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In the past 20 years, the global per capita protein demand has been increasing year by year, and thus the search for sustainable and healthier alternative proteins is the focus of current food research. Yeast proteins are of microbial origin with environmentally friendly advantages. They are high-quality proteins with high bioavailability and are expected to be used as novel alternative proteins for food applications. Although reports on yeast extracts continue to increase, studies on the composition, production methods, and functional properties of yeast proteins lack systematic reviews. In addition, the application of yeast proteins in the food industry has not been summarized previously. This paper reviews the composition of yeast proteins and the approaches for their isolation and extraction, and systematically introduces the functional properties and the wide applications in food fields. Future perspectives for yeast proteins to sustainably and healthily meet the world's growing protein demand are also elucidated. Yeast proteins have great application potential as alternative proteins with a reasonable proportion of amino acid composition. Yeast proteins can be hydrolyzed to produce yeast peptides and can also be used as protein supplements, fining agents, meat extenders, etc. Overcoming the limitations of high nucleic acid content and high cost, and improving the functional properties and sensory acceptability of yeast proteins will greatly promote their market applications. This review will provide ideas and guidance for the research and development of yeast proteins in food applications. Yeast proteins have high nutritional value with an ideal amino acid composition and a wealth of functions and properties. The excellent characteristics allow yeast proteins to be used as sustainable alternative proteins in food applications. [Display omitted] • The compositions and extraction approaches of yeast proteins are overviewed. • The functional properties of yeast proteins are summarized. • The applications of yeast proteins as alternative proteins in food are reviewed. • The strategies to improve the utilization of yeast proteins are emphasized. [ABSTRACT FROM AUTHOR]

Prediction of protein structural class plays an important role in protein structure and function analysis, drug design and many other biological applications. Prediction of protein structural class for low-similarity sequences is still a challenging task. Based on the theory of wavelet denoising, this paper presents a novel method of prediction of protein structural class for the first time. Firstly, the features of the protein sequence are extracted by using Chou’s pseudo amino acid composition (PseAAC). Then the extracted feature information is denoised by two-dimensional (2D) wavelet. Finally, the optimal feature vectors are input to support vector machine (SVM) classifier to predict protein structural classes. We obtained significant predictive results using jackknife test on three low-similarity protein structural class datasets 25PDB, 1189 and 640, and compared our method with previous methods The results indicate that the method proposed in this paper can effectively improve the prediction accuracy of protein structural class, which will be a reliable tool for prediction of protein structural class, especially for low-similarity sequences. [ABSTRACT FROM AUTHOR]

Abstract This paper reviews the main research results on donkey milk quality to highlight the nutritional similarities with human milk, the gold standard for infant feeding. The major differences between donkey and human milk are related to the fat yield, which thus means that quantitative and qualitative supplements are needed in pre-weaned children. The two milks are similar in terms of total protein content and amino acid profile. In addition, both donkey and human milk are poor in casein and rich in lactose and also share a similar unsaturated:saturated fatty acid ratio and cholesterol, sodium, potassium and vitamin C content. The triglyceride profile is also similar. Donkey milk seems to be a promising alternative food targeted at children's health. New, well-designed clinical studies in children and other sensitive groups are needed to examine in depth the clinical and metabolic outcomes and the potential positive health impacts. [ABSTRACT FROM AUTHOR]

Abstract: In contrast to a large number of classically secreted proteins (CSPs) and non-secreted proteins (NSPs), only a few proteins have been experimentally proved to enter non-classical secretory pathways. So it is difficult to identify non-classically secreted proteins (NCSPs), and no methods are available for distinguishing the three types of proteins simultaneously. In order to solve this problem, a data mining has been taken firstly, and mammalian proteins exported via ER-Golgi-independent pathways are collected through extensive literature searches. In this paper, a support vector machine (SVM)-based ternary classifier named SecretP is proposed to predict mammalian secreted proteins by using pseudo-amino acid composition (PseAA) and five additional features. When distinguishing the three types of proteins, SecretP yielded an accuracy of 88.79%. Evaluating the performance of our method by an independent test set of 92 human proteins, 76 of them are correctly predicted as NCSPs. When performed on another public independent data set, the prediction result of SecretP is comparable to those of other existing computational methods. Therefore, SecretP can be a useful supplementary tool for future secretome studies. The web server SecretP and all supplementary tables listed in this paper are freely available at http://cic.scu.edu.cn/bioinformatics/secretp/index.htm. [Copyright &y& Elsevier]

Abstract: Human mitogen-activated protein (MAP) kinase interacting kinase 1b (Mnk1b) is a splice variant of human Mnk1a, which has been identified in our laboratory [A. O’Loghlen, V.M. Gonzalez, D. Pineiro, M.I. Perez-Morgado, M. Salinas, M.E. Martin, Identification and molecular characterization of Mnk1b, a splice variant of human MAP kinase-interacting kinase Mnk1, Exp. Cell Res. 299 (2004) 343–355]. Mnk1b has much higher basal eIF4E kinase activity than Mnk1a. Because Mnk1b presents different features in its C-terminus with respect to Mnk1a, we have studied in this paper the potential role of these structural differences in determining the higher basal eIF4E kinase activity as well as the subcellular localization of Mnk1b. In this paper, we demonstrate that phosphorylation of the Thr209 and Thr214 in the activation loop of Mnk1b is necessary for its activation. However, the different kinase activity between Mnk1a and Mnk1b is independent of the phosphorylation status of the activation loop residues. By deletion of the C-terminal tail in Mnk1a, we confirmed that the absence of this sequence is not responsible for the higher eIF4E kinase activity present in Mnk1b. Moreover, our findings support a crucial role of the 12 amino acids, particularly the Ala344, in the C-terminal specific region of Mnk1b (Mnk1bSR), on the kinase activity of the protein. [Copyright &y& Elsevier]

Abstract: In our previous paper it was shown that the two C-terminal Gln residues of a C-terminal 15-residue fragment, Mel(12–26) (GLPALISWIKRKRQQ-NH2), of melittin and a series of individual substituted analogues might not involved in the interaction with bacterial membranes. In this paper, peptides with one and two Gln residues deletion, respectively, Mel(12–25) and Mel(12–24), were synthesized and characterized. Both of the deletion peptides showed higher antimicrobial activities than the parent peptide, Mel(12–26). If both of the Gln residues of Mel(12–26) were respectively replaced by a hydrophilic amino acid Gly, the antimicrobial activity increased slightly. If the Gln residue of Mel(12–25) was replaced by a hydrophobic amino acid Leu, the antimicrobial activity changed little, although the substituted peptide possessed much higher hydrophobicity and higher α-helical conformation percentage in 1,1,1,3,3,3-hexafluoro-2-propanol/water determined by circular dichroism spectroscopy (CD) than the parent peptide. These results indicated that the two C-terminal residues might be indeed not involved in the binding to bacterial membranes. The antimicrobial activity increasing with the residue deletion may be caused by the decrease of the translational and rotational entropic cost of the binding of the peptides to bacterial membranes because of the lower molecular weights of the deletion peptides. [Copyright &y& Elsevier]

