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Human stuttering is a simple example of the repetition of sounds or symbols, sometimes associated with single letters, and may be used to illustrate the amazing repetition of amino acids (symbolized by a letter, e.g. W) in proteins. A survey of available databases with highly improbable strings of single amino acids is tabulated. This paper concludes with a challenge to the crystallographic community to probe the structural origins of the structure-function relationship in this neglected area. When nature stutters, we should pay attention.

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]

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]

Tryptic and peptic peptides of the L-4 light chain of chicken skeletal muscle myosin were isolated. The amino acid sequences of all the tryptic peptides were determined. The alignment of the tryptic peptides in the protein was deduced from their homology with the primary structure of the A2 (L-4) light chain of rabbit skeletal muscle myosin. The compositions of the peptic peptides confirmed the alignment. Comparing the whole sequence of the L-4 light chain thus established with that of the A2 light chain of rabbit skeletal muscle myosin, 24 amino acid substitutions, were recognized. [ABSTRACT FROM AUTHOR]

The light chain fraction was separated from myosin extracted from chicken cardiac muscle. Two light chain components, L-1 and L-2 in the fraction were isolated by chromatography on a column of DEAE-cellulose (DE-52) in the presence of 4 M urea. After performic acid oxidation, the L-1 chain was digested with trypsin and the resulting peptides were isolated. The amino acid sequences of the peptides were established. The ordering of these tryptic peptides in the L-1 chain was deduced from the amino acid compositions and the partial sequences of peptic peptides from S-carboxymethylated L-1 chain. Comparing the whole sequence of the L-1 chain thus established with that of alkali light chain of rabbit skeletal muscle myosin, 67 amino acid substitutions and two insertions were recognized. [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]

Not all proteins form well defined three-dimensional structures in their native states. Some amino-acid sequences appear to strongly favour the disordered state, whereas some can apparently transition between disordered and ordered states under the influence of changes in the biological environment, thereby playing an important role in processes such as signalling. Although important biologically, for the structural biologist disordered regions of proteins can be disastrous even preventing successful structure determination. The accurate prediction of disorder is therefore important, not least for directing the design of expression constructs so as to maximize the chances of successful structure determination. Such design criteria have become integral to the construct-design strategies of laboratories within the Structural Proteomics In Europe (SPINE) consortium. This paper assesses the current state of the art in disorder prediction in terms of prediction reliability and considers how best to use these methods to guide construct design. Finally, it presents a brief discussion as to how methods of prediction might be improved in the future. [ABSTRACT FROM AUTHOR]

Crystallization is a unique process that occurs at the expense of entropy, including the conformational entropy of surface residues, which become ordered in crystal lattices during formation of crystal contacts. it could therefore be argued that epitopes free of amino acids with high conformational entropy are more thermodynamically favorable for crystal formation. For a protein recalcitrant to crystallization, mutation of such surface amino acids to residues with no conformational entropy might lead to enhancement of crystallization. This paper reports the results of experiments with an important cytosolic regulator of GTPases, human RhoGD1, in which lysine residues were systematically mutated to alanines. Single and multiple mutations were introduced into two different variants of RhoGD1, Nδ23 and Nδ66, in which the first 23 and 66 residues, respectively, were removed by recombinant methods. in total, 13 single and multiple mutants were prepared and assessed for crystallization and all were shown to crystallize using the Hampton Research Crystal Screens I and II, in contrast to wild-type Nδ23 and Nδ66 RhoGD1 which did not crystallize. Four crystal structures were solved (the triple mutants Nδ23:K135,138,141A and Nδ66:K135,138,141A, and two single mutants Nδ66:K113A and Nδ66:K141A) and in three cases the crystal contacts of the new lattices were found precisely at the sites of mutations. These results support the notion that it is, in principle, possible to rationally design mutations which systematically enhance proteins' ability to crystallize. [ABSTRACT FROM AUTHOR]

The complete amino acid sequence of turnip peroxidase TP 7, the principal isoperoxidase during winter in turnip, Brassica napus L., variety Blanc dur d'hiver, has been determined by sequence analysis of cyanogen bromide fragments and of tryptic peptides. The turnip peroxidase TP 7 enzyme is composed of 296 amino acids, one hemin group and one neutral carbohydrate side chain attached through asparagine. The molecular weight of the polypeptide part is 31 060, and including heroin and carbohydrate the molecular weight of the native enzyme is close to 33 400. The isoelectric point of turnip peroxidase TP 7 is 11.6. Comparison of turnip peroxidase TP 7 and horseradish peroxidase HRP C shows that they contain four similarly located disulfide bridges and have pyrrolidone carboxylyl N termini. Their common evolutionary origin is distant as their amino acid sequences are only 49% identical. Furthermore, turnip peroxidase TP 7 differs significantly from three other isoperoxidases of turnip root, turnip peroxidases TP 1, TP 2 and TP 3, and from horseradish peroxidase HRP C in its physico-chemical and enzymatic properties, and its pronounced season-dependent appearance. All these differences of turnip peroxidase TP 7 and of the others suggest they serve separate biological functions. [ABSTRACT FROM AUTHOR]

Herein we provide a guide for adapting the tools developed for protein X-ray crystallography to study the structures and supramolecular assembly of peptides. Peptide crystallography involves selecting a suitable peptide, crystallizing the peptide, collecting X-ray diffraction data, processing the diffraction data, determining the crystallographic phases and generating an electron density map, building and refining models, and depositing the crystallographic structure in the Protein Data Bank (PDB). Advances in technology make this process easy for a newcomer to adopt. This paper describes techniques for determining the X-ray crystallographic structures of peptides: incorporation of amino acids containing heavy atoms for crystallographic phase determination, commercially available kits to crystallize peptides, modern techniques for X-ray crystallographic data collection, and free user-friendly software for data processing and producing a crystallographic structure. [ABSTRACT FROM AUTHOR]

It is an important and desirable capability to be able to control the quality and quantity of biological product by maintaining and adjusting bioreactor performance throughout its production duration. Amino acids are the building blocks of proteins. Scientists will need to ensure sufficient supply of amino acids as the substrates in the bioreactors as well as to control the excess level of undesirable free amino acid byproducts to maintain an optimum growth environment for cell culture. We have developed a compact and robust sample preparation platform capable of interfacing with analytical instruments to achieve bioreactor amino acids monitoring. We demonstrated the feasibility of this concept by incorporating an automatic amino acid sample preparation protocol to a micro sequential injection (μSI) system connected to an ultra-performance liquid chromatography system for real-time, at-line amino acid separation, and quantitation. The μSI system was configured into a 'platform-like' sample preparation system that is able to accommodate future wet chemistry-type sample preparations. Its real-time amino acid results can be readily available to bioprocess scientists for quick decision making and design of their next experiment. Potential automatic feedback control mechanisms can be established through trigger events based on predetermined analytical signal thresholds so the system can communicate with facility infrastructure to control bioreactors in near real-time fashion. The proposed μSI system described in this paper can be widely used as an automatic sample preparation system connected to the front-end of analytical instruments to enable process analytical technology applications. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:607-613, 2015 [ABSTRACT FROM AUTHOR]

