Microenvironment of tryptophan residues in proteins of four structural classes: applications for fluorescence and circular dichroism spectroscopy

Abstract

In this study we examined microenvironment of Trp residues in "dry" sets of nonhomologous proteins that belong to four structural classes, as well as in a "wet" set. In silico experiments showed that residues of Trp demonstrate higher surface accessibility in proteins of "alpha/beta" class where they are rarely included in beta strands. However, this feature has not caused "red" shift in fluorescence spectra in "alpha/beta" proteins in vitro, since there are several factors that should be combined together to cause it: high surface accessibility and high hydrophilicity of the microenvironment, the presence of destabilizing contacts with Asp, Asn, Leu, and multiple Tyr residues, as well as the lack of stabilizing interactions with Arg, Thr, and Pro. The occurrence of Trp residues has the highest value in beta-structural proteins, while they are not involved in aromatic-aromatic interactions with each other as frequently, as they do in proteins of "alpha + beta" class in which Trp residues are overrepresented near each other in the primary sequence. That is why the deformation of circular dichroism spectra because of Trp-Trp interactions is expected to be more frequent in proteins of "alpha + beta" class. In all four classes of proteins Trp residues are involved in long-range interactions with some hydrophobic (Leu, Val, Ile) and aromatic residues (Trp, Phe, and Tyr) more frequently than it is expected. They are involved in long-range interactions with some hydrophilic residues (Asp, Glu, Ser, and Lys) rarely than it is expected. Short-range interactions between Arg and Trp are overrepresented just in alpha-helical proteins.