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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Overview of influenza

The influenza virus is a common virus found in many places around the world and comes in three different subtypes A,B, and C. Influenza A subtype is the most infectious subtype. It causes pandemics with significant mortalities in affected young people for that it has a wide host range including human, pigs, horses, and birds. All the three influenza subtypes contains the same segmental genome and enveloped glycoprotein. The virus is spherically shaped, ranging from 80 to 120 nm in diameter. The viral particles contain 3 proteins on their outer surface, called: H, N, and M2. It also contains a matrix protein M1 below the outer surface. Each protein has a different function that helps the virus to penetrate and enter the animal’s host cell. The virus also contains eight segments of single stranded negative polarity RNA. Once the virus infects the cell, it will travel to the nucleus to replicate its genome, then the viral mRNA will transfer to the cytoplasm to be translated into viral proteins. Once all the viral proteins are formed, they will all aggregate and get released from the host cell (Shors, 2013).

Hemagglutinin (H) protein

(H) protein is the most important glycoprotein found on the virus surface for that it is responsible for the attachment of the influenza to the cells containing sialic acid receptors, such as cells in the upper respiratory tract. It also helps with the fusion between the viral lipid membrane and the host cell endosomal membrane (Shors, 2013). The H protein is a transmembrane protein consisting of two polypeptides, H1 and H2, which are linked by a disulfide bond between two cysteines. Full length protein is referred to as H0 (Shors, 2013).The H0 protein is homotrimer protein consists of three identical polypeptide chains, each polypeptide is 550 amino acids long that get glycosylated then cleaved into two chains (H1,H2) by the removal of arginine 329 along with a conformational change. H1 and H2 chains from one monomer that noncovalently associates with two additional monomers to form one hemagglutinin homotrimer molecule (Proteopedia, 2015).

The H1 subunit consist of 328 amino acid composing eight stranded beta-sheet associated with little alpha-helix (Proteopedia, 2015). The H1 portion forms a globular bulb at the top of the structure and contains the sialic acid binding site. The amino acid of the alpha helix and some other beta sheets compose the binding pocket of the sialic acid subunit, and determine the attachment specificity of the virus to the host cell.

The H2 portion of H0 is called membrane-spanning anchor and it is directly involved in the fusion mechanism. H2 has a hairpin structure composed by two antiparallel alpha-helices. The C- terminal of H2 is embedded in the viral membrane while the N-terminal end contains 10 hydrophobic amino acid forming the fusion peptide (Proteopedia, 2011).

When H protein attaches to sialic acid residues of the ciliated columnar epithelial cell lining the sinuses and airways, the bound virus is endocytosed by the cell and the virions enter the cell within the endosomal vesicle. Then the endosomal vesicle pH level drops and reaches about 5.5 due to the pumping of protons inside the vesicle by the M2 ions channel. As a result, the H1 protein shifts its position, allowing the H2 protein to become embedded in the host cell membrane. Additionally, the C-terminus embedded in the viral membrane rearranges, bringing the two membranes closer together and facilitation fusion (Wilson et. al 1981). The pH induced conformational changes are partially but not completely reversible. As the pH decrease to 5.5, the three globular heads start to dissociate due to the protonation of relevant H protein residues. the change in pH facilitate the releasing of the fusion peptides. Also at low pH the short and long alpha-helix are separated(Thoennes et.al 2008). The shifting of H1 subunit plays an important role in H mediated membrane fusion , H1 protein helps the membrane attachment and fusion, which results in the release of viral RNA’s into the cytoplasm and then into the cell’s nucleus for RNA replication (Racanilllo, 2009).

The Neuraminidase (N) protien

The N protein (neuraminidase), is one of the main antigenic determinants present at the outer surface along with other transmembrane glycoproteins, and it aids in the viral budding process. The N protein is homotetrameric with the substrate binding site containing only single protein. The secondary structure mostly consists of several beta sheets and three short alpha helices (Proteopedia, 2014). The neuraminidase is an enzyme that cleaves sialic acid from the haemagglutinin molecule, neuraminidase molecules, glycoproteins and glycolipids at the cell’s surface. The sialic acid cleavage helps the virus to bud off from the surface of the infected cell (Gürtler, 2006).