The Golgi Apparatus (GA) is a key organelle for protein synthesis within the eukaryotic cell. The main task of GA is to modify and sort proteins for transport throughout the cell. Proteins permeate through the GA on the ER (Endoplasmic Reticulum) facing side (cis side) and depart on the other side (trans side). Based on this phenomenon, we get two types of GA proteins, namely, cis-Golgi protein and trans-Golgi protein. Any dysfunction of GA proteins can result in congenital glycosylation disorders and some other forms of difficulties that may lead to neurodegenerative and inherited diseases like diabetes, cancer and cystic fibrosis. So, the exact classification of GA proteins may contribute to drug development which will further help in medication. In this paper, we focus on building a new computational model that not only introduces easy ways to extract features from protein sequences but also optimizes classification of trans-Golgi and cis-Golgi proteins. After feature extraction, we have employed Random Forest (RF) model to rank the features based on the importance score obtained from it. After selecting the top ranked features, we have applied Support Vector Machine (SVM) to classify the sub-Golgi proteins. We have trained regression model as well as classification model and found the former to be superior. The model shows improved performance over all previous methods. As the benchmark dataset is significantly imbalanced, we have applied Synthetic Minority Over-sampling Technique (SMOTE) to the dataset to make it balanced and have conducted experiments on both versions. Our method, namely, identification of sub-Golgi Protein Types (isGPT), achieves accuracy values of 95.4%, 95.9% and 95.3% for 10-fold cross-validation test, jackknife test and independent test respectively. According to different performance metrics, isGPT performs better than state-of-the-art techniques. The source code of isGPT, along with relevant dataset and detailed experimental results, can be found at https://github.com/srautonu/isGPT. [ABSTRACT FROM AUTHOR]

The molecular interactions that promote the stability of proteins and amino acids in saline solutions is a central topic of molecular biophysics. However, a well-supported molecular picture of the phenomena has not been established yet. In this paper, we studied as model system the mix between DL-Alanine in aqueous solutions of STP (Na 2 S 2 O 3 ·5H 2 O) at different temperatures, from volumetric and viscometric properties. The thermophysical properties obtained indicate the presence of a strong preferential solvation, structure-making action and a possible salt in effect. Quantum chemical calculations and molecular dynamic (MD) simulations provide a new insight to support these arguments. [ABSTRACT FROM AUTHOR]

Objectives: In this paper, a high-quality sequence encoding scheme is proposed for predicting subcellular location of apoptosis proteins.Methods: In the proposed methodology, the novel evolutionary-conservative information is introduced to represent protein sequences. Meanwhile, based on the proportion of golden section in mathematics, position-specific scoring matrix (PSSM) is divided into several blocks. Then, these features are predicted by support vector machine (SVM) and the predictive capability of proposed method is implemented by jackknife test RESULTS: The results show that the golden section method is better than no segmentation method. The overall accuracy for ZD98 and CL317 is 98.98% and 91.11%, respectively, which indicates that our method can play a complimentary role to the existing methods in the relevant areas.Conclusions: The proposed feature representation is powerful and the prediction accuracy will be improved greatly, which denotes our method provides the state-of-the-art performance for predicting subcellular location of apoptosis proteins. [ABSTRACT FROM AUTHOR]

Fucus spiralis, Porphyra sp. and Osmundea pinnatifida are macroalgae consumed as food in some of the Azorean Islands, but little information is available on their nutritional value. This paper presents information on the nutritional aspects in terms of proteins (9.71-24.82%), lipids (5.23-8.88%), soluble carbohydrates (17.59-25.37%), ash (22.31-38.55%), minerals (0.96-1.82 for Na/K ratios) and fat soluble vitamins A (1.20-1.41%) and E (4.86-51.14%) contents on dry weight basis. Fatty acid (SFA, MUFA, PUFA and n6/n3 and h/H ratios) and amino acid profiles, and antioxidant properties were also reported. All the three species contained measurable quantities of 9 of 10 essential amino acids (41.62-63.50% of the total amino acids). The regular consumption of these algae allied with the low level of seawater pollution around Azores Islands will improve human health conditions and will have a protective effect on the most common degenerative diseases. [ABSTRACT FROM AUTHOR]

The physiological functions of essential branched chain amino acids (BCAA) are important in broiler nutrition, but antagonistic BCAA interactions may become evident. Given the increased implementation of reduced-crude protein (CP) diets, this study aimed to investigate whether elevated leucine inclusions in reduced-CP diets would advantage broiler growth performance, provided concomitant elevations in isoleucine and valine were employed. A total of 378 off-sex male Ross 308 broilers were allocated to 9 dietary treatments, each with 7 replicate cages and 6 birds in each. All diets were wheat-based with 190 g/kg CP. The dietary treatments comprised 3 leucine inclusions (12.71, 15.02, 17.33 g/kg) and 3 isoleucine plus valine inclusions (17.21, 20.32, 23.45 g/kg) in a 3 × 3 factorial array. The assessed parameters included growth performance, relative abdominal fat-pad weights, nutrient utilisation, apparent jejunal and ileal digestibility coefficients and disappearance rates of starch, protein (N), amino acids and free amino acid concentrations in systemic plasma. Elevated BCAA inclusions did not enhance growth performance; indeed, elevating isoleucine plus valine from 17.21 to 20.32 g/kg in the 15.02 g/kg leucine diet significantly compromised weight gain by 6.82% (1325 versus 1422 g/bird). However, elevating isoleucine plus valine inclusions from 17.21 to 20.32 g/kg decreased relative fat-pad weights by 8.49% (9.05 versus 9.89 g/kg; P = 0.046). Elevating leucine levels significantly depressed energy utilisation, AME and AMEn, by 0.39 MJ in both instances. Dietary enrichment with leucine had diverse impacts on amino acid digestibility coefficients coupled with free amino acid plasma concentrations. Increasing dietary leucine concentrations improved ileal digestibility of leucine by 4.74% (0.906 versus 0.865) but also significantly increased ileal digestibility coefficients of another 10 amino acids by an average of 3.37% ranging from 1.60% (methionine) to 4.96% (threonine). Overall, elevations of BCAA in wheat-based, reduced-CP diets did not advantage broiler growth performance. The likelihood is that several factors are responsible for this lack of response and consideration is given to these possibilities in this paper. • Elevated dietary leucine inclusions, without or with increases in isoleucine plus valine, did not enhance growth performance. • This was attributed in part to BCAA antagonism. • Dietary leucine enrichment increased ileal digestibility of six essential and six non-essential amino acids. • Leucine enrichment increased free leucine concentrations in plasma but depressed concentrations of isoleucine and valine. • Elevated dietary leucine inclusions depressed energy utilisation (AME and AMEn). [ABSTRACT FROM AUTHOR]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.dsr.2005.05.001 Byline: Sachiko Saijo (a), Eiichiro Tanoue (b) Keywords: Particulate organic matter; Particulate combined amino acids; Proteins; Peptides; Electrophoresis Abstract: Particulate combined amino acids (PCAA) are the most abundant identified constituents of particulate organic matter (POM) in Pacific Ocean surface waters, but their chemical forms are unclear. In the present study, chemical characterization of amino acid-containing materials in surface POM from subarctic to subtropical waters along 165[degrees]E in the Pacific was carried out by one- and two-dimensional gel electrophoresis. At least four chemical forms of amino acid-containing POM were distinguished: proteins, acidic materials containing peptides, protein/peptide-specific dye-stainable low-molecular-mass materials (stainable materials) and non-stainable materials, all of which were considered to be major components of detrital POM. Seventeen distinct protein containing components were distinguished in samples across the transect. A majority of stainable materials was estimated to comprise 6-8 amino acid residues, while less than six amino acid residues made up the non-stainable materials. Among the four chemical forms, acidic materials and non-stainable materials were major components, accounting for 31-42% and 49-63% of PCAA, respectively, along the transect. Proteins were common, but they were quantitatively less than 2% of PCAA. Stainable materials were regionally variable and more abundant in subarctic waters than in subtropical waters. The mechanistic processes by which such amino acid-containing POM occurs as detrital POM are discussed. Author Affiliation: (a) Department of Earth and Environmental Sciences, Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan (b) Department of Earth and Environmental Sciences, Graduate School of Environmental Studies, Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan Article History: Received 15 July 2004; Revised 7 March 2005; Accepted 17 May 2005

