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This work presents an annotation tool that automatically locates mentions of particular amino‐acid residues in published papers and identifies the protein concerned. These matches can be provided in context or in a searchable format in order for researchers to better use the existing and future literature. [ABSTRACT FROM AUTHOR]

We describe a sensitive immunological procedure for the detection of specific proteins in total cell extracts and for the comparison of antigenically related polypeptides. Proteins are fractionated in polyacrylamide gels and transferred electrophoretically to diazophenylthioether paper, to which they bind covalently. Specific proteins are identified by incubation with specific antibody and ⊃125 -labeled protein A from Staphylococcus aureus, followed by autoradiography. High-resolution separation of proteins prior to transfer is achieved by polyacrylamide gradient gel electrophoresis in the presence of sodium dodecyl sulfate or by nonequilibrium pH gradient electrophoresis, followed by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. Further information can be obtained by limited enzymatic proteolysis of the proteins in the gel following polyacryllamide gel electrophoresis in the presence of sodium dodecyl sulfate and analysis of the cleavage products by gel electrophoresis at right angles to the first gel. We show the application of this technique to the detection and comparison in extracts from infected cells of proteins related immunologically to the simian virus 40 capsid proteins VP1 and VP3. [ABSTRACT FROM AUTHOR]

1. A new diagonal etectrophoretic technique for determining the order of the lysine-containing tryptic peptides of a protein is described. The protein is converted into its trifluoracetyl derivative, digested enzymatically (or chemically), and the resulting peptides separated by paper electrophoresis. The paper is then treated with ammonia vapour, which re-exposes the ε-amino groups of the lysine residues, and submitted to a second electrophoresis at right angles to the first direction. Peptides containing lysine residues, together with the N-terminal peptide of the protein, are found to lie off a diagonal formed by all other peptides, whence they may be readily purified. A study of these peptides enables the order of the lysine-containing tryptic peptides in the protein to be deduced. 2. The technique has been successfully tested with insulin. 3. When the method was applied to porcine pepsin, the four tryptic peptides isolated were easily ordered and the carboxyl-terminal sequence of the protein shown to be Arg-Gln-Tyr-TyrThr-Val-Phe-Asp-Arg-Ala-Asn-Asn-Lys-Val-Gly-Leu-Ala-Pro-Val-Ala. The thee basic ammo acid residues in the molecule are thus found clustering towards the C-terminus of the polypeptide chain. 4. A common ancestral gene for porcine pepsin and bovine (calf) rennin is suggested by the close homology between the C-terminal sequents of the two proteins. [ABSTRACT FROM AUTHOR]

Summary: Maize grain is deficient in lysine. While the opaque2 mutation increases grain lysine, o2 is a transcription factor that regulates a wide network of genes beyond zeins, which leads to pleiotropic and often negative effects. Additionally, the drastic reduction in 19 kDa and 22 kDa alpha‐zeins causes a floury kernel, unsuitable for agricultural use. Quality protein maize (QPM) overcame the undesirable kernel texture through the introgression of modifying alleles. However, QPM still lacks a functional o2 transcription factor, which has a penalty on non‐lysine amino acids due to the o2 mutation. CRISPR/cas9 gives researchers the ability to directly target genes of interest. In this paper, gene editing was used to specifically target the 19 kDa alpha zein gene family. This allows for proteome rebalancing to occur without an o2 mutation and without a total alpha‐zein knockout. The results showed that editing some, but not all, of the 19 kDa zeins resulted in up to 30% more lysine. An edited line displayed an increase of 30% over the wild type. While not quite the 55% lysine increase displayed by QPM, the line had little collateral impact on other amino acid levels compared to QPM. Additionally, the edited line containing a partially reduced 19 kDa showed an advantage in kernel texture that had a complete 19 kDa knockout. These results serve as proof of concept that editing the 19 kDa alpha‐zein family alone can enhance lysine while retaining vitreous endosperm and a functional O2 transcription factor. [ABSTRACT FROM AUTHOR]

