Amino acids preferred

Richardson, J.S., Richardson, D.C. Amino acid preferences for specific locations at the ends of a helices. Science 240 1648-1652, 1988. 

From the discussions above, it can be concluded that amino acids prefer to chelate latter transition metals, then to bind to another metal ion via the nonchelating oxygen atom, while the oxygen atom already participating in chelation prefers binding to a Na+ or Ln3+ ion. 

Proteasomes of Thermoplasma contain a single type of p subunit but eukaryotic proteasomes contain subunits with at least three distinct substrate preferences.347 M9c They all appear to use the same hydrolytic mechanism but in their substrate specificities they are chymotrypsin-like, peptidylglutamyl-peptide hydrolyzing, branched chain amino acid preferring, and small neutral amino acid preferring based on the P, amino acid residue. In the spleen some of the P subunits of the proteasomes appear to have been replaced by proteins encoded by the major histocompatibility complex of the immune system (Chapter 31).347 This may alter the properties of the proteasome to favor their function in antigen processing. Proteasomes are also ATP- and ubiquitin-dependent, as discussed in Section 6. 

The. sip-file resulting from the randomise sequence command holds the names of all mutants in the sample population. Since these names contain the randomized positions as well as the substituted amino acids, they can be used to derive the distribution of amino acids for certain positions. By analyzing this distribution for the subset of nondestabilized mutants, it is possible to gain hints about amino acid preferences. 

In the cyclosporin series, addition of specific amino acids in excess to the fermentation medium effects a shift in the ratio of the metabolite composition and the incorporation of the surplus amino acid preferably in position 2 [21]. Systematic trials revealed that an amount of 8 g per litre is a favourable concentration. 

HO Villar, LM Kauvar. Amino acid preferences at protein binding sites. FEBS Lett... 

Pure amino acids Essential amino acids allowed but preferably from materials occurring naturally Essential amino acids allowed but preferably from materials occurring naturally Do not accept synthetic amino acids Preference for natural sources. Concentrated amino acids only when necessary to satisfy normal requirements... 

SI pockets [22], The three major activities, the peptidylglutamil-hydrolyzing (PGPH), trypsin-like and chymotrypsin-like activities, have been assigned to the three active subunits of ySl, yS2 and yS5, respectively, based on mutational and crystal structure analyses. Furthermore, it has been claimed, based on studies with model peptides and inactivation by inhibitors, that mammalian proteasomes also contain two other peptidase activities, referred to as branched-chain amino acid-preferring and small neutral amino acid-preferring (SNAAP). 

Amino acid Preferences for calcium all type (%) Preferences for calciiun side chain (%) Preference as bidentate (%)... 

Poulter and Rine carried out an extensive investigation into the substrate specificity in the two yeast splice variants of the protease, Reel and Afcl [19]. The authors generated a -CaaX library originating from the a-factor oligopeptide, with modifications at each of the ai, a2, and X positions. For each of the splice variants, there was a distinct preference for specific residues at each of the positions. Additionally, there were also library members that were capable of only undergoing proteolysis by one of the enzymes. Despite a sequence similarity between the two splice variants, it appeared that they each possessed unique amino acid preferences however, some overlap was observed. Poulter and coworkers also synthesized CaaX peptides from both yeast and mammalian proteins to further characterize the enzymatic activity of Reel [20], While both farnesylated and... 

An extensive systematic substitution study of the a-factor CaaX motif has revealed amino acid preferences and restrictions of the yeast CaaX... 

The fact that amino acids prefer certain secondary structures does not address the question of why these structural preferences... 

