Amino acid compositions of simian virus 40 structural proteins

The structural proteins of purified SV40 particles were isolated by preparative polyacrylamide gel electrophoresis and the amino acid composition of each protein was obtained. The amino acid composition of VP1 (the major coat protein) was significantly different to that of VP3 (the capsid protein most closely associated with SV40 DNA). The amino acid compositions of VP4, VP5 and VP6 indicated that these proteins were not exclusively histones.     

Amino acid propensities for secondary structures are influenced by the protein structural class

Amino acid propensities for secondary structures were used since the 1970s, when Chou and Fasman evaluated them within datasets of few tens of proteins and developed a method to predict secondary structure of proteins, still in use despite prediction methods having evolved to very different approaches and higher reliability. Propensity for secondary structures represents an intrinsic property of amino acid, and it is used for generating new algorithms and prediction methods, therefore our work has been aimed to investigate what is the best protein dataset to evaluate the amino acid propensities, either larger but not homogeneous or smaller but homogeneous sets, i.e., all-alpha, all-beta, alpha-beta proteins. As a first analysis, we evaluated amino acid propensities for helix, beta-strand, and coil in more than 2000 proteins from the PDBselect dataset. With these propensities, secondary structure predictions performed with a method very similar to that of Chou and Fasman gave us results better than the original one, based on propensities derived from the few tens of X-ray protein structures available in the 1970s. In a refined analysis, we subdivided the PDBselect dataset of proteins in three secondary structural classes, i.e., all-alpha, all-beta, and alpha-beta proteins. For each class, the amino acid propensities for helix, beta-strand, and coil have been calculated and used to predict secondary structure elements for proteins belonging to the same class by using resubstitution and jackknife tests. This second round of predictions further improved the results of the first round. Therefore, amino acid propensities for secondary structures became more reliable depending on the degree of homogeneity of the protein dataset used to evaluate them. Indeed, our results indicate also that all algorithms using propensities for secondary structure can be still improved to obtain better predictive results.     

Amino acid sequence of a mouse mucosal mast cell protease

The amino acid sequence has been determined of a mouse mucosal mast cell protease isolated from the small intestines of mice infected with Trichinella spiralis. The active protease contains 226 residues. Those corresponding to the catalytic triad of the active site of mammalian serine proteases (His-57, Asp-102, and Ser-195 in chymotrypsin) occur in identical positions. A computer search for homology indicates 74.3% and 74.1% sequence identity of the mouse mast cell protease compared to those of rat mast cell proteases I and II (RMCP I and II), respectively. The six half-cystine residues in the mouse mast cell protease are located in the same positions as in the rat mast cell proteases, cathepsin G, and the lymphocyte proteases, suggesting that they all have identical disulfide bond arrangements. At physiological pH, the mouse and rat mucosal mast cell proteases have net charges of +3 and +4, respectively, as compared to +18 for the protease (RMCP I) from rat connective tissue mast cells. This observation is consistent with the difference in solubility between the mucosal and connective tissue mast cell proteases when the enzymes are extracted from their granules under physiological conditions.     

The concentration of retinoic acid determines the differentiated cell types formed by a teratocarcinoma cell line

Retinoic acid (RA) can induce the differentiation of teratocarcinoma cells in culture (S. Strickland and V. Mahdavi, 1978, Cell 15, 393-403; E. M. V. Jones-Villeneuve, M. W. McBurney, K. A. Rogers, and V. I. Kalnins, 1982, J. Cell. Biol. 94, 253-262). With the teratocarcinoma cell line, P19S1801A1 (O1A1), the differentiated cell types formed from cell aggregates exposed to RA are dependent on the concentration of drug used in the treatment. Cultures exposed to low concentrations (10(-9)M) are characterized by an abundance of cardiac muscle. Skeletal muscle becomes abundant at higher drug concentrations (10(-8)M) with neurons and astroglia appearing at very high concentrations (10(-7) to 10(-5) M). These results suggest that during normal embryogenesis, the commitment of pluripotent cells to particular developmental avenues may be determined in part by concentration gradients of substances such as retinoids.     

Amino acid charge distribution influences the assembly of apoprotein into light-harvesting complex II

The light-harvesting complex II of thylakoid membranes channels light energy into the photosynthetic reaction center II. The major apoproteins of this complex are the nuclear encoded light-harvesting chlorophyll a/b-proteins (LHCP). A model for the arrangement of LHCP in the thylakoid membrane predicts three alpha-helical membrane-spanning regions. The first and third putative membrane-spanning regions include oppositely charged amino acid residues. When the first and third helices are altered to carry only positive charges, the in vitro accumulation of LHCP in the complex is reduced. This mutation is partially rescued by the introduction of a new negative charge in the third helix, an arrangement that is reversed from the wild type. An arginine in the first helix is also important in some aspect of the process leading to the successful accumulation of the LHCP in thylakoids.     

Amino acid analysis by gas-liquid chromatography on a single column

A gas-liquid chromatography procedure for analysis of protein amino acids is described. Amino acids are esterified to their n-propyl esters then acylated to their heptafluorobutyryl (HFB) derivatives. These reactions were carried out in a single tube at 100°C. A simple steam-heating apparatus was constructed that heats only the bottom of the reaction vessel. Only 10 min were needed for esterification and 20 min for acylation, respectively. The resulting products, N-HFB-n-propyl esters of amino acids, were chromatographed on a single column. The amino acid compositions of chymotrypsinogen A and casein were analyzed by the present method, and the results were compared with those obtained by ion-exchange chromatography reported previously.     

Amino acid composition and level affect Bt protein concentration in Bt cotton

Low insect resistance has been widely observed in Bacillus thuringiensis (Bt) transgenic cotton. The objective of this study was to investigate the effects of amino acid compositions and their concentration on the Bt toxin content in Bt cotton to gain a better physiological understanding of the observed phenomenon. In the 2010 study, the leaf amino acid composition, contents, and Bt protein concentrations were investigated under high temperature (36?°C) and low temperature(18?°C) at both square and boll stage respectively. In 2011, the leaves were sprayed with ethionone sulfoximine (MSO), aminooxyacetic acid (AOA) or combination of MSO and AOA at the two developing stages, and the leaf amino acid composition and Bt protein concentrations were investigated. In 2012, 17 amino acid compositions were used to spray cotton plants at the same two stages, and the Bt protein concentration were measured. In comparison to the control, more amino acids changed and greater concentration changes had been observed under the extreme temperatures at boll stage compared to that at square stage, which were conformity to the changes of the leaf Bt protein concentration. More amino acids reduced and greater reduction was noted with the application of MSO, AOA or combined MSO and AOA at boll period than that at square period, which resulted in the reduction of the leaf Bt toxin concentration. The external uses of Aspartic acid, Glutamic acid, Glycine, Proline, Tyrosine, Methionine, Phenylalanine, Histidine and Arginin enhanced the leaf Bt toxin level significantly at boll stage. However, only Aspartic acid, Glutamic acid, Proline, Methionine, Arginin could increase Bt protein concentration markedly at square period and the bolstered extent were low. Therefore, it was concluded that cotton amino acid composition and concentration was more sensitive to external factors at boll stage. In addition, there are close relationship between leaf Bt toxin content and Aspartic acid, Glutamic acid, Glycine, Proline, Tyrosine, Methionine, Phenylalanine, Histidine and Arginin and their concentrations.