This review summarizes the recent advances in the analysis of amino acids, peptides, and proteins using hydrophilic interaction chromatography. Various reports demonstrate the successful analysis of amino acids under such conditions. However, a baseline resolution of the 20 natural amino acids has not yet been published and for this reason, there is often a need to use mass spectrometry for detection to further improve selectivity. Hydrophilic interaction chromatography is also recognized as a powerful technique for peptide analysis, and there are a lot of papers showing its applicability for proteomic applications (peptide mapping). It is expected that its use for peptide mapping will continue to grow in the future, particularly because this analytical strategy can be combined with reversed-phase liquid chromatography, in a two-dimensional setup, to reach very high resolving power. Finally, the interest in hydrophilic interaction chromatography for intact proteins analysis is less evident due to possible solubility issues and a lack of suitable hydrophilic interaction chromatography stationary phases. To date, it has been successfully employed only for the characterization of membrane proteins, histones, and the separation of glycosylated isoforms of an intact glycoprotein. From our point of view, the number of hydrophilic interaction chromatography columns compatible with intact proteins (higher upper temperature limit, large pore size, etc.) is still too limited. [ABSTRACT FROM AUTHOR]

Despite being low in crude protein, on a fresh weight basis, given their overall contribution to the North American diet, potatoes contribute approximately 2%–4% of the population's protein intake. However, the quality of the protein remains ill‐defined. To that end, Russet potatoes were secured and subjected to various cooking conditions (raw [control], boiled, baked, microwaved, and fried [3, 6, and 9 min]) to determine the impact of cooking method on protein quality, as determined by amino acid score (AAS) and indices of in vivo true fecal protein digestibility (TFPD%; rodent bioassay) and in vitro protein digestibility (pH‐drop, pH‐Stat, and simulated gastrointestinal digestion both static and dynamic). The AAS of raw Russet potatoes was 0.67 ± 0.01, with histidine being the limiting AA. Frying led to a significant reduction in the AAS, however, other cooking methods yielded similar results to the raw control. The TFPD% of raw potato was low (40.5% ± 3.9%) and was significantly enhanced to over 80% with all cooking methods. Similar patterns were observed with all in vitro measures, however, all methods yielded higher values for the raw control samples. Final protein digestibility‐corrected AAS (PDCAAS; product of AAS and TFPD%) values ranged from 0.27 (raw) to a high of 0.57 (boiled), with cooked values being comparable to other plant‐based protein sources, including grains, and some nuts and pulses. In vitro PDCAAS values followed similar trends. This study defined the protein quality of cooked Russet potatoes and provides data for use in defining the quality of total protein consumed in the North American diet. [ABSTRACT FROM AUTHOR]

Nanofabrication based on biological templates has attracted considerable interest because of its applications in materials science and biomedicine. Herein, a facile method is reported for the synthesis of well‐defined TiO2 nanofibers by using a simple N‐(9‐fluorenylmethoxycarbonyl)‐protected phenylalanine–phenylalanine–aspartic acid tripeptide (Fmoc‐Phe–Phe–Asp‐OH, Fmoc‐FFD) as the template. Compared with other synthetic methods of inorganic nanomaterials, these self‐assembling peptides could control the structure and the catalytic activity of the synthesized nanomaterials produced under mild synthetic conditions. The as‐synthesized peptide‐TiO2 hybrid nanofibers and the calcined TiO2 nanofibers were characterized by using transmission electron microscopy (TEM), scanning electron microscopy (SEM), circular dichroism (CD) spectroscopy, and X‐ray diffraction (XRD). The results show that well‐defined TiO2 nanofibers could form when the pH of the peptide solution was 5–7, whereas nanoparticles formed when the pH was 8. Moreover, the peptide‐templated TiO2 nanofibers showed improved photocatalytic activity for the degradation of methyl orange (MO). Finally, the photocatalytic activity of the TiO2 could be controlled by adjusting the pH of the peptide solution during the synthetic process. Peptide template: TiO2 nanomaterials with tunable photocatalytic activity were prepared by using N‐(9‐fluorenylmethoxycarbonyl)‐protected phenylalanine—aspartic acid tripeptide (Fmoc‐FFD) as the template. By incorporating titanium diisopropoxide bis(acetyl‐acetonate) into the peptide solutions, the TiO2 precursors could mineralize and condense with the peptide assemblages. After removing the peptide templates by calcination, a series of TiO2 nanostructures with enhanced photocatalytic activity were formed. [ABSTRACT FROM AUTHOR]

Nasu-Hakola disease (NHD) was first reported separately by Nasu and Hakola around the same time in the 1970s. It is an autosomal recessive inherited disorder characterized by progressive dementia and repeated pathological fractures during adolescence. It has recently been demonstrated that NHD is caused by a mutation in the TREM2 or DAP12 gene. The present paper demonstrates the first patient reported by Nasu and reviews NHD. The patient was a man who died at the age 38 years. His family history was unremarkable. There was no abnormal developmental history. At the age of 26, the patient suffered a pathological fracture of the right tibia, and X-ray confirmed bone resorption in the right tibia. As for mental status, the patient tended to be euphoric. After that, bone resorption was also seen in other long bones. At the age of 33, the patient could not walk after suffering a right femoral neck fracture. He was apathetic and exhibited behavioral abnormalities. At the age of 38, he could not move or speak and subsequently died. General pathological examination showed yellow opaque gelatinous substances in the medullary cavities, matching translucent cystic lesions in the femur, tibia, and fibula on X-rays. Light microscopy showed numerous membranocystic changes in the substances. The brain weighed 1050 g. Symmetric systemic cerebral atrophy, in particular atrophy of the cerebral white matter in the occipital and temporal lobes, was confirmed. Histological examination showed white matter degeneration and diffuse sclerosis accompanied by astroglial proliferation. Severe demyelination was confirmed. Axonal degeneration and destruction were marked. In demyelinated areas, fat granule cells appeared, and lipid granule-positive cells aggregated around vessels. Cerebral cortical neurons were relatively maintained. In the brain, no membranocystic lesions could be recognized. In the DAP12 gene, the patient had a conversion of nucleotide at position 116 resulting in serine 38 to asparagine substitution. [ABSTRACT FROM AUTHOR]

Serotonin N-acetyltransferase (AANAT) catalyzes the conversion of serotonin to N-acetylserotonin, which is the immediate precursor for formation of melatonin. Although it is known that AANAT is degraded via the proteasomal proteolysis, detailed mechanisms are not defined. In this paper, we tested the in vivo role of proteasome inhibition on AANAT activity and melatonin release and examined the amino acid residues in AANAT that contribute to the proteasome degradation. We have shown that inhibition of proteasome activities in vivo in the intact pineal gland fails to prevent the light-induced suppression of melatonin secretion. Furthermore, in cell lines stably expressing AANAT, inhibition of proteasomal proteolysis, which resulted in a large accumulation of AANAT protein, similarly failed to increase AANAT enzyme activity proportional to the amount of proteins accumulated. Site-directed mutagenesis analysis of AANAT revealed that the AANAT degradation is independent of lysine and the two surface cysteine residues. Deletion analysis of N-terminus identified the second amino acid leucine (L2) as the key residue that contributes to the proteasomal proteolysis of AANAT protein. These results suggest that rat AANAT protein is degraded via the N-end rule pathway of proteasomal proteolysis and the leucine at the N-terminus appears to be the key residue recognized by N-end rule pathway. [ABSTRACT FROM AUTHOR]

