Fedor V. Shirshikov

Personal information

My major is microbiology and molecular biology. My hobby are sciences, such as biology and organic chemistry, but also I like a mountine bike, typographics, graphic design of posters and logos. I can to create the handmade covers on books. During approximately 6 years I was in the boxing school. I was studied at the Secondary School № 43 in Kazan and the School of Arts № 2.

Read more about me here.


PeriodCountry, cityEducation institutionAdditional info
2007–2012 Russia, Kazan Kazan University Diploma with Honors in Microbiology

Scientific interests

Microbiology; molecular biology; structural bioinformatics.

Awards & honors

  • The Special State Scholarship of the Government of the Russian Federation.
  • The Special State Scholarship of the Republic of Tatarstan.
  • Margarita I. Belyaeva Honorary Scholarship for Microbiologists of Kazan University.

Main scientific results

  • Primer set for detection of Dickeya plant pathogens using loop-mediated isothermal amplification (LAMP);
  • Development of software for screening of target genes and designing specific primers using multiple sequence alignment of ortologous nucleotide sequences;
  • Discovery of new plant pathogen genomospecies "Candidatus Pectobacterium maceratum", which able to disseminate using associative symbiosis with fruit flies Drosophila;
  • It was discovered that some cytotoxic ribonucleases contain a hydrophobic segment, which is capable of thermodynamically favorable interaction with a lipid bilayer;
  • It was shown that Leu-32 can play a key role for the dimerization of binase;
  • The new theory of the cytosolic internalization of toxic ribonucleases comprising a hydrophobic segment was proposed.

Scientific societies’ membership

  • The Russian Society of Biochemistry and Molecular Biology of the Russian Academy of Sciences.
  • The Federation of European Biochemical Societies.

Selected publications

  1. Shirshikov F.V., Korzhenkov A.A., Miroshnikov K.K., Kabanova A.P., Barannik A.P., Ignatov A.N., Miroshnikov K.A. (2018). Draft Genome Sequences of New Genomospecies "Candidatus Pectobacterium maceratum" Strains, Which Cause Soft Rot in Plants. Genome Announc 6 (15), e00260–18 [+]

    The article is devoted to the new genomospecies "Candidatus Pectobacterium maceratum", which able to persist the Drosophila gut. This is the first taxon within the Pectobacteriaceae family with unique virulence factor Evf for interaction with flying insect vector.

  2. Shirshikov F.V. (2013). Physicochemical properties of the antitumor ribonucleases. KSSCI Abstracts , 32 [+]

    Here, the homology modeling approach was used to predict the three-dimensional structure of ribonuclease from Bacillus circulans (Bci-RNase), B. coagulans (Bco-RNase), and B. thuringiensis (Bth-RNase). These protein structures have not been experimentally determined. Although the cytotoxic action of above-mentioned ribonucleases is not yet proved, their close homology to barnase and binase suggests that these proteins should be tested as an antitumor drugs.

    The aim of this study is to determine the physicochemical properties of toxic ribonucleases and their close homologs. Few important characteristics, which are necessary for the unrevealing of the mechanism of ribonuclease cytotoxicity, namely charge, dipole moment, water-to-bilayer transfer free energy, and hydrophobic moment values were calculated. The molecular electrostatic maps of toxic ribonucleases were also obtained. The peculiarity of this investigation consists in the complex view on the lipid-protein interaction, which includes not only the electrostatical component, but also the hydrophobic component.

  3. Shirshikov F.V. (2013). Evolutionary role of the hydrophobic segment of bacillar ribonucleases. KSSCI Abstracts , 31 [+]

    By modern computational methods, such as the water-to-bilayer transfer free energy and hydrophobic moment values calculations, was shown that some bacillar ribonucleases with antitumor action, namely barnase and binase, have a hydrophobic segment located in helix II. Interestingly, physicochemical properties of the hydrophobic segment of above-mentioned ribonucleases different significantly.

    The aim of this study is to explain the evolutionary significance of bacillar secretory ribonucleases using the methods of structural bioinformatics. Although attention has long been known to antitumor action of binase, a detailed study of its natural destination in the structure biology aspect had been not observed. Secretory ribonucleases involved in the metabolism of inorganic phosphate, however, the data about the hydrophobic segment suggest that ribonucleases can play subtle biological role. Remarkably, the biosyntesis of binase, not barnase, can be stimulated by addition of dactinomycin.

  4. Shirshikov F.V. (2013). On the molecular basis of the onconase and barnase cytotoxicity. FEBS J 280 (S1), 545–6 [+]

    Ribonucleases are the best-studied proteins in the world of biochemistry. Today, some of these proteins are giving new surprises. It is known that onconase and barnase are water-soluble proteins with antitumor action toward human tumor cell lines. Unfortunately, exact mechanism of the RNases cytotoxicity is still unclear. Here, the structural key, namely the hydrophobic segment, which allows to explain many biological effects of onconase and barnase, was reported.

    The main aim of this investigation is to show that onconase and barnase have special hydrophobic properties, which participated in the apoptosis of tumor cells induction. Here, a clear evidence that onconase and barnase can be mimetics of proapoptotic Bax protein, which belong to the Bcl-2 family proteins, was obtained. It is may be useful for explanation of the mechanism of apoptosis induction.

  5. Shirshikov F.V., Cherepnev G.V., Ilinskaya O.N., Kalacheva N.V. (2013). A hydrophobic segment of some cytotoxic ribonucleases. Med. Hypotheses 81 (2), 328–34 [+]

    The exact mechanism by which cytotoxic ribonucleases reach the cytosol of tumor cells remains unclear. The interaction of ribonucleases with a lipid bilayer is involved in the translocation of ribonucleases across the endosomal membrane. Here, we aimed to study the hydropathy character of toxic antitumor ribonucleases (bovine seminal ribonuclease and binase) and two non-toxic ribonucleases (bovine pancreatic ribonuclease and human pancreatic ribonuclease) by sliding-window hydrophobicity analysis. Comparative hydropathy plot analysis of the non-toxic pancreatic ribonucleases and their toxic variants was also performed. The data obtained indicate that some cytotoxic ribonucleases have a hydrophobic segment, which is sterically available for the hydrophobic interaction with a tumor cell membrane and endosomal membrane. After dissociation, subunits of dimeric ribonucleases are probably capable of thermodynamically favorable interaction with the interfacial region of a lipid bilayer. Remarkably the hydrophobic segment is not identified in the amino acid sequences of non-toxic ribonucleases. The paper describes the hydrophobic properties of toxic RNases that are essential for both the model of a lipid-protein interaction and the cytotoxicity mechanism unraveling.