In this paper, an intelligent hyper framework is proposed to recognize protein folds from its amino acid sequence which is a fundamental problem in bioinformatics. This framework includes some statistical and intelligent algorithms for proteins classification. The main components of the proposed framework are the Fuzzy Resource-Allocating Network (FRAN) and the Radial Bases Function based on Particle Swarm Optimization (RBF-PSO). FRAN applies a dynamic method to tune up the RBF network parameters. Due to the patterns complexity captured in protein dataset, FRAN classifies the proteins under fuzzy conditions. Also, RBF-PSO applies PSO to tune up the RBF classifier. Experimental results demonstrate that FRAN improves prediction accuracy up to 51% and achieves acceptable multi-class results for protein fold prediction. Although RBF-PSO provides reasonable results for protein fold recognition up to 48%, it is weaker than FRAN in some cases. However the proposed hyper framework provides an opportunity to use a great range of intelligent methods and can learn from previous experiences. Thus it can avoid the weakness of some intelligent methods in terms of memory, computational time and static structure. Furthermore, the performance of this system can be enhanced throughout the system life-cycle. [ABSTRACT FROM AUTHOR]

Abstract: Prediction of protein subcellular location is a meaningful task which attracted much attention in recent years. A lot of protein subcellular location predictors which can only deal with the single-location proteins were developed. However, some proteins may belong to two or even more subcellular locations. It is important to develop predictors which will be able to deal with multiplex proteins, because these proteins have extremely useful implication in both basic biological research and drug discovery. Considering the circumstance that the number of methods dealing with multiplex proteins is limited, it is meaningful to explore some new methods which can predict subcellular location of proteins with both single and multiple sites. Different methods of feature extraction and different models of predict algorithms using on different benchmark datasets may receive some general results. In this paper, two different feature extraction methods and two different models of neural networks were performed on three benchmark datasets of different kinds of proteins, i.e. datasets constructed specially for Gram-positive bacterial proteins, plant proteins and virus proteins. These benchmark datasets have different number of location sites. The application result shows that RBF neural network has apparently superiorities against BP neural network on these datasets no matter which type of feature extraction is chosen. [Copyright &y& Elsevier]

Protein aggregation is a major instability that can occur during all stages of protein drug production and development. Protein aggregates may compromise the safety and efficacy of the final protein formulation. In this paper, various new excipients [phenylbutylamino-, benzyl-, and cholesteryl-polyethylene glycols (PEGs)] and their use for the reduction of aggregation of salmon calcitonin (sCT) and hen egg-white lysozyme (HEWL) by noncovalent PEGylation are presented. The ability to suppress aggregation of sCT in various buffer systems at a 1:1 molar ratio was assessed by following changes in protein conformation and aggregation state over time. The results are compared with that of dansyl- and l-tryptophan (Trp)-PEGs described in earlier publications. Furthermore, the influence of the different PEG-based excipients on the aggregation of HEWL was measured. HEWL aggregation was completely suppressed in the presence of cholesteryl-PEGs (2 and 5 kDa), whereas deterioration was observed using benzyl-methoxy polyethylene glycols (mPEGs; 2 and 5 kDa). Phenylbutylamino- and Trp-mPEG (2 kDa), as well as dansyl-PEGs of different molecular weight prolonged the lag phase of aggregation and reduced the aggregation velocity of HEWL. © 2012 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 101:1995-2008, 2012 [ABSTRACT FROM AUTHOR]

Abstract: Chirality is one of the basic, unique, and most appealing features of biological molecules; however, many intriguing chiral phenomena in biological world remains insufficiently revealed yet. In this research, we fabricated chiral surfaces by assembling natural chiral amino acids-cysteine of opposite configurations (D- and L-) onto gold surfaces, respectively, and investigated the adhesion of the L929 fibroblast on them. No significant differences were observed in the density of adherent cells under serum-free culture condition; while in serum-containing condition, significantly more cells adhered on the L-Cys assembled surfaces. This phenomenon suggested that serum protein might play an important role in mediating the selective adhesion of cells on chiral surfaces. Hence, we adopted both radiolabeling and surface plasmon resonance (SPR) techniques to monitor protein adsorption onto the above surfaces. The results evidently showed more proteins adsorbed onto surfaces assembled with L-Cys. We propose that the difference in protein adsorption on chiral surfaces as demonstrated in this paper might not only shed light on the ensuing investigation of bio-related chirality phenomena, but also provide a novel strategy for the rational design and fabrication of novel biomaterials and bio-related devices based on chiral effects. [Copyright &y& Elsevier]

Abstract: In vivo, some proteins exist as monomers (single polypeptide chains) and others as oligomers. Not like monomers, oligomers are composed of two or more chains (subunits) that are associated with each other through non-covalent interactions and, occasionally, through disulfide bonds. These proteins are the structural components of various biological functions, including cooperative effects, allosteric mechanisms and ion-channel gating. However, with the dramatic increase in the number of protein sequences submitted to the public data bank, it is important for both basic research and drug discovery research to acquire the possible knowledge about homo-oligomeric attributes of their interested proteins in a timely manner. In this paper, a high-throughput method, combined support vector machines with discrete wavelet transform, has been developed to predict the protein homo-oligomers. The total accuracy obtained by the re-substitution test, jackknife test and independent dataset test are 99.94%, 96.17% and 96.18%, respectively, showing that the proposed method of extracting feature from the protein sequences is effective and feasible for predicting homo-oligomers. The online service is available at http://bioinfo.ncu.edu.cn/Services.aspx. [Copyright &y& Elsevier]

