Characteristic sequential residue environment of amino acids in proteins

The occurrence of all di- and tripeptide segments of proteins was counted in a large data base containing about 119 000 residues. It was found that the abundance of the amino acids does not determine the frequency of the various di- and tripeptide segments. In addition, the frequency of the various tripeptides cannot be predicted from the observed pair-frequency values. The pair-frequency distribution of amino acids is highly asymmetrical, pairs formed from identical residues are generally preferred and amino acids cannot be clustered on the basis of their first neighbour preferences. These data indicate the existence of general short range regularities in the primary structure of proteins. The consequences of these short range regularities were studied by comparing Chou-Fasman parameters with analogous parameters determined from the results of conformational energy calculations of single amino acids. This comparison shows that Chou-Fasman parameters carry significant information about the environment of each amino acid. The success of the Chou-Fasman's prediction and the properties of the pair and triplet distribution of the amino acid residues suggest that every amino acid has a characteristic sequential residue environment in proteins. The observed preferences could be invoked, for example, in protein design or in the study of the evolutionary relationship of proteins.     

Sea urchin (Anthocidaris crassispina) egg zinc-binding protein. Cellular localization, purification and characterization

Gel-filtration analysis of cytosol fraction obtained from unfertilized sea-urchin (Anthocidaris crassispina) eggs on Sephadex G-75 revealed the presence of two Zn-binding-protein fractions. The major Zn-binding protein fraction had a low molecular weight and a low absorbance at 280 nm, properties similar to those of the metallothionein found in the regenerating rat liver. These fractions were further purified by DEAE-cellulose and Sephadex G-50 chromatography. Homogeneity of the Zn-binding protein was judged by polyacrylamide-disc-gel electrophoresis and gel-permeation chromatography in the presence of 6 M-guanidinium chloride. The molecular weight determined by gel-permeation chromatography was 3900. This value is in good agreement with the minimum molecular weight calculated from the amino acid composition, which was 3655. Zn-binding protein is composed of 36 amino acid residues and the distinctive features include an extremely high content of cysteine, which accounted for one-third of the total amino acid residues, and a complete absence of aromatic amino acids, as well as of methionine, histidine and arginine. Zn-binding protein contained 4.1 g-atoms of zinc per mol and a trace of cadmium, but no copper, iron or calcium. The molar ratio of reactive thiol groups to metal ion was calculated to be 2.73:1. Possible roles of this Zn-binding protein in the homoeostasis of zinc in unfertilized sea-urchin eggs are discussed.     

Strong Correlation Between Statistical Transmembrane Tendency and Experimental Hydrophobicity Scales for Identification of Transmembrane Helices

Direct physical chemistry measurements of the hydrophobicity of amino acids or their derivatives have often been used to estimate the propensity of amino acids to participate in transmembrane helices. In this short note, it is found that there is a very high degree of correlation (r = 0.944–0.965) between an average physical chemistry hydrophobicity scale (an average of scales derived, e.g., from the solubility of amino acid derivatives in organic solvents versus water or their binding to hydrophobic particles) and the statistically based transmembrane tendency scale (derived from the relative abundance of residues in known transmembrane and soluble protein sequences (Zhao and London, Protein Sci 15:1987–2001, 2006)). This correlation indicates that, other than hydrophobicity, amino acid properties/interactions that promote or inhibit transmembrane helix formation in a specific membrane protein largely cancel out when averaged over all transmembrane sequences. In other words, other than hydrophobicity, there are no properties of a specific amino acid residue within a hydrophobic segment that have a strong systematic effect upon transmembrane helix formation independent of the remainder of the sequence in that hydrophobic segment. However, proline is an exception to this rule.     

