Amino acid scales

Calculate/plot amino acid scales (ProtScale)... 

An amino acid scale refers to a numerical value assigned to each amino acid such as polarity, hydrophobicity, accessible/buried area of the residue, and propensity to form secondary structures (e.g., amino acid parameter of AAIndex). For example, selecting (clicking) ProtScale from the list of ExPASy Proteomics tools opens the query page with a list of predefined amino acid scales. Paste the query... 

ProtScale tool of ExPASy computes amino acid scale (physicochemical properties/parameters) and presents the result in a profile plot. Perform ProtScale computations to compare the hydrophobicity/polarity profiles with %buried resi-dues/%accessible residues profiles for human serine protease with the following amino acid sequence. 

Glucose, amino acids Scale-up for High Five cells based on nutrient consumption analysis and specific nutrient supplementation. 29... 

Ten integral membrane proteins of well known structure (BESTP, Methods) have been tested first. Only the Kyte-Doolittle and our modification of the Kyte-Doolittle scale (MODKD, 83) were able to predict all od these ten membrane proteins with 100% correct transmembrane topology, i.e. all transmembrane helices were correctly predicted at their observed sequence locations and there were no overpredicted TMH (Table 7). Only the Chothia buried surface scale (CHOTH, 29) did not recognize one of ten membrane proteins as the membrane protein (the subunit H fi-om the photosynthetic reaction center from R. viridis). Nine long extramembrane helices in these 10 proteins were not predicted as TMH by any of 12 tested amino acid scales. That these sensitive tests of our predictor do not depend on the chosen training procedure was checked by using different training procedures. After... 

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 prediction performance of 12 best amino acid scales... 

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... 

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 subjective choice of attributes can be eliminated also by the procedure of testing all published amino acid scales with respect to the prediction accuracy for transmembrane helices in the chosen training data set of proteins. Our pref suite of algorithms can indeed perform such a task. Such results are beyond the scope of this chapter and will be published elsewhere. 

Campen A, Williams RM, Brown CJ, Meng J, Uversky VN, Dunker AK. TOP-IDP-scale a new amino acid scale measuring propensity for intrinsic disorder. Protein Pept Lett. 2008 15(9) 956-963. 

Coupling onto N-Methylated Amino Acids, Scale ... 

Reagent for the resoln. of chiral amino acids. Scales. 

The first of the two experiments given below illustrates the separation of amino-acids, now an almost classic example of the use of paper chromatography the second illustrates the separation of anthranilic acid and iV-methylanthranilic acid. Both experiments show the micro scale of the separation, and also the fact that a mixture of compounds which are chemically closely similar can be readily separated, and also can be identified by the use of controls. 

The product quaUty considerations for nonphotosynthetic microorganisms are similar to those for algae. Tables 6 and 7 present composition and amino acid analyses, respectively, for selected bacteria, yeasts, molds, and higher fungi produced on a large pilot-plant or commercial scale. Table 8 summarizes results of proteia quaUty and digestibiUty studies. 

The reaction can be used ia the large-scale production of the optically active amino acid detivatives. The chiraUty of the a-carbon is substantially retained and resolution of the product is avoided. 

Fig. 1. Schematic drawing of precursors for selected brain oligopeptides. Shaded areas represent the location of sequences of active peptide products which are normally cleaved by trypsin-like enzymes acting on double-basic amino acid residues. Precursors are not necessarily drawn to scale, (a) CRF precursor (b) proopiomelanocortin (POMC) (c) P-protachykinin (d) proenkephalin A (e) CGRP precursor (f) preprodynorphin, ie, preproenkephalin B. Terms are...

Development of a peptide vaccine is derived from the identification of the immunodominant epitope of an antigen (141). A polypeptide based on the amino acid sequence of the epitope can then be synthesized. Preparation of a peptide vaccine has the advantage of allowing for large-scale production of a vaccine at relatively low cost. It also allows for selecting the appropriate T- or B-ceU epitopes to be included in the vaccine, which may be advantageous in some cases. Several vaccines based on peptide approaches, such as SPf66 (95) for malaria and an HIV-1 peptide (142) have been in clinical trials. No peptide vaccines are Hcensed as yet. 

Amino Acids. Chloroformates play a most important role for the protection of the amino group of amino acids (qv) during peptide synthesis (32). The protective carbamate formed by the reaction of benzyl chloroformate and amino acid (33) can be cleaved by hydrogenolysis to free the amine after the carboxyl group has reacted further. The selectivity of the amino groups toward chloroformates results in amino-protected amino acids with the other reactive groups unprotected (34,35). Methods for the preparation of protected amino acids on an industrial scale have been developed (36,37). A wide variety of chloroformates have been used that give various carbamates that are stable or cleaved under different conditions. 

Resolution of Racemic Amines and Amino Acids. Acylases (EC3.5.1.14) are the most commonly used enzymes for the resolution of amino acids. Porcine kidney acylase (PKA) and the fungaly3.spet i//us acylase (AA) are commercially available, inexpensive, and stable. They have broad substrate specificity and hydrolyze a wide spectmm of natural and unnatural A/-acyl amino acids, with exceptionally high enantioselectivity in almost all cases. Moreover, theU enantioselectivity is exceptionally good with most substrates. A general paper on this subject has been pubUshed (106) in which the resolution of over 50 A/-acyl amino acids and analogues is described. Also reported are the stabiUties of the enzymes and the effect of different acyl groups on the rate and selectivity of enzymatic hydrolysis. Some of the substrates that are easily resolved on 10—100 g scale are presented in Figure 4 (106). Lipases are also used for the resolution of A/-acylated amino acids but the rates and optical purities are usually low (107). 

Advantages of chromatography for protein separations include the large number of possible chemical interactions resulting from variations in the frequency and distribution of the amino-acid side chains on the surfaces of the proteins, and the availability of a wide array of different adsorption media. Chromatography has high efficiency and selectivity, and adequate scale-up potential. 

Hydrophobicity scales measure the degree of hydrophobicity of different amino acid side chains... 

Figure 12.23 Hydropathy plots for the polypeptide chains L and M of the reaction center of Rhodobacter sphaeroides. A window of 19 amino acids was used with the hydrophohicity scales of Kyte and Doolittle. The hydropathy index is plotted against the tenth amino acid of the window. The positions of the transmembrane helices as found by subsequent x-ray analysis by the group of G. Feher, La Jolla, California, ate indicated by the green regions.

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