Amino Acids and Proteins UPDATES

Prion —

There is a commentary and paper in the Nature of 31st of May 2007 on prion of great interest..

Prions are proteins which form insoluble amyloid structures associated with neurodegenerative disorders in mammals. The intriguing place of prions is that they are proteins whose conformation and ability for amyloid formation is self-seeding) and thereby infectious. The conformatiorially converted prion state can be transmitted from cell to cell within or, in some cases, between organisms. Prions, too, can be either deadly or beneficial.

The ability of proteins to form P-.sheet-rich amvloids is associated not only with disease, but also with diverse normal biological functions, including cell adhesion , skin pigmentation, adaptation to environmental stresses and perhaps even long-term neuronal memory.

The first identified prion protein identified was PrP, whose conversion to the prion conformcr (PrPsc) is associated with .several fatal neuro-degenerative diseases. More recently, several prions in yeast and other fungi have been identified that are unrelated to PrP or one another-; some of these may have beneficial effects. The most well-studied is Sup35, a translation-termination factor whose conversion to the prion state reduces its activity. This increases the read-through of stop codons, revealing hidden genetic variation and creating complex new phenotypes in a single step.

Sup35 prions show two of the properties of prion biology that were initially identified for mammalian PrP. First, both Sup35 and PrP can adopt not just one prion conformation, but several related yet structurally distinct conformations (known as strain.or variants). Each conformation self-perpetuates and gives a distinct biological phenotype. Second, the transmission of the prion state between proteins of different species is limited by a species barrier that can occasionally be crossed. In both yeast and mammals the ability to establish and overcome species barriers is, in some unknown way, related to the ability of prions to form distinct Strains.

The carboxy-terminal domain of Sup35 encodes the translation-termination function Whether Sup35 exists in either a prion or a non-prion state is controlled by the interplay of two other domains11″. The middle region (M) has a strong solubilising activity and is very rich in charged residues. The amino (N) terminus is readily forms the amyloid conformation and is of unusually low sequen ce complexity, composed primarily of glutamine, asparagine, glycine and tyrosine residues .

In its non-prion state NM is compact, but plastic , rapidly fluctuating through diverse conformations. The structure of NM in its prion state is of interest. It may be that two discrete regions of the N domain are in self-contact within NM; the region between them is sequestered from intermolecular contacts, whereas elements proximal and distal to the contacts are not part of the amyloid core. Cross-linking NM molecules at one of the intermolecular contacts, but not elsewhere, accelerates nucleation. Other evidence suggests that most residues of the N domain are in jntermolecular contact, stacking in-register on themselves.

Single substitution mutations in certain regions of the N terminus can have profound effects on many aspects of prion biology: they can inhibit replication, bias prion conversion towards the production of distinct strains, and increase or decrease the ability of prions to cross species barriers. Which suggests that precise features of amino acid sequence have critical roles in Sup35 prion biology. Remarkably, however, scrambling the sequence of X docs not prevent prion formation. NM prion formation maybe mainly dependent on the amino acid composition and largely independent of primary sequence.

The authors of this remarkable paper show that only a small subset of ScNM peptides capture the ScNM protein from solution. And this is sufficient to convert soluble proteins to the prion state.

The same sequence elements are responsible for the species seeding activity and formation of distinct prion strains.

Surewicz W 2007 discriminating taste of prions Nature 447, pp 541-2

Tesier PM and Lindquist S 2007 Prion recognition elements govern nucleation, strain recognition and species barrier 447, 556-561

Protein —

Polypeptides after synthesis on the cell’s protein-assembly apparatus require further elaboration for use. Both the peptide backbone and its side chains may need to be altered by post-translational modifications, the covalent attachment of chemical groups that change the properties, and hence the function, of newly generated proteins. Post-translational modifications also control the degradation of aberrant proteins and proteins at the end of their lifespan. Such modifications dramatically expand the compositional and functional complexity of these molecules.

Proteins may exist as a mixture of forms, each incorporating different post-translational modifications.

One intricate form of post-translational modifications is the attachment of carbohydrates, glycans, either to nitrogen atoms (N-linked) in the side chains of asparagine amino acids, or to oxygen atoms (O-linked) on the side chains of serine or threonine. In living cells, glycosidase and glycosyl transferase enzymes first trim N-linked glycans, then extend them with sugars that can branch in several directions, generating numerous variations on a theme. Glycosyl transferases also act on O-linked glycans, imposing similar extensions and modifications. To add to the complexity, each sugar can bear different chemical groups, and the linkages between sugars have specific orientations. Many biological processes, such as cellular differentiation and development, cell adhesion, immune surveillance and inflammation, rely to varying degrees on the correct decoration of proteins with such glycans.

