Protein Type (protein + type)

Distribution by Scientific Domains


Selected Abstracts


Assessment of protein-incorporated arginine methylation in biological specimens by CZE UV-detection

ELECTROPHORESIS, Issue 23 2007
Angelo Zinellu Dr.
Abstract Protein arginine methyltransferases methylate post-translationally arginine residues in proteins to synthesize monomethylarginine (MMA), asymmetric dimethylarginine (ADMA), or symmetric dimethylarginine. Protein arginine methylation is involved in the regulation of signal transduction, RNA export, and cell proliferation. Moreover, upon proteolysis, arginines are released into the cytosol in which they exert important biological effects. Both MMA and ADMA are inhibitors of nitric oxide synthase and especially elevated levels of ADMA are associated with endothelial dysfunction and cardiovascular disease. Quantification of these analytes is commonly performed by HPLC after sample cleanup and derivatization. We propose a CE method in which these steps have been avoided and the procedure for sample preparation has been simplified. After acidic hydrolysis of proteins, samples were dried, resuspended in water, and directly injected in CE. A baseline separation of analytes was reached in a 60 cm×75,,m id uncoated silica capillary, by using a Tris-phosphate run buffer at pH,2.15. This method allows an accurate assessment of protein arginine methylation degree in different biological samples such as whole blood, plasma, red blood cells, cultured cells, and tissue. Moreover, its good sensitivity permits to evaluate the methylation of a single protein type after the opportune purification steps. A method applicability concerns both clinical laboratories, where the evaluation of blood protein from numerous samples could be rapidly performed, and research laboratories where the factors affecting the arginine protein methylation degree could be easily studied. [source]


BSEP and MDR3 haplotype structure in healthy Caucasians, primary biliary cirrhosis and primary sclerosing cholangitis

HEPATOLOGY, Issue 3 2004
Christiane Pauli-Magnus
Primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC) are characterized by a cholestatic pattern of liver damage, also observed in hereditary or acquired dysfunction of the canalicular membrane transporters bile salt export pump (BSEP, ABCB11) and multidrug resistance protein type 3 (MDR3, ABCB4). Controversy exists whether a genetically determined dysfunction of BSEP and MDR3 plays a pathogenic role in PBC and PSC. Therefore, 149 healthy Caucasian control individuals (control group) were compared to 76 PBC and 46 PSC patients with respect to genetic variations in BSEP and MDR3. Sequencing spanned ,10,000 bp including promoter and coding regions as well as 50,350 bp of flanking intronic regions. In all, 46 and 45 variants were identified in BSEP and MDR3, respectively. No differences between the groups were detected either in the total number of variants (BSEP: control group: 37, PBC: 37, PSC: 31; and MDR3: control group: 35; PBC: 32, PSC: 30), or in the allele frequency of the common variable sites. Furthermore, there were no significant differences in haplotype distribution and linkage disequilibrium. In conclusion, this study provides an analysis of BSEP and MDR3 variant segregation and haplotype structure in a Caucasian population. Although an impact of rare variants on BSEP and MDR3 function cannot be ruled out, our data do not support a strong role of BSEP and MDR3 genetic variations in the pathogenesis of PBC and PSC. (HEPATOLOGY 2004;39:779,791.) [source]


Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2009
Ke Chen
Abstract A computational model, IMP-TYPE, is proposed for the classification of five types of integral membrane proteins from protein sequence. The proposed model aims not only at providing accurate predictions but most importantly it incorporates interesting and transparent biological patterns. When contrasted with the best-performing existing models, IMP-TYPE reduces the error rates of these methods by 19 and 34% for two out-of-sample tests performed on benchmark datasets. Our empirical evaluations also show that the proposed method provides even bigger improvements, i.e., 29 and 45% error rate reductions, when predictions are performed for sequences that share low (40%) identity with sequences from the training dataset. We also show that IMP-TYPE can be used in a standalone mode, i.e., it duplicates significant majority of correct predictions provided by other leading methods, while providing additional correct predictions which are incorrectly classified by the other methods. Our method computes predictions using a Support Vector Machine classifier that takes feature-based encoded sequence as its input. The input feature set includes hydrophobic AA pairs, which were selected by utilizing a consensus of three feature selection algorithms. The hydrophobic residues that build up the AA pairs used by our method are shown to be associated with the formation of transmembrane helices in a few recent studies concerning integral membrane proteins. Our study also indicates that Met and Phe display a certain degree of hydrophobicity, which may be more crucial than their polarity or aromaticity when they occur in the transmembrane segments. This conclusion is supported by a recent study on potential of mean force for membrane protein folding and a study of scales for membrane propensity of amino acids. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source]


Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2008
Xuan Xiao
Abstract Using the pseudo amino acid (PseAA) composition to represent the sample of a protein can incorporate a considerable amount of sequence pattern information so as to improve the prediction quality for its structural or functional classification. However, how to optimally formulate the PseAA composition is an important problem yet to be solved. In this article the grey modeling approach is introduced that is particularly efficient in coping with complicated systems such as the one consisting of many proteins with different sequence orders and lengths. On the basis of the grey model, four coefficients derived from each of the protein sequences concerned are adopted for its PseAA components. The PseAA composition thus formulated is called the "grey-PseAA" composition that can catch the essence of a protein sequence and better reflect its overall pattern. In our study we have demonstrated that introduction of the grey-PseAA composition can remarkably enhance the success rates in predicting the protein structural class. It is anticipated that the concept of grey-PseAA composition can be also used to predict many other protein attributes, such as subcellular localization, membrane protein type, enzyme functional class, GPCR type, protease type, among many others. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008. [source]


Using pseudo amino acid composition to predict protein structural classes: Approached with complexity measure factor

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2006
Xuan Xiao
Abstract The structural class is an important feature widely used to characterize the overall folding type of a protein. How to improve the prediction quality for protein structural classification by effectively incorporating the sequence-order effects is an important and challenging problem. Based on the concept of the pseudo amino acid composition [Chou, K. C. Proteins Struct Funct Genet 2001, 43, 246; Erratum: Proteins Struct Funct Genet 2001, 44, 60], a novel approach for measuring the complexity of a protein sequence was introduced. The advantage by incorporating the complexity measure factor into the pseudo amino acid composition as one of its components is that it can catch the essence of the overall sequence pattern of a protein and hence more effectively reflect its sequence-order effects. It was demonstrated thru the jackknife crossvalidation test that the overall success rate by the new approach was significantly higher than those by the others. It has not escaped our notice that the introduction of the complexity measure factor can also be used to improve the prediction quality for, among many other protein attributes, subcellular localization, enzyme family class, membrane protein type, and G-protein couple receptor type. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 478,482, 2006 [source]


Heat-induced Changes in Angel Food Cakes Containing Egg-white Protein or Whey Protein Isolate

JOURNAL OF FOOD SCIENCE, Issue 8 2002
C.W. Pernell
ABSTRACT: Angel food cakes made from egg white or whey protein foams were compared. Cakes were evaluated based on final volume, dynamic volume change, and rheological transitions during baking. Cake expansion during baking was a function of protein concentration regardless of protein type. Cakes containing whey proteins had a lower ability to prevent collapse once starch gelatinization started during baking. Heat-treating whey proteins or adding xanthan gum increases cake volume, but not to the extent of egg-white proteins. Cakes containing egg-white proteins became more elastic at 60 to 85 °C than those containing whey proteins, indicating physical differences in the heat-set protein foam network associated with protein type. [source]


CONSUMER PERCEPTION OF WHEY AND SOY PROTEIN IN MEAL REPLACEMENT PRODUCTS

JOURNAL OF SENSORY STUDIES, Issue 3 2008
JESSICA L. CHILDS
ABSTRACT Meal replacement products including protein bars, shakes and powdered drinks have increased in demand and sales. The objective of this study was to assess the consumer perception of protein content and type and product claims for meal replacement beverages and bars. The impact of exercise frequency on product perception was also investigated. Focus groups were conducted with exercisers and nonexercisers. An adaptive conjoint analysis survey was subsequently developed and conducted (n = 138 consumers, ages 18,35 years). Relative importance of product attributes was determined through a realistic trade-off scenario. Utility scores were extracted and rescaled by the zero-centered differences method, and two-way analysis of variance was conducted to identify the differences between exercise frequency and product attributes. Both groups preferred bars to beverages, and no clear preferences were observed for protein type, which was consistent with focus group results of low knowledge/understanding of specific proteins. All respondents valued the products with low-fat/fat-free, calcium, all-natural, protein, vitamin/mineral, heart health and muscle-building claims. Exercisers viewed muscle-building claims as more important than nonexercisers. Nonexercisers viewed heart health, calcium and vitamin/mineral claims as more important than exercisers. Three distinct consumer clusters were identified, and both exercise groups were found in all three clusters, although exercise frequency influenced membership in two of the three clusters (P < 0.05). These findings can be used to develop and market meal replacement products to specific consumer groups while leveraging their specific and unique needs. PRACTICAL APPLICATIONS Conjoint analysis provides a useful model of how consumers think during the purchase process and an understanding of the motivation for purchase through the testing of possible claims or product attributes. By applying this method to the purchase process of meal replacement bars and beverages, those in the field of development of these products can benefit from this information by being able to understand the motivation for purchase by the targeted consumer. [source]


