Methionine replacement

It is expected that loss of stability will occur for methionine replacements of Leu, lie and Phe because of a reduction in solvent transfer free energy (Table I). In addition, methionine has one or more rotatable bonds than leucine, isoleucine, valine and phenylalanine which may entail a greater loss of side-chain entropy upon folding (Table I). Strain may also be introduced in some cases. The range of destabilization that is observed for the single substitutions (-0.4 to -1.9 kcal/mol) (Table II) shows how the characteristics of the local site of substitution can contribute. 

Figure 5.13 Histone demethylases. Structures and mechanisms are illustrated for the two subclasses of histone lysine demethylases. (a) Views from an X-ray crystal structure of LSDl (PDB ID 2V1D) in complex with cofactor FAD and a peptide substrate analogue, where methionine replaces methylated lysine, and outline mechanism of the LSDl-catalysed demethylation reaction, (b) Views from an X-ray crystal structure of JMJD2A (PDB ID 20Q6) in complex with co-factor analogue N-oxa-lylglycine and histone substrate trimethylated at H3K9 (note that Ni(II) replaces Fe(II) for crystallography), and outline mechanism of JmjC-domain catalysed lysine demethylation. (c) Representative inhibitors of LSDl and JmjC-domain demethylases.

The other useful application of the affinity label derives from the fact that the sulfur in the methionyl residue that is alkylated is not essential for enzyme activity. Therefore in enzyme modified by incorporation of norleucine, the fraction of enzyme which is resistant to alkylation by the reagent is a measure of methionine replacement by norleucine in this locus and in each and every methionine locus in simultaneously synthesized bacterial protein (cf. Cowie et... 

Besides short ELPS, longer ELPs have also been conjugated to synthetic polymers. In one approach, Cu(I)-catalyzed azide-alkyne cycloaddition click chemistry was applied. For this purpose, ELPs were functionalized with azides or alkynes via incorporation of azidohomoalanine and homopropargyl glycine, respectively, using residue-specific replacement of methionine in ELP via bacterial expression [133]. More recently, an alternative way to site-selectively introduce azides into ELPs was developed. Here, an aqueous diazotransfer reaction was performed directly onto ELP[V5L2G3-90] using imidazole-1-sulfonyl azide [134]. 

Not all proteins are nutritionally equivalent. Mote of some than of others is needed to maintain nittogen balance because different proteins contain different amounts of the various amino acids. The body s requirement is for specific amino acids in the correct proportions to replace the body proteins. The amino acids can be divided into two groups essential and nonessential. There are nine essential or indispensable amino acids, which cannot be synthesized in the body histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. If one of these is lacking or inadequate, then—regardless of the total intake of protein—it will not be possible to maintain nitrogen balance since there will not be enough of that amino acid for protein synthesis. 

The introduction of redox activity through a Co11 center in place of redox-inactive Zn11 can be revealing. Carboxypeptidase B (another Zn enzyme) and its Co-substituted derivative were oxidized by the active-site-selective m-chloroperbenzoic acid.1209 In the Co-substituted oxidized (Co111) enzyme there was a decrease in both the peptidase and the esterase activities, whereas in the zinc enzyme only the peptidase activity decreased. Oxidation of the native enzyme resulted in modification of a methionine residue instead. These studies indicate that the two metal ions impose different structural and functional properties on the active site, leading to differing reactivities of specific amino acid residues. Replacement of zinc(II) in the methyltransferase enzyme MT2-A by cobalt(II) yields an enzyme with enhanced activity, where spectroscopy also indicates coordination by two thiolates and two histidines, supported by EXAFS analysis of the zinc coordination sphere.1210... 

The building blocks of proteins are the alpha-amino acids, and exclusively those with the L-configuration. There are 20 that occur in na- ture. They too all consist of the four elements C, H, N, and 0 two amino acids additionally contain sulfur (cysteine and methionine). In certain, but vital, enzymes (the peroxidases), sulfur is replaced by selenium. 

In one set of experiments a titration of compound is performed to assess its potency in vivo. HeLa cells are maintained in DMEM supplemented with 10% fetal bovine serum (FBS) at 37° in 5% C02. One day prior to labeling, the cells are seeded in 24-well plates at approximately 60,000 cells per well. The next day, cells are washed with warm (37°) PBS and the medium replaced with 250 41 of methionine-free DMEM containing 10% dialyzed serum (Invitrogen). After a 15-min incubation at 37°, different concentrations of compound are added to the cells (which can range from 1 nM to 50 fiM) and the incubation continued for another 45 min. Anisomycin is used as a positive control at a final concentration of 50 /iM. Fifty-five microcuries of 35S-methionine/cysteine [35S-methionine/cysteine express protein labeling mix (1175 Ci/mmol) (Per-kin-Elmer)] is added to each well (220 /(Ci/ml) and the incubation continued for another 15 min. 

