Ligation sites

LI ligase s large intrinsic flexibility was revealed by the recent crystal structure of the ligation product of a reduced size variant with two vastly different conformers, differing by reorientation of one of the stems by around 80 A, that were resolved in the same asymmetric cell [106], Based on the presence/absence of specific contacts between distant conserved parts including the ligation site and a totally conserved residue, U38, one of the conformers was postulated to represent the catalytically active or on conformation, the other the inactive or off one [106],... 

Figure 14-11. Snapshots from the conformational switch path explored in the vicinity of the active conformation (unfolded docked conformation) and starting from the inactive (undocked) conformation found in crystal. Stems A and B were aligned (best fitted) and are shown in yellow, different instances of stem C are shown in stick representation with different colors. A schematic of the non-canonical binding scheme of the ligation site is shown in the right panel and the general mechanism of ligation in the left panel...

His residues in the peptide sequence are fundamental for Ni11 ion interactions with peptides. When the His residue is relatively distant from the N terminus, it may compete as a primary ligation site with the N-terminal amino nitrogen. However, even the higher number of His residues inserted inside the peptide sequence may be not able to compete with the albumin-like N terminus, unless the specific peptide structure is established. 

The coordination chemistry of diazaphospholes has attracted much attention during the last decade. Among various categories of diazaphospholes, coordination behavior of [1,2,3]- and [l,2,4]diazaphospholes has been investigated. They provide a variety of ligating sites, in addition to the phosphorus and =N- lone pairs n coordination of the type if and if is also possible. In 4-phosphino-[ 1,2,3] diazaphospholes, coordination takes place via exocyclic phosphino phosphorus. Accordingly, complexation reactions can be subdivided into two categories-... 

The ionization is the rds. The spontaneous rate is considered to be accelerated by both inter-molecular (from the buffer) and intramolecular (from His-64) proton transfer. Cadmium can replace the native zinc from metalloenzymes and Cd nmr is being used increasingly to probe metal ligation sites in metalloproteins. The cadmium product often does not show enzyme activity however. 

Fig. 7. Helical wheel and sequence representation of the parental homodimeric coiled coil. The substitution positions within the hydrophobic domain are highlighted with open squares and those in the charged domain with open circles. Their interaction partners are highlighted with shaded squares and circles, respectively. The arrows mark the ligation site of nucleophilic and electrophilic fragments. (See Colour Plate Section at the end of this book.)...

Other very important applications of C-terminal thioester-functionalized peptides include their usage in the condensation of large unprotected peptide fragments (ligation see Vol. E22a, Section 4.1.5). 4,5,74 In this process the thioester-modified unprotected peptide reacts with the N-terminal cysteine of a second unprotected peptide giving a thioester intermediate. This step is followed by a rapid intramolecular S—>N shift with formation of the thermodynamically favored amide bond at the ligation site. 

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