Because protein is a primary element responsible for biological or biochemical roles in living bodies, protein function is the core and basis information for biomedical studies. However, recent advances in bio technologies have created an explosive increase in the amount of published literature; therefore, biomedical researchers have a hard time finding needed protein function information. In this paper, a classification system for biomedical literature providing protein function evidence is proposed. Note that, despite our best efforts, we have been unable to find previous studies on the proposed issue. To classify papers based on protein function evidence, we should consider whether the main claim of a paper is to assert a protein function. We, therefore, propose two novel features -- protein and assertion. Our experimental results show a classification performance with 71.89% precision, 90.0% recall, and a 79.94% F-measure. In addition, to verify the usefulness of the proposed classification system, two case study applications are investigated -- information retrieval for protein function and automatic summarization for protein function text. It is shown that the proposed classification system can be successfully applied to these applications. [ABSTRACT FROM AUTHOR]

Discusses two studies on hypertension. "Effect of Soybean Protein on Blood Pressure: A Randomized, Controlled Trial," by J. He et al published in the 2005 issue of "Annals of Internal Medicine"; "North American Ginseng Exerts a Neutral Effect on Blood Pressure in Individuals With Hypertension," by P. M. Stavro et al published in the 2005 issue of "Hypertension."

We have previously described a partial cDNA sequence encoding a RhoGAP protein, GAP25 that is homologous to the recently reported ArhGAP9 and ArhGAP12. We now describe a related new member ArhGAP15 that shares a number of domain similarities, including a pleckstrin homology (PH) domain, a RhoGAP domain and a novel motif N-terminal to the GAP domain. This novel motif was found to be responsible for nucleotide-independent Rac1 binding. Using swop mutants of Rac/Cdc42, we have established that the binding is through the C-terminal half of Rac1. The GAP domain of ArhGAP15 showed specificity towards Rac1 in vitro. The PH domain is required for ArhGAP15 to localize to cell periphery and over-expression of the full-length ArhGAP15, but not the mutant with a partial deletion of the PH domain, resulted in an increase in actin stress fibers and cell contraction. These morphological effects can be attenuated by the co-expression of dominant negative Rac1N17. HeLa cells expressing ArhGAP15 were also resistant to phorbol myristatate acetate treatment, suggesting that ArhGAP15 is a potential regulator of Rac1. [Copyright &y& Elsevier]

Proteins produced by cap‐independent translation mediated by an internal ribosome entry site (IRES) in circular RNAs (circRNAs) play important roles in tumour progression. To date, numerous studies have been performed on circRNAs and the proteins they encode. In this review, we summarize the biogenesis of circRNAs and the mechanisms regulating circRNA‐encoded proteins expression. We also describe relevant research methods and their applications to biological processes such as tumour cell proliferation, metastasis, epithelial‐mesenchymal transition (EMT), apoptosis, autophagy and chemoresistance. This paper offers deeper insights into the roles that circRNA‐encoded proteins play in tumours. It also provides a theoretical basis for the use of circRNA‐encoded proteins as biomarkers of tumorigenesis and for the development of new targets for tumour therapy. [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]

The article lists several research papers that would be published in the coming issues of the European Journal of Biochemistry. Some of the articles and topics are related to glucogen synthase, protein phosphates, DNA sequences, etc.

The article presents a list of forthcoming papers related to immunology. Some of the papers include "Inhibitory p41 Isoform of Invariant Chain and Its Potential Target Enzymes Cathepsins L and H in Distinct Populations of Macrophages in Human Lymph Nodes," by V. Zavašnik-Bergant, A. Schweiger, T. Bevec, R. Golouh, V. Turk, J. Kos, and " Echinococcus Multilocularis Proliferation in Mice and Respective Parasite 14-3-3 Gene Expression is Mainly Controlled by an CD4 + T cell Mediated Immune Response," by W. Dei, A. Waidvogel, M. Siles-Lucas, Bruno Gottistein.

A neurodepressing hormone has been isolated and purified to homogeneity from aqueous extracts of 2000 eyestalks of the Mexican crayfish Procambarus bouvieri (Ortmann). Purification was achieved by gel filtration on Sephadex G-25 and G-15, and preparative paper electrophoresis at four pH values (1.8, 3.6, 6.0 and 10.0). The recovery of hormone activity was 85% and the specific activity was 4.0 × 104 limes that of the starting material. The hormone is a thermostable peptide of approximately 1200 molecular weight and composed of neutral amino acids. No N-terminal group could be found. From its electrophoretic behavior it is concluded that the C-terminal group is also blocked. [ABSTRACT FROM AUTHOR]

The article presents information on various research papers which will be published in the forthcoming issue of the "European Journal of Biochemistry". Some of the papers discusses are "Enzymatic Synthesis of Neolactotetraosylceramide by the N-Acctyllactosamine Synthase of Human Serum". "Rate of Transplantation and Kinetics of Processing of Newly Synthesized Molecules of Two Major Outer-Membrane Proteins, the OmpA and OmpF Proteins of Escherichia Coli," by the researchers I. Crowlesmith and K. Gamon.