氨基酸的分子结构与遗传密码简并及二维集合分类

根据氨基酸遗传密码子的简并程度,可将64个遗传密码子分为高简并度类（3,4,6度简并组）和低简并度类（1,2度简并组）两大类。高简并度类有9个氨基酸,其分子量比较小,等电点的分布比较集中。低简并度类有11个氨基酸,其分子结构比较复杂,参考Taylor对氨基酸特性的分类图,本文提出以分子量（M）及等电点（P）作为氨基酸的化学特性坐标,作出其二维集合MP分类图,MP分类图可以反映出氨基酸的各种属性,如分子量的大小,简并度的高低,极性与非极性、带电荷或不带电荷,疏水性与亲水性,以及氨基酸残基的种类等。根据氨基酸的分类分析,可以认为：高简并度氨基酸多数是脂烃类和羟脂烃类的氨基酸,分子量比较小,分子结构比较简单,大部分为疏子性,主要组成跨膜结构或蛋白质的结构域,可能是出现较早的氨基酸;而低简并度的氨基酸,分子结构比较复杂,分子量比较大,多数是和蛋白质功能有密切联系的基团,可能是进化出现较晚的结构。     

Glycoproteines sulfates des membranes de l'oeuf de poule et de l'oviducte Isolement et caracterisation de glycopeptides sulfatesSulfated glycoproteins form egg shell membranes and hen oviduct. Isolation and characterization of sulfated glycopeptides

Sulfated glycopeptides were isolated from pronaisc and tryptic digests of egg shell membranes and hen oviduct. They were precipitated by cationic detergents and separated by preparative electrophoresis, after removal of small quantities of glucuronoglycosaminoglycans detected only in the oviduct (isthmus and magnum). The principal isolated sulfated glycopeptides were divided according to increasing electrophoretic mobilities into two groups A and B. The homogeneity of the purified glycopeptides was confirmed by gel filtration and polyacrylamide gel electrophoresis.Glycopeptides from pool preparation of tissue are analysed and carbohydrate and amino acids average values are estimated. Hexosamines (mainly N-acetylglucosamine), hexoses (galactose, glucose, mannose) and fucose were found in Glycopeptides A. The molar ratio of hexose/hexosamine was 0.4. N-Acetylneuraminic acid and sulfate were also present in Glycopeptides A. The molar ratio of sulfate/hexosamine ranged from 0.1 to 0.25. The Glycopeptides A composition indicated the presence of chains with many glycosyl groups and a few of amino acids residues. The carbohydrate components of Glycopeptides B from egg shell membranes and magnum were found to be hexosamines (N-acetylgalactosamine and N-acetylglucosamine in equimolar proportions), hexoses (galactose mainly and glucose), N-acetylneuraminic acid, and fucose. The molar ratio of hexose/hexosamine was 1. Sulfate was also present and the molar ratio of N-acetylneuraminic acid and sulfate to hexosamine was ranged from 0.8 to 1. The main amino acid residues in these glycopeptides were serine and threonine with destruction of these hydroxyamino acids during alkali treatment. Glycopeptides B probably consist of short carbohydrate chains, linked to the polypeptide through O-glycosidic bonds involving N-acetylgalactosamine and serine and threonine. Approximately 40% of the amino acid residues were linked to carbohydrate chains.Glycopeptides B from egg shell membranes magnum and egg white were very similar in their carbohydrate and amino acid composition and in their properties.Gylcopeptides A from egg shell membranes, isthmus and magnum showed similarities and divergences especially in the amino acid composition. These results suggest that magnum and isthmus in oviduct are both concerned with the synthesis of egg shell membrane glycoproteins.     

Purification and characterization of zinc-binding protein from the liver of the partially hepatectomized rat.

Zn-binding protein in liver of the partially hepatectomized rat was purified by column chromatography on Sephadex G-75 and DEAE-cellulose. Homogeneity was judged by polyacrylamide-disc-gel electrophoresis. The molecular weight determined by gel-permeation chromatography in 6 M-guanidine hydrochloride was 6700. This value is in good agreement with the molecular weight calculated from the amino acid composition, which was 6073. Zn-binding protein was composed of 61 amino acid residues, and the distinctive features include an extremely high content of cysteine, which accounted for one-third of the total amino acid residues, and an absolute absence of aromatic amino acids as well as of histidine, leucine and arginine. The amino acid composition was similar to that of the metallothioneins previously isolated from rat liver and mouse liver. These observations suggest that the Zn-binding protein can be classified as a type of metallothionein. Zn-binding protein contained 8.2g-atoms of zinc per mol and traces of copper, but no cadmium. The molar ratio of thiol groups to zinc was calculated to be 2.5:1. Possible roles of this Zn-binding protein in the transport and storage of zinc in the liver are discussed.     

