Site Directed moiety

In the three-dimensional stmcture of actin, the environment of the phosphate moiety of the nucleotide appears roughly the same when CaADP or CaATP is bound. This observation argues against two different conformations. The reason why this is so is unclear. However, it must be stressed that the three-dimensional stmcture is derived from X-ray diffraction of crystals of the DNasel-actin complex, which, like G-actin, is unable to hydrolyze ATP. The conformation obtained may therefore correspond to G-actin frozen in the G-ATP state independently of the bound nucleotide. Stmctural studies in conjunction with site-directed mutagenesis experiments should eventually solve this problem. 

X-ray crystallographic structures of myoglobin and hemoglobin were first completed in 19662 and 19753, respectively. Since then, many other X-ray crystallographic studies of deoxy- and oxy- as well as met-myoglobin and hemoglobin have been carried out.22,24 Additionally, researchers have studied the carbon monoxide bound moieties MbCO and HbCO as well as MbNO. Site-directed mutagenesis of residues near the active sites of Mb and Hb have yielded... 

The most promising tools developed for this sort of analysis are active-site-directed irreversible inhibitors of DUBs. These inhibitors are ubiquitin or ubiquitin-like proteins chemically modified at the C-terminus by an electrophilic moiety such as a Michael acceptor or alkyl halide. The modified ubiquitin can be incubated with a purified DUB or a cell lysate containing DUB activity. Ubiquitin vinyl sul-fone (UbVS) is one such irreversible inhibitor because the vinyl sulfone moiety reacts with the active-site cysteine of the DUB, forming a thioether linkage. The covalent adduct is stable and can be detected in a variety of ways. Labeling of DUBs is specific, as only a DUB active-site cysteine will efficiently react with the vinyl sulfone moiety. 

Some studies have been reported where individual aromatic groups of a protein have been systematically replaced using site-directed mutagenesis, allowing the contributions of the individual chomophores to be determined. Craig et al. [106] have systematically relaced all the Trp moieties in interleukin-ip (IL-lp). Earlier work of Elwell and Schellman [107] replaced the tryptophan in T4 lysozyme with tyrosine. 

With site-directed mutation and femtosecond-resolved fluorescence methods, we have used tryptophan as an excellent local molecular reporter for studies of a series of ultrafast protein dynamics, which include intraprotein electron transfer [64-68] and energy transfer [61, 69], as well as protein hydration dynamics [70-74]. As an optical probe, all these ultrafast measurements require no potential quenching of excited-state tryptophan by neighboring protein residues or peptide bonds on the picosecond time scale. However, it is known that tryptophan fluorescence is readily quenched by various amino acid residues [75] and peptide bonds [76-78]. Intraprotein electron transfer from excited indole moiety to nearby electrophilic residue(s) was proposed to be the quenching... 

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