Evolutionary divergence in the two kinds of subunits of ribulose diphosphate carboxylase isolated from different species ofNicotiana

A ² analysis was made of previously reported values for the amino acid composition of the large and small subunits of ribulose diphosphate carboxylase (E.C. 4, 1, 1, 39) isolated from five species ofNicotiana. The distributions of these values were then compared with published values for hemoglobin chains and cytochromec's of diverse origins. It was concluded that evolutionary diversity in the large and small subunits of RuDP carboxylase occurs even within the limited taxonomic category of the genusNicotiana. The large subunit was as stable towards mutation during evolution as the chains and cytochromes, whereas the small subunit was much less stable. The hypothesis is discussed that the large subunit played a more significant role than the small subunit in the enzyme function and/or structural integrity of the oligomeric protein. It was also speculated that the addition of small subunits to the molecule, which may have been a recent evolutionary event, enables the fixation of many evolutionarily favorable mutations. Thus, survival of the enzymatic activity in changing environments is favored.     

野苋菜的氨基酸含量与营养评价

野苋菜含有１８种氨基酸,其中有营养必需的８种氨基酸。含硫氨基酸ＡＡＳ＝０．５１,为第一限制氨基酸。Ｅ／Ｅ＋Ｎ＝４１．６％,Ｅ／Ｎ＝０．７１,接近ＷＨＯ／ＦＡＯ提出的参考蛋白模式。     

鱼类抗冻蛋白的研究 Ⅰ.黄盖鲽血清抗冻蛋白的特性及分离

本文首次报道了中国沿海鱼类中有含抗冻蛋白的鱼种存在。从产于中国黄海的黄盖鲽血清中分离提纯了抗冻蛋白,并对其进行了研究分析。黄盖鲽抗冻蛋白具有十分明显的降低血液冰点的作用,存在特征性的热滞现象。该蛋白的分子量为4500道尔顿左右,经Sephsdex G-25柱层析及高效液相色谱逆向层析法二步提纯。氨基酸组成分析结果表明它含有60％左右的丙氨酸。抗冻蛋白产生于黄盖鲽的冬季血清中,而不存在于夏季血清中。从肝脏中提取mRNA。Northern杂交证实,黄盖鲽抗冻蛋白是一类在转录水平上受到调控的蛋白。该蛋白的提纯及对其特性的研究,对研究抗冻基因的克隆及表达都具有重要的意义。     

PPS: A computing engine to find Palindromes in all Protein sequences

The primary structure of a protein molecule comprises a linear chain of amino acid residues. Certain parts of this linear chain are unique in nature and function. They can be classified under different categories and their roles studied in detail. Two such unique categories are the palindromic sequences and the Single Amino Acid Repeats (SAARs), which plays a major role in the structure, function and evolution of the protein molecule. In spite of their presence in various protein sequences, palindromes have not yet been investigated in detail. Thus, to enable a comprehensive understanding of these sequences, a computing engine, PPS, has been developed. The users can search the occurrences of palindromes and SAARs in all the protein sequences available in various databases and can view the three-dimensional structures (in case it is available in the known three-dimensional protein structures deposited to the Protein Data Bank) using the graphics plug-in Jmol. The proposed server is the first of its kind and can be freely accessed through the World Wide Web.

Availability

URL http://pranag.physics.iisc.ernet.in/pps/     

Using support vector machines to distinguish enzymes: Approached by incorporating wavelet transform

The enzymatic attributes of newly found protein sequences are usually determined either by biochemical analysis of eukaryotic and prokaryotic genomes or by microarray chips. These experimental methods are both time-consuming and costly. With the explosion of protein sequences registered in the databanks, it is highly desirable to develop an automated method to identify whether a given new sequence belongs to enzyme or non-enzyme. The discrete wavelet transform (DWT) and support vector machine (SVM) have been used in this study for distinguishing enzyme structures from non-enzymes. The networks have been trained and tested on two datasets of proteins with different wavelet basis functions, decomposition scales and hydrophobicity data types. Maximum accuracy has been obtained using SVM with a wavelet function of Bior2.4, a decomposition scale j=5, and Kyte-Doolittle hydrophobicity scales. The results obtained by the self-consistency test, jackknife test and independent dataset test are encouraging, which indicates that the proposed method can be employed as a useful assistant technique for distinguishing enzymes from non-enzymes.     

