N-terminal residues

Thin layer chromatography of the dansylamino acid obtained from the hydrolysate together with a series of samples of authentic dansylamino acids and 

Finally, the important principle of subtractive analysis should be mentioned. Selective decomposition of the N-terminal residue is possible, for instance by deamination with nitrous acid or through oxidative deamination with ninhy-drin. Quantitative amino acid analysis before and after the reaction will show the absence of one amino acid in the hydrolysate of the treated sample. Obviously this is the residue with the free amino group hence it must have occupied the N-terminal position in the sequence. 

Determination of N-terminal amino acid residues by use of 2,4-dinitrofluorobenzene (Sanger s reagent). 

CHAPTER 3 Protein Isolation and Determination of Amino Acid Sequence 

Dansyl derivative of N-terminal amino acid (highly fluorescent) 

The dansyl amino acid is separated and identified by chromatographic methods. The dansyl procedure is about 100 times more sensitive than the DNFB method because the dansyl amino acids are highly fluorescent and therefore detectable in minute quantities. 

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Several chemical methods have been devised for identifying the N terminal ammo acid They all take advantage of the fact that the N terminal ammo group is free and can act as a nucleophile The a ammo groups of all the other ammo acids are part of amide linkages are not free and are much less nucleophilic Sanger s method for N terminal residue analysis involves treating a peptide with 1 fluoro 2 4 dimtrobenzene which is very reactive toward nucleophilic aromatic substitution (Chapter 23)... 

When Sanger s method for N terminal residue analysis was discussed you may have wondered why it was not done sequentially Simply start at the N terminus and work steadily back to the C terminus identifying one ammo acid after another The idea is fine but It just doesn t work well m practice at least with 1 fluoro 2 4 dimtrobenzene... 

A major advance was devised by Pehr Edman (University of Lund Sweden) that has become the standard method for N terminal residue analysis The Edman degrada tion IS based on the chemistry shown m Figure 27 12 A peptide reacts with phenyl iso thiocyanate to give a phenylthwcarbamoyl (PTC) denvative as shown m the first step This PTC derivative is then treated with an acid m an anhydrous medium (Edman used mtromethane saturated with hydrogen chloride) to cleave the amide bond between the N terminal ammo acid and the remainder of the peptide No other peptide bonds are cleaved m this step as amide bond hydrolysis requires water When the PTC derivative IS treated with acid m an anhydrous medium the sulfur atom of the C=S unit acts as... 

The polypeptide chain of the 92 N-terminal residues is folded into five a helices connected by loop regions (Figure 8.6). Again the helices are not packed against each other in the usual way for a-helical structures. Instead, a helices 2 and 3, residues 33-52, form a helix-turn-helix motif with a very similar structure to that found in Cro. 

What is the N-terminal residue on a peptide that gives the following PTH derivative on Edmau degradation ... 

The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. Proteins with destabilizing N-terminal residues such as arginine and leucine are recognized by a RING-type ubiquitin ligase (termed N-recognin or E3-a) that, together with a specific ubiquitin c, mediates poly-ubiquitylation. 

Threonine peptidases (and some cysteine and serine peptidases) have only one active site residue, which is the N-terminus of the mature protein. Such a peptidase is known as an N-terminal nucleophile hydrolase or Ntn-hydrolase. The amino group of the N-terminal residue performs the role of the general base. The catalytic subunits of the proteasome are examples of Ntn-hydrolases. 

Another way in which to gain structural information concerning the N-terminal residue of glycophorins A" and A is to study the N-terminal, mono[ C]methyl derivatives these are produced by using limited amounts of [ C]formaldehyde. There are distinct differences between the N, N -di[ C]methylamino and N -mono[ C]methylamino species (i) a significant, chemical-shift difference exists between the N-terminal dimethyl and monomethyl species (43 and 34 p.p.m.) (li) all of the C resonances of the N-terminal dimethyl species move upheld as the pH is increased (if they move at all), whereas all of the C resonances of the N-terminal, monomethyl species move downfield as the pH is increased and (in) A for the N-terminal monomethyl species tends to be much larger than that for the N-terminal dimethyl species. Point (in) would tend to indicate that it may be more advantageous to study the N-terminal monomethyl species. However, because of allowable protein concentrations, detection limits on available instruments, and technical difficulties, it has thus far... 