Introduces the research papers to be published in the "European Journal of Biochemistry," succeeding the May 15, 1985. "Primer-independent abortive initiation by wheat-germ RNA polymerase B," by H. Mosig et al; "Protein structure and gene organization of mouse lactate dehydrogenase-A isozyme," S.S.-L. Li et al; "A model for intracellular complexation between gene-5 protein and bacteriophage fd DNA," by G.D. Bayer et al.

Streptococcus sanguinis is an important cause of infective endocarditis. In strain SK36, the ABC-family manganese transporter, SsaACB, is essential for virulence. We have now identified a ZIP-family protein, TmpA, as a secondary manganese transporter. A tmpA mutant had no phenotype, but a ΔssaACB ΔtmpA mutant was more attenuated for serum growth and for virulence in a rabbit model than its ΔssaACB parent. The growth of both mutants was restored by supplemental manganese, but the ΔssaACB ΔtmpA mutant required twenty-fold more and accumulated less. Although ZIP-family proteins are known for zinc and iron transport, TmpA-mediated transport of either metal was minimal. While ssaACB appears ubiquitous in St. sanguinis, tmpA was present in a majority of strains and a mntH gene encoding an NRAMP-family transporter was identified in relatively few, including VMC66. As in SK36, deletion of ssaACB greatly diminished VMC66 endocarditis virulence and serum growth, and deletion of tmpA from this mutant diminished virulence further. Virulence was not significantly altered by deletion of mntH from either VMC66 or its ΔssaACB mutant. This and the accompanying paper together suggest that SsaACB is of primary importance for endocarditis virulence while secondary transporters TmpA and MntH contribute to growth under differing conditions. [ABSTRACT FROM AUTHOR]

Presents research articles on biochemistry to be published in the "European Journal of Biochemistry." "Secondary and Tertiary Structure Characteristic of Megasphaera elsdenii Flavodoxin in the Reduced State as Determined by Two-Dimensional 1H NMR," by C. P. M. van Mierlo, F. M¨ller, and J. Vervoort; "Presence and Characterization of Glycolipid Sulfotransferase in Human Cancer Serum," by S. Gasa, M. -T. Casl, A. Makita, N. Sakakibara, T. Koyanagi, and T. Atsuta; "Interaction of Hemin With Placental Glutathione Transferase," by A. M. Caccuri; A. Aceto, F. Piemonte, C. di Ilio, N. Rosato, and G. Federici.

Lists articles about biochemistry. "Modulation of the interaction between the two halves of troponin C by the other troponin subunits," by C.-L.A. Wang and J. Gergely; "Sequence determinants of cytosolic N-terminal protein processing," by C. Flinta, B. Persson, H. Jornvall and G. von Heijne; "Effect of benzoate on the metabolism of fructose 2,6-biphosphate in yeast," by J. Francois, E. van Schaftingen and H.-G. Hers; "Isolation and properties of porcine cholesterol acyltransferase," G. Knipping; Others.

Lists the titles of papers that will be published in future issues of the "European Journal of Biochemistry." "Regulation of the ontogeny of rat liver metallothionein mRNA by zinc," by G.K. Andrews et al; "Processing of a plant vacuolar protein precursor in vitro," by T. Hattori et al "Structural studies of the putatitve O-specific polysaccharide of Serratia marcescens 09," by D. Oxley and S.G. Wilkinson.

Lists papers that will published in the upcoming issues of the "European Journal of Biochemistry". "Eurabutoxin b--Initial protein refinement and sequence analysis at 0.140-nm resolution," by P.E. Bourne and colleagues; "Preferential conformation of substance P in solution," by G. Chassaing and colleagues; "Interaction of actinogelin with actin--No nucleation but high gelation activity".

The article presents a list of forthcoming research papers including "Kinetic Studies of Proton Transfer in the Microenvironment of a Binding Site," by M. Gutman, D. Huppert and E. Nachliel," "The Substrate Binding Site of Aldehyde Reductase From Pig Liver: Stereochemical Investigations Using NADP-2-Oxodiacid Adducts As Probe," by G. Branlant and "Membranes of Protein Bodies: I. Isolation from Cotyledons of Germinating Cucumber Seeds" by U. A. K. Kara and H. Kindl.

