利用伪氨基酸组分和支持向量机预测抗冻蛋白

抗冻蛋白是一类具有提高生物抗冻能力的蛋白质。抗冻蛋白能够特异性的与冰晶相结合,进而阻止体液内冰核的形成与生长。因此,对抗冻蛋白的生物信息学研究对生物工程发展。提高作物抗冻性有重要的推动作用。本文采用由400条抗冻蛋白序列和400条非抗冻蛋白序列构成数据集,以伪氨基酸组分为特征,利用支持向量机分类算法预测抗冻蛋白,对训练集预测精度达到91．3％,对测试集预测精度达到78．8％。该结果证明伪氨基酸组分能够很好的反映抗冻蛋白特性,并能够用于预测抗冻蛋白。     

Molecular weight and amino acid composition of purified spinach beet phenolase

The purification of spinach beet phenolase has been modified to include equilibration of the crude macerate with 0.5% cetyl-trimethylammonium bromide a     

Preparative separation and amino acid composition of neurofilament triplet proteins

Abstract: Intact neurofilaments were isolated from bovine spinal cord white matter, washed by sedimentation in 0.1 m -NaCl, and extracted with 8 m -urea. Solubilized neurofilament triplet proteins of molecular weights approximately 68,000 (P68), 150,000 (P150), and 200,000 (P200) were purified by preparative electrophoresis, using an LKB 7900 Uniphor apparatus. The method provides for an enhanced yield of purified protein and has markedly reduced admixture of electrophoresed protein with acrylamide and associated protein contaminants. Amino acid compositions of the purified neurofilament triplet proteins are reported and compared.     

Dietary deficiencies of single amino acids: Whole-body amino acid composition of adult rats

Abstract

To ascertain whether chronic amino acid deficiency alters the amino acid composition of the body, 44 adult female rats were randomly allocated to one of 11 treatments which included one control group, ingesting an adequate diet with balanced protein, and ten deficient groups in which one group received protein-deficient diets and the other groups consumed diets each deficient in a single essential amino acid. The degree of deficiency was adjusted to achieve a gradual decline in body weight to 85% of the initial weight and was then adjusted so that this weight was maintained until the end of the experiment at 93 days, when the rats were killed. Deficient rats had lower absolute weights of liver, gastrointestinal tract and muscle than animals given the adequate diet but greater relative weights (% of body weight) of heart and kidneys. There were no significant differences amongst groups in percentages of lipid, nitrogen, protein plus lipid or dry matter. Chronic marginal amino acid deficiencies did not selectively alter amino acid composition.     

Predicting the cofactors of oxidoreductases based on amino acid composition distribution and Chou's amphiphilic pseudo-amino acid composition

Predicting the cofactors of oxidoreductases plays an important role in inferring their catalytic mechanism. Feature extraction is a critical part in the prediction systems, requiring raw sequence data to be transformed into appropriate numerical feature vectors while minimizing information loss. In this paper, we present an amino acid composition distribution method for extracting useful features from primary sequence, and the k-nearest neighbor was used as the classifier. The overall prediction accuracy evaluated by the 10-fold cross-validation reached 90.74%. Comparing our method with other eight feature extraction methods, the improvement of the overall prediction accuracy ranged from 3.49% to 15.74%. Our experimental results confirm that the method we proposed is very useful and may be used for other bioinformatical predictions. Interestingly, when features extracted by our method and Chou's amphiphilic pseudo-amino acid composition were combined, the overall accuracy could reach 92.53%.     

Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species

We studied the correlations between amino acid composition and mononucleotide and dinucleotide frequencies in 115 bacterial genomes of varying G+C content. Observed amino acid frequencies were compared with those expected from the actual mononucleotide and dinucleotide frequencies. Both mononucleotide and dinucleotide frequencies correlate well with the amino acid frequency, with dinucleotide frequencies doing so better. Despite the strong correlations, some of the observed amino acid frequencies, in particular for Arg, Val, Asp, Glu, Ser, and Cys, were consistently different from predicted values in all genomes. We suggest that this variation from predicted values is a consequence of selection pressure at the level of amino acids, while the close correspondence to the predictions in residues such as Thr, Phe, Lys, and Asn arises only from mutation and selection pressure at the level of the nucleic acid sequences.     

