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

  • Vladislav Victorovich KhrustalevEmail author
  • Victor Vitoldovich Poboinev
  • Aleksander Nicolaevich Stojarov
  • Tatyana Aleksandrovna Khrustaleva
Original Article
  • 45 Downloads

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.

Keywords

Tryptophan Amino acid residues Fluorescence Circular dichroism Aromatic–aromatic interactions Cation–pi interactions 

Notes

Supplementary material

249_2019_1377_MOESM1_ESM.xlsx (18 kb)
Supplementary material 1 (XLSX 18 kb)

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Copyright information

© European Biophysical Societies' Association 2019

Authors and Affiliations

  1. 1.Department of General ChemistryBelarusian State Medical UniversityMinskBelarus
  2. 2.Department of Radiomedicine and EcologyBelarusian State Medical UniversityMinskBelarus
  3. 3.Biochemical Group of the Multidisciplinary Diagnostic LaboratoryInstitute of Physiology of the National Academy of Sciences of BelarusMinskBelarus

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