Presents a list of research papers to be published in the upcoming issues of the "European Journal of Biochemistry." "Extraction and Translation of Collagen mRNA From Fetal Calf Skin," by R. Kaufman, A. Belayew, B. Nusgens, and C. M. Lapie&rgrave;e; "Messenger RNA For Ribosomal Proteins in Xenopus laevis Oocytes," by P. Pierandrei-Amaldi and E. Beccari; "Purification and Characterization of Esterase 2B of the House Mouse, Mus musculus," by U. Lexow, A. Ronai, and O. von Deimling.

In this paper, the effects of peroxyl radical oxidation on the physicochemical and functional properties of walnut protein were investigated. Walnut protein isolate (WPI) containing 2,2′‐azobis(2‐amidinopropane) dihydrochloride (AAPH) was oxidatively stressed under aerobic conditions in peroxyl radical‐generating media. Incubation of walnut protein with increasing concentration of AAPH resulted in gradual carbonyl generation and free sulfhydryl group degradation. The results of surface hydrophobicity implied that oxidation leads to protein aggregation thus decreasing protein solubility in an AAPH concentration‐dependent manner (P < 0.05). Emulsifying properties exhibited a significant increase (P < 0.05) at AAPH concentrations up to 0.2 mM and higher AAPH concentrations reduced the emulsifying capacity of WPI. These results indicate that appropriate oxidation is helpful to improve the emulsifying properties of protein, and with an increase of oxidation degree, emulsifying functional will damage. [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]

The methylation of HeLa cell ribosomal proteins has been studied by paper electrophoresis separation of the peptides produced after trypsin digestion of individual ribosomal proteins. Methylation in vivo was detected by 3H labeling of peptides from cells that had been incubated with a mixture of [methyl-3H]methionine plus [35S]methionine, the incorporation of the 3H-labeled amino acid methionine being corrected by the 35S uptake. Each methylated peptide thus represented at least one methylation site (one or more methylated amino acids and their adjacent amino acid sequence). Eleven ribosomal proteins were found to be methylated. As many as five methylation sites were present in one ribosomal protein. In several ribosomal proteins some sites were methylated when ribosome synthesis was suppressed with low levels of actinomycin D, while other sites were not. Therefore, some of the sites in a given protein were apparently methylated in mature ribosomes, while other sites were methylated during ribosome processing. The methyl-group-specific labeling of some sites, but not others, was suppressed by cycloheximide, thus suggesting that the methylation of some sites was dependent on protein synthesis. A cell-free system from cultured HeLa cells is described, which reproduces the methylation pattern of ribosomal proteins in vivo in two ways: methylation was observed both in vivo and in vitro (a) in the same ribosomal proteins; and (b) in the same methylation sites of a given ribosomal protein. In addition, our data in vitro suggest that the methylation of some human ribosomal protein sites may involve a methyl donor other than S-adenosylmethionine. [ABSTRACT FROM AUTHOR]

A series of bacterial cell wall glycopeptides of low molecular weight and cell wall nucleotide precursors have been tested for their inhibitory action on the digestion by T4 lysozyme of a radioactively labeled linear uncrosslinked peptidoglycan. The disaccharide-peptides GlcNAc-MurNAc- L-Ala-D-Glu(A2pm) (C5) and GlcNAc-MurNAc-L-Ala-D-Glu(A2pm-D-Ala) (C6) as well as the monosaccharide-peptide MurNAc-L-Ala-D-Glu(A2pm) were found to be good competitive in- hibitors (with similar Ki values) whereas the disaccharide-pentapeptide GlcNAcMurNAc-L-Ala-D Glu-Gly [This symbol cannot be represented into ASCII Text]-L-Lys-D-Ala was a poor inhibitor. T4 lysozyme did not catalyse transglycosylation reactions from Escherichia coli B peptidoglycan to the disaccharide-peptide C6. No changes were seen in the circular dichroism spectra (200–250 nm) or fluorescence emission spectra upon binding of the good inhibitors. The results obtained indicate that T4 lysozyme has a small active site capable of recognizing a unit consisting of MurNAc-L-Ala-D-Glu(A2pm). [ABSTRACT FROM AUTHOR]

