THE CHARACTERISTIC PROPERTIES OF AMINO ACID CONTENT OF ALPHA HELICES FRAGMENTS IN POLYPEPTIDE CHAINS OF DIFFERENT STRUCTURAL CLASSES OF PROTEINS
Abstract
In this study we analyzed the amino acid content of alpha helices from proteins that belong to four structural classes in nonhomologous sets of 3D structures. Comparison of probability scales revealed that lysine, arginine and histidine show high probabilities to be included in alpha helices only in certain structural classes of proteins, unlike the constant formers of alpha helices: alanine, leucine, glutamic acid, glutamine and methionine. Alpha helices of beta structural proteins show lower usage of leucine and higher usage of glutamine, as well as the elevated usage of combinations of hydrophilic and hydrophobic amino acids that are characteristic to beta strands, relative to alpha helices from alpha helical proteins. The properties of amino acid content of alpha helices situated between two beta strands in beta structural and mixed proteins show that they are protected from the shift to beta strands. Obtained data are important in the process of the selection of antigenic fragments of proteins that contain alpha helices with highly stabilized secondary structure, with the aim to use them in vaccine design studies.
Keywords
alpha helix,
structural class of a protein,
hydrophobic amino acid residue,
hydrophilic amino acid residue,
beta strand
Supporting agencies: This work was financially supported by the grant of the Belarusian Republican Foundation for Fundamental Research no. B16M-083.
About the Authors
V. V. Poboinev
Belarusian State Medical University, Minsk
Belarus
Belarus
Undergraduate
83, Dzerzhynskiy Ave., 220116
V. V. Khrustalev
Belarusian State Medical University, Minsk
Belarus
Belarus
Assistant Professor, Head of the Department
83, Dzerzhynskiy Ave., 220116
T. A. Khrustaleva
Institute of Physiology of the National Academy of Sciences of Belarus, Minsk
Belarus
Belarus
Senior researcher
28, Aсademicheskaya Str., 220072
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