Grotenbreg and Ploegh Nature 2007, vol 446, pp 993-995.

Protein 2

The molecular mechanism of protein translocation, is the focus of a Rapoport in Nature.

Proteins transported across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane include soluble proteins, such as those ultimately secreted from the cell or localized to the endoplasmic reticulum lumen, and membrane proteins, such as those in the plasma membrane or in other organelles of the secretory pathway. Soluble proteins cross the membrane completely and usually have amino-terminal, cleavable signal sequences, the major feature of which is a segment of 7-12hydrophobic amino acids.

Membrane proteins have different topologies in the lipid bilayer, with one or more transmembrane segments composed of about 20 hydrophobic amino acids; the hydrophilic regions of these proteins either cross the membrane or remain in the cytosol.

Both types of proteins are handled by the same machinery within the membrane: a protein-conducting channel. The channel allows soluble polypeptides to cross the membrane and hydrophobic transmembrane segments of membrane proteins to exit laterally into the lipid phase.

An important step in the biosynthesis of many proteins is the partial or complete translocation across the endoplasmic reticulum membrane. Most of these proteins are translocated through a protein-conducting channel that is formed by a conserved, heterotrimeric membrane-protein complex, the Sec61 or SecY complex. Depending on channel binding partners, polypeptides are moved by different mechanisms: the polypeptide chain is transferred directly into the channel by the translating ribosome, a ratcheting mechanism is used by the endoplasmic reticulum chaperone BiP. Structural, genetic and biochemical data show how the channel opens across the membrane, releases hydrophobic segments of membrane proteins laterally into lipid, and maintains the membrane barrier for small molecules.

Rapoport 2007, Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature vol 450, 663-669.

Sulphur Amino Acids

The sulfur amino acids, methionine and cysteine, are implicated in numerous biological functions and diseases, aside from their role in protein synthesis
Methionine is an indispensable amino acid and is transmethylated intracellularly to homocysteine via S-adenosylmethionine, the principal biological methyl donor in mammalian cells and a precursor for polyamine synthesist. Reduced -adenosylmethionine concen¬trations, as a consequence of low methionine intake or folate deficiency, mainly lead to a deregulation in DNA methylation.

Homocysteine is a sulfur-containing amino acid present in the blood and tissues but not incorporated into protein. Homo¬cysteine can be converted into cy teine via cystathionine through the trans-sulfuration pathway, an irreversible process Homocysteine can also be methylated back to methionine via the remethylation pathway. The combination of transmethylation and remethylation pathways comprises the methionine cycle which occurs in most cells. However, the trans-sulfuration pathway has a limited tissue distribution and is restricted to the liver, kidney, intestine, pancreas and adrenals.

Cysteine is considered a semi-indispensable amino acid whose availability is dependent upon methionine intake. However, dietary cysteine can satisfy a proportion of the sulfur amino acid requirement, the so-called cysteine-sparing effect on dietary methionine requirernent. Cysteine is a constituent amino acid of the tripeptide glutathione (?-Glu-Cys-Gly), the major cellular antioxidant in mammals, and serves also as a precursor for the synthesis of taurine, pyruvate, sulfate and hydrogen sulfide (H2S) .

The gastrointestinal tract is a metabolically significant site of sulfur amino acid metabolism in the body and metabolises about 20 % of the dietary methionine intake which is mainly transmethylated to homocysteine and trans-sulfurated to .cysteine. The gastrointestinal tract accounts for about 25 % of the whole-body transmethylation and trans-sulfurarion.

The gut also utilises 25 % of the dietary cysteine intake and the cysteine uptake by the gut represents about 65% of the splanchnic first-pass uptake.

Sulfur amino acids deficiency significantly suppresses intestinal mucosal growth and reduces intestinal epithelial cell proliferation, and increases intestinal oxidant stress in piglets.

Suggesting that intestinal metabolism of dietary methionine and cysteine is nutritionally important for intestinal mucosal growth. Besides their role in protein synthesis, methionine and cysteine are precursors of important molecules. S-adenosylmethionine, a metabolite of methionine, is the principal biological methyl donor in mammalian cells and a precursor for polyamine synthesis. Cysteine is the rate-limiting amino acid for glutathione synthesis, the major cellular antioxidant in mammal .

Bauchart-Thevret et al 2009 Intestinal metabolism of sulphur amino acids Nutrition Research Review vol 22 pp 175-187


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