Chemical and catalytical properties of thermal polymers of amino acids (proteinoids)

The significance of thermal polyamino acids (proteinoids) as abiotic predecessors of proteins is reviewed on the basis of new experimental results. Most proteinoids yield only 50% to 80% amino acid upon acid hydrolysis. They contain 40% to 60% less peptide links than typical proteins, whereas their average nitrogen content is like that of proteins. The arrangement of amino acid residues is nonrandom. The degree of nonrandomness is difficult to determine because unusual crosslinks disturb most of the sequencing methods typically applied, in protein chemistry. The products obtained in a polymerization experiment are heterogeneous. They can be separated into a limited number of related fractions by chromatography or electrophoresis and other separation methods applied in protein chemistry. Their molecular weights are typically between 400 and 10 000. The number of free NH₂-groups, is usually smaller than in comparable proteins A significant fraction of NH₂-groups yields imidazole-type bases during the thermal polymerization. Optically active amino acids racemize during the same process. So far no helicity could be detected. Proteinoids are thus clearly distinct from proteins However, many of them exhibit weak catalytic activities and tend to undergo self-assembly into microstructures. Their properties of which only a few have been mentioned still support their role as possible candidates for ancestors of first proteins.     

Dual-specificity protein kinases: will any hydroxyl do?

Protein kinases are classified by the target amino acid in their substrates. Those protein kinases that phosphorylate hydroxyamino acids comprise two groups, the protein-tyrosine and protein-serine/threonine kinases, which, until recently, had been thought to be mutually exclusive. However, several new protein kinases have been discovered that, by the criterion of primary structure, would be classified as protein-serine/threonine kinases but which, surprisingly, are able to phosphorylate tyrosine residues. Even more surprising, there are reports of protein kinases that are capable of phosphorylating both tyrosine and serine/threonine residues. We review and discuss recent developments concerning these 'dal-specificity' protein kinases.     

The polypeptide composition of bovine epidermal alpha-keratin.

1. The polypedtide chains that comprise the subunits of the tonofilaments, or th alpha-keratin component, of bovine epidermis were fractionated by combination of chromatography on DEAE-cellulose and preparative polyacrylamide-gel electrophoresis. 2. The seve polypeptide chains investigated had generalyy similar properties; all contained two residues per molecule of tryptophan and N-acetylserine was the common N-terminal amino acid residue. 3. On the basis of close similarities in alpha-helix content and amino acid composition, the polypeptide chains were classified into three distinct groups. Each group contained approximately one-third of the total polypeptides on a molar basis. The groups and designated polypeptides chain numbers were: group one, polypeptides 1a and 1b, which had moleculae weights of 58,000, contained about 25% alpha-helix, 86 glutamic acid and 8 cysteine residues per molecule, but which differed in net charge, extinction coefficients and tyrosine contents; group two, polypeptides 2, 3, and 4, which hadmolecular weights within thewithin the range of 52,00-56,000, contained about 48% alpha-helix, 54 glutamic acid and 6 cysteine residues per molecule, but which differed in extinction coefficients and tryosine contents; and group, polypeptides 5 and 6, which had molecular weights of 47000-48000, contained about 56% alpha-helix, 64 glutamic acid and 4 cysteine residues per molecule, but which differed in extinction coefficients and tyrosine contents...     

Azuki bean (Vigna angularis) protease inhibitors: isolation and amino acid sequences

