Evolution of the amino acid substitution in the mammalian myoglobin gene

Summary Multivariate statistical analyses were applied to 16 physical and chemical properties of amino acids. Four of these properties; volume, polarity, isoelectric point (charge), and hydrophobicity were found to explain adequately 96% of the total variance of amino acid attributes. Using these four quantitative measures of amino acid properties, a structural discriminate function in the form of a weighted difference sum of squares equation was developed. The discriminate function is weighted by the location of each particular residue within a given tertiary structure and yields a numerical discriminate or difference value for the replacement of these residues by different amino acids. This resulting discriminate value represents an expression of the perturbation in the local positional environment of a protein when an amino acid substitution occurs. With the use of this structural discriminate function, a residue by residue comparison of the known mammalian myoglobin sequences was carried out in an attempt to elucidate the positions of possible deviations from the known tertiary structure of sperm whale myoglobin. Only 11 of the 153 residue positions in myoglobin demonstrated possible structural deviations. From this analysis, indices of difference were calculated for all amino acid exchanges between the various myoglobins. All comparisons yielded indices of difference that were considerably lower than would be expected if mutations had been fixed at random, even if the organization of the genetic code is taken into consideration. On the basis of these results, it is inferred that some form of selection has acted in the evolution of mammalian myoglobins to favor amino acid substitutions that are compatible with the retention of the original conformation of the protein.     

Amino acid composition analysis of secondary transport proteins from Escherichia coli with relation to functional classification,ligand specificity and structure

We have performed an amino acid composition (AAC) analysis of the complete sequences for 235 secondary transport proteins from Escherichia coli, which have functions in the uptake and export of organic and inorganic metabolites, efflux of drugs and in controlling membrane potential. This revealed the trends in content for specific amino acid types and for combinations of amino acids with similar physicochemical properties. In certain proteins or groups of proteins, the so-called spikes of high content for a specific amino acid type or combination of amino acids were identified and confirmed statistically, which in some cases could be directly related to function and ligand specificity. This was prevalent in proteins with a function of multidrug or metal ion efflux. Any tool that can help in identifying bacterial multidrug efflux proteins is important for a better understanding of this mechanism of antibiotic resistance. Phylogenetic analysis based on sequence alignments and comparison of sequences at the N- and C-terminal ends confirmed transporter Family classification. Locations of specific amino acid types in some of the proteins that have crystal structures (EmrE, LacY, AcrB) were also considered to help link amino acid content with protein function. Though there are limitations, this work has demonstrated that a basic analysis of AAC is a useful tool to use in combination with other computational and experimental methods for classifying and investigating function and ligand specificity in a large group of transport or other membrane proteins, including those that are molecular targets for development of new drugs.     

Butyric acid mediated induction of enhanced transendothelial resistance in an in vitro model blood-brain barrier system.

Previously we reported that the co-culture of non-brain vascular endothelial cells with glioma cells leads to the induction of a more differentiated endothelial cell phenotype which exhibits important properties of the blood-brain barrier (BBB). Recognising the potential for improving the model barrier system with agents known to modify the growth and differentiation of cells in culture we examined the effects of four differentiating agents (butyric acid, dexamethasone, retinoic acid, and dimethyl sulfoxide) on barrier function. Of these agents only butyric acid and dexamethasone resulted in an enhancement (depending on the dose used) of transendothelial electrical resistance (barrier function). The greatest effect was observed with butyric acid in a dose-dependent manner and was slow in onset and only occurred in the endothelial/glial cell co-cultures. These data indicate that butyric acid may be a beneficial agent in optimising conditions necessary for induction of BBB properties in in vitro barrier systems.     

Antioxidant alpha-keto-carboxylate pyruvate protects low-density lipoprotein and atherogenic macrophages