Procedures are described for the assay of collagen galactosyltransferase and collagen glucosyltransferase activities. The methods are based on the transfer of [14C]galactose or [14C]glucose from the corresponding radioactive UDP-glycoside to hydroxylysyl or galactosylhydroxylysyl residues in calf-skin gelatin substrate, and on the specific assay of the products of the enzymic reactions. The assay of the products includes precipitation of the protein, and removal of most of the radioactivity present in the free UDP-glycoside by several washings of the precipitate. The [14C]galactosylhydroxylysine or [14C]glucosylgalactosylhydroxylysine is then liberated by alkaline hydrolysis, and purified further by a modified Dowex chromatography and by paper electrophoresis. The procedure is entirely specific when judged by amino acid analysis, and it is possible to assay a series of 36 samples in 2 days. The sensitivity of the method permits assays in extracts from several tissues, including tissues with low transferase activities, such as liver. Preliminary characterization of the transferases from chick embryo cartilage indicated that the galactosyltransferase did not catalyze the transfer of galactose to free hydroxylysine. Dialyzable peptides were found to act as substrates for both transferases. The Km for the gelatinized collagen substrate was 150 g/1 in the reaction with the galactosyltransferase, and 14 g/1 in that with the glucosyltransferase. The Km for UDP-galactose or UDP-glucose in the reaction with the corresponding transferase was about 30 μM. Both transferases required a metal co-factor, and manganese was found to be far more effective than any other metal tested. The optimal manganese concentration for both transferases was 10 mM. No stimulation of the glucosyltransferase activity was found with folate, which has recently been reported to stimulate collagen glucosyltransferase from rat kidney. [ABSTRACT FROM AUTHOR]

The Yes-associated protein ( YAP) is an important transcriptional co-activator that mediates the cellular response to mechanical and cytoskeletal cues. In two recent papers published in The EMBO Journal, Dae-Sik Lim and colleagues show how YAP activity affects cancer formation and metastasis via a crosstalk with myocardin-related transcription factors (MRTFs; Kim et al, 2017) and SKP2-dependent cell cycle progression (Jang et al, 2017). [ABSTRACT FROM AUTHOR]

Synthetic biology is an interdisciplinary field that uses well‐established engineering principles for performing the analysis of the biological systems, such as biological circuits, pathways, controllers and enzymes. Conventionally, the analysis of these biological systems is performed using paper‐and‐pencil proofs and computer simulation methods. However, these methods cannot ensure accurate results due to their inherent limitations. Higher‐order‐logic (HOL) theorem proving is proposed and used as a complementary approach for analysing linear biological systems, which is based on developing a mathematical model of the genetic circuits and the bio‐controllers used in synthetic biology based on HOL and analysing it using deductive reasoning in an interactive theorem prover. The involvement of the logic, mathematics and the deductive reasoning in this method ensures the accuracy of the analysis. It is proposed to model the continuous dynamics of the genetic circuits and their associated controllers using differential equations and perform their transfer function‐based analysis using the Laplace transform in a theorem prover. For illustration, the genetic circuits of activated and repressed expressions and autoactivation of protein, and phase lag and lead controllers, which are widely used in cancer‐cell identifiers and multi‐input receptors for precise disease detection, are formally analyzed. [ABSTRACT FROM AUTHOR]

