Bioinformatics Helps Create Zika Virus 3D Model

Researchers from Novosibirsk State University contributed to the creation of the first detailed 3D model of Zika virus worked out by a Russian company Visual Science. A detailed prototype made in atomic resolution was created based on the scientific information published using the methods of structural bioinformatics. The model will help researchers diagnose the fever and develop a vaccine for this dangerous disease caused by a tropical virus.

The 3D model of Zika virus is a part of the non-commercial educational project Viral Park, which was launched by the Visual Science in 2009 and includes models of HIV, influenza A/H1N1, adenovirus, Ebola and papilloma viruses. Such models sum up all the available information about the structure of the most widespread and dangerous human viruses and may act as kind of visual scientific reviews.

The Laboratory of Structural Bioinformatics and Molecular Modelling at NSU engaged in modelling the virus. Our researchers created models for some proteins and analyzed scientific data about related viruses in order to identify the positions of various Zika components, such as proteins, RNA, or the lipid membrane, in the structure of the virion.

The Head of the Laboratory and the head molecular modeler Anastasia Bakulina, PhD, tells us about the virus and her work for Visual Science:

Zika virus belongs to the same systematic group, Flaviviridae, as the hepatitis C, Dengue, yellow fever, West Nile and Chikungunya viruses. The most reliable method of diagnosing virus infections is to identify the genetic material of the virus in the patient’s blood. However, it can only be done with the help of sophisticated equipment and experienced doctors. More common diagnostic methods, such as enzyme immunoassay EIA, are based on finding antibodies against the virus. It is particularly useful for epidemiological studies as it testifies to the fact of the person’s meeting the virus in the past.

 The major surface protein E (in the model — different shadows of blue on the surface of the virion) has a strong resemblance to the corresponding protein of yellow fever, West Nile and Dengue. The difference is in fewer than half amino-acid residues in the proteins with many of them either hidden in the membrane or glycosylated (in the model — dark grey spots on the surface of the virion). Experiments show that the antibodies against Zika bind to Dengue and vice versa, which makes it difficult to diagnose the fever.

It is still not quite clear how Zika may cause microcephaly, which is a challenge for our researchers. We guess it is connected with some special properties of protein E. If we “spoil” it with some mutations while leaving the virus viable, we may work out a good vaccine.