The amino acid composition and the physicochemical and functional properties of quinoa flour proteins (QFP) were evaluated during storage (at 20, 30 and 40 °C). Quinoa flour showed a protein content of 14.2 ± 0.1 g 100 g−1 and high levels of essential amino acids as lysine. SDS–PAGE of the QFP presented ten major band, and native-PAGE of the QFP showed similar banding; there was a little variation due to time-temperature. TCA-protein solubility variation (%) was small and the values of water activity were low, a non-significant endogenous hydrolysis was observed. Differential scanning calorimetry flour analysis allowed determining two endotherms, starch and protein. Important structural changes of protein soluble fractions were not detected by UV and fluorescence spectroscopy due to temperature and time of storage. It was found during storage time loss of protein solubility and water absorption. These changes could be to influence in the manufacture of quinoa flour based products. For avoid changes in these functional properties (solubility and water holding capacity), quinoa flour can be stored at ambient temperature (between 20 and 30 °C) and packed in double kraft paper bags (2 months). [ABSTRACT FROM AUTHOR]

Numerous studies were carried out about aminoacidic composition of vegetable proteins, but information about the free amino acid pool and the role of these substances is very incomplete. The aim of this paper was to contribute to the scarce knowledge concerning the composition of free amino acids in botanicals and botanical preparations widely used as food, in dietary supplements, and in pharmaceutical products. This work studied the composition of free amino acids, identified the major components of 19 species of plants, and evaluated the influence of different types of extraction on the amino acid profile. Amino acids were determined using an automatic precolumn derivatization with fluorenylmethyl-chloroformate and reversed-phase liquid chromatography with fluorescence and ultraviolet detection. The amounts of total free amino acids varied widely between plants, from approximately 12 g in 100 g of Echinacea pallida extract to less than 60 mg in the same amount of Coleus forskohlii, Garcinia cambogia, and Glycine max. In 13 plants arginine, asparagine, glutamine, proline, and γ-aminobutyric acid were the free amino acids found in preponderant quantities. The levels of free amino acids above the quantification limit in 36 assayed samples of botanicals, extracts, and supplements are shown. [ABSTRACT FROM AUTHOR]

A nine-octapeptide insertion in the prion protein (PrP) gene is associated with an inherited form of human prion disease. Transgenic (Tg) mice that express the mouse homolog of this mutation (designated PG14) spontaneously accumulate in their brains an insoluble and weakly protease-resistant form of the mutant protein. This form (designated PG14Spon) is highly neurotoxic, but is not infectious in animal bioassays. In contrast, when Tg(PG14) mice are inoculated with the Rocky Mountain Laboratory (RML) strain of prions, they accumulate a different form of PG14 PrP (designated PG14RML) that is highly protease resistant and infectious in animal transmission experiments. We have been interested in characterizing the molecular properties of PG14Spon and PG14RML, with a view to identifying features that determine two, apparently distinct properties of PrP aggregates: their infectivity and their pathogenicity. In this paper, we have subjected PG14Spon and PG14RML to a panel of assays commonly used to distinguish infectious PrP (PrPSc) from cellular PrP (PrPC), including immobilized metal affinity chromatography, precipitation with sodium phosphotungstate, and immunoprecipitation with PrPC- and PrPSc-specific antibodies. Surprisingly, we found that aggregates of PG14Spon and PG14RML behave identically to each other, and to authentic PrPSc, in each of these biochemical assays. PG14Spon however, in contrast to PG14RML and PrPSc, was unable to seed the misfolding of PrPC in an in vitro protein misfolding cyclic amplification reaction. Collectively, these results suggest that infectious and non-infectious aggregates of PrP share common structural features accounting for their toxicity, and that self-propagation of PrP involves more subtle molecular differences. [ABSTRACT FROM AUTHOR]

The proteins structure can be mainly classified into four classes: all-α, all-β, α/β, and α + β protein according to their chain fold topologies. For the purpose of predicting the protein structural class, a new predicting algorithm, in which the increment of diversity combines with Quadratic Discriminant analysis, is presented to study and predict protein structural class. On the basis of the concept of the pseudo amino acid composition (Chou, Proteins: Struct Funct Genet 2001, 43, 246; Erratum: Proteins Struct Funct Genet 2001, 44, 60), 400 dipeptide components and 20 amino acid composition are, respectively, selected as parameters of diversity source. Total of 204 nonhomologous proteins constructed by Chou (Chou, Biochem Biophys Res Commun 1999, 264, 216) are used for training and testing the predictive model. The predicted results by using the pseudo amino acids approach as proposed in this paper can remarkably improve the success rates, and hence the current method may play a complementary role to other existing methods for predicting protein structural classification. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [ABSTRACT FROM AUTHOR]

This work presents the architecture of PROSIDIS, a special purpose processor designed to search for the occurrence of substrings similar to a given ‘template string’ within a proteome. Similarity is determined by means of a weighting matrix which measures the degree of similarity between any two amino acids. The paper recalls the basis of the PHG (Parallel Hardware Generator) tool, developed in the framework of the HADES project (Hardware Design for Scientific Applications). Through PHG it is possible to design, in a nearly automatic way, a parallel hardware which efficiently implements an algorithm described through recurrence equations; PHG is able to generate a synthesizable VHDL which represents a parallel system derived from the System of Affine Recurrence Equations (SARE) describing the problem. In this work we illustrate the advantages derived from designing a special purpose processor to face the protein similarity discovery problem. Some preliminary results are given, reporting the time spent by several conventional computing architectures and by the PROSIDIS processor hosted by a personal computer to solve the same protein analysis problem. The results show that PROSIDIS, implemented on a Xilinx XV1000 FPGA, gives speedup figures ranging from 5.6 up to 55.6. Copyright © 2004 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The protein kinase CK1 phosphorylates serine residues that are located close to another phosphoserine in the consensus pSer-Xaa-Xaa-Ser. This specificity generates regions in its target proteins containing two or more neighbouring phosphoserine residues, termed here multisite phosphorylation domains (MPDs). In this paper, we demonstrate that D4476 is a potent and rather selective inhibitor of CK1 in vitro and in cells. In H4IIE hepatoma cells, D4476 specifically inhibits the phosphorylation of endogenous forkhead box transcription factor O1a (FOXO1a) on Ser322 and Ser325 within its MPD, without affecting the phosphorylation of other sites. Our results indicate that these residues are targeted by CK1 in vivo and that the CK1 -mediated phosphorylation of the MPD is required for accelerated nuclear exclusion of FOXO1a in response to IGF-1 and insulin. D4476 is much more potent and specific than 1C261 or CKI-7, and is therefore the most useful CK1 inhibitor currently available for identifying physiological substrates of CK1. [ABSTRACT FROM AUTHOR]