publisher‐imprint‐name Springer volume‐issue‐count 1 issue‐article‐count 0 issue‐toc‐levels 0 issue‐pricelist‐year 2016 issue‐copyright‐holder The Author(s) issue‐copyright‐year 2016 article‐contains‐esm No article‐numbering‐style Unnumbered article‐registration‐date‐year 2016 article‐registration‐date‐month 2 article‐registration‐date‐day 19 article‐toc‐levels 0 toc‐levels 0 volume‐type Regular journal‐product ArchiveJournal numbering‐style Unnumbered article‐grants‐type OpenChoice metadata‐grant OpenAccess abstract‐grant OpenAccess bodypdf‐grant OpenAccess bodyhtml‐grant OpenAccess bibliography‐grant OpenAccess esm‐grant OpenAccess online‐first false pdf‐file‐reference BodyRef/PDF/40169_2016_Article_87.pdf target‐type OnlinePDF issue‐type Regular article‐type ReviewPaper journal‐subject‐primary Medicine & Public Health journal‐subject‐secondary Medicine/Public Health, general journal‐subject‐collection SC11 open‐access true --> Extracellular microvesicles (ExMVs) are part of the cell secretome, and evidence has accumulated for their involvement in several biological processes. Fourteen years ago our team demonstrated for the first time that ExMVs carry functional RNA species and proteins from one cell to another, an observation that opened up the new research field of horizontal transfer of bioactive molecules in cell‐to‐cell communication. Moreover, the presence of mRNA, noncoding RNA, and miRNA in ExMVs in blood and other biological fluids opened up the possibility of employing ExMVs as new detection markers for pathological processes, and ExMVs became a target for "liquid biopsy" approaches. While ExMV‐derived mRNAs may be translated in target cells into appropriate proteins, miRNAs regulate expression of corresponding mRNA species, and both RNA‐depended ExMV‐mediated mechanisms lead to functional changes in the target cells. Following from this observation, several excellent papers have been published that confirm the existence of the horizontal transfer of RNA. Moreover, in addition to RNA, proteins, bioactive lipids, infectious particles and intact organelles such as mitochondria may follow a similar mechanism. In this review we will summarize the impressive progress in this field—14 years after initial report. [ABSTRACT FROM AUTHOR]

Features the new semi-dry electrophoretic transfer system PhastTransfer from Pharmacia LKB Biotechnology AB. Usability of the system; Operational function; Contact information.

Lists articles about biochemistry. "Impact of altered protein structures on the intracellular traffic of a mutated vasopressin precursor from Brattleboro rats," by H. Schmale et al; "Direct electron transfer of redox proteins at the bare classy carbon electrode," by W.R. Hagen; "Molecular cloning of preproacrosin and analysis of its expression pattern in spermatogenesis," by I.M. Adham; "Reduced temperature does not prevent transport of lysosomal integral membrane proteins from endoplasmic reticulum and through the Golgi system to lysosomes," by P.G. Morales; Others.

Offers information on articles for publication in future issues of the "European Journal of Biochemistry". Synthesis of two proteins in chloroplasts and messenger RNA; Types of acids from Mycobacterium thamnopheos; Use of the inhibition of enzymatic antioxidant systems in order to evaluate their physiological importance.

Presents several articles to be published in the "European Journal of Biochemistry." "Modification of Ribosomal Proteins in Sea Urchin Eggs Following Fertilization," by K. Takeshima and E. Nakano; "A Phosphotyrosyl-Protein Phosphatase Activity Associated With Acid Phosphatase From Human Prostate Gland," by H.-C. Li, J. Chernoff, L. B. Chen and A. Kirschonbaum; "Molecular Characterization of the Gene Coding for Major Outer Membrane Protein OmpA from Enterobacter Aerogenes," by G. Braun and S. T. Cole; "Nidogen: A New, Self-Aggregating Basement Membrane Protein," by R. Timpl, M. Dziadek, S. Fujiwara, H. Nowack and G. Wick; Others.

In a Eukaryotic gene, identification of exon regions is crucial for protein formation. The periodic‐3 property of exon regions has been used for its identification. An anti‐notch infinite impulse response (IIR) filter is mostly employed to recognise this periodic‐3 property. The lattice structure realisation of anti‐notch IIR filter requires less hardware over direct from‐II structures. In this study, a hardware implementation of IIR anti‐notch filter lattice structure is carried out on Zynq‐series (Zybo board) field programmable gate array (FPGA). The performance of hardware design has been improved using techniques like retiming, pipelining and unfolding and finally assessed on various Eukaryotic genes. The hardware implementation reduces the time frame to analyse the DNA sequence of Eukaryotic genes for protein formation, which plays a significant role in detecting individual diseases from genetic reports. Here, the performance evaluation is carried out in MATLAB simulation environment and the results are found similar. Application‐specific integrated circuit (ASIC) implementation of the anti‐notch filter lattice structure is also carried out on CADENCE‐RTL compiler. It is observed that the FPGA implementation is 31 to 34 times faster and ASIC implementation is 58 to 64 times faster compared to the results generated by MATLAB platform with similar prediction accuracy. [ABSTRACT FROM AUTHOR]

Crystallographic models of biological macromolecules have been ranked using the quality criteria associated with them in the Protein Data Bank (PDB). The outcomes of this quality analysis have been correlated with time and with the journals that published papers based on those models. The results show that the overall quality of PDB structures has substantially improved over the last ten years, but this period of progress was preceded by several years of stagnation or even depression. Moreover, the study shows that the historically observed negative correlation between journal impact and the quality of structural models presented therein seems to disappear as time progresses. [ABSTRACT FROM AUTHOR]

