures at neutral pH and maize and rice proteins do so in aqueous ethanol or at acidic pH, respectively. [ABSTRACT FROM AUTHOR]

With the aim of establishing a starting point for the determination of the complete amino acid sequence of the major parvalbumin from hake muscle, the peptides resulting bom the tryptic digestion of the S-sulfo-derivative and of the performic, acid-oxidized protein were examined. A total of 20 peptides were thus obtained m sufficient quantity and m a state of purity adequate for further studies. Their complete or partial sequence is reported. When due account is taken of obvious overlaps, the total of these peptides fully accounts for the composition of the whole molecule with the exception of one alanine residue, and for the number of peptides expected from the presence of 12 lysines and 1 arginine in this parvalbumin. [ABSTRACT FROM AUTHOR]

Porcine secretin is a heptacosapeptide with the amino acid sequence His-Ser-Asp-Gly-Thr- Phe -Thr- Ser -Glu -Leu -Ser -Arg -Leu -Arg -Asp-Ser -Ala -Arg -Leu -Gin -Arg -Leu -Leu-Gln-Gly-Leu- Va1NH2. Fourteen of its twenty-seven amino acids occur in the same position as they do in porcine glucagon. [ABSTRACT FROM AUTHOR]

Eukaryotic cells are highly compartmentalized, requiring elaborate transport mechanisms to facilitate the movement of proteins between membrane‐bound compartments. Most proteins synthesized in the endoplasmic reticulum (ER) are transported to the Golgi apparatus through COPII‐mediated vesicular trafficking. Sar1, a small GTPase that facilitates the formation of COPII vesicles, plays a critical role in the early steps of this protein secretory pathway. Sar1 was characterized in yeast, animals and plants, but no Sar1 homolog has been identified and functionally analyzed in algae. Here we identified a putative Sar1 homolog (CrSar1) in the model green alga Chlamydomonas reinhardtii through amino acid sequence similarity. We employed site‐directed mutagenesis to generate a dominant‐negative mutant of CrSar1 (CrSar1DN). Using protein secretion assays, we demonstrate the inhibitory effect of CrSar1DN on protein secretion. However, different from previously studied organisms, ectopic expression of CrSar1DN did not result in collapse of the ER‐Golgi interface in Chlamydomonas. Nonetheless, our data suggest a largely conserved role of CrSar1 in the ER‐to‐Golgi protein secretory pathway in green algae. [ABSTRACT FROM AUTHOR]

This paper describes the use of Principal Component Analysis (PCA) as a tool for modeling chromatographic separations. PCA is an analytical technique developed to extract key information out of large data sets and to develop relationships and correlations. The basis of the proposed model is the use of PCA to correlate experimental chromatographic data across different process variables or scales. The generated correlations are then used to provide for the simulation of additional chromatographic runs not included in the initial dataset. The approach is demonstrated by application to the cation exchange separation of a four protein component feed comprising ovalbumin, ovatransferrin, lysozyme, and myoglobin. A good fit between modeled and experimental data was found, and the ability of the method to model additional chromatographic separations not within the original dataset is demonstrated. The technique has the potential to accommodate changing system variables such as column dimensions as well as process variables including sample volume and salt gradient. It provides a potentially powerful tool for the rapid investigation of scale-up effects and for the minimization of the material inventories needed for such studies. [ABSTRACT FROM AUTHOR]

Crystallographers are increasingly determining structures of protein constructs that include His tags. Many have taken for granted that these tags have little effect on the native structure. This paper surveys and compares crystal structures with and without His tags. It is observed that actual refined tag residues fitted into density occur in less that 10% of the tagged sequences. However, higher resolution crystals are observed when this occurs. It is shown that these purification tags generally have no significant effect on the structure of the native protein. Resolution and R factors are not affected, but the overall B factors are slightly higher. Additional annotation in the PDB format to make tag definition explicit is suggested. [ABSTRACT FROM AUTHOR]

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]

The design and development of soft biomaterials based on amino acid and short‐peptide have gained much attention due to their potent biomedical applications. A slight alteration in the side‐chain of single amino acid in a peptide or protein sequence has a huge impact on the structure and function. Phenylalanine is one of the most studied amino acids, which contains an aromatic phenyl group connected through a flexible −CH2− unit. In this work, we have examined whether flexibility and aromatic functionality of phenylalanine (Phe) are important in gel formation of model gelator Fmoc‐Phe‐OH or not. To examine this hypothesis, we synthesized Fmoc‐derivatives of three analogues unnatural amino acids including cyclohexylalanine, phenylglycine, and homophenylalanine; which are slightly varied from Phe. Interestingly, all these three new analogues formed hydrogels in phosphate buffer at pH 7.0 having different gelation efficacy and kinetics. This study suggests that the presence of aromatic side‐chain and flexibility are not mandatory for the gelation of this model gelator. Newly synthesized unnatural amino acid derivatives have also exhibited promising antimicrobial activity towards gram‐positive bacteria by inhibiting cellular oxygen consumption. We further determined the biocompatibility of these amino acid derivatives by using a hemolysis assay on human blood cells. Overall studies described the development of single amino acid‐based new injectable biomaterials with improved antimicrobial activity by the slight alteration in the side‐chain of amino acid. [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]