In this work, the protein quality of defatted hemp hearts and protein‐enriched hemp fractions was determined. Protein quality was assessed using a rodent bioassay to evaluate growth and protein digestibility, while amino acid composition was determined via HPLC. A method for determining in vitro protein digestibility was compared to in vivo methodology and used to generate an in vitro protein quality score. The true protein digestibility of hemp protein 2, a hemp protein concentrate, was significantly lower than that of either defatted hemp hearts or hemp protein 1, a hemp protein concentrate (p <.05). While there was no relationship between the in vivo and in vitro measurements of protein digestibility (R2 =.293, p =.459), there was a significant correlation between the protein digestibility‐corrected amino acid score (PDCAAS) determined in vivo and in vitro PDCAAS (R2 =.989, p =.005). The protein efficiency ratio of hemp protein 1 was significantly lower than that of either defatted hemp hearts or hemp protein 2 (p <.05). These data highlight the nutritional capacity of hemp protein sources while also demonstrating the relationship between in vivo and in vitro methods for determining protein quality. [ABSTRACT FROM AUTHOR]

Goat milk proteins are unique in their nutritional and functional properties and have become increasingly popular in recent years. A variety of methods have been studied for extracting and isolating these proteins, with coprecipitation being a particularly effective approach. Compared to cow milk proteins, goat milk proteins contain higher levels of certain amino acids such as tryptophan and cysteine, while maintaining similar nutritional properties. Additionally, they have superior functional properties, including better emulsifying and foaming properties, which make them an attractive option for developing new food products. Research has shown that goat milk proteins have several health benefits, including immunomodulatory effects, allergy management, anti‐inflammatory, and antioxidant effects, as well as antimicrobial and anticancer properties. They have the potential to be used as a treatment for autoimmune diseases, allergies, and other immune system disorders due to their ability to modulate the production of cytokines and other immune system components. Furthermore, their antimicrobial properties can help prevent the growth of harmful bacteria and reduce the risk of infection. Future research will focus on the potential of goat milk proteins as a functional food ingredient, their effects on gut health and microbiota, and their therapeutic potential for various health conditions. This research may lead to the development of new functional foods that promote health and prevent disease, and potentially pave the way for the use of goat milk proteins as a therapeutic agent for various health conditions. [ABSTRACT FROM AUTHOR]

This paper presents the first purification of the mitochondrial branched‐chain amino acid aminotransferase (BCATm) from sheep placenta. It is a homodimer with an apparent subunit molecular mass of 41 kDa. The enzyme differs from those of the rat and human as it appears to form at least one intermolecular disulfide bond. The sheep BCATm cDNA (1.4 kb) encodes a mature polypeptide of 366 amino acids with a calculated molecular mass of 41 329 Da and a partial mitochondrial targeting sequence of seven amino acids. The sheep BCATm sequence shares higher identity with other mammalian BCATm isoenzymes (82–85%) than with the cytosolic isoenzymes (60%). By Northern blot analysis, a message of 1.7 kb was detected in sheep placenta and skeletal muscle. Measurements of BCAT activity, mRNA and BCATm protein in sheep placenta and skeletal muscle revealed that BCATm is the sole BCAT isoenzyme expressed in placenta, whereas it contributes 57 and 71% of the BCAT activity in tensor fascia latae and masseter muscles from weaned lambs respectively. Skeletal muscle, the main site of branched‐chain amino acid transamination, exhibits significantly lower BCAT activity in sheep than in rat. Our results suggest that the low BCATm mRNA level probably accounts for the low BCAT activity in sheep skeletal muscle, and that the metabolic scheme for branched‐chain amino acid catabolism is specific to each species. [ABSTRACT FROM AUTHOR]

The enhancement of the catalytic power of enzymes is a subject of enormous interest both for science and for industry. The latter, in particular, due to the vast applications enzymes can have in industrial processes, for instance in the desulfurization of crude oil, which is mandatory by law in many developed countries and is currently performed using costly chemical processes. In this work we sought to enhance the turnover rate of DszD from Rhodococcus erythropolis, a NADH-FMN oxidoreductase responsible for supplying FMNH2 to DszA and DszC in the biodesulfurization process of crude oil, the 4S pathway. For this purpose, we replaced the wild type spectator residue of the rate limiting step of the reduction of FMN to FMNH2, a process catalysed by DszD and known to play an important role in the reaction energy profile. As replacements, we used all the naturally occurring amino acids, one at a time, using computational methodologies, and repeated the above-mentioned reaction with each mutant. To calculate the different free energy profiles, one for each mutated model, we applied quantum mechanics/molecular mechanics (QM/MM) methods within an ONIOM scheme. The free energy barriers obtained varied between 15.1 and 29.9 kcal mol−1. Multiple factors contributed to the different Δ G values. The most relevant were electrostatic interactions and the induction of a favourable alignment between substrate and cofactor. These results confirm the great potential that chirurgic mutations have for increasing the catalytic power of DszD in relation to the wild type ( wt) enzyme. [ABSTRACT FROM AUTHOR]

The primary structure of the major parvalbumin (pI = 4.45) from the cartilaginous fish Raja clavata has been determined. The amino acid sequence was deduced by the analysis of peptides derived from tryptic digestion of the oxidized protein. These peptides were aligned by comparison with (a) overlapping peptides produced by limited tryptic and chymotryptic digestion, and (b) by comparison with the known structures of other fish parvalbumins. The molecular evolution of thornback ray parvalbumin is briefly discussed. [ABSTRACT FROM AUTHOR]

Sheep-serum transferrin shows marked polymorphism and more than 20 alleles have been identified although only 4 or 5 of these have a frequency higher than 1%. Each of the alleles has two bands in starch-gel electrophoresis, corresponding to a major and a minor fraction. This paper describes the isolation and partial characterisation of the two fractions from the transferrin of sheep homozygous for Tf B. The purification consisted of: (a) precipitation by ammonium sulphate, (b) chromatography on CM-cellulose and, finally (c) chromatography on DEAE-Sephadex. The purification procedure had no effect on the electrophoretic mobility of the two fractions and they appeared homogeneous by starch-gel and polyamide-gel electrophoresis and by immuno-electrophoresis. The amino-acid compositions of both fractions were very similar and the sequences of the first eight amino-acid residues: Ser-Pro-Glu-Lys-Thr-Val-Arg-Trp-were identical for both bands. These results, and the fact that the two fractions are found in all genetic variants and always have the same relative mobility strongly suggest that the differences do not lie in the polypeptide chain. From the results of hydrolysis by neuraminidase and assay of sialic acid, the major and minor fractions most probably contain two and three sialic acid residues (exclusively N-acetylneuraminic acid) respectively, thus explaining the different electrophoretic mobilities. The sialic-acid content has been calculated on the basis of a molecular weight of 77500 as determined both by low-speed equilibrium ultracentrifugation and by Archibald's method. The following physico-chemical constants have been established: absorption coefficient at 280nm, A1 mg/cm³1 cm = 1.25 ± 0.01 cm² · mg-1; partial specific volume, &vmacr; = 0.734 cm³ · g-1; sedimentation coefficient s20.wo = 5.15 S; refractive-index increment, dn/dc = 0.173 cm³ · g-1. [ABSTRACT FROM AUTHOR]