Oxidative modification of low-density lipoprotein (oxLDL) plays a pathogenic role in atherogenesis. Classical antioxidants such as L-ascorbic acid can inhibit formation of oxLDL. Alpha-Keto-carboxylates such as pyruvate and congeners also display antioxidant properties in some cell-free and intact cell systems. We tested the hypothesis that pyruvate or alpha-keto-glutarate may function as antioxidants with respect to LDL incubated with 5 or 10 microM Cu2+ alone or in combination with THP-1-derived macrophages. alpha-Hydroxy-carboxylates (L-lactate), linear aliphatic monocarboxylates (acetate/caprylate) and L-ascorbic acid served as controls. The oxLDL formation was ascertained by electrophoretic mobility and oxLDL cytotoxicity was judged by macrophage viability and thiobarbituric acid reactive substances (TBARS) formation. Cu2+ alone was not cytotoxic but increased electrophoretic mobility of cell-free LDL, stimulating TBARS. Millimolar pyruvate, alpha-ketoglutarate, or micromolar L-ascorbic acid partially inhibited oxLDL formation, while alpha-hydroxy-carboxylate or the aliphatic mono-carboxylates had no measurable antioxidant properties in cell-free LDL. Co-culture of LDL with macrophages and Cu2+ augmented TBARS release and resulted in 95% macrophage death. Pyruvate improved macrophage viability with 5 microM Cu2+ up to 60%. L-Ascorbic acid (> or = 100 microM) protected macrophages up to 80%. When > or = 100 microM L-ascorbic acid was combined with pyruvate, oxLDL formation and macrophage death were fully prevented. Thus, alpha-keto-carboxylates, but not physiological alpha-hydroxy-carboxylates or aliphatic monocarboxylates qualify as antioxidants in LDL systems. Since alpha-keto-carboxylates enhanced the antioxidant power of L-ascorbic acid, our findings may have implications for strategies attenuating atherosclerosis.     

In vitro linoleic acid activation of protein kinase C

The importance of membrane fluidity in the activation of protein kinase C (PKC) was examined using the membrane fluidizer, linoleic acid, in a well-defined model membrane system. Biochemical and biophysical properties of the system were monitored. Linoleic acid activated PKC to a level of 50% of that observed for diacylglycerol. In contrast, linoleic acid did not directly interact with the phorbol ester binding site as did diacylglycerol. This was determined by the lack of involvement of the ionizable group of the fatty acid with activity and the enhancement of phorbol ester binding by linoleic acid and its ester analogs. The membrane fluidity of this model membrane system in the presence of linoleic acid was increased as determined by fluorescence polarization. This increased the availability of phospholipids, thus, explaining the linoleic acid-induced enhancement of phorbol ester binding. The PKC conformation as determined from intrinsic tryptophan fluorescence spectra was different for lipid mixtures containing linoleic acid or diacylglycerol correlating with the difference in biochemical activation properties. This study provides evidence that membrane fluidization is not the predominant function of the lipid activator in PKC activation, but may play a role in obtaining the preferred membrane state for maximal activation.     

THE ANTICONVULSANT ACTION OF GABA-ELEVATING AGENTS: A RE-EVALUATION

Abstract— The GABA-elevating agents, aminooxyacetic acid, hydrazine, and hydroxylamine, all possessed anticonvulsant properties, although to a widely varying degree. Aminooxyacetic acid was the most efficacious in delaying drug-induced seizures in mice whereas hydroxylamine brought about only a slight delay in the onset of seizures. The anticonvulsant action was observed against various convulsant agents regardless of whether the convulsant mechanism might involve a deranged GABA metabolism (allylglycine, isonicotinic acid hydrazide, hydrazine), an interference with GABA function (picrotoxin) or some other mechanism (pentylenetetrazol). The anticonvulsant action was not related in a simple manner to either GABA levels or glutamic acid decarboxylase (GAD) activities but the anomalous situation whereby seizures occurred when the GABA content of brain was above normal could be resolved on the basis of an expression which included changes in both GABA levels and GAD activity. The possibility was proposed that the anticonvulsant action of aminooxyacetic acid involved two separate mechanisms.     

Function of the conserved triad residues in the class C beta-lactamase from Citrobacter freundii GN346

The conserved KTG triad in the class C beta-lactamase from Citrobacter freundii GN346 was examined as to its function by means of site-directed mutagenesis. The following conversions were performed; Lys-315 to arginine, alanine or glutamic acid, Thr-316 to valine, and Gly-317 to alanine, proline or isoleucine. The resultant mutant enzymes revealed that a basic amino acid at position 315 and a small uncharged residue at position 317 are essential for the enzyme activity, but a hydroxyl group at residue 316 is not required for the enzymatic catalysis. The kinetic properties of the purified Arg-315 and Val-316 enzymes provided information on the function of these residues.     

The rheology of pig small intestinal and colonic mucus: weakening of gel structure by non-mucin components.