Biochemical and biophysical experiments are essential for uncovering the three‐dimensional structure and biological role of a protein of interest. However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an uncharacterized protein based on their evolutionary relatedness. These predictions are helpful in developing specific hypotheses to guide wet‐laboratory experiments. Commonly used bioinformatics resources include methods to identify and predict conserved sequence motifs, protein domains, transmembrane segments, signal sequences, and secondary as well as tertiary structure. Here, several such methods available through the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) are described and how their combined use can provide meaningful information on a protein of unknown function is demonstrated. In particular, the identification of homologs of known structure using HHpred, internal repeats using HHrepID, coiled coils using PCOILS and DeepCoil, and transmembrane segments using Quick2D are focused on. [ABSTRACT FROM AUTHOR]

Proteolytic instability is a critical limitation for peptide‐based products. Although significant efforts are devoted to stabilize sequences against proteases/peptidases in plasma/serum, such approaches tend to be rather empirical, unspecific, time‐consuming, and frequently not cost‐effective. A more rational and potentially rewarding alternative is to identify the chemical grounds of susceptibility to enzymatic degradation of peptides so that proteolytic resistance can be tuned by manipulation of key chemical properties. In this regard, we conducted a meta‐analysis of literature published over the last decade reporting experimental data on the lifetimes of peptides exposed to proteolytic conditions. Our initial database contained 579 entries and was curated with regard to amino acid sequence, chemical modification, terminal half‐life (t1/2) or other stability readouts, type of stability assay, and biological application of the study. Although the majority of entries in the database corresponded to (slightly or substantially) modified peptides, we chose to focus on unmodified ones, as we aimed to decipher intrinsic characteristics of peptide proteolytic susceptibility. Specifically, we developed a multivariable regression model to unravel those peptide properties with most impact on proteolytic stability and thus potential t1/2 predicting ability. Model validation was done by two different approaches. First, a library of peptides spanning a large interval of properties that modulate stability was synthesized and their t1/2 in human serum were experimentally determined. Second, the t1/2 of 21 selected peptides approved for clinical use or in clinical trials were recorded and matched with the model‐estimated values. With both approaches, good correlation between experimental and predicted t1/2 data was observed. [ABSTRACT FROM AUTHOR]

The Cd(II)‐, Pb(II)‐, Ni(II)‐ and Zn(II)‐complexes of small terminally protected peptides containing CXXX, XXXC, XCCX, CXnC (n=1–3) sequences have been studied with potentiometric, UV/Vis and CD spectroscopic techniques. The cysteine thiolate group is the primary binding site for all studied metal ions, but the presence of a histidyl or aspartyl side chain in the molecule contributes to the stability of the complexes. For two‐cysteine containing peptides the (S−,S−) coordinated species are formed in the physiological pH range and the stability increases in the Ni(II)

1. Adenylate kinase (ATP: AMP phosphotransferase) has been purified 490-fold from porcine muscle with a final yield of 60 mg/kg muscle. 2. The amino-acid composition is Asp11 Asn2, Thr14, Ser11, Glu19,, Gln6, Pro6, Gly19>, Ala6, Cyst2, Val17, Met6, Ile9, Leu18, Tyr7, Phe5, Lys21, His2, Arrg11. 3. The protein molecules a single polypeptide chain of 194 amino-acid residues with an acetylmethionine at the N-terminus and a lysine residue at the C-terminus. 4. Cyanogen bromide cleavage of carboxymethylated adenylate kinase yielded six fragments which were further degraded by using trypsin, chymotrypsin, thermolysin, subtilisin or α-protease. Sequence data on the resulting peptides are summarized in the present report, full details are given in a supplementary paper which has been deposited at CNRS from where copies can be obtained. 5. The primary structure of porcine adenylate kinase was given. [ABSTRACT FROM AUTHOR]

The structure of a new antibiotic of the iturin group, bacillomycin F, has been demonstrated. It is a mixture of homologous peptidolipids, essentially C51H80N12O14 and C52N82N12O14. The lipid moiety consists of minor isoC15, anteisoC15 β-amino acids and major isoC16, isoC17 and anteisoC17 β-amino acids. The peptide sequence was determined by studying the peptides obtained after mild HCl hydrolysis and by Edman degradation of bacillomycin F treated with N-bromosuccinimide. The sequence was confirmed by two-dimensional NMR spectrometry and fast-atom-bombardment mass spectrometry gave the molecular masses of the homologous compounds. Bacillomycin F is a cyclic peptidolipid; its complete structure is given in the paper. [ABSTRACT FROM AUTHOR]