Location Of Tryptophan Residues Research Articles

Role of Tryptophan in Protein–Nanocrystals Interaction: Energy or Charge Transfer

Abstract The understanding of the interaction between the semiconductor nanocrystals (NCs) and the proteins are essential for design and fabrication of nanocomposites for application in the field of biotechnology. Herein, we have studied the interaction between CdTe NCs and the proteins by steady-state and time-resolved photoluminescence (PL) spectroscopy. The steady-state PL intensity of CdTe NCs is quenched and enhanced in the presence of lysozyme and bovine serum albumin, respectively. However, the PL intensity of CdTe NCs is not affected with α-synuclein, indicating the role of tryptophan moiety in the protein–NCs interaction. The detailed analysis of PL data allows us to elucidate the dominant mechanism of interaction, i.e. charge or energy transfer, depending on the location of tryptophan residues in the protein. Assuming a Poisson statistic of lysozymes around NCs, the Poisson binding model is used to understand the kinetics of charge transfer from CdTe NCs to the lysozyme. It provides the average number of lysozymes present on the surface of one CdTe NC.

The Off-rate of Monomers Dissociating from Amyloid-β Protofibrils

The interconversion of monomers, oligomers, and amyloid fibrils of the amyloid-β peptide (Aβ) has been implicated in the pathogenesis of Alzheimer disease. The determination of the kinetics of the individual association and dissociation reactions is hampered by the fact that forward and reverse reactions to/from different aggregation states occur simultaneously. Here, we report the kinetics of dissociation of Aβ monomers from protofibrils, prefibrillar high molecular weight oligomers previously shown to possess pronounced neurotoxicity. An engineered binding protein sequestering specifically monomeric Aβ was employed to follow protofibril dissociation by tryptophan fluorescence, precluding confounding effects of reverse or competing reactions. Aβ protofibril dissociation into monomers follows exponential decay kinetics with a time constant of ∼2 h at 25 °C and an activation energy of 80 kJ/mol, values typical for high affinity biomolecular interactions. This study demonstrates the high kinetic stability of Aβ protofibrils toward dissociation into monomers and supports the delineation of the Aβ folding and assembly energy landscape.

Location of tryptophan residues in free and membrane bound Escherichia coli α-hemolysin and their role on the lytic membrane properties

α-Hemolysin (HlyA) is an extracellular protein toxin secreted by Escherichia coli that acts at the level of plasma cell membranes of target eukaryotic cells. Previous studies showed that toxin binding to the bilayers occurs in at least two ways, a reversible adsorption and an irreversible insertion. Studies of HlyA insertion into bilayers formed from phosphatidylcholine show that insertion is accompanied by an increase in the protein intrinsic fluorescence. In order to better define structural parameters of the membrane-bound form, the location of tryptophan residues was studied by means of quenchers of their intrinsic fluorescence located at 7, 12 and 16 positions of the acyl chain of phosphatidylcholine. The quenching was progressively weaker suggesting an interfacial location of the Trp. In parallel, HlyA was subjected to oxidation with N-bromosuccinimide to study the role of Trp residues exposed to aqueous media in its structure–function relationship. In the folded toxin molecule, a single residue was susceptible to oxidation with NBS, whereas incubation with LUV of the toxin prior modification prevents its oxidation, suggesting that Trp residue(s) are directly involved in toxin binding and insertion. Finally, the modification of residues exposed to solvent resulted in a complete impairment of the lytic activity. It was concluded that the modification-sensitive Trp residues are essential for the structure and function of native HlyA. These results are consistent with the model proposed by Soloaga et al. (Mol. Microbiol. 31 (1999) 1013–1024) according to which HlyA is bound to a single monolayer through a number of amphipathic instead of inserted transmembrane helices.

Contribution of separate tryptophan residues to intrinsic fluorescence of actin. Analysis of 3D structure

The location of tryptophan residues in the actin macromolecule was studied on the basis of the known 3D structure. For every tryptophan residue the polarity and packing density of their microenvironments were evaluated. To estimate the accessibility of the tryptophan residues to the solvent molecules it was proposed to analyze the radial dependence of the packing density of atoms in the macromolecule about the geometric center of the indole rings of the tryptophan residues. The proposed analysis revealed that the microenvironment of tryptophan residues Trp-340 and Trp-356 has a very high density. So these residues can be regarded as internal and inaccessible to solvent molecules. Their microenvironment is mainly formed by non-polar groups of protein. Though the packing density of the Trp-86 microenvironment is lower, this tryptophan residue is apparently also inaccessible to solvent molecules, as it is located in the inner region of macromolecule. Tryptophan residue Trp-79 is external and accessible to the solvent. All residues that can affect tryptophan fluorescence were revealed. It was found that in the close vicinity of tryptophan residues Trp-79 and Trp-86 there are a number of sulfur atoms of cysteine and methionine residues that are known to be effective quenchers of tryptophan fluorescence. The most essential is the location of SG atom of Cys-10 near the NE1 atom of the indole ring of tryptophan residue Trp-86. On the basis of microenvironment analysis of these tryptophan residues and the evaluation of energy transfer between them it was concluded that the contribution of tryptophan residues Trp-79 and Trp-86 must be low. Intrinsic fluorescence of actin must be mainly determined by two other tryptophan residues – Trp-340 and Trp-356. It is possible that the unstrained conformation of tryptophan residue Trp-340 and the existence of aromatic rings of tyrosine and phenylalanine and proline residues in the microenvironments of tryptophan residues Trp-340 and Trp-356 are also essential to their blue fluorescence spectrum.