Mechanical spectroscopy has been used to study the structure and properties of pig small intestinal and colonic adherent mucus gel. Both mucus secretions had properties of viscoelastic gels, but that from the small intestine was substantially weaker in quality. Small intestinal mucus gel was disrupted by acid (pH 1), detergents (bile) and protein denaturants while that from the colon remained stable following these treatments. Concentration of purified colonic mucin produced a gel with the same rheological properties as the native secretion. Purified small intestinal mucin when concentrated produced a stronger gel than the native secretion and, in contrast to the latter, one which was not disrupted by acid or denaturants. The instability of native small intestinal mucus was shown not to be a function of the mucin components (which alone could account for the gel-forming properties), but to arise from the presence of insoluble material largely from sloughed mucosal cells. These studies show (1) that mucus gels from the colon and small intestine have similar mechanical behaviour and properties to those from the stomach and duodenum, and (2) emphasise the caution that should be exercised when interpreting the rheological properties of mucus preparations, particularly with respect to their content of mucosal cellular material.     

Biologically active peptides of the vesicular stomatitis virus glycoprotein.

A peptide corresponding to the amino-terminal 25 amino acids of the mature vesicular stomatitis virus glycoprotein has recently been shown to be a pH-dependent hemolysin. In the present study, we analyzed smaller constituent peptides and found that the hemolytic domain resides within the six amino-terminal amino acids. Synthesis of variant peptides indicates that the amino-terminal lysine can be replaced by another positively charged amino acid (arginine) but that substitution with glutamic acid results in the total loss of the hemolytic function. Peptide-induced hemolysis was dependent upon buffer conditions and was inhibited when isotonicity was maintained with mannitol, sucrose, or raffinose. In sucrose, all hemolytic peptides were also observed to mediate hemagglutination. The large 25-amino acid peptide is also a pH-dependent cytotoxin for mammalian cells and appears to effect gross changes in cell permeability. Conservation of the amino terminus of vesicular stomatitis virus and rabies virus suggests that the membrane-destabilizing properties of this domain may be important for glycoprotein function.     

悦目金蛛和棒络新妇卵袋丝物理化学结构表征及其力学性能研究

蜘蛛丝是一种具有优良机械性能的天然动物蛋白纤维,它特有的结构和性能与其生物学功能密切相关。作者采用氨基酸自动分析仪、傅立叶转换红外光谱仪、扫描电镜和电子单纤强力仪对悦目金蛛（Argiope amoena）和棒络新妇（Nephila clavata）的卵袋丝进行了物理化学结构表征与力学性能的研究,结果表明两种蜘蛛卵袋均由微米级柱状腺丝、大壶状腺丝、亚微米级或纳米级葡萄状腺丝构成。卵袋丝的表面形貌特征、极性氨基酸含量、大侧链与小侧链氨基酸的比值、无定型区、β-折叠结构与结晶结构的含量等氨基酸组成种类与蛋白质二级结构特征,均满足各自生物学功能对断裂强度、延展性、初始模量等力学性能的要求。     

Comprehensive analysis of the numbers,lengths and amino acid compositions of transmembrane helices in prokaryotic,eukaryotic and viral integral membrane proteins of high-resolution structure

We report a comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in 235 high-resolution structures of integral membrane proteins. The properties of 1551 transmembrane helices in the structures were compared with those obtained by analysis of the same amino acid sequences using topology prediction tools. Explanations for the 81 (5.2%) missing or additional transmembrane helices in the prediction results were identified. Main reasons for missing transmembrane helices were mis-identification of N-terminal signal peptides, breaks in α-helix conformation or charged residues in the middle of transmembrane helices and transmembrane helices with unusual amino acid composition. The main reason for additional transmembrane helices was mis-identification of amphipathic helices, extramembrane helices or hairpin re-entrant loops. Transmembrane helix length had an overall median of 24 residues and an average of 24.9 ± 7.0 residues and the most common length was 23 residues. The overall content of residues in transmembrane helices as a percentage of the full proteins had a median of 56.8% and an average of 55.7 ± 16.0%. Amino acid composition was analysed for the full proteins, transmembrane helices and extramembrane regions. Individual proteins or types of proteins with transmembrane helices containing extremes in contents of individual amino acids or combinations of amino acids with similar physicochemical properties were identified and linked to structure and/or function. In addition to overall median and average values, all results were analysed for proteins originating from different types of organism (prokaryotic, eukaryotic, viral) and for subgroups of receptors, channels, transporters and others.     

Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica

The neutral theory of molecular evolution predicts that variation within species is inversely related to the strength of purifying selection, but the strength of purifying selection itself must be related to physical constraints imposed by protein folding and function. In this paper, we analyzed five enzymes for which polymorphic sequence variation within Escherichia coli and/or Salmonella enterica was available, along with a protein structure. Single and multivariate logistic regression models are presented that evaluate amino acid size, physicochemical properties, solvent accessibility, and secondary structure as predictors of polymorphism. A model that contains a positive coefficient of association between polymorphism and solvent accessibility and separate intercepts for each secondary-structure element is sufficient to explain the observed variation in polymorphism between sites. The model predicts an increase in the probability of amino acid polymorphism with increasing solvent accessibility for each protein regardless of physicochemical properties, secondary-structure element, or size of the amino acid. This result, when compared with the distribution of synonymous polymorphism, which shows no association with solvent accessibility, suggests a strong decrease in purifying selection with increasing solvent accessibility.     

Physicochemical properties of the exocellular polysaccharide from Cyanospira capsulata

This paper reports on the chemical structure and on some physicochemical properties of a new exopolysaccharide, CC-EPS, secreted by a filamentous nitrogen-fixing cyanobacterium, Cyanospira capsulata. Solution properties of CC-EPS were studied with the aim of characterizing the conformational state of the polysaccharide in water and in aqueous salt solution, in view of the peculiar rheological properties. Because the molecule has two different uronic acid residues, a variation of pH and/or ionic strength was considered to be the best perturbation to disclose any possible ordered structures. We found no evidence for a cooperative conformational transition from the change of the chiro-optical properties or from the smooth increase of pKa as a function of the degree of ionization, alpha, of the polyacid. The same conclusion was drawn from the study of the temperature dependence and ionic strength dependence (in the range up to 0.1 M NaCl) of solution properties. The data suggest that the solution conformation of CC-EPS is a random coil with a chain flexibility comparable to that of alginate.     

Coffee polyphenols extracted from green coffee beans improve skin properties and microcirculatory function

Coffee polyphenols (CPPs), including chlorogenic acid, exert various physiological activities. The purpose of this study was to investigate the effects of CPPs on skin properties and microcirculatory function in humans. In this double-blind, placebo-controlled study, 49 female subjects with mildly xerotic skin received either a test beverage containing CPPs (270 mg/100 mL/day) or a placebo beverage for 8 weeks. The ingestion of CPPs significantly lowered the clinical scores for skin dryness, decreased transepidermal water loss, skin surface pH, and increased stratum corneum hydration and the responsiveness of skin blood flow during local warming. Moreover, the amounts of free fatty acids and lactic acid in the stratum corneum significantly increased after the ingestion of CPPs. These results suggest that an 8-week intake of CPPs improve skin permeability barrier function and hydration, with a concomitant improvement in microcirculatory function, leading to efficacy in the alleviation of mildly xerotic skin.     

Lipid composition and physical properties of membranes from C-6 glial cells with altered phospholipid polar headgroups

Growth of C-6 glial cells in media enriched in the polar headgroup precursors N,N-dimethylethanolamine, N-monomethylethanolamine or ethanolamine for 24 h resulted in the accumulation of the corresponding phospholipids to about 30% of total membrane phospholipid. Under these conditions the cholesterol to phospholipid ratios were unaffected. With the exception of arachidonic acid, which was significantly reduced in the lipids from cells grown in the presence of N-monomethylethanolamine, the fatty acid composition of cells grown under the various conditions was identical. The physical properties of membranes prepared from these cells were compared by electron spin resonance spectroscopy using spin-labelled stearic acid. Modifications in cellular phospholipid composition did not affect either the order parameter or the correlation time of fatty acid spin labels. Since there are no significant effects on the other membrane lipids and since the physical properties of the membranes are maintained, these modifications in phospholipid composition provide a valuable means for studying the role of phospholipid polar headgroups in the function of membrane-bound enzymes and hormone receptors in C-6 cells.     