The primary structure of protein S8 from the 30-S ribosomal subunit of Escherichia coil was determined mainly by automatic Edman degradation using a modified Beckman protein sequenator and the solid-phase sequenator of Laursen. The complete sequence, containing 109 amino acids, was derived by analysing peptides from tryptic, chymotryptic, thermolysin, staphylococcal protease and cyanogen bromide digestion of the protein. The amino acid composition was found to be (aspartic acid)6, (asparagine)3, (threonine)5, (serine)5, (glutamic acid)7, (glutamine)6, (proline)5, (glycine)6, (alanine)11, (valine)9, (methionine)4, (isoleucine)7, (leucine)9, (tyrosine)3, (phenylalanine)3, (lysine)11, (arginine)8, (cysteine)1. S8 is a basic protein and binds to the 16-S RNA; knowledge of its sequence is necessary for a detailed study of its interaction with the ribosomal RNA. [ABSTRACT FROM AUTHOR]

The amino acid sequence of the light chain of the mouse monoclonal MOPC 173 immunoglobulin molecule (IgG2a,χ) is presented. This kappa chain contains 214 residues. Comparisons of this sequence with murine kappa chains already published by other workers bring a confirmation of the large size of the murine Vχ chain pool. A complete identity was found with the constant region of the light chain of MOPC 21 from residue 97 to residue 214. [ABSTRACT FROM AUTHOR]

Extracellular protein secretion by the main terminal branch of the general secretory pathway in Pseudomonas aeruginosa requires a secretion machinery comprising the products of at least 12 genes. One of the components of this machinery, the XcpR protein, belongs to a large family of related proteins distinguished by the presence of a highly conserved nucleotide binding domain (Walker box A). The XcpR protein is essential for the process of extracellular secretion and amino acid substitutions within the Walker A sequence result in inactive XcpR. The same mutations exert a dominant negative effect on protein secretion when expressed in wild-type bacteria. Transdominance of XcpR mutants suggests that this protein is involved in interactions with other components of the secretion machinery or that it functions as a multimer. In this study, the amino-terminal portion of the cl repressor protein of phage λ was used as a reporter of dimerization in Escherichia coli following fusion to full-length as well as a truncated form of XcpR. The cl-XcpR hybrid proteins were able to dimerize, as demonstrated by the immunity of bacteria expressing them to killing by λ phage. The full-length XcpR as well as several deletion mutants of XcpR were able to disrupt the dimerization of the chimeric cl-XcpR protein. The disruption of cl-XcpR dimers using the deletion mutants of XcpR, combined with the analysis of their dominant negative effects on protein secretion, was used to map the minimal dimerization domain of XcpR, which is located within an 85 amino acid region in its N-terminal domain. Taken together, the data presented in this paper suggest that the XcpR protein dimerizes via its N-terminus and that this dimerization is essential for extracellular protein secretion. [ABSTRACT FROM AUTHOR]

Group B Streptococcus (GBS) is the foremost cause of neonatal sepsis and meningitis in the United States. A major virulence factor for GBS is its capsular polysaccharide, a high molecular weight polymer of branched oligosaccharide subunits. N-acetylneuraminic acid (Neu5Ac or sialic acid), at the end of the polysaccharide side chains, is critical to the virulence function of the capsular polysaccharide. Neu5Ac must be activated by CMP-Neu5Ac synthetase before it is incorporated into the polymer. We showed previously that a transposon mutant of a serotype III GBS strain which had no detectable capsular Neu5Ac was deficient in CMP-Neu5Ac-synthetase activity (Wessels et al., 1992). In this paper, we report the identification and characterization of cpsF, a gene interrupted by transposon insertion in the previously described Neu5Ac-deficient mutant. The predicted amino acid sequence of the cpsF gene product shares 57% similarity and 37% identity with CMP-Neu5Ac synthetase encoded by the Escherichia coli K1 gene, neuA. The enzymatic function of the protein encoded by cpsF was established by cloning the gene in E. coli under the control of the T7 polymerase/promoter. Lysates of E. coli in which the cpsF gene product was expressed, catalysed the condensation of CTP with Neu5Ac to form CMP-Neu5Ac. In addition, when a CMP-Neu5Ac synthetase-deficient mutant of E. coli K1 was transformed with cpsF, K1 antigen expression was restored. We conclude that cpsF encodes CMP-Neu5Ac synthetase in type III GBS, and that the GBS enzyme can function in the capsule-synthesis of a heterologous bacterial species. [ABSTRACT FROM AUTHOR]

Secretion of haemolysin (HlyA) is secA independent, but depends upon two accessory membrane proteins, HlyB and HlyD. encoded by the hly determinant. A fourth (cytoplasmic) protein, HlyC, is required to activate HlyA post-translationally, but has no role in export. Deletion studies have previously shown that the HlyA molecule contains a targeting signal close to the C-terminus which specifically directs its secretion to the medium. This targeting signal has been variously located within the terminal 27, 53, 60 or 113 amino acids. In this paper, we have sought to confirm the presence of a C-terminal targeting signal and to analyse the specificity of the Hly transport system through fusion of C-terminal fragments of HlyA to heterologous polypeptides. A C-terminal fragment (23 kDa) of HlyA. when fused at the C-terminus, efficiently promoted the secretion of the eukaryotic protein prochymosin (PCM) to the medium via HlyB and HlyD. This result is in contrast to previous findings that prochymosin, preceded by the alkaline phosphatase signal sequence, cannot be translocated across the Escherichia coli inner membrane. The HlyA targeting domain was also used to secrete to the medium varying portions of chloramphenicol acetyltransferase (CAT) and 98 per cent of the β-galactosidase (LacZ) molecule (both E. coli cytoplasmic proteins). In the case of the PCM and CAT fusions the efficiency of secretion was reduced as the proportion of the PCM and CAT molecule increased. This result is consistent with inhibition of secretion through the irreversible folding of the larger passenger protein fragments, or the occlusion of the HlyA targeting signal by upstream sequences. Analysis of the nature of the C-terminal domain promoting secretion of prochymosin, demonstrated that shortening the signal domain from 218 to 113 amino acids significantly reduced the efficiency of secretion. This result may also reflect the importance of maintaining an independent... [ABSTRACT FROM AUTHOR]

