Cellular folding

VIII. Role of Prolyl Isomerase for Cellular Folding... 

A retarding effect of CsA on cellular folding, mediated possibly by the inhibition of PPI activity, was observed for two large proteins, collagen and transferrin. Both are secreted proteins that mature to their native oligomeric structure in the endoplasmic reticulum. 

The conformation of Xaa-Pro peptide bonds in the newly synthesized polypeptide chains prior to cellular folding is not known. The product of protein biosynthesis could be a uniform chain with all peptide bonds in the trans conformation. If this chain starts to fold immediately, then the trom-prolines would be in the correct conformation already, the cis-prolines would be in the incorrect isomeric state, and their trans — cis isomerization would be involved in the folding of all molecules. Alternatively, if there is sufficient time available for the Xaa-Pro bonds of the nascent chains to reach a cis/trans equilibrium (e.g., when folding is transiently arrested by binding to other proteins, such as heat-shock protein (HSP70), then the distribution of prolyl cis and trans isomers prior to cellular folding could be similar to the distribution found in the unfolded protein in vitro. Such a case was encountered in the maturation... 

Direct inspection of the pattern of desolvation of the main chain clearly reveals that the cellular fold of the human prion [39] (Fig. 5.11) is too vulnerable to water attack and at the same time too sticky to avert aggregation. Clearly, its sequence has not been optimized to keep the backbone hydrogen bonds dry in the folded state. In fact, their extent of exposure of backbone hydrogen bonds is the highest among soluble proteins in the entire PDB, with the sole exception of some toxins whose stable fold is held together by a profusion of disulfide bridges, as shown in Chap. 2. 

Most reactions in cells are carried out by enzymes [1], In many instances the rates of enzyme-catalysed reactions are enhanced by a factor of a million. A significantly large fraction of all known enzymes are proteins which are made from twenty naturally occurring amino acids. The amino acids are linked by peptide bonds to fonn polypeptide chains. The primary sequence of a protein specifies the linear order in which the amino acids are linked. To carry out the catalytic activity the linear sequence has to fold to a well defined tliree-dimensional (3D) stmcture. In cells only a relatively small fraction of proteins require assistance from chaperones (helper proteins) [2]. Even in the complicated cellular environment most proteins fold spontaneously upon synthesis. The detennination of the 3D folded stmcture from the one-dimensional primary sequence is the most popular protein folding problem. 

Hartl, F.U. Molecular chaperones in cellular protein folding. Nature 381 571-580, 1996. 

As stated above, calcium is an extremely important cellular ion for several cellular functions. The concentration of calcium in human extracellular fluid is about 2.5 mM, while the intracellular concentration is only 100-200 nM depending on the cell type. Thus, there is 10 000-20 000 fold concentration difference between the cell interior and exterior that has to be maintained by cellular pumping mechanisms. This requires a large amount of energy. " ... 

Protein trafficking is the transport of proteins to their correct subcellular compartments or to the extracellular space ( secretory pathway ). Endo- and exocytosis describe vesicle budding and fusion at the plasma membrane and are by most authors not included in the term protein trafficking. Protein quality control comprize all cellular mechanisms, monitoring protein folding and detecting aberrant forms. 

Proteosomal degration is the process by which improperly folded proteins or proteins with altered post-translational modifications are removed from a cell before they have a detrimental effect on cellular function. This is performed in small organelles known as proteosomes. Proteins are targeted for destruction in the proteosome by having a number of small ubiquitin molecules added. 

SUMOylation. Figure 1 SUMOylation is a reversible and regulated process. Target protein modification by SUMO can be initiated and terminated by different cues. Sumoylation leads to changes in the behavior of the modified protein, for example, different cellular localization, enhanced/reduced activity, or increased stability. These changes are due to alterations either in protein interactions or protein folding. 

Both the heat and cold shock response are universal and have been studied extensively. The major heat shock proteins (HSPs) are highly conserved. They are involved in the homeostatic adaptation of cells to harsh environmental conditions. Some act as molecular chaperones for protein folding, while others are involved in the processing of denatured polypeptides whose accumulation would be deleterious. The cold shock results in the transient induction of cold shock proteins (CSPs), which include a family of small acidic proteins carrying the cold shock domain. The CSPs appear to be involved in various cellular functions such as transcription, translation and DNA recombination. 

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