Tryptophan residue

The conformation of bovine myelin basic protein (MBP) in AOT/isooctane/water reversed micellar systems was studied by Waks et al. 67). This MBP is an extrinsic water soluble protein which attains an extended conformation in aqueous solution 68 but is more density packed at the membrane surface. The solubilization of MBP in the AOT reversed micelles depends on the water/AOT-ratio w0 68). The maximum of solubilization was observed at a w0-value as low as 5.56. The same value was obtained for another major protein component of myelin, the Folch-Pi proteolipid 69). According to fluorescence emission spectra of MBP, accessibility of the single tryptophane residue seems to be decreased in AOT reversed micelles. From CD-spectra one can conclude that there is a higher conformational rigidity in reversed micelles and a more ordered aqueous environment. 

Kulinski, T., Visser, A. J. W. G., O Kane, D. J., and Lee, J. (1987). Spectroscopic investigations of the single tryptophan residue and of riboflavin and 7-oxolumazine bound to lumazine apoprotein from Photobacterium leiognathi. Biochemistry 26 540-549. 

Fig. 15. The two Fe-S clusters are some 12-13 A apart and within possible electron transfer range. A tyrosine residue, Y493, is situated roughly halfway between the two clusters, but whether it plays a role in any electron transfer is unclear. Two adjacent tryptophan residues are also located close to cluster 2 again, their possible roles in any enzymatic reaction remain to be defined.

The one residue most extensively studied is tryptophan. It is very easily modified, indicating that tryptophan residue is exposed 5-8). Raman spectroscopic analysis of a sea snake neurotoxin indicated that a single tryptophan residue is indeed exposed (2). The tryptophan residue lies in the important loop consisting of segment 4. Modification of the tryptophan residue induces the loss of AChR binding ability as well as the loss of toxicity 5-8). 

Additional evidence for conformational changes in the transporter has come from measurement of the intrinsic fluorescence of the protein tryptophan residues, of which there are six, in the presence of substrates and inhibitors of transport. The fluorescence emission spectrum of the transporter has a maximum at about 336 nm, indicating the presence of tryptophan residues in both non-polar environments (which would emit maximally at about 330 nm) and in polar environments (which would emit at 340-350 nm) [154], The extent of quenching by the hydrophilic quencher KI indicates that more than 75% of the fluorescence is not available for quenching, and so probably stems from tryptophan residues buried within the hydrophobic interior of the protein or lipid bilayer [155]. Fluorescence is quenched... 

Aromatic amine-containing haptens are converted to diazonium salts with ice-cold nitrous acid. Diazonium salts can then react with a protein at alkaline pH (around 9) through electrophilic attack of the diazonium salt at histidine, tyrosine and(or) tryptophan residues of the carrier protein (Table 7). 

Fluorescence spectroscopy offers several inherent advantages for the characterization of molecular interactions and reactions. First, it is 100-1000 times more sensitive than spectrophotometric techniques. Second, fluorescent compounds are extremely sensitive to their environment. Tryptophan residues that are buried in the hydrophobic interior of a... 

The six major proteins of milk, asl-, o s2-, and /c-casein, jS-lactoglobulin, and a-lactalbumin, contain at least one tryptophan residue [57], the fluorescence of which allows the monitoring of the structural modifications of proteins and their physicochemical environment during the coagulation processes. Emission fluorescence spectra of the protein tryptophanyl residues were recorded for the milk coagulation kinetics induced by... 

Figure 3.35 presents TR spectra obtained with varying time delays between the pump and probe pulses following photolysis of HbCO. The Raman band features have been attributed to tyrosine (Y) and tryptophan (W) vibrational modes as indicated at the top of Figure 3.35. These Raman bands change with time and provide information about the environment of the typrosine and tryptophan residues in the heme. Inspection of Figure 3.35 reveals that the negative difference Raman...

The starting point for much of the work described in this article is the idea that quinone methides (QMs) are the electrophilic species that are generated from ortho-hydro-xybenzyl halides during the relatively selective modification of tryptophan residues in proteins. Therefore, a series of suicide substrates (a subtype of mechanism-based inhibitors) that produce quinone or quinonimine methides (QIMs) have been designed to inhibit enzymes. The concept of mechanism-based inhibitors was very appealing and has been widely applied. The present review will be focused on the inhibition of mammalian serine proteases and bacterial serine (3-lactamases by suicide inhibitors. These very different classes of enzymes have however an analogous step in their catalytic mechanism, the formation of an acyl-enzyme intermediate. Several studies have examined the possible use of quinone or quinonimine methides as the latent... 