Locahzed motion can also lead to local variations in correlation times. Folded peptides with unfolded C- or N-terminal residues, for example, will have varying correlation times for the rigid and flexible parts of the molecule, resulting in different cross-relaxation rates. Such effects can usually be distinguished by the Unewidths and intensities of the corresponding diagonal signals, since the autorelaxation rates also depend on the correlation time. 

Figure 10-5. Representative conformations of the (5 amyloid peptide (10-42) under different pH conditions. The conformations were obtained as centroids of the most populated clusters from the replica-exchange CPHMD folding simulations [43, 44]. The N-terminal residues 10-28 are shown in blue the C-terminal residues 29-42 are shown in red. In the most aggregation-prone state (pH 6), the side chains of the central hydrophobic cluster Leu-17, Val-18, Phe-19, Phe-20 and Ala-21 are shown as van der Waals spheres in pink, grey, cyan, purple and green, respectively...

Proline dipeptidase cleaves dipepetides where proline is adjacent to the N-terminal residue. The enzyme is a homodimer, with one Co ion tightly bound in each subunit. However, it has been shown that an additional Co11 ion must be added (per subunit) for activity. This second ion is relatively weakly bound and may be substituted by Mn11 with somewhat attenuated activity. Curiously, the active site ligands identified in metallohydrolases such as MetAP are conserved in this enzyme despite a generally low sequence similarity. 

There is a second long interface stretching between the threefold and fourfold axes, involving both hydrophobic and hydrophilic interactions. Close to the threefold axis is an intersubunit salt bridge between Asp-139 of subunit I and His-128 in III, which links the N-terminal end of helix D (III) to a position near the kink in helix D (I). Further along the interface, N-terminal residues 6-12 of subunit III make several interactions with the C-helix of subunit I, including several which are mediated... 

A truncated version of PTH (tradenames Forsteo and Forteo) has been approved for the treatment of osteoporosis in postmenopausal women. This 4 kDa polypeptide is identical in sequence to the N-terminal residues 1-34 of endogenous hPTH, it binds to the native PTH receptor and triggers the same effects. The product is produced in E. coli, purified and presented as a sterile solution containing 250 pg active substance per millilitre. 

Figure 10.10 Amino acid sequence of human adrenocorticotrophin. The amino acid residues in this polypeptide hormone are linked by peptide bonds and each residue is given a number starting with the N-terminal residue (number 1) to the C-terminal residue (number 39).

One of the most intriguing recent examples of disordered structure is in tomato bushy stunt virus (Harrison et ah, 1978), where at least 33 N-terminal residues from subunit types A and B, and probably an additional 50 or 60 N-terminal residues from all three subunit types (as judged from the molecular weight), project into the central cavity of the virus particle and are completely invisible in the electron density map, as is the RNA inside. Neutron scattering (Chauvin et ah, 1978) shows an inner shell of protein separated from the main coat by a 30-A shell containing mainly RNA. The most likely presumption is that the N-terminal arms interact with the RNA, probably in a quite definite local conformation, but that they are flexibly hinged and can take up many different orientations relative to the 180 subunits forming the outer shell of the virus particle. The disorder of the arms is a necessary condition for their specific interaction with the RNA, which cannot pack with the icosahedral symmetry of the protein coat subunits. 

To analyze the role of the N-terminal residue of MyoD as a ubiquitination site, we fused to WT MyoD, upstream to the N-terminal residue, a 6 x Myc tag, and monitored the stability of the tagged protein. We showed that it is stable both in vitro and in vivo. It should be noted that the two first N-terminal residues of the Myc tag, methionine and glutamate, are identical to the first two N-terminal residues in MyoD. In addition, the Myc tag also contains a lysine residue. Thus, altogether, six additional lysine residues were added to WT MyoD in addition to its own nine native residues. Nevertheless, the tag stabilizes it, probably by blocking access to a specific N-terminal residue, and, as became clear later (see below), to its neighboring domain. 

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