几种海洋微藻的氨基酸含量

分析测定分属硅藻,绿藻和蓝藻的７种海洋饵料微藻氮和氨基酸含量。氮含量范围为４．０４％～９．８６％,总氨基酸中共测出１７种氨基酸,含量范围为１．２３％～９．７４％。名藻的总氨基酸含量顺序与氮含量相同     

γ-Glutamyl semialdehyde and 2-amino-adipic semialdehyde: biomarkers of oxidative damage to proteins

Reactive oxygen species are formed in the body by several natural processes and by induced oxidative stress. The reactive oxygen species may react with the various biomolecules of the body, including proteins. In order to assess the impact of oxidative damage to proteins, we have tried to identify oxidized amino acids in blood proteins which might serve as biomarkers of oxidative damage. When oxidative damage is induced into bovine serum albumin by metal-catalysed oxidation systems, the aldehyde groups formed can be derivatized by fluoresceinamine (FINH₂). Following acid hydrolysis of FINH₂-derivatized protein, two major oxidation products, γ-glutamyl semialdehyde (GGS) and 2-amino-adipic semialdehyde (AAS), were found and identified by HPLC and MS. Isolation and identification of oxidized amino acids from homopolymers (poly-Arg,-Pro,-Lys,-Trp or -Leu) confirmed that GGS can originate from Arg or Pro, while AAS is an oxidation product of Lys. When oxidative stress was induced in rats by treatments with t-butyl hydroperoxide or acrolein, rat plasma protein levels of GGS and AAS were found to be significantly higher compared with control rats. The AAS-content in serum albumin or in total plasma proteins collected from eight different mammalian species was found to be inversely proportional to their maximum lifespan potential. The content of AAS in plasma proteins of untreated adult rats showed a positive correlation with the age of the rat. In young rats a negative correlation with age was found for both GGS and AAS. We conclude that GGS or AAS may be useful novel biomarkers of oxidative damage to proteins in vivo.     

Protein Architecture Chronology Deduced From Structures of Amino Acid Synthases

Abstract

Inferring the protein architecture chronology is one of central topics in origin of life study and has been given much attention. Based on an amino acid evolutionary model that late amino acids were bio-synthesized prior to early counterparts, we addressed the issue by examining the structures of amino acid synthases. Despite the limited structural information on amino acid synthases, our deduction revealed that α/β was the oldest protein class, which is in good agreement with the prior fold-usage-based conclusion.     

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

The canonical set of amino acids leads to an exceptionally wide range of protein functionality. Nevertheless, the set of residues still imposes limitations on potential protein applications. The incorporation of noncanonical amino acids can enlarge this scope. There are two complementary approaches for the incorporation of noncanonical amino acids. For site-specific incorporation, in addition to the endogenous canonical translational machineries, an orthogonal aminoacyl-tRNA-synthetase-tRNA pair must be provided that does not interact with the canonical ones. Consequently, a codon that is not assigned to a canonical amino acid, usually a stop codon, is also required. This genetic code expansion enables the incorporation of a noncanonical amino acid at a single, given site within the protein. The here presented work describes residue-specific incorporation where the genetic code is reassigned within the endogenous translational system. The translation machinery accepts the noncanonical amino acid as a surrogate to incorporate it at canonically prescribed locations, i.e., all occurrences of a canonical amino acid in the protein are replaced by the noncanonical one. The incorporation of noncanonical amino acids can change the protein structure, causing considerably modified physical and chemical properties. Noncanonical amino acid analogs often act as cell growth inhibitors for expression hosts since they modify endogenous proteins, limiting in vivo protein production. In vivo incorporation of toxic noncanonical amino acids into proteins remains particularly challenging. Here, a cell-free approach for a complete replacement of L-arginine by the noncanonical amino acid L-canavanine is presented. It circumvents the inherent difficulties of in vivo expression. Additionally, a protocol to prepare target proteins for mass spectral analysis is included. It is shown that L-lysine can be replaced by L-hydroxy-lysine, albeit with lower efficiency. In principle, any noncanonical amino acid analog can be incorporated using the presented method as long as the endogenous in vitro translation system recognizes it.     

