Human adenovirus 3D model
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Adenoviruses are not deadly pathogens. Rather, though they occasionally cause the common cold and resulting complications, they are a promising tool for the development of new medical technologies and gene therapy techniques. Human adenoviruses are part of the Adenoviridae family, whose representatives also infect animals such as cows, ducks, bats, geckoes, and even sturgeons. In human bodies, adenoviruses attack cells of the upper respiratory tract predominantly, causing flu-like symptoms: runny nose, coughing, pain and inflammation in the nose and throat and — sometimes — conjunctivitis [1,2]. To date, more than fifty different types of adenoviruses have been described in humans [4]. These viruses may be transmitted by aerosol or can be found in water reservoirs.Despite their abundance, however, less than 5% of all common cold cases are the result of adenoviral infection [3]. Adenoviral particles are not much smaller than HIV or influenza particles. However, they are relatively big for non-enveloped viruses. The adenoviral capsid has the shape of a rounded icosahedron (a polyhedron with 12 vertices, 20 faces, and 30 edges), and each vertex has a spike that allows the virus to interact with the surface of a host cell [5]. Packed inside this capsid lies the adenovirus genome. Its structure allows to use adenovirus as a tool in gene therapy. Selected foreign genes can be substituted for certain adenoviral genes before infection. In this case the virus may still be able to enter the cells and deliver the foreign genes into the cell nucleus.

The particle structure

Adenoviruses are not surrounded by the lipid envelope, but they incorporate a large set of proteins and a long DNA molecule (4 times longer than HIV genome) that make the virion relatively big (about 90 nm in diameter). The capsid has an icosahedral shape with rounded edges. The trimeric spikes that are located at each vertex interact with the cellular receptors to make the entry of the virus possible [6]. The adenoviral genome is comprised of double-stranded linear DNA that is approximately 35000 bp in length, though highly variable [7]. The outer shell of the adenovirus is composed of 7 protein types. Some of them form the core of the capsid’s faces, some provide additional stability, and still others constitute its vertices. Another subset of five proteins is involved in genome packaging [8, 9, 10, 11].

The major structural component of the adenovirus capsid’s faces is the hexon protein (protein II). Three molecules of this protein form a basic structural unit called the “hexon”. One face is comprised of a group of nine hexons [12], though this group of nine (GON) has several other structural proteins thatare needed to stabilize the structure. Among them are polypeptides VI, VIII and IX, which are located under the hexon proteins, closer to the center of the virion [8]. There are three more hexons attached to each GON near the vertices, which differ from those of the faces by their stabilizing proteins. These GONs are connected to the vertex regions by the IIIa protein [13]. Bases of the vertices are composed of the pentameric penton base protein (protein III) [14]. Each penton is the base for the vertex’s spike, which is made of trimers of the glycosylated fiber protein (protein IV) [15, 16]. The spike consists of the very flexible shaft and the globular knob, which can connect to the CAR receptor (Coxsackie virus and adenovirus receptor) on a host cell’s surface [26]. After the interaction with CAR, the adenovirus enters the cell via the clathrin-dependent, or macropinocytosis, pathway [29].

One controversial question remains concerning the outer morphology of the adenovirus. Many icosahedral viruses and phages have a special portal structure in the place of one of the vertices. This portal serves an important role in loading the viral DNA into the capsid. While we know that the adenoviruses have such machinery — the hexamer of the IVa2 protein — it remains unclear whether this structure replaces one of the penton base and fiber complexes or is located under them [17].

The genome

The size of an adenovirus genome affects the stability of the virion and may vary widely, from 26 to 46 kilobases [18]. Most of the transcriptional units are expressed in early stages of the viral life cycle and play a role in the regulation of viral transcription and replication. (They also downregulate the cellular response to the infection) [19, 20]. Most of the late transcriptional units encode structural proteins [21].