Introduction: Dental pulp with special structure has become a good reference sample in paleomicrobiology‐related blood‐borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins. Objectives: This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20 years following the first detection of an ancient microbe. Methods: The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: "ancient," "dental pulp," "teeth," "anatomy," "structure," "collection," "preservation," "selection," "photography," "radiography," "contamination," "decontamination," "DNA," "protein," "extraction," "bone," "paleomicrobiology," "bacteria," "virus," "pathogen," "molecular biology," "proteomics," "PCR," "MALDI‐TOF," "LC/MS," "ELISA," "immunology," "immunochromatography," "genome," "microbiome," "metagenomics." Results: The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty‐seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species. Conclusions: Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics. [ABSTRACT FROM AUTHOR]

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The paper 'Interaction of N‐acetyl‐l‐glutamate kinase with the PII signal transducer in the non‐photosynthetic alga Polytomella parva: Co‐evolution towards a hetero‐oligomeric enzyme' by Selim et al. highlights how the study of a true taxonomic oddity, the heterotrophic unicellular alga P. parva, has been instrumental in uncovering the large potential for adaptive variation in the signaling complex of PII with the enzyme N‐acetylglutamate kinase (NAGK). This complex modifies the regulatory properties of NAGK, allowing nitrogen stockpiling as arginine. In P. parva, a stable PII‐NAGK complex is formed which lacks regulation by canonical PII effectors but which exhibits novel adaptive responses to nitrogen abundance mediated by glutamine, a neo‐effector of PII proteins of photosynthetic eukaryotes. [ABSTRACT FROM AUTHOR]

A new approach of predicting structural classes of protein domain sequences is presented in this paper. Besides the amino acid composition, the composition of several dipeptides, tripeptides, tetrapeptides, pentapeptides and hexapeptides are taken into account based on the stepwise discriminant analysis. The result of jackknife test shows that this new approach can lead to higher predictive sensitivity and specificity for reduced sequence similarity datasets. Considering the dataset PDB40-B constructed by Brenner and colleagues, 75.2% protein domain sequences are correctly assigned in the jackknife test for the four structural classes: all-α, all-β, α/β and α + β, which is improved by 19.4% in jackknife test and 25.5% in resubstitution test, in contrast with the component-coupled algorithm using amino acid composition alone (AAC approach) for the same dataset. In the cross-validation test with dataset PDB40-J constructed by Park and colleagues, more than 80% predictive accuracy is obtained. Furthermore, for the dataset constructed by Chou and Maggiona, the accuracy of 100% and 99.7% can be easily achieved, respectively, in the resubstitution test and in the jackknife test merely taking the composition of dipeptides into account. Therefore, this new method provides an effective tool to extract valuable information from protein sequences, which can be used for the systematic analysis of small or medium size protein sequences. The computer programs used in this paper are available on request. [ABSTRACT FROM AUTHOR]

LINKED CONTENT: This article is linked to Hey et al paper. To view this article, visit https://doi.org/10.1111/apt.17917 [ABSTRACT FROM AUTHOR]

An editorial is presented on challenges related to protein provision for the growing global population, which include improving the environmental impact of traditional protein supply chains; and considering the environmental impact with the need to reduce greenhouse gas emissions.

This study investigated the possibility of using amaranth protein isolate (API) as a plant‐based substitute for egg yolk (EY) in the preparation of low‐fat mayonnaise (LFM). The alkali extraction/acidic precipitation method was used to isolate amaranth protein; its functional properties were then studied. The results showed that besides its great water and oil absorption capacities, API had better emulsifying capacity and significantly higher (p <.05) emulsion stability at pH 2.0 than alkali pH values. Five mayonnaise samples with different API/EY combination ratios (%) (i.e., 0/0.75, 0.25/0.5, 0.375/0.375, 0.5/0.25, and 0.75/0) were prepared. The color, emulsion stability (ES), freeze–thaw stability (FTS), droplet size, structure, rheology, and sensory properties of samples were examined. API replacement showed no adverse effects on the L* value, ES, and sensory attributes (p >.05). Low API concentrations (0.25% and 0.375%) significantly (p <.05) increased the droplet size and decreased the FTS of LFM emulsion. High API concentrations (0.5% and 0.75%) had no significant effect (p >.05) on droplet size and formed emulsions with more tightly packed oil droplets. The Cross model was chosen best to describe the flow behavior of LFM samples (R2 = 0.99). The sample with 0.75% API had significantly (p <.05) the highest values of ηo (zero‐shear viscosity) and λ (relaxation time), indicating greater interaction between the emulsion particles. All samples showed a weak gel structure (G' > G"). In conclusion, API can be considered an appropriate substitute for EY in LFM production, which can benefit human health and offer a new strategy for preparing vegan products. [ABSTRACT FROM AUTHOR]