A new sequence representation as applied in better specificity elucidation for human immunodeficiency virus type 1 protease

Factor analysis scales of generalized amino acid information (FASGAI) involving hydrophobicity, alpha and turn propensities, bulky properties, compositional characteristics, local flexibility, and electronic properties were derived from 516 property parameters of 20-coded amino acids, and was then employed to represent sequence structures of 746 peptides with 8 amino acid residues. Cleavage site prediction models for human immunodeficiency virus type 1 protease by linear discriminant analysis and support vector machine with radial basis function kernel were constructed to identify if they could be cleaved or not, and were further utilized to investigate the cleavage specificity. These diversified properties, including the bulky properties, secondary conformation characteristics, electronic properties, and hydrophobicity at the first, the second, the fourth, the fifth, and the sixth residue, are possibly important factors in determining HIV PR cleavage or not. Particularly, maximal positive and negative influences result from the bulky properties of different sites. Further results from analysis of variance also likely reflect that the HIV PR recognizes diversified key properties of various sites in the octameric sequences. Satisfactory results show that FASGAI can not only be used to represent sequence structures of various functional peptides, but alsoprovide a potential feasible measure for exploring relationship between protein motif sequences and their functions.     

Polyunsaturated fatty acid supplements modulate mast cell membrane microdomain composition

In the present study, the lipid raft composition of a canine mastocytoma cell line (C2) was analyzed. Lipid rafts were well separated from non-raft plasma membranes using a detergent-free isolation technique. To study the influence of n-3 and n-6 polyunsaturated fatty acids (PUFA) on raft fatty acid composition in comparison to non-raft cell membrane, C2 were supplemented with one of the following: α-linolenic acid, eicosapentaenoic acid, docosahexaenoic acid, linoleic acid or arachidonic acid. Enrichment of the culture medium with a specific PUFA resulted in an increase in the content of this fatty acid both in rafts and non-raft membranes. Contents of cholesterol and protein were found not to be affected by the changes in the fatty acid profiles. In conclusion, our data provide strong evidence that PUFA modulate lipid composition and physiological properties of membrane micro domains of mast cells which in turn may have effects on mast cell function.     

Uteroferrin: A protein in search of a function

Uteroferrin, a purple-colored, iron-containing acid phosphatase, with many of the properties of a lysosomal hydrolase, transports iron from the mother to the conceptus in pregnant pigs. Uteroferrin, however, is but one member of what may be a broad class of iron-containing phosphatases with unusual spectral properties which result from a novel type of di-iron active site. The biological function of uteroferrin is unknown. We argue here that the in vivo function of uteroferrin, despite its undoubted ability to act as a potent acid phosphatase, is that of a transplacental iron transporter.     

Antioxidant α-Keto-carboxylate Pyruvate Protects Low-density Lipoprotein and Atherogenic Macrophages

Oxidative modification of low-density lipoprotein (oxLDL) plays a pathogenic role in atherogenesis. Classical antioxidants such as l -ascorbic acid can inhibit formation of oxLDL. &#102 -Keto-carboxylates such as pyruvate and congeners also display antioxidant properties in some cell-free and intact cell systems. We tested the hypothesis that pyruvate or &#102 -keto-glutarate may function as antioxidants with respect to LDL incubated with 5 or 10 &#119 M Cu 2+ alone or in combination with THP-1-derived macrophages. &#102 -Hydroxy-carboxylates ( l -lactate), linear aliphatic mono-carboxylates (acetate/caprylate) and l -ascorbic acid served as controls. The oxLDL formation was ascertained by electrophoretic mobility and oxLDL cytotoxicity was judged by macrophage viability and thiobarbituric acid reactive substances (TBARS) formation. Cu 2+ alone was not cytotoxic but increased electrophoretic mobility of cell-free LDL, stimulating TBARS. Millimolar pyruvate, &#102 -keto-glutarate, or micromolar l -ascorbic acid partially inhibited oxLDL formation, while &#102 -hydroxy-carboxylate or the aliphatic mono-carboxylates had no measurable antioxidant properties in cell-free LDL. Co-culture of LDL with macrophages and Cu 2+ augmented TBARS release and resulted in 95% macrophage death. Pyruvate improved macrophage viability with 5 &#119 M Cu 2+ up to 60%. l -Ascorbic acid ( &#83 100 &#119 M) protected macrophages up to 80%. When &#83 100 &#119 M l -ascorbic acid was combined with pyruvate, oxLDL formation and macrophage death were fully prevented. Thus, &#102 -keto-carboxylates, but not physiological &#102 -hydroxy-carboxylates or aliphatic mono-carboxylates qualify as antioxidants in LDL systems. Since &#102 -keto-carboxylates enhanced the antioxidant power of l -ascorbic acid, our findings may have implications for strategies attenuating atherosclerosis.