The spatial structure of the adenovirus genome remains poorly described. However, it is known that the viral DNA interacts with several structural proteins, including major and minor core proteins, which are mainly responsible for the packaging of the whole molecule, as well as the protein μ and the DNA terminal protein that fixes the ends of the genome [22]. Virions also incorporate proteases that are necessary for viral unpacking [23]. The exact location, functions, and number of these proteins require further investigation. Some data indicates that the adenoviral genome is more likely to be organized in a loop rather than in a spiral form, which is found in several bacteriophages [24, 25]. Existing models predict that there are approximately 1100-1300 pVII proteins inside the adenovirus particle. These proteins are thought to form hexamers, which then play the role of viral nucleosomes. The pV protein may serve as a linker between these nucleosome-like structures and mediate the connection between the DNA and outer capsid components, such as the pVI protein located under each hexon [22].

Life cycle and use

Adenovirus entry into the host cell is mediated by the surface receptor CAR (Coxsackievirus and adenovirus receptor), which normally connects cells to one another or to intercellular matrix components [26, 27, 28]. After entry and unpacking inside the cytoplasm, the viral DNA enters the cell nucleus.

Adenovirus enters cells via clathrin-dependent endocytosis or via micropinocytosis [29]. After partial unpacking in the cytoplasm, the remaining capsid structures carry the genome to the nucleus in a complex with VII-protein [22, 30]. Early genes of adenovirus are united in several groups — transcriptional units. These encode regulatory proteins that activate DNA synthesis in the cell and block the interferon response, thereby preventing the cell from triggering apoptosis [31]. Some of these early transcriptional products also trigger the synthesis of the late structural proteins.

Adenoviruses are well-equipped to play the role of vectors for the transformation of human cells in medicine. Genes that are needed for viral replication may be easily substituted for by the DNA of interest, and adenovirus particles may be used for its delivery [32, 33, 34, 35, 36]. The simplest variant of this procedure is to delete the adenoviral DNA region that triggers the transcription of most viral proteins (E1A gene), thereby eliminating the virus’s ability to replicate and infect new cells while retaining its ability to express the transgene.

More complicated vector systems require more significant changes to the adenoviral genome. Immense effort has been invested in the development of a virus that could replicate in tumor cells and selectively kill them. The working principle of such therapy is based on the interaction between the viral E1B protein and the cellular p53 protein, which is usually inactivated in tumor cells. In a normal adenoviral infection, viral E1B-55 blocks cellular p53 to prevent cellular apoptosis from precluding viral replication. A therapy which infects tumor cells with a virus lacking the E1B region of its genome may lead to the selective elimination of those cells because viruses with truncated genome could not kill the normal cells with active p53 [37, 38, 39]. Other medical application for adenoviruses is tumor immunotherapy. This approach uses adenoviruses to deliver the toll-like receptor TLR5 and flagellin genes to the tumor cell. Flagellin is a component of bacterial flagella and is also a main ligand for the TLR5 receptor. The interaction between these proteins in the tumor tissue may activate a targeted immune response against the tumor [40, 41]. This approach is briefly described on our website.

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  • Author and manager of the project, 3D-visualization, 3D-technology:
    Ivan Konstantinov
  • Science consultant, texts:
    Yury Stefanov, PhD
  • Senior molecular modeller:
    Anastasia Bakulina, PhD
  • 3D-modeling:
    Dmitri Scherbinin, PhD
  • 3D-modeler:
    Alex Kovalevsky
  • Web-technologists:
    Kirill Grishanin, Gleb Kondratenko
  • Corrector:
    Amy Gordon

Visual Science team is grateful to Drs. Carmen San Martin from Spanish National Center of Biotechnology in Madrid, Michael Imperiale from University of Michigan Health System, Vijay Reddy from the Scripps University and Hong Zhou from the University of California in Los-Angeles for the useful comments and communication.

Congratulation for your very succesful 3D HIV model
Prof. Françoise BARRÉ-SINOUSSI
Nobel Prize in Medicine 2008, Pasteur Institute, Paris, France