半滑舌鳎受精卵、卵黄囊仔鱼和开口仔鱼氨基酸及脂肪酸的变化

采用气相色谱仪和氨基酸分析仪测定了半滑舌鳎(Cynoglossus semilaevis)受精卵、卵黄囊仔鱼和开口仔鱼的氨基酸与脂肪酸组成的变化。结果表明:总氨基酸组成在受精卵和卵黄囊仔鱼之间变化明显,但是在卵黄囊仔鱼和开口仔鱼之间只有细微的变化。开口仔鱼与其摄食的轮虫的总必需氨基酸组成相关。受精卵、卵黄囊仔鱼、开口仔鱼的游离氨基酸含量分别为139 mg/g、3.6 mg/g和2.5 mg/g,占总氨基酸含量的22.3%、3.6%和2.5%。饱和脂肪酸的总量从受精卵到卵黄囊仔鱼明显下降,但是发育到开口仔鱼含量无显著变化。单不饱和脂肪酸和多不饱和脂肪酸的总量在不同发育阶段无显著变化,而EPA和DHA的含量从卵黄囊仔鱼到开口仔鱼有明显下降。这表明在早期发育阶段半滑舌鳎主要利用饱和脂肪酸作为能量代谢的基质,对饱和脂肪酸的利用程度大于单不饱和脂肪酸和多不饱和脂肪酸。半滑舌鳎似乎需要长链的多不饱和脂肪酸如EPA、DHA和ARA。     

Protein location prediction using atomic composition and global features of the amino acid sequence

Subcellular location of protein is constructive information in determining its function, screening for drug candidates, vaccine design, annotation of gene products and in selecting relevant proteins for further studies. Computational prediction of subcellular localization deals with predicting the location of a protein from its amino acid sequence. For a computational localization prediction method to be more accurate, it should exploit all possible relevant biological features that contribute to the subcellular localization. In this work, we extracted the biological features from the full length protein sequence to incorporate more biological information. A new biological feature, distribution of atomic composition is effectively used with, multiple physiochemical properties, amino acid composition, three part amino acid composition, and sequence similarity for predicting the subcellular location of the protein. Support Vector Machines are designed for four modules and prediction is made by a weighted voting system. Our system makes prediction with an accuracy of 100, 82.47, 88.81 for self-consistency test, jackknife test and independent data test respectively. Our results provide evidence that the prediction based on the biological features derived from the full length amino acid sequence gives better accuracy than those derived from N-terminal alone. Considering the features as a distribution within the entire sequence will bring out underlying property distribution to a greater detail to enhance the prediction accuracy.     

Unexpected amino acid composition of modern Reptilia and its implications in molecular mechanisms of dinosaur extinction

Dinosaur extinction is a great challenge to evolutionary biology. Although accumulating evidence suggests that an abrupt change of environment, such as a long period of low temperature induced by asteroid hit or other disasters, may be responsible for dinosaur extinction, little is known about the underlying molecular mechanisms. By analyzing the amino acid compositions of 13 biological classes, we found that the charged amino acid content of modern Reptilia, the sibling of dinosaur, is strikingly different from those of other classes, which inspires us to propose a possible molecular mechanism for dinosaur extinction.     

Evaluation of the Chinese indigenous pig breed Dahe and crossbred Dawu for growth and carcass characteristics, organ weight, meat quality and intramuscular fatty acid and amino acid composition

The objectives of the experiment were to evaluate growth and carcass characteristics, organ weight, meat quality and intramuscular fatty acid (FA) and amino acid composition between the Chinese indigenous pig breed Dahe and the crossbred Dawu. The Dahe pigs had lower average daily gain (P < 0.001) and a higher feed conversion ratio (P < 0.001) compared with the Dawu pigs. The Dahe pigs contained less lean meat percentage (P < 0.001) and more carcass fat percentage (P < 0.001) compared with the Dawu pigs. For organ weight, the Dahe pigs had lower relative heart weight and small intestine weight, respectively, compared with that of the Dawu pigs (P < 0.001). In addition, the Dahe pigs showed higher pH values (at 45 min and 24 h, P < 0.001 and P < 0.001, respectively), higher Marbling score (P < 0.05), lower Minolta L values (at 45 min and 24 h, P < 0.001 and P < 0.05, respectively) and lower muscle fiber area (P < 0.05) than did the Dawu pigs. C18:1, C16:0, C18:0 and C18:2 were the main FAs and nine essential amino acids were found in the Longissimus dorsi of the two breeds.     