However, diffusion of the reactive QM out of the enzyme active site is a major concern. For instance, a 2-acyloxy-5-nitrobenzylchloride does not modify any nucleophilic residue located within the enzyme active site but becomes attached to a tryptophan residue proximal to the active site of chymotrypsin or papain.23,24 The lack of inactivation could also be due to other factors the unmasked QM being poorly electrophilic, active site residues not being nucleophilic enough, or the covalent adduct being unstable. Cyclized acyloxybenzyl molecules of type a could well overcome the diffusion problem. They will retain both the electrophilic hydroxybenzyl species b, and then the tethered QM, in the active site throughout the lifetime of the acyl-enzyme (Scheme 11.1). This reasoning led us to synthesize functionalized... 

Horton, H. R. Koshland, D. E. Jr. A highly reactive coloured reagent with selectivity for the tryptophan residue in proteins 2-hydroxy-5-nitrobenzyl bromide. J. Amer. Chem. Soc. 1965, 87, 1126-1132. 

Kostic el al. discovered that Pd11 complexes, when attached to tryptophan residues, can rapidly cleave peptides in acetone solutions to which a stoichiometric amount of water is added, for hydrolysis.436 The indole tautomer in which a hydrogen has moved from the nitrogen to C(3) is named indolenine. Its palladium(II) complexes that are coordinated via the nitrogen atom have been characterized by X-ray crystallography and spectroscopic methods.451 Binuclear dimeric complexes between palladium(II) and indole-3-acetate involve cyclopalladation.452 Bidentate coordination to palladium(II) through the N(l) and the C(2) atoms occurs in binuclear complexes.453 Reactions of palladium(II) complexes with indole-3-acetamide and its derivatives produced new complexes of unusual structure. Various NMR, UV, IR, and mass spectral analyses have revealed bidentate coordination via the indole carbon C(3) and the amide oxygen.437... 

Khorana et al. 233) also carried out a sequence of bacteriorhodopsin, which was largely in agreement with the earlier study but which found another tryptophan residue... 

Chakraborty, S., Ittah, V., Bai, P., Luo, L., Haas, E., and Peng, Z. Y (2001). Structure and dynamics of the alpha-lactalbumin molten globule Fluorescence studies using proteins containing a single tryptophan residue. Biochemistry 40, 7228-7238. 

Also recently, Liao and collaborators [89] proposed a homogeneous noncompetitive assay of a protein in biological samples based on FRET by using its tryptophan residues as intrinsic donors and its specific fluorescent ligand as the FRET acceptor, which was defined as an analytical FRET probe. To evaluate this method, a naphthylamine derivative, namely /V-biotinyl-/V -(l -naphthylj-ethylene-diamine (BNEDA) 33 was used as an analytical FRET probe for the homogeneous noncompetitive assay of streptavidin. 

Liao F, Xie Y, Yang X et al (2009) Homogeneous noncompetitive assay of protein via Forster-resonance-energy-transfer with tryptophan residue(s) as intrinsic donor(s) and fluorescent ligand as acceptor. Biosens Bioelectron 25 112-117... 

Chen J, Callis PR, King J (2009) Mechanism of the very efficient quenching of tryptophan fluorescence in human gamma D- and gamma S-crystallins the gamma-crystallin fold may have evolved to protect tryptophan residues from ultraviolet photodamage. Biochemistry 48(17) 3708-3716... 

L-tryptophan is compulsory, the biosynthetic machinery displays wide latitude in its ability to condense a second auxiliary amino acid—L-alanine in the case of (+)-ll,ll -dideoxyverticillin A (1)—to afford a tryptophan-derived diketopiperazine intermediate 13. Mirroring Woodward and Robinson s biogenetic hypothesis for the calycanthaceous alkaloids, single-electron oxidation of the electron-rich tryptophan residue would likely initiate an oxidative dimerization of the diketopiperazine precursor with concomitant cyclization to yield the octacyclic intermediate 17. Subsequent A-methylation of the amides would then yield an unembellished skeletal core of the dimeric epipolythiodiketopiperazine alkaloids. The first step en route... 

The organization of lipids around the plasma membrane Ca2+-transport ATPase of erythrocytes has been also determined by FRET. Taking advantage of the intrinsic fluorescence of the ATPase due to tryptophan residues and labeling different types of lipids with pyrene, it was demonstrated that the transporter is preferentially surrounded by negatively charged lipids such as phosphoinositides [167],... 

Some peptide sensors were based on binding to the zinc chelate of ligands such as 79, with specific quenching of the fluorescence of nearby tryptophan residues in the peptide... 

Sodium periodate also may affect tryptophan residues in some proteins. The oxidation of tryptophan can result in activity losses if the amino acid is an essential component of the active site. For instance, avidin and streptavidin may be severely inactivated by treatment with periodate, since tryptophan is important in forming the biotin-binding pocket. In addition, many other amino acid residues are susceptible to oxidation by periodate (Chapter 1, Section 1.1). Limiting the time of oxidation is important to restricting oxidation to diol groups while not affecting other protein structures. 

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