γ-Glutamyl semialdehyde and 2-amino-adipic semialdehyde: biomarkers of oxidative damage to proteins

Reactive oxygen species are formed in the body by several natural processes and by induced oxidative stress. The reactive oxygen species may react with the various biomolecules of the body, including proteins. In order to assess the impact of oxidative damage to proteins, we have tried to identify oxidized amino acids in blood proteins which might serve as biomarkers of oxidative damage. When oxidative damage is induced into bovine serum albumin by metal-catalysed oxidation systems, the aldehyde groups formed can be derivatized by fluoresceinamine (FINH₂). Following acid hydrolysis of FINH₂-derivatized protein, two major oxidation products, γ-glutamyl semialdehyde (GGS) and 2-amino-adipic semialdehyde (AAS), were found and identified by HPLC and MS. Isolation and identification of oxidized amino acids from homopolymers (poly-Arg,-Pro,-Lys,-Trp or -Leu) confirmed that GGS can originate from Arg or Pro, while AAS is an oxidation product of Lys. When oxidative stress was induced in rats by treatments with t-butyl hydroperoxide or acrolein, rat plasma protein levels of GGS and AAS were found to be significantly higher compared with control rats. The AAS-content in serum albumin or in total plasma proteins collected from eight different mammalian species was found to be inversely proportional to their maximum lifespan potential. The content of AAS in plasma proteins of untreated adult rats showed a positive correlation with the age of the rat. In young rats a negative correlation with age was found for both GGS and AAS. We conclude that GGS or AAS may be useful novel biomarkers of oxidative damage to proteins in vivo.     

灵芝氨基酸研究

采用日立８３５－５０型氨基酸自动分析仪,测定了泰山地区的五种灵芝成品的氨基酸含量。结果表明,除色氨酸被水解破坏而未检出外,其它１７种氨基酸含量丰富,其氨基酸的总含量最高为１２．８７％,低的为４．６７６％,并含有７种人体必需氨基酸,值得深度开发利用。     

基于序列疏水值震荡的折叠速率预测

蛋白质折叠速率的正确预测对理解蛋白质的折叠机理非常重要。本文从伪氨基酸组成的方法出发,提出利用序列疏水值震荡的方法来提取蛋白质氨基酸的序列顺序信息,建立线性回归模型进行折叠速率预测。该方法不需要蛋白质的任何二级结构、三级结构信息或结构类信息,可直接从序列对蛋白质折叠速率进行预测。对含有62个蛋白质的数据集,经过Jack．knife交互检验验证,相关系数达到0．804,表示折叠速率预测值与实验值有很好的相关性,说明了氨基酸序列信息对蛋白质折叠速率影响重要。同其他方法相比,本文的方法具有计算简单,输入参数少等特点。     

双丙磷测定方法的改进

本文探讨了用氨基酸自动分析仪测定生物除草剂双丙磷的方法。结果表明,本方法能有效克服干扰,回收率为９７～１０２％。变异系数０．６９～１．０％,线性相关系数为０．９９９８。     

Human Alanine-Glyoxylate Aminotransferase 2 Lowers Asymmetric Dimethylarginine and Protects from Inhibition of Nitric Oxide Production