One day prior to the isolation of polysomes, approximately 5 million HeLa cells are plated into 10-cm dishes. The following day, the media is replaced with fresh DMEM and compound is added to a concentration previously determined to inhibit translation in vivo by 35S-methionine metabolic labeling (see previously). 

Once a suitable crystal is obtained and the X-ray diffraction data are collected, the calculation of the electron density map from the data has to overcome a hurdle inherent to X-ray analysis. The X-rays scattered by the electrons in the protein crystal are defined by their amplitudes and phases, but only the amplitude can be calculated from the intensity of the diffraction spot. Different methods have been developed in order to obtain the phase information. Two approaches, commonly applied in protein crystallography, should be mentioned here. In case the structure of a homologous protein or of a major component in a protein complex is already known, the phases can be obtained by molecular replacement. The other possibility requires further experimentation, since crystals and diffraction data of heavy atom derivatives of the native crystals are also needed. Heavy atoms may be introduced by covalent attachment to cystein residues of the protein prior to crystallization, by soaking of heavy metal salts into the crystal, or by incorporation of heavy atoms in amino acids (e.g., Se-methionine) prior to bacterial synthesis of the recombinant protein. Determination of the phases corresponding to the strongly scattering heavy atoms allows successive determination of all phases. This method is called isomorphous replacement. 

Sulfur-bound L-Met, as opposed to S,N-chelated L-Met, is more reactive as a ligand on Pt(II) and can be slowly replaced by N7 of G (95, 96). Transfer of Pt onto DNA via Met-containing peptides or proteins may therefore be possible. Monofunctional adducts of the type [Pt(en)(G)(L-Met-S)] appear to be very stable (97) and so methionine may play a role in trapping these adducts. Also, the high trans influence of S as a Pt(II) ligand can lead to the facile labilization of trans-am(m)ine ligands and this allows cisplatin to react with GMP faster in the presence of L-Met then in its absence (98), which introduces another route to DNA platination. 

By the 1930s many workers had shown that nutritionally inadequate proteins, such as zein from maize, could be effective as a source of nitrogen if supplemented by additional amino acids (for zein, tryptophan). Even if it contained all the essential amino acids, the amount of protein in the diet influenced the results. Osbome and Mendel found that if the diet contained 18% by weight casein, which is low in cystine, young rats grew, but if the amount of protein was diminished, added cystine was required to offset the relative deficiency of this amino acid. Later, after methionine had been discovered, it was shown to replace the need for cystine. 

Another interesting blue protein is stellacyanin (FW = 20 000) from the Japanese lacquer tree Rhus vernicifera, in which, with respect to the other cupredoxins, glutamine replaces the methionine ligand.64 Stellacyanin also bears an overall positive charge (p/=9.9). It, therefore, gives a reversible Cu(II)/Cu(I) response at a glassy carbon electrode in aqueous solution (pH 7.6).61 The formal electrode potential of the Cu(II)/Cu(I) reduction (E01 = + 0.18 V vs. NHE) is the lowest among cupredoxins. 

Amino acid variants of IL-2 have been used to investigate the relationship between retention and protein structure in gradient RPLC.22 The protein contains three cysteine residues in its primary sequence at positions 58, 105, and 125. The two located at positions 58 and 105 are linked in a disulfide bridge in the native molecule. A series of variants in which the three cysteinyl residues were replaced with serines were compared. Substitution with serine at positions 58 or 105 forces the molecule to form an unnatural disulfide between positions 125 and 58 or 105. A methionine residue located at position 104 can also be oxidized to the sulfoxide... 

ESl-MS of cysteine solutions yields only the singly protonated hexamer [(Cys)6-H]. No preference for the chirality of the individual aminoacidic components is observed." Addition of cysteine to a serine solution yields abundant homochiral mixed octamer [(L-Ser)g m(L-Cys) -H] (m = 0-2). No [(L-Ser)g. (D-Cys)m H]+ (m = 1,2) octamers, but only [(L-Ser)g-H]+ are observed by using the wrong D-cysteine enantiomer. A similar picture is observed by replacing cysteine with other aminoacid, such as aspartic acid, asparagine, leucine, and methionine. 

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