Trypanosoma brucei contains an ATP-dependent phosphofructokinase (PFK), located in its glycosomes, which are peroxisome-like organelles sequestering the majority of its glycolytic enzymes. In this paper, we report the cloning and sequencing of the single-copy gene encoding this enzyme. Its amino-acid sequence is more similar to pyrophosphate (PPi)-dependent PFKs than to other ATP-dependent PFKs. a phylogenetic analysis suggests that the enzyme must have been derived from a PPi-dependent ancestral PFK, which changed its phospho-donor specificity during evolution. The enzyme is no longer capable of using PPi as phospho substrate, nor can it catalyze the reverse reaction as PPi-PFKs generally can. Moreover, the presence of a high pyrophosphatase activity in the cell renders it unlikely that PPi can function as free-energy source in present-day trypanosomes. It remains to be determined which mutations were responsible for the chage in phospho-substrate specificity of the trypanosomatid PFK. As a result of its particular evolutionary hitory, the T. brucei PFK shows many structural differences, even at the active site, when compared with other ATP-dependent PFKs. These differences offer great potential for the structure-based design of trypanocidal drugs. [ABSTRACT FROM AUTHOR]

We have previously isolated a form of protein phosphatase-1 (PP1M) from avian smooth muscle myofibrils that is composed of the catalytic subunit of PP1 (PP1C) bound to an M-complex consisting of 110-kDa (M110) and 21-kDa (M21) subunits. The interaction of PP1C with an N-terminal region of the M110 subunit enhances the dephosphorylation of myosin and suppresses the dephosphorylation of other substrates [Alessi, D. R., MacDougall, L. K., Sola, M. M., Ikebe, M. & Cohen, P. (1992) Eur. J. Biochem. 210, 1023–1035; Chen, Y. H., Chen, M. X., Alessi, D. R., Campbell, D. G., Shanahan, C., Cohen, P. & Cohen, P. T. W. (1994) FEBS Lett. 356, 51–56; Johnson, D. F., Moorhead, G., Caudwell, F. B., Cohen, P., Chen, Y. H., Chen, M. X. & Cohen, P. T. W. (1996) Eur. J. Biochem. 239, 317–325]. In this paper, we establish that PP1M accounts for nearly all the myosin phosphatase activity in myofibrils, that the M110 and M21 subunits are present at similar concentrations in the myofibritlar fraction, and that these subunits are entirely bound to PP1. We demonstrate that the M21 subunit does not interact with PP1C, but with the C-terminal 72 residues of the M110 m subunit, a region which is 43 % identical to residues 87–161 of the M21 subunit. A fragment of the M21 subunit, M21-(M1–L146), which lacks the C-terminal leucine zipper, also bound to the M110 subunit, but two other fragments M21-(M1–E110) and M21-(E110–K186) did not. The M110 and M21 subunits were both found to be myosin-binding proteins. The C-terminal 291 residues of the M110 subunit, but not the C-terminal 72 residues, bound to myosin, but the N-terminal fragments M110-(M1—E309) and M110-(M1—S477) did not. Thus, the region of the M110 subunit that stimulates the dephosphorylation of myosin by PP1C is distinct from the region that targets PP1M to myosin. Remarkably, each myosin dimer was capable of binding about 20 tool M21 subunit and many of the M21-binding sites were located in the myosin rod domain. The potential significance of this observation is discussed. [ABSTRACT FROM AUTHOR]

Preparations of bovine lung surfactant D (SP-D) and conglutinin were examined by electron microscopy, gel-filtration and SDS/PAGE. SP-D is composed of non-covalently linked subunits, of 160 kDa, which each contain three, disulphide-linked, 44-kDa polypeptide chains. In the electron microscope a single 160-kDa subunit of SP-D appears as a 45.8 ± 3-nm-long rod connected to a small globular ‘head’. Particles were also seen which correspond to non-covalently linked dimmers, trimers and tetramers of the 160-kDa monomer subunit of SP-D. The tetramer structure contains 12 polypeptide chains and is very similar to the electron microscopy images and model reported by Strang et al. [Strang, C. J., Slayter, US., Lachmann, P. J. and Davis, A. E. (1986) Biochem. J. 236, 3811–389] for bovine conglutinin in which four 160-kDa subunits are disulphide-linked to give a molecule of expected molecular mass of 528 kDa. This study confirmed the findings by Strang et al. in the above paper for intact conglutinin and also emphasized that the rod-like structures, of length 37.6 ± 3.7 nm. Seen in the conglutinin subunits were significantly shorter than those in SP-D despite the close similarity in amino acid sequence (79% identity) and chain length between the two proteins. In addition, a truncated form of conglutinin was found in the conglutinin preparations, due to limited proteolysis of the Arg-Ala bond at position 54 in the 44-kDa chains. These truncated conglutinin chains yield a subunit composed of three shortened, non-disulophide-linked, chains and this subunit appears as a monomer with a rod length of 34.2 ± 2.8 nm in the electron microscope. On gel-filtration, a proportion of the SP-D preparation behaved, as expected, as a molecule with an apparent molecular mass of 600 kDa. The remainder of the SP-D preparation behaved as aggregated material with a molecular mass greater than 900 kDa which yielded no distinct structures in the electron microscope. Intact conglutinin was wluted at a position greater than 900 kDa but yet provided clear electron microscopy images of the tetramer structure described above. Although it is difficult to explain fully the anomalous behaviour of SP-D and conglutinin on gel-filtration, it is proposed that the natural form of both Sp-D and conglutinin is the highest distinct oligomer form seen in the electron microscope, i.e. a tetramer of the 160-kDa subunits in which the four rod-like elements are linked in a tail-to-tail fashion to a central core. [ABSTRACT FROM AUTHOR]

A protein is usually classified into one of the following four structural classes: all α, all β, (a + B) and α/β. In this paper, based on the maximum correlation-coefficient principle, a new formulation is proposed for predicting the structural class of a protein according to its amino acid composition. Calculations have been made for a development set of proteins from which the amino acid compositions for the standard structural classes were derived, and an independent set of proteins which are outside the development set. The former can test the self consistency of a method and the latter can test its extrapolating effectiveness. In both cases, the results showed that the new method gave a considerably higher rate of correct prediction than any of the previous methods, implying that a significant improvement has been achieved by implementing the maximum-correlation-coefficient principle in the new method. [ABSTRACT FROM AUTHOR]

1. The abundance of tyrosine sulfate in membrane proteins was quantified in four different cell lines and compared to that in soluble cellular and secreted proteins. 2. Upon metabolic labelling of HepG2, Ltk-, AtT20 and PC12 cells with [35S]sulfate or [³H]tyrosine, a fraction enriched in integral membrane proteins was found to contain small, but significant, amounts of protein-bound tyrosine sulfate (up to 2.5% of the total cellular plus secreted protein-bound tyrosine sulfate). On the other hand, the frequency of sulfation of tyrosine residues of membrane proteins was within the same order of magnitude as that of secreted proteins, indicating that the low abundance of tyrosine sulfate in membrane proteins was largely a reflection of the low abundance of these proteins themselves. Consistent with this conclusion were the results of an analysis showing that 14 out of 32 selected membrane-spanning proteins contain potential tyrosine sulfation sites. 3. In HepG2 cells, three tyrosine-sulfated integral membrane glycoproteins of molecular mass 100, 125 and 150 kDa were identified. Characterization of the 150-kDa tyrosine-sulfated membrane protein revealed that it was protected from proteolysis in intact cells, suggesting a localization in an intracellular organelle. 4. Together with the results reported in the preceding paper in this journal, our data suggest that tyrosine sulfation occurs in various classes of trans-Golgi-derived proteins, soluble as well as membrane, and extracellularly exposed as well as intracellularly retained, proteins. This suggests that tyrosine sulfation may have a variety of physiological functions, depending on the individual tyrosine-sulfated protein or protein class. [ABSTRACT FROM AUTHOR]