Protein Sequences as Literature Text

MACROMOLECULAR THEORY AND SIMULATIONS, Issue 5 2006
Valentina V. Vasilevskaya
Abstract Summary: We have performed analysis of protein sequences treating them as texts written in a "protein" language. We have shown that repeating patterns (words) of various lengths can be identified in these sequences. It was found that the maximum word lengths are different for proteins belonging to different classes; therefore, the corresponding values can be used to characterize the protein type. The suggested technique was first applied to analyze (decompose into words) normal (literature) texts written as a gapless symbolic sequence without spaces and punctuation marks. The tests using fiction, scientific, and popular scientific English texts proved the relative efficiency of the technique. Maximum word length for various proteins: ,fibrillar proteins, ,globular proteins, ,membrane proteins. [source]


Role of protein and carbohydrate sources on acute appetite responses in lean and overweight men

NUTRITION & DIETETICS, Issue 2008
Jane BOWEN
Abstract Dietary protein induces greater satiety compared with carbohydrate in lean subjects, which may involve appetite-regulatory gut hormones. Little is known about the duration of effect, influence of protein and carbohydrate source and relevance to non-lean individuals. We compared the effect of various dietary proteins and carbohydrates on post-prandial appetite ratings, ad libitum energy intake (EI) and appetite hormones in lean and overweight men. Three randomised double-blinded cross-over studies examined appetite response (appetite ratings, ghrelin, glucagon-like peptide-1 (GLP-1) and cholecystokinin) to liquid preloads over three to four hours followed by a buffet meal to assess ad libitum EI. The 1-MJ preloads contained ,55 g of protein (whey, casein, soy and gluten), carbohydrate (glucose, lactose and fructose) or combined whey/fructose. EI was 10% higher following glucose preloads compared with protein preloads, observed at three hours but not four hours. Protein ingestion was followed by prolonged elevation of cholecystokinin and GLP-1 (two hours) and suppression of ghrelin (three to four hours) compared with glucose and independent of protein type. Replacing some whey with fructose attenuated the effect of protein on these hormones. Treatment effects on EI and appetite hormones were independent of bodyweight status, despite higher GLP-1 and lower ghrelin in overweight subjects. Protein-rich liquid preloads reduce EI over three hours in overweight men compared with glucose. These findings suggest a potential application for protein-rich drinks and/or foods to facilitate reduced EI. Future studies should explore additional dietary manipulations that may enhance this relationship, and confirm these effects within the context of energy-restricted dietary patterns. [source]


Fishing new proteins in the twilight zone of genomes: The test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria

PROTEIN SCIENCE, Issue 6 2003
Rita Casadio
Abstract We address the problem of clustering the whole protein content of genomes into three different categories,globular, all-,, and all-, membrane proteins,with the aim of fishing new membrane proteins in the pool of nonannotated proteins (twilight zone). The focus is then mainly on outer membrane proteins. This is performed by using an integrated suite of programs (Hunter) specifically developed for predicting the occurrence of signal peptides in proteins of Gram-negative bacteria and the topography of all-, and all-, membrane proteins. Hunter is tested on the well and partially annotated proteins (2160 and 760, respectively) of Escherichia coli K 12 scoring as high as 95.6% in the correct assignment of each chain to the category. Of the remaining 1253 nonannotated sequences, 1099 are predicted globular, 136 are all-,, and 18 are all-, membrane proteins. In Escherichia coli 0157:H7 we filtered 1901 nonannotated proteins. Our analysis classifies 1564 globular chains, 327 inner membrane proteins, and 10 outer membrane proteins. With Hunter, new membrane proteins are added to the list of putative membrane proteins of Gram-negative bacteria. The content of outer membrane proteins per genome (nine are analyzed) ranges from 1.5% to 2.4%, and it is one order of magnitude lower than that of inner membrane proteins. The finding is particularly relevant when it is considered that this is the first large-scale analysis based on validated tools that can predict the content of outer membrane proteins in a genome and can allow cross-comparison of the same protein type between different species. [source]