Conservation of the basic pattern of cellular amino acid composition of archaeobacteria during biological evolution and the putative amino acid composition of primitive life forms

Summary. Previous studies showed that the cellular amino acid composition obtained by amino acid analysis of whole cells, differs such as eubacteria, protozoa, fungi and mammalian cells. These results suggest that the difference in the cellular amino acid composition reflects biological changes as the result of evolution. However, the basic pattern of cellular amino acid composition was relatively constant in all organisms examined. In the present study, we examined archaeobacteria, because they are considered important in understanding the relationship between biological evolution and cellular amino acid composition. The cellular amino acid compositions of Archaeoglobus fulgidus, Pyrococcus horikoshii, Methanobacterium thermoautotrophicum and Methanococcus jannaschii differed slightly from each other, but were similar to those determined from codon usage data, based on the complete genomes. Thus, the cellular amino acid composition reflects biological evolution. We suggest that primitive forms of life appearing on earth at the end of prebiotic evolution had a similar-cellular amino acid composition. Received November 28, 2000 Accepted January 30, 2001     

Relationship between G + C in silent sites of codons and amino acid composition of human proteins

Summary We have investigated the relationship between the G + C content of silent (synonymous) sites in codons and the amino acid composition of encoded proteins for approximately 1,600 human genes. There are positive correlations between silent site G + C and the proportions of codons for Arg, Pro, Ala, Trp, His, Gln, and Leu and negative ones for Tyr, Phe, Asn, Ile, Lys, Asp, Thr, and Glu. The median proteins coded by groups of genes that differ in silent-site G + C content also differ in amino acid composition, as do some proteins coded by homologous genes. The pattern of compositional change can be largely explained by directional mutation pressure, the genetic code, and differences in the frequencies of accepted amino acid substitutions; the shifts in protein composition are likely to be selectively neutral.Offprint requests to: D.W. Collins     

The classification of various organisms according to the free amino acid composition change as the result of biological evolution

Summary. The free amino acid compositions in archaeobacteria, eubacteria, protozoa, blue-green alga, green alga, slime mold, plants and mammalian cells were analyzed, to investigate whether changes in their free amino acid compositions reflect biological evolution. Cell homogenates were treated with 80–90% ethanol to separate cellular proteins and free amino acids contained in the cells. Different patterns of the free amino acid compositions were observed in the various organisms. Characteristic differences were observed between plant and mammalian cells, and between archaeobacteria and eubacteria. The patterns of the free amino acid composition in blue-green alga, green alga, protozoa and slime mold differed from each other and from those of eubacteria and archaeobacteria. Rat hepatoma cells (R-Y121B) were cultured in Eagle's minimum essential medium (MEM) containing 5% serum or in a modified MEM lacking arginine, tyrosine and glutamine. No significant difference in the free amino acid composition was observed between the two cell groups cultured under two different conditions. It is suggested that the free amino acid composition reflects apparent biological changes as the result of evolution. Received July 5, 2000 Accepted July 31, 2001     

胞外多肽信使的氨基酸偏好特征研究及应用

植物细胞外多肽信使已经被证实是植物信号转导中重要的第一信使。通过运用生物信息学的方法,分析比较了已知的植物、动物及微生物的胞外多肽信使的氨基酸序列,发现这些来自不同种的胞外多肽信使具有共同的氨基酸偏好特征。利用在线工具对胞外多肽信使的氨基酸偏好特征进行了验证,并根据细胞外多肽信使的氨基酸偏好特征推测了新的植物胞外多肽信使,这些结果对发现新的植物胞外多肽信使将会有所帮助。     

基于氨基酸和二肽组成的蛋白质四级结构分类研究

基于最近邻居算法,从蛋白质一级序列出发,利用蛋白质序列氨基酸组成、二肤组成以及混合组成方法对蛋白质单聚体、二聚体、三聚体、四聚体、五聚体、六聚体和八聚体进行分类研究。结果表明:采用二肽组成编码方法的预洲效果最好,Jackknife检验和独立测试集检验的总体预测精度分别达到90.83%和95.48%,比相同数据集上基于伪氨基酸组成和组分耦合预测的方法提高了12和15个百分点;特别是对于五聚体蛋白,预测精度分别提高了90和50个百分点;说明二肽组成对于蛋白质四级结构分类研究是一种非常有效的特征提取方法。     

Nonrandom amino acid substitution and estimation of the number of nucleotide substitutions in evolution

Summary A method of estimating the number of nucleotide substitutions from amino acid sequence data is developed by using Dayhoff's mutation probability matrix. This method takes into account the effect of nonrandom amino acid substitutions and gives an estimate which is similar to the value obtained by Fitch's counting method, but larger than the estimate obtained under the assumption of random substitutions (Jukes and Cantor's formula). Computer simulations based on Dayhoff's mutation probability matrix have suggested that Jukes and Holmquist's method of estimating the number of nucleotide substitutions gives an overestimate when amino acid substitution is not random and the variance of the estimate is generally very large. It is also shown that when the number of nucleotide substitutions is small, this method tends to give an overestimate even when amino acid substitution is purely at random.     