1. The abundance of tyrosine sulfate in secretory proteins and in various classes of cellular proteins has been quantified and compared to protein-bound carbohydrate sulfate. 2. HepG2 cells and fibroblasts, two cell types showing only the constitutive pathway of secretion, and PC12 cells, which show both the constitutive and the regulated pathway of secretion, were subjected to pulse-chase and/ or long-term labelling with [35S]sulfate and [³H]tyrosine, followed by analysis of proteins in the cells and medium. Under both conditions of labelling, 65-92% of the protein-bound tyrosine sulfate and 44-84% of the protein bound carbohydrate sulfate were found to be secretory. In HepG2 cells, the frequency of sulfation of tyrosine residues, which can be determined independently from protein abundance and the rate of protein synthesis, was 8-22 times higher in proteins secreted into the medium than in cellular proteins. 3. All cell lines studied contained significant amounts, not only of carbohydrate sulfate, but also of tyrosine sulfate in specific cellular proteins. As shown for fibroblasts, these tyrosine-sulfated proteins were retained within the cells for at least 100 min of chase following a pulse with [35S]sulfate and were almost completely recovered in a light membrane fraction after subcellular fractionation. 4. Lysosomes were found to contain small, but significant, amounts of protein-bound tyrosine sulfate in addition to protein-bound carbohydrate sulfate. Protein-bound tyrosine sulfate in lysosomes reached a peak at 20 min of chase and rapidly disappeared thereafter, whereas protein-bound carbohydrate sulfate accumulated after 20 min of chase. Examination of the known sequences of eleven lysosomal enzymes revealed the presence of potential tyrosine sulfation sites in five of them. 5. Our results show that secretory proteins are the most abundant, but not exclusive, in vivo substrates for tyrosine sulfation and suggest the presence of soluble tyrosine-sulfated proteins in lysosomes and other, as yet unidentified, organelles of the secretory pathway. In the following paper in this journal we describe the abundance of tyrosine sulfate in integral membrane proteins. [ABSTRACT FROM AUTHOR]

The identities of the protein phosphatases involved in the regulation of hepatic glycolysis, gluconeogenesis and aromatic amino acid breakdown were investigated using 6-phosphofructo-1-kinase, fructose-1,6-biphosphatase, L-pyruvate kinase, phenylalanine hydroxylase and the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase as substrates. Purified preparations of protein phosphatases-1, 2A, 2B and 2C exhibited activity towards all five substrates in vitro, although phosphatases-1 and 2B were only weakly active. Studies in liver extracts using inhibitor-2 and trifluoperazine, which inhibit protein phosphatase-1 and 2B, respectively, confirmed that these phosphatases are unlikely to be important in dephosphorylating these substrates in vivo. Sequential fractionation of rat liver extracts by anion-exchange chromatography and gel-filtration failed to resolve any protein phosphatases acting on each substrate, apart from protein phosphatases-2A and 2C. The present results, together with those described in the following paper (in this journal) indicate that under the assay conditions used, protein phosphatase-2A is the most powerful phosphatase acting on each substrate, although protein phosphatase-2C contributes a significant percentage of the activity towards 6-phophofructor-1-kinase. No clear evidence was obtained for a role of metabolites in the regulation of dephosphorylation of the five substrates. This study reinforces our contention that only a few serine-specific and threonine-specific protein phosphatase catalytic subunits participate in cellular regulation. [ABSTRACT FROM AUTHOR]

According to the signal hypothesis, a signal sequence, once having initiated export of a growing protein chain across the rough endoplasmic reticulum, is cleaved from the mature protein at a specific site. It has long been known that some part of the cleavage specificity resides in the last residue of the signal sequence, which invariably is one with a small, uncharged side-chain, but no further specific patterns of amino acids near the point of cleavage have been discovered so far. In this paper, some such patterns, based on a sample of 78 eukaryotic signal sequences, are presented and discussed, and a first attempt at formulating rules for the prediction of cleavage sites is made. [ABSTRACT FROM AUTHOR]

The brain specific S-100 protein is a mixture of two components S-100a and S-100 b with a subunit composition αβ or β2 respectively. The amino acid sequence of the β subunit has been previously determined. This paper presents the sequence of the α subunit in the S-100a protein. The α subunit consists of 93 amino-acid residues and has a relative molecular mass of 10400. The sequence shows extensive homology (58 %) with that of the β-subunit and shares an apparent calcium binding site in the C-terminal half of the molecule, suggesting a close evolutionary relationship between these subunits. [ABSTRACT FROM AUTHOR]

Describes an application of two-dimensional, nuclear magnetic resonance techniques for the study of proteins. Amino acid residue; Molecular weight; Glycyl residue spin systems; Spin-spin coupling constants; Protein conformation.

The complete primary structure of the constant part of the μ-chain-disease protein, BOT, was established. It includes the whole CH2, CH3 and CH4 domains. Two amino acid changes were found, at positions 309 (Ser ↵ Gly) and 333 (Val ↵ Gly) (GAL numbering). In two additional monoclonal n chains (SCO and CO), the same positions showed an amino acid variability. From these data it may be concluded that four types of μ chains exist in the human: (1) GAL type with Ser-309 and Val-333; (2) OU type with Gly-309 and Val-333; (3) SCO type with Ser-309 and Gly-333; (4) BOT/CO type with Gly-309 and Gly-333. The meaning of this molecular polymorphism is discussed. [ABSTRACT FROM AUTHOR]

We have developed a semi-empirical method to determine the subunit molecular weight of a protein. The method is a minor modification of the Edman degradation and is based on a simple chemical procedure to modify specifically the N-terminal NH2 group. Initially, all NH2 groups, including the ε-NH2 groups of lysine residues and the N-terminal α-NH2 group, are reacted with phenylisothiocyanate and the protein derivative is subjected to one step of the Edman degradation. The newly exposed N terminus is then reacted with radioactively labelled phenylisothiocyanate. A value for the subunit molecular weight can be obtained from an analysis of the incorporated radioactivity and the amount of the protein in the sample. The molecular weight of five different proteins have been determined by this method. Our method is particularly useful for proteins containing lipid or sugar components and also for relatively small peptides. The procedure described in this paper for the specific modification of the N terminus has been found to be a powerful tool for protein sequencing. [ABSTRACT FROM AUTHOR]