Elevated blood concentrations of asymmetric dimethylarginine (ADMA), an endogenous inhibitor of nitric-oxide (NO) synthase, are found in association with diabetes, hypertension, congestive heart failure, and atherosclerosis. ADMA levels are controlled by dimethylarginine dimethylaminohydrolases (DDAHs), cytosolic enzymes that hydrolyze ADMA to citrulline and dimethylamine. ADMA also has been proposed to be regulated through an alternative pathway by alanine-glyoxylate aminotransferase 2 (AGXT2), a mitochondrial aminotransferase expressed primarily in the kidney. The goal of this study was to define the subcellular localization of human AGXT2 and test the hypothesis that overexpression of human AGXT2 protects from ADMA-induced inhibition in nitric oxide (NO) production. AGXT2 was cloned from human kidney cDNA and overexpressed in COS-7 cells and human umbilical vein endothelial cells with a C-terminal FLAG epitope tag. Mitochondrial localization of human AGXT2 was demonstrated by confocal microscopy and a 41-amino acid N-terminal mitochondrial cleavage sequence was delineated by N-terminal sequencing of the mature protein. Overexpression of human AGXT2 in the liver of C57BL/6 mice using an adenoviral expression vector produced significant decreases in ADMA levels in plasma and liver. Overexpression of human AGXT2 also protected endothelial cells from ADMA-mediated inhibition of NO production. We conclude that mitochondrially localized human AGXT2 is able to effectively metabolize ADMA in vivo resulting in decreased ADMA levels and improved endothelial NO production.     

The Allosteric Regulatory Mechanism of the Escherichia coli MetNI Methionine ATP Binding Cassette (ABC) Transporter

The MetNI methionine importer of Escherichia coli, an ATP binding cassette (ABC) transporter, uses the energy of ATP binding and hydrolysis to catalyze the high affinity uptake of d- and l-methionine. Early in vivo studies showed that the uptake of external methionine is repressed by the level of the internal methionine pool, a phenomenon termed transinhibition. Our understanding of the MetNI mechanism has thus far been limited to a series of crystal structures in an inward-facing conformation. To understand the molecular mechanism of transinhibition, we studied the kinetics of ATP hydrolysis using detergent-solubilized MetNI. We find that transinhibition is due to noncompetitive inhibition by l-methionine, much like a negative feedback loop. Thermodynamic analyses revealed two allosteric methionine binding sites per transporter. This quantitative analysis of transinhibition, the first to our knowledge for a structurally defined transporter, builds upon the previously proposed structurally based model for regulation. This mechanism of regulation at the transporter activity level could be applicable to not only ABC transporters but other types of membrane transporters as well.     

Crystal Structure and Mutational Analysis of Aminoacylhistidine Dipeptidase from Vibrio alginolyticus Reveal a New Architecture of M20 Metallopeptidases

Aminoacylhistidine dipeptidases (PepD, EC 3.4.13.3) belong to the family of M20 metallopeptidases from the metallopeptidase H clan that catalyze a broad range of dipeptide and tripeptide substrates, including l-carnosine and l-homocarnosine. Homocarnosine has been suggested as a precursor for the neurotransmitter γ-aminobutyric acid (GABA) and may mediate the antiseizure effects of GABAergic therapies. Here, we report the crystal structure of PepD from Vibrio alginolyticus and the results of mutational analysis of substrate-binding residues in the C-terminal as well as substrate specificity of the PepD catalytic domain-alone truncated protein PepD^CAT. The structure of PepD was found to exist as a homodimer, in which each monomer comprises a catalytic domain containing two zinc ions at the active site center for its hydrolytic function and a lid domain utilizing hydrogen bonds between helices to form the dimer interface. Although the PepD is structurally similar to PepV, which exists as a monomer, putative substrate-binding residues reside in different topological regions of the polypeptide chain. In addition, the lid domain of the PepD contains an “extra” domain not observed in related M20 family metallopeptidases with a dimeric structure. Mutational assays confirmed both the putative di-zinc allocations and the architecture of substrate recognition. In addition, the catalytic domain-alone truncated PepD^CAT exhibited substrate specificity to l-homocarnosine compared with that of the wild-type PepD, indicating a potential value in applications of PepD^CAT for GABAergic therapies or neuroprotection.     