Double-headed protease inhibitors I, IIa, and IIc (AB I, AB IIa, and AB IIc) have been purified from azuki beans "Takara" (Vigna angularis) by conventional chromatographic methods and their amino acid sequences have been determined. AB I, AB IIa, and AB IIc had molecular weights of 9,166, 8,661, and 8,756 daltons, consisting of 82, 78, 79 amino acid residues, respectively. The molecular weights of these inhibitors, determined by gel filtration at pH 8.0, were 18,000 for AB I and 17,000 for both AB IIa and AB IIc, indicating that the inhibitors are dimers. The inhibitors had isoelectric points of 4.7 (AB I), 6.8 (AB IIa), and 6.2 (AB IIc). AB I stoichiometrically inhibited both trypsin and chymotrypsin at a molar ratio of 1 : 1. On the other hand, AB IIa and AB IIc both inhibited trypsin at a molar ratio of about 1 : 2 and also inhibited chymotrypsin, though only weakly. Sequence comparison with other double-headed inhibitors indicated the reactive sites of AB IIa and AB IIc for trypsin to be Lys26-Ser27 and Arg53-Ser54, and those of AB I for trypsin and chymotrypsin to be Lys26-Ser27 and Tyr53-Ser54, respectively. The differences between AB IIa and AB IIc were that AB IIa lacked the C-terminal aspartic acid residue, and that Glu10 and Arg60 in AB IIa were replaced by Gln10 and His60 in AB IIc. A comparison between AB IIa and AB I revealed 25 variant amino acids among the 78 residues of AB IIa; further, Ab IIa lacked 4 amino acid residues in the C-terminal region of AB I.     

Characterization of pig pancreatic kallikreins A and B.

Pig pancreatic kallikreins A and B are both composed of the same 229 amino acids, a figure resembling the number of amino acid residues found in other serine proteinases of pancreas. Both forms of the enzyme contain N-terminal isoleucine and alanine and C-terminal leucine/serine (about half a mol each per mol kallikrein) and proline. Values for the glucosamine content of the kallikreins obtained on the amino acid analyzer after hydrolysis with p-toluenesulfonic acid, a procedure also used for the determination of amide ammonia, agreed with those determined by a gas-chromatographic method. Neuraminidasetreated kallikrein B differs from the A form only in containing roughly double the amount (on the average a total of 11.5 vs. 5.6% by weight) of carbohydrate (glucosamine, mannose, galactose, and fucose) and possibly by a higher content (20 vs. 17 residues) of amide ammonia. From the composition, molecular weights of 26800 and 28600 are calculated for sialic-acid-free kallikreins A and B, respectively, and of 25300 for the protein part of kallikrein. The molar absorbance of both forms of the enzyme has been determined as (50.6 +/- 1.3) X 10(3)M-1 cm-1 at 280 nm. A comparison of kallikreins A and B with kallikreins d1 and d2 described by Zuber and Sache reveals as principal difference a much lower specific activity of the latter preparations with all reagents tested. Conceivably, the reported lower carbohydrate contents of kallikreins d1 and d2 and their separation into three instead of two major subunits are related to this finding.     

Statistical analysis of the physical properties of the 20 naturally occurring amino acids

In order to describe the conformational and other physical properties of the 20 naturally occurring amino acid residues with a minimum number of parameters, several multivariate statistical analyses were applied to 188 of their physical properties and ten orthogonal properties (factors) were obtained for the 20 amino acids without losing the information contained in the original physical properties. The analysis consisted of three main steps. First, 72 of the physical properties were eliminated from further consideration because they did not pass statistical tests that they follow a normal distribution. Second, the remaining 116 physical properties of the amino acids were classified by a cluster analysis to eliminate duplications of highly correlated physical properties. This led to nine clusters, each of which was characterized by an average characteristic property, namely bulk, two hydrophobicity indices for free amino acids, one hydrophobicity index for amino acid residues in a protein, two types of -structure preference, -helix preference, and two types of bend-structure preference. The physical properties within a given cluster were highly correlated with each other, but the correlation between clusters was low. Third, a factor analysis was applied to the nine average classified properties and 16 additional physical properties to obtain a small number of orthogonal properties (ten factors). Four of these factors arise from the nine characteristic properties, and the remaining six factors were obtained from the 16 physical properties not included in the nine characteristic properties. Finally, most of the 188 physical properties could be expressed as a sum of these ten orthogonal factors, with appropriate weighting factors. Since these factors contain information relating almost all properties of all 20 amino acids, it is possible to estimate the numerical values of a property for one or two amino acids for which experimental data for this property are not available. For example, the estimated values for the Zimm-Bragg parameters at 20°C are 0.66 and 0.92 for proline and cysteine, respectively, computed from the first four factors.     