Abstract: Secondary Ion Mass Spectrometry (SIMS) is a well established method for sensitive surface atomic and molecular analysis. Protein analysis with conventional SIMS has been attempted numerous times; however it delivers exclusively fragment peaks assigned to α-amino acids or immonium ions. In this paper we report experiments where direct sequence information could be measured thanks to a combination of HPLC separation with matrix enhanced SIMS (ME-SIMS) on tryptic digests of intact proteins. We employ peptide mass fingerprinting (PMF) and protein identification through the detection of HPLC-separated digests of Savinase (Sav.) and bovine serum albumin (BSA), followed by MASCOT search. This is the first time that the possibility of full protein identification using LC-ME-SIMS is demonstrated in a classic proteomics workflow and that a 69kDa protein is identified with SIMS. These results demonstrate both the relevance and the potential of LC-ME-SIMS in future high resolution proteomics studies. [Copyright &y& Elsevier]

Abstract: This review outlines and discusses the recent development of thermochemolysis (or thermally assisted hydrolysis and methylation (THM)) since the review paper by Challinor in this journal in 2001. The concept and practice of thermochemolysis using quaternary ammonium base reagents, e.g., tetramethylammonium hydroxide (TMAH), is given. The application review is categorized based on either the class of compounds, or popular sample types, e.g., soils, pollen etc. using thermochemolysis gas chromatography–mass spectrometry (GC–MS). Quantitative analysis, a relatively new aspect of thermochemolysis, is discussed separately, where appropriate, at the end of some of application sections. The wide variety of applications includes synthetic polymers, lipids, materials in art and conservation, lignin, carbohydrates, amino acids, proteins and nucleic acids, flavonoids, soil/sediments, atmosphere particulates, human samples, and others. A section is devoted to chemometric techniques and data analysis of thermochemolysis products. [ABSTRACT FROM AUTHOR]

Abstract: Mammalian olfactory system is the archetype of smell sensor devices. Its complexity resides both in the odorant mechanism of capture by the single olfactory receptor (OR) and in the space organization and codification of the information. The result is a unique profile for each odorant. Our aim is to partially mimick this system, in order to produce a biosensor on nanometric scale. In this paper, we present a microscopic theoretical framework in which the experimental results should be embedded. It consists of the description of the protein at the level of the amino-acid structure in terms of an impedance network able to simulate the electrical characteristics associated with the protein topology. [Copyright &y& Elsevier]

Abstract: This paper presents a GC–MS analytical procedure for determining proteinaceous materials, glycerolipids, natural waxes and terpenoid resins in the same paint micro-sample. The procedure is also reliable when high amounts of interfering inorganic pigments, dryers and charges are present. The characterisation of proteinaceous binders in a paint sample can be subject to analytical interferences by inorganic materials. Such materials may form complexes with functional groups of proteins, thus preventing their efficient derivatisation, which is necessary prior to GC analysis. For this reason an analytical procedure has been developed based on two extractions and a clean-up step, in order to obtain two fractions: a lipid-resinous fraction and a proteinaceous fraction. The lipid-resinous fraction is subjected to salification/saponification assisted by microwaves, followed by acidification, extraction, derivatisation and GC–MS analysis. The proteinaceous fraction is analysed by GC–MS after hydrolysis and derivatisation of the freed amino acids. The desalting step is applied before the hydrolysis, and is based on the use of the monolithic sorbent tip technology with a C4 stationary phase. Reference paint replicas of egg, casein and animal glue were prepared with and without several metals containing pigments, and used to develop and validate the analytical procedure. The procedure proved to be efficient in desalting the proteinaceous materials both from cations and anions. Although non quantitative, it is reliable in the analysis of samples whose content of extractable proteins is <1μg, thus showing it to be suitable for the characterisation of paint samples. An example of how the analytical procedure was used to characterise a sample from a 15th century panel painting is also discussed. [Copyright &y& Elsevier]

Abstract: In this work, genetic algorithms concepts along with a rotamer library dependent of backbone and implicit solvation potential are used to study the tertiary structure of peptides. We starting from known primary sequence and optimize the structure of the backbone while the side chains allowed adopting the conformations present in a rotamer library. The GA, implemented with two force fields with a growing complexity, was used predict the structure of a polyalanine and a polyisolueucine. This paper presents good and interesting results about the study of peptides structures and about the development of computational tools to study peptides structures. [Copyright &y& Elsevier]

Abstract: Protein–protein complex, composed of hydrophobic and hydrophilic residues, can be divided into hydrophobic and hydrophilic amino acid network structures respectively. In this paper, we are interested in analyzing these two different types of networks and find that these networks are of small-world properties. Due to the characteristic complementarity of the complex interfaces, protein–protein docking can be viewed as a particular network rewiring. These networks of correct docked complex conformations have much more increase of the degree values and decay of the clustering coefficients than those of the incorrect ones. Therefore, two scoring terms based on the network parameters are proposed, in which the geometric complementarity, hydrophobic–hydrophobic and polar–polar interactions are taken into account. Compared with a two-term energy function, a simple scoring function HPNet which includes the two network-based scoring terms shows advantages in two aspects, not relying on energy considerations and better discrimination. Furthermore, combing the network-based scoring terms with some other energy terms, a new multi-term scoring function HPNet-combine can also make some improvements to the scoring function of RosettaDock. [Copyright &y& Elsevier]

Abstract: Inclusion body refolding processes play a major role in the production of recombinant proteins. Improvement of the size-exclusion chromatography refolding process was achieved by combining a decreasing urea gradient with an increasing arginine gradient (two gradients) for the refolding of NTA protein (a new thrombolytic agent) in this paper. Different refolding methods and different operating conditions in two gradients gel filtration process were investigated with regard to increasing the NTA protein activity recovery and inhibition of aggregation. The refolding of denatured NTA protein showed this method could significantly increase the activity recovery of protein at high protein concentration. The activity recovery of 37% was obtained from the initial NTA protein concentration up to 20 mg/ml. The conclusions presented in this study could also be applied to the refolding of lysozyme. [Copyright &y& Elsevier]

Abstract: Three-dimensional structures of proteins are the support of their biological functions. Their folds are stabilized by contacts between residues. Inner protein contacts are generally described through direct atomic contacts, i.e. interactions between side-chain atoms, while contact prediction methods mainly used inter-Cα distances. In this paper, we have analyzed the protein contacts on a recent high quality non-redundant databank using different criteria. First, we have studied the average number of contacts depending on the distance threshold to define a contact. Preferential contacts between types of amino acids have been highlighted. Detailed analyses have been done concerning the proximity of contacts in the sequence, the size of the proteins and fold classes. The strongest differences have been extracted, highlighting important residues. Then, we studied the influence of five different side-chain conformation prediction methods (SCWRL, IRECS, SCAP, SCATD and SCCOMP) on the distribution of contacts. The prediction rates of these different methods are quite similar. However, using a distance criterion between side chains, the results are quite different, e.g. SCAP predicts 50% more contacts than observed, unlike other methods that predict fewer contacts than observed. Contacts deduced are quite distinct from one method to another with at most 75% contacts in common. Moreover, distributions of amino acid preferential contacts present unexpected behaviours distinct from previously observed in the X-ray structures, especially at the surface of proteins. For instance, the interactions involving Tryptophan greatly decrease. [Copyright &y& Elsevier]

