Carboxy-terminal side

Two domains, t1 and t2, exist which affect the GR post-DNA binding transcription activity (37). The major (t1) transactivation domain is 185 amino acid residues ia length with a 58-tesidue a-heUcal functional cote (38). The t1 domain is located at the N terminus of the proteia the minor (t2) trans activation domain residues on the carboxy-terminal side of the DNA binding domain. 

Chymotrypsin-like proteinases are serine proteinases that recognize pqDtide residues with aromatic side chains (phyenylalanyl or tyrosyl residues) and that effect hydrolysis of the polypeptide chain on the carboxy-terminal side of these residues. Examples of chymotrypsin-like proteinases are chymotrypsin and cathepsin-G. 

The amino acid spacer between ligands Li and L2 is X, that between L3 and nearest ligand Li or L2 is Y, and that between L3 and L4 is Z. The symbol N indicates that L3 is located on the amino (N) side of L2. If no letter is present, L3 is located on the carboxy-terminal side of L2. The subscripts a, refer to the a-or 3io helix and /9-sheet structure that supplies the ligand. The subscript L denotes an amino acid sequence of < 6 residues between two structural elements. The subscripts a and b indicate the ligand is either one (or two) residues after or before the secondary structural element. 

Trypsin cleaves proteins at the carboxy terminal side of lysine and arginine residues. Arg-Pro or Lys-Pro sites are trypsin resistant. Also, trypsin only slowly attacks peptide bindings between a basic amino acid (Lys, Arg) and an acidic one (Glu, Asp). The pH optimum of trypsin lies between 8 and 9, and the optimum relation of enzyme to substrate is 1 50 to 100. Ca ions inhibit the self-digestion of trypsin. The trypsin must not contain any chymotrypsin activity (i.e., TPCK must be treated and highly purified). Lysine residues can be protected from trypsin by derivatization (e.g., with citraconic acid), and in reverse, treating the cysteine groups with iodoethylene trifluoroacetamide introduces new trypsin cleaving sites. 

The P2X receptor subunits are unusual in having only two transmembrane domains with both the amino terminal and carboxy terminal located intracellularly. The ion channel is proposed by analogy with the structure of some potassium channels to be formed by a short loop which enters the membrane from the extracellular side (North and Surprenant 2000). 

Fig. 5. Proposed topology of K channel subunits inserted into the membrane. COO carboxy-terminal. The proposed membrane-spanning segments SI-S6 in the core region of channel proteins are displayed linearly. H5 may be part of the K channel pore. The amino-terminal inactivation gate is symbolized by a positively charged ball which could occlude the pore region. The extracellular side is thought to be at top and the intracellular side at bottom.

NFH, and to a lesser extent NFM, has a large number of consensus phosphorylation sites for proline-directed kinases in this carboxy-terminal extension (>50 on NFH and >10 on NFM in many species). In large myelinated axons, most, if not all, of these sites are phosphorylated [21, 22]. This phosphorylation of NFH and NFM side-arms alters the charge density on the NF surface, repelling adjacent NFs with similar charge. Such mutual repulsion by the sidearms of NFs is thought to be a major determinant of axonal caliber [24],... 

The next residues were attached successively by dicyclohexylcarbodiimide-mediated coupling of Boc-amino acids with the free amino groups. The use of excess Boc-amino acid eliminated the need for capping after coupling. The last Boc-group and the benzyl-based side chain and carboxy-terminal protectors were removed at the end of the synthesis by acidolysis with hydrogen bromide in trifluoroacetic acid the latter was used instead of acetic acid to avoid acetylation of hydroxymethyl side chains (see Section 6.6). Catalytic hydrogenolysis of the peptide removed the nitro... 

The structure of PaFd was the first to be crystallographically determined (Adman et ai, 1973). The basic fold of the protein may be described as a pair of two stranded antiparallel )3 sheets. The two 4Fe 4S clusters are sandwiched between these /3 strands on one side and several helical segments on the other side. The clusters are packed in a predominantly hydrophobic environment. The internal sequence homology is clearly reflected in the structure the two clusters and much of the polypeptide chain are related by an approximate internal twofold rotation axis. The two clusters are ligated by the two sets of four cysteines in the two halves of the molecule. Surprisingly, each cluster is liganded by cysteines from both halves of the sequence, rather than cysteines from only one half (which are adjacent in the sequence). Cluster 1 is coordinated by Cys-8, -11, and -14 in the amino-terminal half and Cys-45 of the carboxy-terminal half, while cluster 2 is coordinated by Cys-35, -38, and -41 of the carboxy-terminal half and Cys-18 of the amino-terminal half. 

The main advantage of ferr-alkyl esters as linkers is their stability towards nucleophiles. For instance, no diketopiperazine formation is observed during the preparation of peptides containing carboxy-terminal proline, an otherwise common side reaction when using benzyl alcohol linkers (Section 15.22.1). 

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