Two of the hydrophihcity scales in Table 2 were derived from experimental measures of the behavior of amino acids in various solvents, namely partitioning coefficients [K-D index of Kyte and Doolittle (30)] or mobility in paper chromatography [Rf index of Zimmerman et al. (31)]. By contrast, the Hp index was obtained from quantum mechanics (QM) calculations of electron densities of side chain atoms in comparison with water (32). The Hp index is correlated highly with these two established hydrophobicity scales (Table 4). Therefore, like the polarizability index, it is possible to represent fundamental chemical properties of amino acids (hydrophUicity, Hp) with parameters derived from ab initio calculations of electronic properties. However, in contrast to polarizabihty (steric effects), hydrophihcity shows significant correlation with preference for secondary structure. Thus, hydrophobic amino acids prefer fi-strands (and fi-sheet conformations) and typically are buried in protein structures, whereas hydrophilic residues are found commonly in turns (coil structure) at the protein surface. 

Proteinase K Serine P-1 1 Pi P-1 = non-specific but aromatic or hydrophobic amino acids preferred. Pi = non-specific. 5-50 pg/p.1... 

The cleavage/attachment site consists of 3 amino acids. The first amino acid is the site of attachment and can be glycine, alanine, serine, cysteine, aspartic acid, or asparagine. Only these small amino acids are permissible in chimeric studies [105,108,109] and are the only ones reported in the C-terminal tails of sequenced GPI-anchored proteins [5,104-106]. Serine is most favorable [109] and is present in over half of the known GPI anchor proteins. The second amino acid, on the C-terminal side, can be any amino acid except proline. In contrast, the third amino acid is restricted to only small amino acids, preferably glycine or alanine, although serine and to a lesser extent cysteine, threonine and valine are possible [105,108]. 

Pridzun L, Wiesmiiller K-H, Kienle S, Jung G, Walden P (1996) Amino acid preferences in the octa-peptide subunit of the major histocompatibility complex class 1 heterotrimer H-2LJ, Eur J Biochem 236 249-253. 

Fig. 10 Comparison of amino acid preferences in hot spots from Bullock et al. [67] and Bogan and Thom [25] (Reprinted with permission from Bullock et al. [67], Copyright (2011) American Chemical Society)...

Degradation of a-amino acids. a-Amino acids (preferably the sodium salts) are converted into carbonyl compounds by reaction with N-sulfinylaniline in DMSO (80°) (equation 1). Esters are degraded to a-keto esters (rather low... 

L. Zhong and W. C. Johnston, Jr., Environment affects amino acid preference for secondary strnctnre, Proc. Natl. Acad. Sci. USA 89, 4462-4465 (1992). 

Eizert H, Bander P, Bagossi P, Sperka T, MMossy G, Boross P, Eber IT, Tozser J. Amino acid preference of retroviral proteases for amino-terminal positions in a type 1 cleavage site. J Virol. 2998 82 10111-10117. 

Closer examination of the carboxy-terminal domain reveals a tendency for it to be able to form an amphiphilic O-strand. There are also strong amino acid preferences in positions -3 to +1 (shaded in Fig.4) these positions contain very few turn-promoting residues (Gly, Pro, Asn) have a rather low Ser-content, and acidic residues start appearing in abundance only in position +2. Conversely, Ala is very frequent in positions -1 and +1, and Ihe branched hydrophobic residues He and Val are frequently found in position -3, Fig.4. 

There are two basic reasons that allow delineation of reading or protein coding frames in nucleotide sequences, namely (1) the distribution of the 20 amino acids in proteins is not uniform and (ii) the degenerate but different codons for a particular amino acid are not uniformly selected. In other words, proteins display amino acid preferences and the coding sequences display codon preferences. These genetic facts result obviously in different expected frequencies for given codons and different expected positional base frequencies in the three codon nucleotide sites. As an example, the third position is almost uniformly occupied by the four bases as the amino acid code is generally insensitive to the nucleic acid selection at this site. 

As reported by Lifson and Sander (1979, 1980a,b), residue contact in antiparallel and in parallel j8 strands differs in amino acid preference. The correlations were investigated between nearest neighbors (ij) in adjacent strands (see Fig. 2.18). Pair correlation among groups of similar polarity has been reported by von Heijne and Blomberg (1977,1978). Parallel jS strands impose more severe constraints on amino acid content than antiparallel P strands. 

---