Abstract: Glu is highly conserved as the first amino acid of E-helix of the EF-hand protein. In this paper, Glu 101, the first amino acid of E-helix of the third EF-hand motif in Euplotes octocarinatus centrin (EoCen) was mutated to be Lys by the method of site direct mutation. Tb3+ and TNS were used as fluorescence probes in the study of the effect of this mutation to the metal binding characteristic of EoCen by fluorescence spectra. Results indicate that compared with EoCen, the mutation protein (E101K) displays a different Tb3+ binding characteristic and an increased hydrophobic exposure surface. Polyacrylamide gels electrophoresis indicated that the electrophoretic mobilities of EoCen and E101K are distinctly different. It can be deduced that the conformation of EoCen has been altered by this mutation. The general conditional binding constant of Tb3+ to the three loops of EF-hand sites I–III in E101K was calculated to be (5.64±0.57)×105 M−1 according to the modified equation of the single binding process. [Copyright &y& Elsevier]

An additive that is highly effective in small amounts for controlling protein inactivation and aggregation has long been demanded. In this paper we show amidated amino acids as new potent additives. In the presence of 100 mM amidated amino acids, e.g., Ala, Arg, Asn, Met, and Val, the heat-induced inactivation and aggregation of lysozyme at pH 7.1 are one order of magnitude slower than those in the absence of additives. Although a high Arg concentration (>1 M) has been used to prevent aggregation among amino acids, it is worth mentioning that above amidated amino acids can prevent aggregation at submolar concentrations. The data obtained suggest the importance of amino and amide groups rather than the guanidium group as an aggregation suppressor. [Copyright &y& Elsevier]

Abstract: This paper gives a summary of different aspects for predicting protein behaviour in hydrophobic interaction chromatography (HIC). First, a brief description of HIC, hydrophobic interactions, amino acid and protein hydrophobicity is presented. After that, several factors affecting protein chromatographic behaviour in HIC are described. Finally, different approaches for predicting protein retention time in HIC are shown. Using all this information, it could be possible to carry out computational experiments by varying the different operating conditions for the purification of a target protein; and then selecting the best conditions in silico and designing a rational protein purification process involving an HIC step. [Copyright &y& Elsevier]

A water-soluble chlorophyll-binding protein (WSCP) is the single known instance of a putative chlorophyll (Chl) carrier in green plants. Recently the photoprotective function of WSCP has been demonstrated by EPR measurements; the light-induced singlet-oxygen formation of Chl in the WSCP tetramer is about four times lower than that of unbound Chl. This paper describes the crystal structure of the WSCP-Chl complex purified from leaves of Lepidium virginicum (Virginia pepperweed) to clarify the mechanism of its photoprotective function. The WSCP-Chl complex is a homotetramer comprising four protein chains of 180 amino acids and four Chl molecules. At the center of the complex one hydrophobic cavity is formed in which all of the four Chl molecules are tightly packed and isolated from bulk solvent. With reference to the novel Chl-binding mode, we pro- pose that the photoprotection mechanism may be based on the inhibition of physical contact between the Chl molecules and molecular oxygen. [ABSTRACT FROM AUTHOR]

Although the field of protein methylation enjoys widespread interest in the scientific literature of today, this is a recent phenomenon. Papers on ‘protein methylation’ were first published in the 1960s. By the early 1980s, it was known that lysine, arginine, histidine and dicarboxylic amino acids were post-translationally methylated by highly specific methyltransferases. However, despite these early advances, the biological importance of these reactions remained largely unproven. With the introduction of modern molecular biology techniques in the mid-1990s, an enormous surge of interest in protein methylation occurred. It is now clear that protein methylation carries many important biological functions, including gene regulation and signal transduction. Thus, the story of protein-methylation research is a testament to both modern molecular biology and the importance of continuing to pursue lines of research in which the precise biological function might not be currently known. [Copyright &y& Elsevier]

Abstract: Exciting with the Nd:YAG laser line at 1064nm allows to receive high-quality, fluorescence-free Raman spectra of biomaterials. The paper presents investigations of Raman scattering from the bone irradiated with γ radiation up to the dose of 1000kGy. Results of Raman spectra studies of γ-irradiated bone allowed to show that inorganic component of the animal bone are more sensitive to γ radiation than the organic component. The changes in the irradiated bone were evaluated on the basis of the changes in the intensities of line, changes in their position and changes in some important ratios. Independent determination of the protein content and the content of some important amino acids were compared with the data obtain in the Raman studies. The majority of the bands assigned to organic component of bone were affected by doses higher than 100kGy. [Copyright &y& Elsevier]

This study was undertaken to determine the relationship between measured net portal absorptions (NPA) and flows of digestible essential amino acids (EAA) predicted with the National Research Council model (NRC, 2001) or the Cornell Net Carbohydrate and Protein System model (CNCPS, version 5.0.34). Net portal absorption data were obtained from 33 measurements of portal-arterial plasma EAA concentration differences among 8 treatments in lactating dairy cows, with plasma flow estimated from downstream dilution of para amino-hippurate. The predicted digestible flows from NRC (2001) related better than CNCPS to NPA observed in our studies, as shown by the lower standard errors on the slopes for all EAA and lower root mean prediction errors for all EAA except Met and Phe. However, the partitioning of the prediction error indicated a systematic underprediction (mean bias) for the NRC model (2001), with the exception of Ile. It is important to note that a relationship of unity was not expected, as discussed in the paper, because of losses of EAA through portal-drained viscera metabolism. A revised set of predictive equations for digestible EAA was obtained using a subset of data from NRC (2001) limited to trials conducted with dairy cows. This increased the predicted flows of digestible EAA by only 2%. Flows of digestible EAA were also estimated using a factorial approach, assuming an AA composition for each fraction of the duodenal flow estimated by NRC (undegradable, microbial, and endogenous proteins). This resulted in a slight improvement in the slope of the regression between predicted flows and measured NPA, but still yielded predicted digestive flows that were too low to support observed NPA. Finally, on the basis of literature values, increment of the digestibility of the undegradable fraction of forages and of microbial protein is suggested to improve the relationship between predicted digestible flows and NPA. Overall, this study indirectly confirms, across EAA, smaller losses through gut metabolism for His, Met, and Lys, intermediate losses for the branched-chain AA with the higher losses for Thr. [ABSTRACT FROM AUTHOR]

