Modification, folding and transport of released polypeptide

Content
Expression of Gene : Protein Synthesis 4. Translation in Prokaryotes and Eukaryotes
Formation of amino-acyl tRNA
Initiation of polypeptide 
Initiation in prokaryotes
Initiation in eukaryotes
Kozak's scanning hypothesis
Elongation of polypeptide
Binding of AA-tRNA at site 'A' of ribosome
Formation of peptide bond
Translocation of peptidyl tRNA from 'A' to 'P' site
Termination of polypeptide
Modification, folding and transport of released polypeptide
Translation in chloroplasts and mitochondria


Modification, Folding and Transport of Released Polypeptide
Modification of released polypeptide
The released polypeptide is modified in various ways. An enzyme deformylase removes the formyl group of first amino acid methionine. (Fig. 34.13). Due to the action of certain other enzymes, exo-amino-peptidases, amino acids may be removed from either the N-terminal end or the C-terminal end or both. Due to this modification, therefore, the N-terminal amino acid may not be methionine in some cases (Fig. 34.13), although in protein synthesis, the first amino acid is always methionine. The polypeptide chain singly or in association with other chains also folds to take up a tertiary structure. In this manner, these proteins ultimately become functional enzymes.

Chaperones in folding and assembly of proteins
Molecular chaperones represent a diverse class of protein molecules (recently discovered), which play a significant role in folding of individual polypeptides and in assembly of multimeric proteins, but are not themselves components of the final functional structures. These chaperones function by inhibiting incorrect molecular interactions, which are often possible in their absence (word chaperone, rather chaperon is used in english to describe 'a person' usually a married or elderly woman who for the sake of propriety, accompanies a young unmarried lady in public, as guide and protector). Some molecular chaperones (but not all of them) are also stress proteins, so that it is possible that all stress proteins act as molecular chaperones. Another term 'chaperonin' is sometimes used interchangeably with 'molecular chaperones' , but refers to only one of the different classes of molecular chaperones. (Table 34.6). Many chaperonins are ATPases, whose function was demonstrated by in vitro folding and assembly of RUBISCO, which required groEL and groES proteins of E. coli. Another chaperonin encoded by a nuclear gene is hsp60 (heat shock protein) which is translated in the cytosol and imported into the mitochondrion, where it is folded and assembled into a tetradecameric structure. Some chaperonins can induce their own folding and self assembly (e.g. groEL protein); there are others (e.g. hsp60), which can fold and assemble only in the presence of other pre-existing functional chaperonins.
 
Removal of formyl group from released polypeptide and a subsequent removal of methionine, so that the second amino acid becomes terminal (modified from Lewin's 'Genes').
Fig. 34.13. Removal of formyl group from released polypeptide and a subsequent removal of methionine, so that the second amino acid becomes terminal (modified from Lewin's 'Genes').

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Protein sorting or protein trafficking using signal proteins
The proteins synthesized in the cell have to be translocated to appropriate location within the same cell or other cells. This process is called protein sorting or protein trafficking and involves interaction of celt membranes either with some parts of newly synthesized protein or with a protein sequence added to this new protein. These protein sequences interacting with membranes are called signal sequences or transit peptides, or leader sequences, which are recognized by receptors located within the membrane. The transfer of proteins may be coupled with translation- co-translational transfer (proteins synthesized on ribosomes attached to endoplasmic reticulum = rough ER) or may take place after the translation- post-translational transfer (proteins synthesized on free ribosomes).

Proteins that are imported into mitochondria and chloroplasts possess N-terminal leader sequences that target them to organelle envelope or to inside the organelle. The leader sequence may have regions, which comprise envelope targeting signal and matrix targeting signal. For instance, cytochrome C, which is bound on inner membrane of mitochondria facing the intermembrane space has a leader sequence of 61 amino acids, of which 32 N-terminal amino, acids (mainly charged) make matrix targeting signal and the next 19 amino acids (uncharged) make envelope targeting signal. These regions of leader sequence decide the ultimate location of protein. Eventually, the leader sequence is cleaved by a protease and degraded. The entire process requires ATP as a source of energy.

The proteins synthesized on rough ER are transported, while still being synthesized. A signal hypothesis has been proposed for this transport. According to this hypothesis ribosomes synthesizing proteins are attached to the membrane via the leader sequence. In the protein, the presence of a signal recognition particle (SRP) in the form of a ribonucleoprotein complex (IIS), and in the membrane, the presence of a SRP receptor help in the transfer of a ribosome (engaged in protein synthesis) to the membrane. The function of SRP and, SRP receptor, is now over and transport of protein is facilitated by membrane bound ribosomes.

Several other mechanisms for protein transport or protein trafficking have been discovered. The function of signal sequences has been confirmed in many cases by joining a specific signal sequence to an unrelated protein (using a hybrid gene). In these cases the signal sequence directs the transport of unrelated proteins to cell organelles. For more details, readers are advised to consult Lewin's "Genes . V".