Bond formation, protein

Disulfide bond formation, protein folding, and assembly of multimeric proteins, which take place exclusively In the rough ER, also are discussed in this section. Only properly folded and assembled proteins are transported from the rough ER to the Golgi complex and ultimately to the cell surface or other final destination. Unfolded, misfolded, or partly folded and assembled proteins are selectively retained In the rough ER. We consider several features of such quality control in the latter part of this section. 

There are numerous references in the literature to irreversible adsorption from solution. Irreversible adsorption is defined as the lack of desotption from an adsoibed layer equilibrated with pure solvent. Often there is no evidence of strong surface-adsorbate bond formation, either in terms of the chemistry of the system or from direct calorimetric measurements of the heat of adsorption. It is also typical that if a better solvent is used, or a strongly competitive adsorbate, then desorption is rapid and complete. Adsorption irreversibility occurs quite frequently in polymers [4] and proteins [121-123] but has also been observed in small molecules and surfactants [124-128]. Each of these cases has a different explanation and discussion. 

When both building block units are m place on the acyl carrier protein carbon-carbon bond formation occurs between the a carbon atom of the malonyl group and the carbonyl carbon of the acetyl group This is shown m step 1 of Figure 26 3 Carbon-carbon bond formation is accompanied by decarboxylation and produces a four carbon acetoacetyl (3 oxobutanoyl) group bound to acyl earner protein... 

Figure 6.8 Schematic diagram of the enzyme DsbA which catalyzes disulfide bond formation and rearrangement. The enzyme is folded into two domains, one domain comprising five a helices (green) and a second domain which has a structure similar to the disulfide-containing redox protein thioredoxin (violet). The N-terminal extension (blue) is not present in thioredoxin. (Adapted from J.L. Martin et al.. Nature 365 464-468, 1993.)...

Martin, J.E., Bardwell, J.C.A., Kuriyan, J. Crystal structure of the DsbA protein required for disulphide bond formation in vivo. Nature 365 464-468, 1993. 

In addition to being a remarkable demonstration of the power of computer-based combinatorial design of a protein fold, this designed peptide is the shortest known peptide consisting entirely of naturally occurring amino acids that folds into a well-ordered structure without metal binding, oligomerization or disulfide bond formation. 

FIGURE 1.9 (a) Amino acids build proteins by connecting the n-carboxyl C atom of one amino acid to the n-amino N atom of the next amino acid in line, (b) Polysaccharides are built by combining the C-1 of one sugar to the C-4 O of the next sugar in the polymer, (c) Nucleic acids are polymers of nucleotides linked by bonds between the 3 -OH of the ribose ring of one nucleotide to the 5 -P04 of its neighboring nucleotide. All three of these polymerization processes involve bond formations accompanied by the elimination of water (dehydration synthesis reactions). 

Protein-Free 50S Ribosomal Subunits Catalyze Peptide Bond Formation In Vitro... 

Perhaps the most significant case of catalysis by RNA occurs in protein synthesis. Harry F. NoIIer and his colleagues have found that the peptidyl transferase reaction, which is the reaction of peptide bond formation during protein synthesis (Figure 14.24), can be catalyzed by 50S ribosomal subunits (see Chapter 12) from which virtually ail of the protein has been removed. These... 

Schemes are available, however, that start from the free carboxylic acid, plus an activator . Dicyclohexylcarbodiimide, DCC, has been extensively employed as a promoter in esterification reactions, and in protein chemistry for peptide bond formation [187]. Although the reagent is toxic, and a stoichiometric concentration or more is necessary, this procedure is very useful, especially when a new derivative is targeted. The reaction usually proceeds at room temperature, is not subject to steric hindrance, and the conditions are mild, so that several types of functional groups can be employed, including acid-sensitive unsaturated acyl groups. In combination with 4-pyrrolidinonepyridine, this reagent has been employed for the preparation of long-chain fatty esters of cellulose from carboxylic acids, as depicted in Fig. 5 [166,185,188] ...

Post-translation modification Changes that occur to proteins after peptide-bond formation has occurred, e.g. glycosylation and acylation. 

Disulfide bonds between and within polypeptides stabilize tertiary and quaternary structure. However, disulfide bond formation is nonspecific. Under oxidizing conditions, a given cysteine can form a disulfide bond with the —SH of any accessible cysteinyl residue. By catalyzing disulfide exchange, the rupture of an S— bond and its reformation with a different partner cysteine, protein disulfide isomerase facilitates the formation of disulfide bonds that stabilize their native conformation. 

Elongation is a cycUc process on the ribosome in which one amino acid at a time is added to the nascent peptide chain. The peptide sequence is determined by the order of the codons in the mRNA. Elongation involves several steps catalyzed by proteins called elongation factors (EFs). These steps are (1) binding of aminoacyl-tRNA to the A site, (2) peptide bond formation, and (3) translocation. 

Polyacrylamide gel electrophoresis results suggest that p-LG undergoes a greater conformational loss as a fimction of extrusion temperature than a-LA, presumably due to intermolecular disulfide bond formation. Atomic force microscopy indicates that texturization results in a loss of secondary structure of aroimd 15%, total loss of globular structure at 78 °C, and conversion to a random coil at 100 °C (Qi and Onwulata, 2011). Moisture has a small effect on whey protein texturization, whereas temperature has the largest effect. Extrusion at or above 75 °C leads to a uniform densely packed polymeric product with no secondary structural elements (mostly a-helix) remaining (Qi and Onwulata, 2011). 

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