Abstract: We previously reported chromatographic evidence supporting the similarity of yellow chromophores isolated from aged human lens proteins, early brunescent cataract lens proteins and calf lens proteins ascorbylated in vitro [Cheng, R. et al. Biochimica et Biophysica Acta 1537, 14–26, 2001]. In this paper, new evidence supporting the chemical identity of the modified amino acids in these protein populations were collected by using a newly developed two-dimensional LC-MS mapping technique supported by tandem mass analysis of the major species. The pooled water-insoluble proteins from aged normal human lenses, early stage brunescent cataract lenses and calf lens proteins reacted with or without 20 mM ascorbic acid in air for 4 weeks were digested with a battery of proteolytic enzymes under argon to release the modified amino acids. Aliquots equivalent to 2.0 g of digested protein were subjected to size-exclusion chromatography on a Bio-Gel P-2 column and four major A 330 nm-absorbing peaks were collected. Peaks 1, 2 and 3, which contained most of the modified amino acids were concentrated and subjected to RP-HPLC/ESI-MS, and the mass elution maps were determined. The samples were again analyzed and those peaks with a 104–106 response factor were subjected to MS/MS analysis to identify the daughter ions of each modification. Mass spectrometric maps of peaks 1, 2 and 3 from cataract lenses showed 58, 40 and 55 mass values, respectively, ranging from 150 to 600 Da. Similar analyses of the peaks from digests of the ascorbylated calf lens proteins gave 81, 70 and 67 mass values, respectively, of which 100 were identical to the peaks in the cataract lens proteins. A total of 40 of the major species from each digest were analyzed by LC-MS/MS and 36 were shown to be identical. Calf lens proteins incubated without ascorbic acid showed several similar mass values, but the response factors were 100 to 1000-fold less for every modification. Based upon these data, we conclude that the majority of the major modified amino acids present in early stage brunescent Indian cataract lens proteins appear to arise as a result of ascorbic acid modification, and are presumably advanced glycation end-products. [Copyright &y& Elsevier]

Abstract: This paper discusses the importance of the Maillard reaction for food quality and focuses on flavour compound formation. The most important classes of Maillard flavour compounds are indicated and it is shown where they are formed in the Maillard reaction. Some emphasis is given on the kinetics of formation of flavour compounds. It is concluded that the essential elements for predicting the formation of flavour compounds in the Maillard reaction are now established but much more work needs to be done on specific effects such as the amino acid type, the pH, water content and interactions in the food matrix. It is also concluded that most work is done on free amino acids but hardly anything on peptides and proteins, which could generate peptide- or protein-specific flavour compounds. [Copyright &y& Elsevier]

Abstract: This paper focuses on the prediction of the dimensionless retention time of proteins (DRT) in hydrophobic interaction chromatography (HIC) by means of mathematical models based on characteristics of the surface hydrophobicity distribution. We introduce a new parameter, called hydrophobic imbalance (HI), obtained from the three-dimensional structure of proteins. This parameter quantifies the displacement of the superficial geometric centre of the protein when the effect of the hydrophobicity of each amino acid is considered. This parameter is simpler and less expensive than those reported previously. We use HI as a way to incorporate information about the surface hydrophobicity distribution in order to improve the prediction of DRT. We tested the performance of our DRT predictive models in a set of 15 proteins. This set includes four proteins whose DRTs are known as very difficult to predict. By means of the variable HI, it was possible to improve the predictive characteristics obtained by models based on the average surface hydrophobicity (ASH) by 9.1%. Also, we studied linear multivariable models based on characteristics determined from the HI. By using this multivariable model, a correlation coefficient of 0.899 was obtained. With this model, we managed to improve the predictive characteristics shown by previous models based on ASH by 31.8%. [Copyright &y& Elsevier]

Abstract: This paper focuses on the prediction of the dimensionless retention time (DRT) of proteins in hydrophobic interaction chromatography (HIC) by means of mathematical models based on the statistical description of the amino acid surface distribution. Previous models characterises the protein surface as a whole. However, most of the time it is not the whole protein but some of its specific regions that interact with the environment. It seems much more natural to use local measurements of the characteristics of the surface. Therefore, the statistical characterisation of the distribution of an amino acid property on the protein surface was carried out from the systematic calculation of the local average of this property in a neighbourhood placed sequentially on each of the amino acids on the protein surface. This process allowed us to characterise the distribution of this property quantitatively using three main statistics: average, standard deviation and maximum. In particular, if the property considered is a hydrophobicity scale, these statistics allowed us to characterise the average hydrophobicity and the hydrophobic content of the most hydrophobic cluster or hotspot, as well as the heterogeneity of the hydrophobicity distribution on the protein surface. We tested the performance of the DRT predictive models based on these statistics on a set of 15 proteins. We obtained better predictive results with respect to the models previously reported. The best predictive model was a linear model based on the maximum. This statistic was calculated using an index of the mobilities of amino acids in chromatography. The predictive performance of this model (measured as the Jack Knife MSE) was 26.9% better than those obtained by the best model which does not consider the amino acid distribution and 19.5% better than the model based on the hydrophobic imbalance (HI). In addition, the best performance was obtained by a linear multivariable model based on the HI and the maximum. The difference between the experimental data and the prediction carried out by this model was smaller than those observed previously. In fact, this model obtained better predictive capacities than a previous linear multivariable model decreasing the Jack Knife MSE in 8.7%. In addition, this model allowed us to diminish the number of variables required, increasing, in this way, the degrees of freedom of the model. [Copyright &y& Elsevier]

Summary: This paper describes a convergent mechanism for the feedback control of cholesterol synthesis and uptake mediated by SREBPs, membrane bound transcription factors. Endoplasmic reticulum (ER) bound SREBPs form complexes with Scap, a polytopic ER protein. In sterol-overloaded cells, Scap/SREBP binds to Insig-1, which retains the complex in the ER. Upon sterol deprivation, the Scap/SREBP complex dissociates from Insig-1, which is then ubiquitinated on lysines 156 and 158 and degraded in proteasomes. Scap/SREBP moves to the Golgi, where SREBP is processed to liberate a nuclear fragment that activates genes for cholesterol synthesis and uptake and the gene for Insig-1. Ubiquitination is not necessary for release of Scap/SREBP from Insig-1, but it establishes a requirement for synthesis of new Insig-1 for feedback inhibition. When the new Insig-1 and cholesterol converge on Scap, Scap/SREBP binds to Insig-1, preventing ubiquitination. The Insig-1/Scap/SREBP complex accumulates in the ER, ready for liberation when the cell is again sterol deprived. [Copyright &y& Elsevier]

Abstract: This paper focuses on the prediction of the dimensionless retention time of proteins (DRT) in hydrophobic interaction chromatography (HIC) by means of mathematical models based, essentially, only on aminoacidic composition. The results show that such prediction is indeed possible. Our main contribution was the design of models that predict the DRT using the minimal information concerning a protein: its aminoacidic composition. The performance is similar to that observed in models that use much more sophisticated information such as the three-dimensional structure of proteins. Three models that, in addition to the amino acid composition, use different assumptions about the amino acids tendency to be exposed to the solvent, were evaluated in 12 proteins with known experimental DRT. In all the cases analyzed, the model that obtained the best results was the one based on a linear estimation of the aminoacidic surface composition. The models were adjusted using a collection of 74 vectors of aminoacidic properties plus a set of 6388 vectors derived from these using two mathematical tools: k-means and self-organizing maps (SOM) algorithms. The best vector was generated by the SOM algorithm and was interpreted as a hydrophobicity scale based partly on the tendency of the amino acids to be hidden in proteins. The prediction error (MSEJK) obtained by this model was almost 35% smaller than that obtained by the model that supposes that all the amino acids are completely exposed and 40% smaller than that obtained by the model that uses a simple correction factor considering the general tendency of each amino acid to be exposed to the solvent. In fact, the performance of the best model based on the aminoacidic composition was 5% better than that observed in the model based on the three-dimensional structure of proteins. [Copyright &y& Elsevier]