Two feeding trials were performed to evaluate the apparent digestibility coefficients (ADCs) of dry matter, protein, and amino acids of three animal‐origin and four plant‐origin ingredients in Totoaba macdonaldi. In the first feeding trial, the animal‐origin ingredients were evaluated using totoaba juveniles with an initial weight of 529.7 ± 104.2 g, and for the second feeding trial 745.9 ± 210.6 g. Evaluated ingredients were: poultry by‐product meal, meat and bone meal, feather meal (FM), soy protein concentrate, soybean meal (SBM), corn gluten (CG), and wheat gluten (WG). Each experimental ingredient was evaluated in triplicate. ADCs of dry matter ranged from 35.9% for FM to 67.9% for poultry by‐product, while the protein ADCs values ranged from 41.7% for CG to 83.2% for poultry by‐product. Fish meal ADC (79.6%) was similar to poultry by‐product but significantly higher than WG and soy protein concentrate (72.5% and 72.6%, respectively). The ADCs for lysine were significantly higher for WG, sardine meal, poultry by‐product, and SMB (94.5%, 79.8%, 79.4%, and 79.4%, respectively). Based on the results from the present study, poultry by‐product, WG, and soy protein concentrate are the most promising alternative ingredients (i.e., to the fishmeal) for the formulation of totoaba grow‐out feeds. [ABSTRACT FROM AUTHOR]

Conventional protein engineering methods for modifying protein nanopores are typically limited to 20 natural amino acids, which restrict the diversity of the nanopores in structure and function. To enrich the chemical environment inside the nanopore, we employed the genetic code expansion (GCE) technique to site‐specifically incorporate the unnatural amino acid (UAA) into the sensing region of aerolysin nanopores. This approach leveraged the efficient pyrrolysine‐based aminoacyl‐tRNA synthetase‐tRNA pair for a high yield of pore‐forming protein. Both molecular dynamics (MD) simulations and single‐molecule sensing experiments demonstrated that the conformation of UAA residues provided a favorable geometric orientation for the interactions of target molecules and the pore. This rationally designed chemical environment enabled the direct discrimination of multiple peptides containing hydrophobic amino acids. Our work provides a new framework for endowing nanopores with unique sensing properties that are difficult to achieve using classical protein engineering approaches. [ABSTRACT FROM AUTHOR]

The Molecular Fractionation with Conjugate Caps (MFCC) method is a popular fragmentation method for the quantum-chemical treatment of proteins. However, it does not account for interactions between the amino acid fragments, such as intramolecular hydrogen bonding. Here, we present a combination of the MFCC fragmentation scheme with a second-order many-body expansion (MBE) that consistently accounts for all fragment--fragment, fragment--cap, and cap--cap interactions, while retaining the overall simplicity of the MFCC scheme with its chemically meaningful fragments. We show that with the resulting MFCC-MBE(2) scheme, the errors in the total energies of selected polypeptides and proteins can be reduced by up to one order of magnitude and relative energies of different protein conformers can be predicted accurately. [ABSTRACT FROM AUTHOR]

Proteinaceous matter (PrM) is a substantial constituent in bioaerosols. However, the sources and atmospheric processes of PrM remain large uncertainties. The characterizations, sources, and potential atmospheric processes of free amino acids (FAAs) and combined amino acids (CAAs) were investigated via a set of 1‐year fine particle (PM2.5) samples collected in suburban Guiyang (a hilly basin area in Southwest China). The annual average concentrations of FAAs and CAAs were 156.31 ± 41.52 and 315.36 ± 147.66 ng m−3, respectively. The dominant FAA and CAA species were proline, which was different from previous observations with glycine as a major species. The results indicated that the sources or atmospheric processes of aerosol PrM at this study site were different from previous observations in the urban and suburban areas. The analysis of AA‐nitrogen isotope compositions and air mass back trajectories suggested that the abundances of aerosol FAAs and CAAs were highly controlled by primary sources (particularly plants) with less impact from long‐range transport. Furthermore, the contributions of PrM degradation by ozone‐ and hydroxyl radical‐related processes to total FAAs were found to be minor. The overall results suggested that the long‐range transport and atmospheric degradation of PrM were insignificant factors affecting aerosol PrM abundance in this suburban area with the weak atmospheric oxidation capacity, high cloud cover rate, and frequent precipitation. Thus, the findings improve our understanding of the sources and atmospheric processes of aerosol PrM. Plain Language Summary: Aerosol proteinaceous matter (PrM) consists of free amino acids (FAAs) and combined amino acids (CAAs). It is well documented that FAAs and CAAs have a large variety of natural sources. Moreover, the atmospheric degradation of CAAs has been regarded as a new potential source of aerosol FAAs. However, the relative contribution of primary and secondary sources to FAAs remains poorly understood. Based on a 1‐year investigation of PrM in PM2.5 collected in suburban Guiyang (a hilly basin area in Southwest China), we found that proline was the dominant species in both FAAs and CAAs. This result was different from previous observations with glycine as a major species. Further, our analysis showed that aerosol PrM in this hilly basin area was mainly derived from local primary sources (particularly plants) with less influence from long‐range transport of PrM. Moreover, the contribution of oxidative degradation of PrM to total FAAs was found to be minor. In general, the long‐range transport and atmospheric degradation of PrM have an insignificant contribution to aerosol PrM abundance in this hilly basin area. Our findings provide new insights into the sources and atmospheric transformation of aerosol PrM. Key Points: Proline is the dominant species in both free amino acids and combined amino acidsAerosol Proteinaceous matter (PrM) was largely originated from local primary sources with less impact from long‐range transportThe oxidative degradation of aerosol PrM was insignificant in suburban Guiyang [ABSTRACT FROM AUTHOR]

The bank vole (BV) prion protein (PrP) can function as a universal acceptor of prions. However, the molecular details of BVPrP's promiscuity for replicating a diverse range of prion strains remain obscure. To develop a cultured cell paradigm capable of interrogating the unique properties of BVPrP, we generated monoclonal lines of CAD5 cells lacking endogenous PrP but stably expressing either hamster (Ha), mouse (Mo), or BVPrP (M109 or I109 polymorphic variants) and then challenged them with various strains of mouse or hamster prions. Cells expressing BVPrP were susceptible to both mouse and hamster prions, whereas cells expressing MoPrP or HaPrP could only be infected with species‐matched prions. Propagation of mouse and hamster prions in cells expressing BVPrP resulted in strain adaptation in several instances, as evidenced by alterations in conformational stability, glycosylation, susceptibility to anti‐prion small molecules, and the inability of BVPrP‐adapted mouse prion strains to infect cells expressing MoPrP. Interestingly, cells expressing BVPrP containing the G127V prion gene variant, identified in individuals resistant to kuru, were unable to become infected with prions. Moreover, the G127V polymorphic variant impeded the spontaneous aggregation of recombinant BVPrP. These results demonstrate that BVPrP can facilitate cross‐species prion replication in cultured cells and that a single amino acid change can override the prion‐permissive nature of BVPrP. This cellular paradigm will be useful for dissecting the molecular features of BVPrP that allow it to function as a universal prion acceptor. [ABSTRACT FROM AUTHOR]