Amino acid attributes

Several scales of amino acid attributes used in this report... 

What are the best scales of amino acid attributes ... 

Test of best 12 amino acid attributes in predicting TMH in membrane proteins of known structure ... 

Tested proteins (BESTP, Methods) had 28 observed TMH with 717 residues in the TMH conformation. Standard training procedure was used with each choice of amino acid attribute. Code numbers for amino acid scales are listed in Table 5... 

The observation that conformational preferences are specified by the contexts - local segment primary structure, amino acid attributes, the three-dimensional environment in protein and environmental media, has been discussed before [102-105] Algorithms that do take into account context-dependence of preferences [106] generally perform better for secondary structure prediction In this report simple mathematical representation of context dependence is obtained through preference flmctions that are analytical fiinctions of the surrounding sequence hydrophobicity or of any other amino acid attribute. Furthermore, preference functions are used to predict secondary structure motifs. It has turned out that for integral membrane proteins preference functions are excellent predictors of transmembrane segments in helical conformation In fact preference functions are much better predictors than the hydrophobicity scale chosen to extract these functions. 

Our algorithm can give partial answer to the question what attributes are optimal predictors for specific folding motifs. Kyte-Doolittle type hydropathy values and Chou-Fasman type conformational preferences are two obvious answers to the question what amino acid attributes are good predictors for majority of transmembrane helices. Indeed, three such scales MODKD, KYTDO and CPREF (Table 4), are on the very top of the list of the best amino acid scales (Table 5). Performance parameters that punish overprediction (A-j y and Qp) give advantage to hydropathy values. Modifications to the Kyte-Doolittle values in the MODKD... 

Well known Kyte-Doolittle scale [17] can be used throughout, except in the case when specific need exists to test other amino acid attributes. 

As the set of amino acid attributes, any hydrophobicity scale or any statistical, physical, chemical, or mathematical property of the 20 natural amino acid types may be used. Many amino acid scales either are obtained experimentally (by determining properties of individual amino acids) or are computed by statistical analysis on a certain set of membrane proteins. However, it is not clear in advance which one among... 

The physical properties of a typical amino acid such as glycine suggest that it is a very polar substance much more polar than would be expected on the basis of its formula tion as H2NCH2CO2H Glycine is a crystalline solid it does not melt but on being heated It eventually decomposes at 233°C It is very soluble m water but practically insoluble m nonpolar organic solvents These properties are attributed to the fact that the stable form of glycine is a zwittenon, or inner salt... 

Upon carefully controlled hydrolysis with hydrochloric acid at room temperature, the corresponding serine methyl esters 4 are obtained in reasonable yields. Higher yields of 4 arc obtained by hydrolyzing with dilute trifluoroacetic acid5. In some cases, the diastereomeric ratio of 4 does not exactly correspond to the d.r. of the adduct 3, which is attributed to different kinetics in the hydrolysis of the diastereomers 4. Subsequent treatment of the methyl ester with excess 5 N hydrochloric acid and methyloxirane as an acid scavenger results in the free amino acid 54,7. 

The Rh2(DOSP)4 catalysts (6b) of Davies have proven to be remarkably effective for highly enantioselective cydopropanation reactions of aryl- and vinyl-diazoacetates [2]. The discovery that enantiocontrol could be enhanced when reactions were performed in pentane [35] added advantages that could be attributed to the solvent-directed orientation of chiral attachments of the ligand carboxylates [59]. In addition to the synthesis of (+)-sertraline (1) [6], the uses of this methodology have been extended to the construction of cyclopropane amino acids (Eq. 3) [35], the synthesis of tricyclic systems such as 22 (Eq. 4) [60], and, as an example of tandem cyclopropanation-Cope rearrangement, an efficient asymmetric synthesis of epi-tremulane 23 (Eq. 5) [61]. 

Extensive studies of stereoselective polymerization of epoxides were carried out by Tsuruta et al.21 s. Copolymerization of a racemic mixture of propylene oxide with a diethylzinc-methanol catalyst yielded a crystalline polymer, which was resolved into optically active polymers216 217. Asymmetric selective polymerization of d-propylene oxide from a racemic mixture occurs with asymmetric catalysts such as diethyzinc- (+) bomeol218. This reaction is explained by the asymmetric adsorption of monomers onto the enantiomorphic catalyst site219. Furukawa220 compared the selectivities of asymmetric catalysts composed of diethylzinc amino acid combinations and attributed the selectivity to the bulkiness of the substituents in the amino acid. With propylene sulfide, excellent asymmetric selective polymerization was observed with a catalyst consisting of diethylzinc and a tertiary-butyl substituted a-glycol221,222. ... 

Similarly, the rate of inhibition of phosphoenzyme formation by diethylpyrocarbonate (DEPC) was much slower than the loss of ATPase activity [368], Even when the reaction approached completion with more than 90% inhibition of ATP hydrolysis, about 70% of the Ca -ATPase could still be phosphorylated by ATP (2.3nmoles of E P/mg protein). The remaining 30% of E P formation and the corresponding ATPase activity was not reactivated by hydroxylamine treatment, suggesting some side reaction with other amino acids, presumably lysine. When the reaction of the DEPC-modified ATPase with P-ATP was quenched by histidine buffer (pH 7.8) the P-phosphoenzyme was found to be exceptionally stable under the same conditions where the phosphoenzyme formed by the native ATPase underwent rapid hydrolysis [368]. The nearly normal phosphorylation of the DEPC-trea-ted enzyme by P-ATP implies that the ATP binding site is not affected by the modification, and the inhibition of ATPase activity is due to inhibition of the hydrolysis of the phosphoenzyme intermediate [368]. This is in contrast to an earlier report by Tenu et al. [367], that attributed the inhibition of ATPase activity by... 

Thus, a reversal of the diastereoseleetivity of the reaetion was observed if the enolate was prepared in the presenee of a lithiated base. The different behaviour of the base could be attributable to the geometry of the enolate. It was assumed that the use of KOH as a base would give predominantly the E enolate, whereas the Z enolate would be formed with a lithiated base such as LiN(TMS)2- This methodology was applied to the asymmetric synthesis of quaternary a-amino acids starting from an imino alaninate compound. 

Diffusion-mediated release of root exudates is likely to be affected by root zone temperature due to temperature-dependent changes in the speed of diffusion processes and modifications of membrane permeability (259,260). This might explain the stimulation of root exudation in tomato and clover at high temperatures, reported by Rovira (261), and also the increase in exudation of. sugars and amino acids in maize, cucumber, and strawberry exposed to low-temperature treatments (5-10°C), which was mainly attributed to a disturbance in membrane permeability (259,262). A decrease of exudation rates at low temperatures may be predicted for exudation processes that depend on metabolic energy. This assumption is supported by the continuous decrease of phytosiderophore release in Fe-deficient barley by decreasing the temperature from 30 to 5°C (67). 

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