As shown in the preceding paper [Ito, M., Ikegami, Y., Tai, T. & Yamagata, T. (1993) Eur. J. Biochem. 218, 637–643], endoglycoceramidase (EGCase: EC,3,3,1,123) was found to hydrolyze the cell-surface glycosphingolipids (GSLs) of erythrocytes without any damage to other cell membrane components. This paper represent the kinetics of EGCase action toward cell-surface GSLs of erythrocytes. Without activator or detergents, cell-surface GSLs were found to be hydrolyzed by EGCase II very slowly at pH 7.0. The initial reaction velocity of EGCase II under this condition was 0.038 pmol⋅min ¹ ⋅ mU ¹ for horse erythrocyte cell-surface GM3 and 0.032 pmol ⋅ min ¹ ⋅ mU ⋅ for guinea pig erythrocyte cell-surface Gg3Cer. The addition of activator protein (60 μM), which stimulates EGCase II in the absence of detergents, increased the initial reaction velocity of the enzyme 616-fold for cell-surface GM3 and 468-fold for Gg3Cer, while no increased hemolysis was observed with the addition of activator. However, even in the presence of the activator, the cell-surface GSLs were very resistant to hydrolysis by EGCase II compared to GSL vesicles (or micelles) under same conditions. In contrast to the activator, Triton X-100 (0.4%, mass/vol.) not only stimulated the enzyme activity but also solubilized erythrocyte GSLs into detergent micelles, inducing further increment of the enzyme activity but also solubilized erythrocyte GSLs into detergent micelles, inducing further increment of the enzyme reaction velocity. The apparent Km and Vmax values of EGCase II were calculated from the Lineweaver­Burk plot as 47 μM and 35 pmol min ¹ mU ¹ for horse erythrocyte cell-surface GM3 and 44 μM and 27 pmol ⋅ min ¹ ⋅ mU ¹ for guinea pig erythrocyte cell-surface Gg3Cer, at pH 7.0 in the presence of activator at a concentration of 60 μM. [ABSTRACT FROM AUTHOR]

The electron transfer kinetics between the hydrogenase from Desulfovibrio vulgaris (strain Hildenborough) and the mediators methyl viologen, di-(n-aminopropyl) viologen and propyl viologen sulfonate have been investigated by chronoamperometry. Second-order rate constants were calculated on basis of the theory for a simple catalytic mechanism and are compared with the results obtained before by cyclic voltammetry (preceding paper in this journal). From the ionic-strength dependence and the observed differences in the rate constants for the differently charged viologens, the existence of an electrostatic interaction between mediator and a negatively charged part of the protein is confirmed. Chronoamperometry (computer-controlled) was found to possess advantages over cyclic voltammetry in the determination of homogeneous rate constants (faster, more accurate, and better reproducibility). [ABSTRACT FROM AUTHOR]

This paper is a further study of ion binding to protein surfaces and builds on the studies of the binding of [Crk(CN)6]3- and [Fe(edta)(H2O)]- previously reported [Williams et al. (1982) FEBS Lett. 15, 293-299; Eley et al. (1982) Eur. J. Biochem. 124, 295-303]. In the present paper the binding of polyaminocarboxylate complexes of gadolinium have been studied. Eight ion-binding sites have been identified on the surface of cytochrome c. These exhibit different binding specificities which, in some cases, are not fully understood. However it is clear that simple outer-sphere interactions are not the sole determining factor for the association of metal ion complexes with proteins. The NMR paramagnetic difference spectrum method has been shown to be good at locating binding sites and revealing qualitative differences in their relative affinities for a range of complex types. However the use of relaxation probes is not a good method for the quantitative determination of binding constants; for this, isostructural shift probes must be sought. [ABSTRACT FROM AUTHOR]