Regulation of amino acid transport in growing cells of Streptomyces hydrogenans

(1) The active uptake of different amino acids by growing cells of Streptomyces hydrogenans was shown to be correlated with the physiological age of the cells. During the lag phase of growth the transport capacity increased and attained its highest level when the growth rate was maximum. During further growth the transport capacity declined progressively. The lowest transport activity was observed when the culture shifted into the stationary growth phase. (2) Such modulation of transport capacity was independent on the presence or absence of amino acids in the growth medium of the cells. (3) The size and the composition of the pool of free intracellular amino acids was also undergoing substantial variations during the growth cycle of the culture. In the lag phase, the levels of all amino acids decreased markedly and attained their lowest values at the end of this phase. During further growth the pool size was slowly replenished. (4) Removal of the pool resulted in a considerable gain of transport capacity. Therefore, it was concluded that active amino acid transport in growing Streptomyces hydrogenans is under feedback control by intracellular amino acids. (5) Quantitatively, the modulation of the pool size could not fully account for the variation of the transport capacity. Since a pool-independent stimulation of transport was found to be correlated with the increase of the growth rate of the cells, the possibility is discussed that the stimulation of transport is either due to increased levels of distinct RNA species, which might provide positive feedback signals for transport, or by increased rates of de novo synthesis of transport limiting proteins.List of Abbreviations AIB 2-aminoisobutyric acid - CM complete medium - MM mineral medium     

Unique amino acid composition of proteins in halophilic bacteria

The amino acid compositions of proteins from halophilic archaea were compared with those from non-halophilic mesophiles and thermophiles, in terms of the protein surface and interior, on a genome-wide scale. As we previously reported for proteins from thermophiles, a biased amino acid composition also exists in halophiles, in which an abundance of acidic residues was found on the protein surface as compared to the interior. This general feature did not seem to depend on the individual protein structures, but was applicable to all proteins encoded within the entire genome. Unique protein surface compositions are common in both halophiles and thermophiles. Statistical tests have shown that significant surface compositional differences exist among halophiles, non-halophiles, and thermophiles, while the interior composition within each of the three types of organisms does not significantly differ. Although thermophilic proteins have an almost equal abundance of both acidic and basic residues, a large excess of acidic residues in halophilic proteins seems to be compensated by fewer basic residues. Aspartic acid, lysine, asparagine, alanine, and threonine significantly contributed to the compositional differences of halophiles from meso- and thermophiles. Among them, however, only aspartic acid deviated largely from the expected amount estimated from the dinucleotide composition of the genomic DNA sequence of the halophile, which has an extremely high G+C content (68%). Thus, the other residues with large deviations (Lys, Ala, etc.) from their non-halophilic frequencies could have arisen merely as "dragging effects" caused by the compositional shift of the DNA, which would have changed to increase principally the fraction of aspartic acid alone.     

The effects of guanine and cytosine variation on dinucleotide frequency and amino acid composition in the human genome

Summary One hundred twelve human DNA sequences were analyzed with respect to dinucleotide frequency and amino acid composition. The variation in guanine and cytosine (G+C) content revealed: (1) at 2–3 and 3-1 doublet positions CG discrimination is attenuated at high G+C, but TA disfavor is enhanced, and (2) several amino acids are subject to G+C change. These findings have been reported in part for collections of sequences from various species. The present study confirms that in a single organism-the human-the G+C effects do exist. Aspects of the argument that connects G+C with protein thermal stability are also discussed.     

Amino acid composition and the evolutionary rates of protein-coding genes

Summary Based on the rates of amino acid substitution for 60 mammalian genes of 50 codons or more, it is shown that the rate of amino acid substitution of a protein is correlated with its amino acid composition. In particular, the content of glycine residues is negatively correlated with the rate of amino acid substitution, and this content alone explains about 38% of the total variation in amino acid substitution rates among different protein families. The propensity of a polypeptide to evolve fast or slowly may be predicted from an index or indices of protein mutability directly derivable from the amino acid composition. The propensity of an amino acid to remain conserved during evolutionary times depends not so much on its being features prominently in active sites, but on its stability index, defined as the mean chemical distance [R. Grantham (1974) Science 185862–864] between the amino acid and its mutational derivatives produced by single-nucleotide substitutions. Functional constraints related to active and binding sites of proteins play only a minor role in determining the overall rate of amino acid substitution. The importance of amino acid composition in determining rates of substitution is illustrated with examples involving cytochrome c, cytochrome b₅,ras-related genes, the calmodulin protein family, and fibrinopeptides.