Gamma-carboxyglutamic acid

Summary Gamma-carboxyglutamic acid is an amino acid with a dicarboxylic acid side chain. This amino acid, with unique metal binding properties, confers metal binding character to the proteins into which it is incorporated. This amino acid has been discovered in blood coagulation proteins (prothrombin, Factor X, Factor IX, and Factor VII), plasma proteins of unknown function (Protein C, Protein S, and Protein Z), and proteins from calcified tissue (osteocalcin and bone-Gla protein). It has also been observed in renal calculi, atherosclerotic plaque, and the egg chorioallantoic membrane, among other tissues. Gamma-carboxyglutamic acid is synthesized by the post-translational modification of glutamic acid residues. This reaction, catalyzed by a hepatic carboxylase, requires reduced vitamin K, oxygen, and carbon dioxide. The function of -carboxyglutamic acid is uncertain. In prothrombin y-carboxyglutamic acid residues bound to metal ions participate as an intramolecular non-covalent bridge to maintain protein conformation. Additionally, these amino acids participate in the calcium-dependent molecular assembly of proteins on membrane surfaces through intermolecular bridges involving y-carboxyglutamic acid and metal ions.     

The proteinaceous components of the gum exudates from some phyllodinous Acacia species

Acacia gum exudates are proteinaceous polysaccharides; their protein content ranges from ca 0.2 to 45%.The data presented show that the amino acid compositions of the gums from 12 phyllodinous species (10 from Bentham's sub-series Uninerves racemosae, two from sub-series Juliflorae) also vary considerably, particularly in respect of their hydroxyproline content (55 residues per 1000 residues in A. aestivalis gum, 287 residues per 1000 in A. saliciformis gum). The proportions of some other amino acids, e.g. alanine, aspartic acid, proline and serine also vary considerably, but the proportions of others, e.g. cystine, methionine, histidine, threonine, tyrosine and valine, are remarkably constant. The amino acid composition of gums with a very low protein content (e.g. A. victoriae and A. mycrobotrya) is similar to that for a highly proteinaceous gum (A. tumida). There are, however, considerable differences between the amino acid compositions of the gums from A. saligna and A. pycnantha (South African and Western Australian specimens). This strengthens previous chemotaxonomic evidence, based on the polysaccharide parameters of their gums, that these two species are not as close taxonomically as was originally believed from morphological considerations.     

一种快速非比对的蛋白质序列相似性与进化分析方法

本文提出了一种新的快速非比对的蛋白质序列相似性与进化分析方法。在刻画蛋白质序列特征时,首先将氨基酸的10种理化性质通过主成分分析浓缩为6个主成分,并且将每条蛋白质序列里的氨基酸数目作为权重对主成分得分值进行加权平均,然后再融合氨基酸的位置信息构成一个26维的蛋白质序列特征向量,最后利用欧式距离度量蛋白质序列间的相似性及进化关系。通过对3个蛋白质序列数据集的测试表明,本文提出的方法能将每条蛋白质序列准确聚类,并且简便快捷,说明了该方法的有效性。     

Viscosity B-coefficients and standard partial molar volumes of amino acids, and their roles in interpreting the protein (enzyme) stabilization

This review systematically surveys the viscosity B-coefficients and standard partial molar volumes of amino acids at various temperatures as these data are quite important for interpreting the hydration and other properties of peptides and proteins. The effect of organic solutes and various ions on the viscometric and volumetric properties of amino acids has also been discussed in terms of their kosmotropic ('structure-making') effects on the hydration of amino acids. The comparison of these effects on the amino acid hydration enables us to have a better understanding of the influence of organic solute and salt on the protein stabilization. In addition, the viscometric and volumetric behaviors of amino acid ions (cations and anions) are also summarized because these ions have recently been incorporated as part of novel ionic liquids, which have wide applications in biocatalysis and protein stabilization.     

Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins

Summary. Thermophilic proteins show substantially higher intrinsic thermal stability than their mesophilic counterparts. Amino acid composition is believed to alter the intrinsic stability of proteins. Several investigations and mutagenesis experiment have been carried out to understand the amino acid composition for the thermostability of proteins. This review presents some generalized features of amino acid composition found in thermophilic proteins, including an increase in residue hydrophobicity, a decrease in uncharged polar residues, an increase in charged residues, an increase in aromatic residues, certain amino acid coupling patterns and amino acid preferences for thermophilic proteins. The differences of amino acids composition between thermophilic and mesophilic proteins are related to some properties of amino acids. These features provide guidelines for engineering mesophilic protein to thermophilic protein. Authors’ addresses: Yuan-Jiang Pan, Institute of Chemical Biology and Pharmaceutical Chemistry, Zhejiang University, Zhejiang University Road 38, Hangzhou 310027, China; Wei-Fen Li, Microbiology Division, College of Animal Science, Zhejiang University, Hangzhou 310029, China     

Two amino acid residues determine the low substrate affinity of human cationic amino acid transporter-2A

Mammalian cationic amino acid transporters (CAT) differ in their substrate affinity and sensitivity to trans-stimulation. The apparent Km values for cationic amino acids and the sensitivity to trans-stimulation of CAT-1, -2B, and -3 are characteristic of system y+. In contrast, CAT-2A exhibits a 10-fold lower substrate affinity and is largely independent of substrate at the trans-side of the membrane. CAT-2A and -2B demonstrate such divergent transport properties, even though their amino acid sequences differ only in a stretch of 42 amino acids. Here, we identify two amino acid residues within this 42-amino acid domain of the human CAT-2A protein that are responsible for the apparent low affinity of both the extracellular and intracellular substrate-binding sites. These residues are located in the fourth intracellular loop, suggesting that they are not part of the translocation pathway. Rather, they may be responsible for the low affinity conformation of the substrate-binding sites. The sensitivity to trans-stimulation is not determined by the same amino acid residues as the substrate affinity and must involve a more complex interaction between individual amino acid residues. In addition to the 42-amino acid domain, the adjacent transmembrane domain X seems to be involved in this function.     

Purification and properties of plaice metallothionein, a cadmium-binding protein from the liver of the plaice (Pleuronectes platessa).

A low-molecular-weight protein induced in the liver of the plaice (Pleuronectes platessa) by exposure to cadmium was purified and characterized. It is closely similar to mammalian metallothioneins in all of its properties in that it is a single-chain cadmium-binding protein of approx. 7000 mol.wt. with a high cysteine content (31 mol%) and no aromatic amino acid residues. The thiol groups of the cysteine residues complex with the cadmium in a SH/Cd molar ratio of 3:1 and produce a characteristic absorption maximum at 250 nm. Unlike the mammalian metallothioneins, however, metal analyses reveal only traces of zinc and copper in addition to cadmium. The presence of carbohydrate previously assumed from a positive reaction with periodic acid/Schiff reagent has now been disproved, and the positive reaction attributed to interaction with the thiol groups in the protein.     

Fluorescence analysis study of the lability of biomembranes and their components. III. Kinetics of complex formation between bovine serum albumin molecules and higher saturated fatty acids]

Kinetic peculiarities of the sorption of natural limited fatty acids on the molecules of bovine serum albumine (BSA) were studied by investigating fluorescent parameters of ionic (1-anilinonaphtalin-8-sulphonate-ANS) and neutral (N-phenyl-1-naphtylamine-PNA) probes. The following regularities were found: 1. The parameters which characterize the microsurroundings of both probes (quantum yield of fluorescence, the binding constant) did not change significantly during the sorption of the fattyn acids (laurinic, palmitinic and methyl ether of the stearinic acid). An exponential character of BSA fluorescent titration with fatty acids points to a competitive character of the relationship dye -- fatty acid for the binding sites in hydrophobic sacks of BSA. 2. The study of the character of the effect of solution ionic strength on the sorption of fatty acids showed that along with hydrophobic interactions the electrostatic interaction between carboxyl residues of fatty acids and charged protein groups also significantly contributed to this process. 3. Temperature relationship of AMS and PNA fluorescence intensity in the complex BSA -- laurinic acid correlates well with temperature relationship obtained from a pure protein system.