SUMO (small ubiquitin-like modifier)/Smt3 (suppressor of mif two) is a member of the ubiquitin-related protein family and is known to conjugate with many proteins. In the sumoylation pathway, SUMO/Smt3 is transferred to substrate lysine residues through the thioester cascade of E1 (activating enzyme) and E2 (conjugating enzyme), and E3 (SUMO ligase) functions as an adaptor between E2 and each substrate. Yeast Ull1 (ubiquitin-like protein ligase 1)/Siz1, a PIAS (protein inhibitor of activated STAT)-type SUMO ligase, modifies both cytoplasmic and nuclear proteins. In this paper, we performed a domain analysis of Ull1/Siz1 by constructing various deletion mutants. A novel conserved N-terminal domain, called PINIT, as well as the RING-like domain (SP-RING) were required for the SUMO ligase activity in the in vitro conjugation system and for interaction with Smt3 in an in vitro binding assay. The most distal N-terminal region, which contains a putative DNA-binding SAF-A/B, Acinus, and PIAS (SAP) motif, was not required for the ligase activity but was involved in nuclear localization. A strong SUMO-binding motif was identified, which interacted with Smt3 in the two-hybrid system but was not necessary for the ligase activity. The most distal C-terminal domain was important for stable localization at the bud neck region and thereby for the substrate recognition of septins. Furthermore, the C-terminal half conferred protein instability on Ull1/Siz1. Taken together, we conclude that the SP-RING and PINIT of Ull1/Siz1 are core domains of the SUMO ligase, and the other domains are regulatory for protein stability and subcellular localization. [ABSTRACT FROM AUTHOR]

Abstract: The subcellular location of a protein is closely correlated with it biological function. In this paper, two new pattern classification methods termed as Nearest Feature Line (NFL) and Tunable Nearest Neighbor (TNN) have been introduced to predict the subcellular location of proteins based on their amino acid composition alone. The simulation experiments were performed with the jackknife test on a previously constructed data set, which consists of 2427 eukaryotic and 997 prokaryotic proteins. All protein sequences in the data set fall into four eukaryotic subcellular locations and three prokaryotic subcellular locations. The NFL classifier reached the total prediction accuracies of 82.5% for the eukaryotic proteins and 91.0% for the prokaryotic proteins. The TNN classifier reached the total prediction accuracies of 83.6 and 92.2%, respectively. It is clear that high prediction accuracies have been achieved. Compared with Support Vector Machine (SVM) and Nearest Neighbor methods, these two methods display similar or even higher prediction accuracies. Hence, we conclude that NFL and TNN can be used as complementary methods for prediction of protein subcellular locations. [Copyright &y& Elsevier]

Abstract: A key process in the development of new drugs is elucidation of the interaction between the drug molecule and the target protein. Such knowledge then makes it possible to make systematic structural modifications of the drug molecule to optimize the interaction. Many analytical techniques can be applied to proteins in solution such as circular dichroism, ultraviolet, and fluorescence spectroscopy but these all have limitations. In this paper, we investigate the feasibility of using relatively simple, visible light Raman spectroscopic methods to investigate amino acids and related biopolymers. [Copyright &y& Elsevier]

Abstract: The TGF-β superfamily signaling pathway regulates many important biological processes, including cell growth, differentiation and embryonic pattern formation. Smad1, a member of this signaling pathway that functions downstream of serine/threonine kinase receptors, has ability to interact with carboxyl terminus of Hsc70-interacting protein (CHIP), which is an E3 ubiquitin ligase in other cases. It has been reported that Smurf1, a member of the Hect family E3 ubiquitin ligases, can target Smad1 to 26S proteasome for degradation. In this paper, we studied the interaction of Smad1 and CHIP by combination of surface plasmon resonance and supported monolayer approach. The specific binding of Smad1 to CHIP indicates that the degradation of Smad1 may also be mediated by CHIP, and CHIP may play an essential role in the TGF-β signaling pathway. [Copyright &y& Elsevier]

Nitric oxide (NO) transduces most of its biological effects through activation of the heterodimeric enzyme, soluble guanylyl cyclase (sGC). Activation of sGC results in the production of cGMP from GTP. In this paper, we demonstrate a novel protein interaction between CCT (chaperonin containing t-complex polypeptide) subunit η and the α1β1 isoform of sGC. CCTη was found to interact with the β1 subunit of sGC via a yeast-two-hybrid screen. This interaction was then confirmed in vitro with a co- immunoprecipitation from mouse brain. The interaction between these two proteins was further supported by a co-localization of the proteins within rat brain. Using the yeast two-hybrid system, CCTη was found to bind to the N-terminal portion of sGC. In vitro assays with purified CCTη and Sf9 lysate expressing sGC resulted in a 30-50% inhibition of diethylamine diazeniumdiolate-NO-stimulated sGC activity. The same assays were then performed using BAY41-2272, an NOindependent allosteric sGC activator, and CCTη had no effect on this activity. Furthermore, CCTη had no effect on basal or sodium nitroprusside-stimulated αβCys-105 sGC, a constitutively active mutant that only lacks the heine group. The N-terminal 94 amino acids of CCTη seem to be critical for the mediation of this inhibition. Lastly, a 45% inhibition of sGC activity by CCTη was seen in vivo in BE2 cells stably transfected with CCTη and treated with sodium nitroprusside. These data suggest that CCTη binds to sGC and, in cooperation with some other factor, inhibits its activity by modifying the binding of NO to the heme group or the subsequent conformational changes. [ABSTRACT FROM AUTHOR]

Peroxiredoxin Q, as a member of peroxiredoxin gene family, was most recently cloned from plants. However, its molecular characteristics remain unclear. In this paper, we cloned a peroxiredoxin Q gene from a 400 mM NaCl-treated cDNA library of Suaeda salsa. The SsPrx Q gene (1 003 bp) contains an open reading frame of 214 amino acids with a molecular mass of 23.6 kDa. SsPrx Q showed high homology to the Prx Q of Sedum lineare, with 76% identities in deduced amino acid sequence. Southern blot analysis indicated that SsPrx Q gene has a single copy in S. salsa genome. Northern blot analysis showed that SsPrx Q gene expression was up-regulated by NaCl, mannitol, low temperature, H2O2, methyl viologen, and ABA. Studies of the recombinant protein produced in E. coli cells exhibited that it actually had a thioredoxin-dependent peroxidase activity, the characteristic of the Prx family. These results indicated that SsPrx Q may play an important role in protecting S. salsa from environmental stresses. [Copyright &y& Elsevier]

