Productive folding pathways proteins

Plant-based production systems are now being used commercially for the synthesis of foreign proteins [1-3]. Post-translational modification in plant cells is similar to that carried out by animal cells plant cells are also able to fold multimeric proteins correctly. The sites of glycosylation on plant-produced mammalian proteins are the same as on the native protein however, processing of N-linked glycans in the secretory pathway of plant cells results in a more diverse array of glycoforms than is produced in animal expression systems [4]. Glycoprotein activity is retained in plant-derived mammalian proteins. 

Have we exhausted catalases as a source of information about protein structure and the catalatic mechanisms The answer is clearly no. With each structure reported comes new information, often including structural modifications seemingly unique to catalases and with roles that remain to be explained. Despite a deeply buried active site, catalases exhibit one of the fastest turnover rates determined. This presents the as yet unanswered question of how substrate can access the active site while products are simultaneously exhausted with a potential turnover rate of up to 10 per second. The complex folding pathway that produces the intricate interwoven arrangement of subunits also remains to be fully clarified. 

Since plastids have a limited set of protein degradation pathways, foreign proteins that exhibit harmful effects to the plant in the cytoplasm may be more stable when they accumulate within the chloroplast (Heifetz, 2000). For example, the vaccine protein cholera toxin B subunit was shown to be toxic even when it accumulated to very low levels within the plant cytoplasm, but was nontoxic when it accumulated to large quantities within the chloroplast. Plastids also possess the ability to form disulfide bonds, a requirement for many correctly folded mammalian proteins (Daniell et al., 2005a). These properties have made them attractive for the production of biopharmaceuticals in plants. 

Structure analysis of several proteases involved in blood coagulation and fibrinolysis reveals a diverse, sometimes repetitive, assembly of discrete protein modules (Fig. 9.4) [56]. While these modules represent independent structural units with individual folding pathways, their concerted action contributes to function and specificity in the final protein product. On the genetic level, these individual modules are encoded in separate exons. Over the course of modular protein evolution, new genes are created by duplication, deletion, and rearrangement of these exons. Mechanistically, the exon shuffling actually takes place in the intervening intron sequences (intronic recombination - for further details see [10]). 

Figure 3. Intracellular folding pathway of P22 tailspike proteins. The newly synthesized wild type or mutant polypeptide chains at 30°C first fold into partially folded monomeric intermediates. These species fold and associate to form a protrimer intermediate. Further folding results in a thermostable native tailspike. At 40°C, the folding is inhibited and tsf mutants act by blocking an early step in chain folding, prior to association. However, if infected cells are shifted to 30 C, the mutant chains continue through the productive pathway.

At this stage, production of humanized glycoproteins through bacterial glycoengineering techniques has not been explored in depth. There are some difficulties that may hamper this endeavor, such as the expression of properly folded human proteins in the bacterial periplasm, as well as the intricacy inherent to the biosynthesis of complex human oligosaccharides. This goal maybe achieved in the future when complete details of bacterial protein glycosylation pathways are revealed. 

Yet the unfolded 1-D chain does fold into a functionally active unit, which maintains a reasonably well defined structure, within certain limits. It does so in a very short time, far shorter than any estimated time that would have been required by the random selection of a folding pathway. This means that there exists not only a thermodynamic force leading from the unfolded to the folded state, but there must be some dynamical forces, at least in part of the folding pathway, that direct the protein to move toward the final product. 

The term "structural genomics" is used to describe how the primary sequence of amino acids in a protein relates to the function of that protein. Currently, the core of structural genomics is protein structure determination, primarily by X-ray crystallography, and the design of computer programs to predict protein fold structures for new proteins based on their amino acid sequences and structural principles derived from those proteins whose 3-dimensional structures have been determined. Plant natural product pathways are a unique source of information for the structural biologist in view of the almost endless catalytic diversity encountered in the various pathway enzymes, but based on a finite number of reaction types. Plants are combinatorial chemists par excellence, and understanding the principles that relate enzyme structure to function will open up unlimited possibilities for the... 

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