Expression of Functional Recombinant Mussel Adhesive Protein Type 3A in Escherichia coli

BIOTECHNOLOGY PROGRESS, Issue 3 2005
Dong Soo Hwang
Mussel adhesive proteins, including the 20-plus variants of foot protein type 3 (fp-3), have been suggested as potential environmentally friendly adhesives for use in aqueous conditions and in medicine. Here we report the novel production of a recombinant Mytilus galloprovincialis foot protein type 3 variant A (Mgfp-3A) fused with a hexahistidine affinity ligand in Escherichia coli and its ,99% purification with affinity chromatography. Recombinant Mgfp-3A showed a superior purification yield and better apparent solubility in 5% acetic acid (prerequisites for large-scale production and practical use) compared to those of the previously reported recombinant M. galloprovincialis foot protein type 5 (Mgfp-5). The adsorption abilities and adhesion forces of purified recombinant Mgfp-3A were compared with those of Cell-Tak (a commercial mussel extract adhesive) and recombinant Mgfp-5 using quartz crystal microbalance analysis and modified atomic force microscopy, respectively. These assays showed that the adhesive ability of recombinant Mgfp-3A was comparable to that of Cell-Tak but lower than that of recombinant Mgfp-5. Collectively, these results indicate that recombinant Mgfp-3A may be useful as a commercial bioadhesive or an adhesive ingredient in medical or underwater environments. [source]


Prediction of coenzyme specificity in dehydrogenases/ reductases

FEBS JOURNAL, Issue 6 2006
A hidden Markov model-based method, its application on complete genomes
Dehydrogenases and reductases are enzymes of fundamental metabolic importance that often adopt a specific structure known as the Rossmann fold. This fold, consisting of a six-stranded ,-sheet surrounded by ,-helices, is responsible for coenzyme binding. We have developed a method to identify Rossmann folds and predict their coenzyme specificity (NAD, NADP or FAD) using only the amino acid sequence as input. The method is based upon hidden Markov models and sequence pattern analysis. The prediction sensitivity is 79% and the selectivity close to 100%. The method was applied on a set of 68 genomes, representing the three kingdoms archaea, bacteria and eukaryota. In prokaryotes, 3% of the genes were found to code for Rossmann-fold proteins, while the corresponding ratio in eukaryotes is only around 1%. In all genomes, NAD is the most preferred cofactor (41,49%), followed by NADP with 30,38%, while FAD is the least preferred cofactor (21%). However, the NAD preponderance over NADP is most pronounced in archaea, and least in eukaryotes. In all three kingdoms, only 3,8% of the Rossmann proteins are predicted to have more than one membrane-spanning segment, which is much lower than the frequency of membrane proteins in general. Analysis of the major protein types in eukaryotes reveals that the most common type (26%) of the Rossmann proteins are short-chain dehydrogenases/reductases. In addition, the identified Rossmann proteins were analyzed with respect to further protein types, enzyme classes and redundancy. The described method is available at http://www.ifm.liu.se/bioinfo, where the preferred coenzyme and its binding region are predicted given an amino acid sequence as input. [source]


Comparison of the protein composition of breast milk and the nutrient intake between Thai and Japanese mothers

NURSING & HEALTH SCIENCES, Issue 2 2009
Venus Leelahakul dsc
Abstract This study compared the protein composition of breast milk and the nutrient intake between Thai and Japanese lactating mothers. The breast milk was collected from 15 Thai and 14 Japanese mothers at the fifth day post-partum. Twenty-four-hour dietary records were performed from the second-to-the-fourth day post-partum. The nutrient intake was calculated by using the nutrient content of a food table. The protein composition of the whey was separated by gel electrophoresis and was identified by mass spectrometry and two-dimensional electrophoresis. The results showed that the concentrations of the major protein types in the breast milk were not significantly different between the two groups. The concentrations of the minor protein types varied markedly with the individuals, with higher concentrations in the breast milk of the Thai mothers. There were no significant differences in terms of the energy and protein intake; however, the sources of energy were different. The results indicate that the total protein and lactoferrin concentrations in the breast milk could be predicted by the maternal daily energy and fat intake. [source]