The modification of the lysine moieties of proteins to Nε-carboxymethyllysine (CML) is supposed to play a major role in the development of long-term complications in patients with diabetes mellitus. This paper presents an analytical method for the quantitative determination of CML in plasma proteins, which could be used for studying the development of diabetic complications. The method is based on isolating proteins from plasma by precipitation with trichloroacetic acid and hydrolysing these under acidic conditions (6 M hydrochloric acid at 110 °C for 20 h) to the individual amino acids. After hydrolysis, CML is derivatised along with the other amino acids to 9-fluorenylmethoxycarbonyl (FMOC) derivatives, which are subsequently separated by reversed-phase column liquid chromatography using a 150 mm × 4.6 mm C8 column and a mobile phase of 25 mM potassium phosphate buffer (pH 2.0) and acetonitrile (80:20 (v/v)) and detected using fluorescence detection (excitation at 260 nm and emission at 310 nm). Quantification of the protein-bound CML content of a plasma sample is achieved using standard addition. The impact of several aspects of the sample preparation and chromatography on method performance is discussed. Method evaluation results are reported and show that this method is capable of determining CML with good accuracy and precision (below 10%) in the relevant concentration range (1–10 μg/ml), with a limit of detection of 0.2 μg/ml. [Copyright &y& Elsevier]

We developed a method to follow the metabolic fate of [14C]-labeled Euglena gracilis protein amino acids in Aedes aegypti mosquitoes under three different adult nutritional regimes. Quantitative analysis of blood meal protein amino acid metabolism showed that most of the carbon of the amino acids was either oxidized to CO2 or excreted as waste. Under the three different adult nutritional regimes, no significant differences in the metabolism of amino acids were found, which indicated that the female A. aegypti mosquitoes possess a substantial capacity of maintaining metabolic homeostasis during a gonotrophic cycle. The amount of maternal glycogen and lipid after egg laying were significantly lower in the mosquitoes that underwent a partial starvation before a blood meal and/or starvation after the blood meal. The content of egg lipid or protein or the number of eggs laid did not show a significant difference among the three different regimes, which indicates that stable fecundity of A. aegypti under the partial starvation before a blood meal and/or starvation after the blood meal seemed to result from a trade-off between current fecundity and future survival after the eggs laid. The methods described in this paper can be applied to a wide range of questions about the effects of environmental conditions on the utilization of blood meal amino acids. [Copyright &y& Elsevier]

The present paper describes a method for radiolabeling Artemia that has potential applicability in the study of food intake, Artemia digestibility, protein and amino acid (AA) metabolism in early stages of marine fish larvae. Artemia nauplii were labeled by adding a uniformly labeled 14C protein hydrolysate to its hatching or enrichment media. Both newly hatched and enriched nauplii assimilated rapidly the radiolabel and a very high proportion of the uptaken label was incorporated into the TCA precipitate (mostly protein) fraction after a short period of time—84–91%, at the end of the hatching period and 81–87%, after 12 h of enrichment. In addition, it was observed that the amount of radiolabel per Artemia, as well as its distribution between the TCA precipitate and soluble (free AA) fractions, was relatively stable (up to 8 h) in conditions simulating transfer to larval feeding tanks. During the radiolabeling trials a substantial amount of the total initial radioactivity in the media was not recovered at the end of the hatching or enrichment period (38% and 29%, respectively). An experiment was designed to study the release of the radiotracer into the atmosphere, as 14CO2. It was concluded that although the Artemia catabolism may be responsible for some release of the radiolabel into the atmosphere, bacterial activity in the enrichment media has a major impact, being responsible for the loss of 19.2% of the total initial radiolabel from the system. The digestibility and transfer rates of the labeled nutrients from Artemia to fish larvae was analysed “in vivo” by feeding radiolabeled newly hatched nauplii to herring (Clupea harengus) larvae and following the metabolic fate of the label. The results revealed a high digestibility (around 60%) of the Artemia, with 20% being retained in the body and 39% catabolised by the larvae, 24 h after feeding. The digestion process and subsequent absorption of the digested radiolabeled nutrients were quite rapid, given that 40% was recovered in the body only 2 h after feeding and 6% was found in the CO2 trap at this time. [Copyright &y& Elsevier]

A method to suppress the interference of pigments in the analysis of proteinaceous media used in paintings is presented in this paper. This method is based on the formation of metallic ion–ethylenediaminetetraacetic acid (EDTA) complexes previous to the derivatisation process, using ethyl chloroformate (ECF), to transform the amino acids in N(O,S)-ethoxycarbonyl (EOC) ethyl esters. Test specimens, containing different proteinaceous media such as albumin, porcine gelatine and casein mixed with lead white, chalk, verdigris and raw Sienna have been prepared for carrying out this study. Different pH conditions have been probed for the different pigments studied. Values of peak area ratio of amino acids relative to the alanine, obtained using the proposed method on a series of protein–pigment test specimens, have been compared to those from specimens of pure protein in which direct method of derivatisation was applied. Finally, the method has been successfully applied to the analysis of 18th century wall paintings in which animal glue was used as binding medium. [Copyright &y& Elsevier]

It is well known that the gene distribution is non-uniform in the human genome, reaching the highest concentration in the GC-rich isochores. Also the amino acid frequencies, and the hydrophobicity, of the corresponding encoded proteins are affected by the high GC level of the genes localized in the GC-rich isochores. It was hypothesized that the gene expression level as well is higher in GC-rich compared to GC-poor isochores [Mol. Biol. Evol. 10 (1993) 186]. Several features of human genes and proteins, namely expression level, coding and non-coding lengths, and hydrophobicity were investigated in the present paper. The results support the hypothesis reported above, since all the parameters so far studied converge to the same conclusion, that the average expression level of the GC-rich genes is significantly higher than that of the GC-poor genes. [Copyright &y& Elsevier]

Hydrophobic interaction chromatography (HIC) is widely used in the downstream processing of proteins. Resolution of HIC is very good, but sometimes not as high as expected. Resolution values could be increased if good operating conditions were selected. In this paper we present a methodology for selecting good operating conditions. First, it is necessary to predict the dimensionless retention time (DRT) of each protein in the mixture. We use a correlation such as DRT=A+Bφ+Cφ2, where φ is the superficial hydrophobicity of the protein, which is calculated considering the hydrophobicity of the superficial amino acids using the Miyazawa–Jernigan scale. Considering that there was little interaction amongst proteins in a mixture at the concentrations investigated (2 g/l of each protein), the behaviour of the proteins in the mixture was considered to be similar to that of the individual proteins. Using simulations it was possible to test different operating conditions for the purification of a target protein from a mixture of proteins and it was possible to select ideal conditions. The methodology developed was also tested for the purification of a recombinant protein from a fermentation extract of yeast producing human superoxide dismutase and the results have been satisfactory. [Copyright &y& Elsevier]