氨基酸自动分析仪测定血浆中牛磺酸程序的改进及其应用

<正> 牛磺酸是一种由胱氨酸转化而来的β—氨基酸。已有研究证实,牛磺酸与生长发育、体温调节、营养作用、学习记忆及某些疾病有关。由于牛磺酸具有调节生理功能的作用,目前牛磺酸代谢方面的     

Biochemical Evaluation of the Decarboxylation and Decarboxylation-Deamination Activities of Plant Aromatic Amino Acid Decarboxylases

Plant aromatic amino acid decarboxylase (AAAD) enzymes are capable of catalyzing either decarboxylation or decarboxylation-deamination on various combinations of aromatic amino acid substrates. These two different activities result in the production of arylalkylamines and the formation of aromatic acetaldehydes, respectively. Variations in product formation enable individual enzymes to play different physiological functions. Despite these catalytic variations, arylalkylamine and aldehyde synthesizing AAADs are indistinguishable without protein expression and characterization. In this study, extensive biochemical characterization of plant AAADs was performed to identify residues responsible for differentiating decarboxylation AAADs from aldehyde synthase AAADs. Results demonstrated that a tyrosine residue located on a catalytic loop proximal to the active site of plant AAADs is primarily responsible for dictating typical decarboxylase activity, whereas a phenylalanine at the same position is primarily liable for aldehyde synthase activity. Mutagenesis of the active site phenylalanine to tyrosine in Arabidopsis thaliana and Petroselinum crispum aromatic acetaldehyde synthases primarily converts the enzymes activity from decarboxylation-deamination to decarboxylation. The mutation of the active site tyrosine to phenylalanine in the Catharanthus roseus and Papaver somniferum aromatic amino acid decarboxylases changes the enzymes decarboxylation activity to a primarily decarboxylation-deamination activity. Generation of these mutant enzymes enables the production of unusual AAAD enzyme products including indole-3-acetaldehyde, 4-hydroxyphenylacetaldehyde, and phenylethylamine. Our data indicates that the tyrosine and phenylalanine in the catalytic loop region could serve as a signature residue to reliably distinguish plant arylalkylamine and aldehyde synthesizing AAADs. Additionally, the resulting data enables further insights into the mechanistic roles of active site residues.     

PylSn and the Homologous N-terminal Domain of Pyrrolysyl-tRNA Synthetase Bind the tRNA That Is Essential for the Genetic Encoding of Pyrrolysine

Pyrrolysine is represented by an amber codon in genes encoding proteins such as the methylamine methyltransferases present in some Archaea and Bacteria. Pyrrolysyl-tRNA synthetase (PylRS) attaches pyrrolysine to the amber-suppressing tRNA^Pyl. Archaeal PylRS, encoded by pylS, has a catalytic C-terminal domain but an N-terminal region of unknown function and structure. In Bacteria, homologs of the N- and C-terminal regions of archaeal PylRS are respectively encoded by pylSn and pylSc. We show here that wild type PylS from Methanosarcina barkeri and PylSn from Desulfitobacterium hafniense bind tRNA^Pyl in EMSA with apparent K_d values of 0.12 and 0.13 μm, respectively. Truncation of the N-terminal region of PylS eliminated detectable tRNA^Pyl binding as measured by EMSA, but not catalytic activity. A chimeric protein with PylSn fused to the N terminus of truncated PylS regained EMSA-detectable tRNA^Pyl binding. PylSn did not bind other D. hafniense tRNAs, nor did the competition by the Escherichia coli tRNA pool interfere with tRNA^Pyl binding. Further indicating the specificity of PylSn interaction with tRNA^Pyl, substitutions of conserved residues in tRNA^Pyl in the variable loop, D stem, and T stem and loop had significant impact in binding, whereas those having base changes in the acceptor stem or anticodon stem and loop still retained the ability to complex with PylSn. PylSn and the N terminus of PylS comprise the protein superfamily TIGR03129. The members of this family are not similar to any known RNA-binding protein, but our results suggest their common function involves specific binding of tRNA^Pyl.