The M1 protien

The M1 protein is one of the major components of the virus by playing an essential role in viral budding. It also forms an intermediate layer between the viral envelope containing the integral membrane proteins and the genomic ribonucleoproteins (RN). The structure of M1 protein has two domain protein with an N-terminal domain containing residues 1–164 and a C-terminal domain with residues 165–252 (Arzt et.al, 2003). The N terminus of M1 has a polybasic sequence at the one side of the molecule, this polybasic sequence sometimes is beta strand and sometimes is alpha helical (Ruigrok et.al, 1999).

The M1 protein functions as self-polymerization, M1 proteins must bind to both the membrane and the viral RNA simultaneously. Some other functions include: a role in the export by the viral ribonucleoproteins from the host cell nucleus, and entering the nucleus through its own nuclear localization signal, which is needed for the export for the newly formed ribonucleoproteins (Arzt et.al, 2003). The proteins that are involved in this export process are the NS2 or NEP proteins, for nuclear export protein inhibition of viral transcription, as well as partaking in the virus assembly and budding. This is done in the form of asexual reproduction that the influenza virus practices (Holsinger et. al 1994).

The M2 protien

The structure of the M2 protein consists of a four-helix bundle with a 25-degree tilt. Since the H protein undergoes a conformational change, M2 proteins act as an ion channel by allowing the proton ions to penetrate the viron (Pinto, Lamb 2006). The pumping of the protons will weakens the interaction between the viral matrix proteins and the viral RNA and nucleoproteins. The eight segments of the viral ribonuclease are then released into the cytoplasm and exported to the nucleus. The ability of opening and closing the M2 ion channel depends on the action of single transmembrane domain residue Trp 41. When the pH exceeds pH 7, the channel will be closed, and when the pH is lower than pH 6.5, the channel will be opened. Trp 41 is a key residue in opening and closing ion channel pore (Pinto, Lamb 2006).

Influenza treatment

There are two antiviral treatments nowadays that triggers the M2 channel and stops its function, Amantadine and Rimantadine (Shors, 2013). By stopping the function of M2 proteins, the release of the viral genome and proteins will be incomplete or terminally stopped. As a result, the uncoating process and the spread of the viral genome will be impaired and the virus replication will be stopped. This can be done by changing the formation of the ion channel or stopping the M2 protein function entirely. In addition to the above treatments, there are other antiviral drugs which targets the sialic acid receptor, the RNA dependent RNA polymerase, Neuraminidase (N) protein.

References

1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

AArzt, S., Petit, I., Burmeister, W. P., Ruigrok, R. W. H., & Baudin, F. (2004). Structure of a knockout mutant of influenza virus M1 protein that has altered activities in membrane binding, oligomerisation and binding to NEP (NS2). Virus Research, 99(2), 115-119. doi:http://dx.doi.org/10.1016/j.virusres.2003.10.010

Gray, C., & Tamm, L. K. (1998). pH-induced conformational changes of membrane-bound influenza hemagglutinin and its effect on target lipid bilayers. Protein Science : A Publication of the Protein Society, 7(11), 2359.

Gürtler, L. (2006). In Kamps B. S., Hoffmann C. and Preiser W. (Eds.), Virology of human influenza Flying publisher.

Hemagglutinin (influenza). (2015). Retrieved 11/13, 2015, from https://en.wikipedia.org/wiki/Hemagglutinin_(influenza)

Holsinger, L., Nichani, D., Pinto, L., & Lamb, R. (1994). Influenza A virus M2 ion channel protein: A structure-function analysis. Journal of Virology, 68(3), 1551.

Influenza hemagglutinin. (2011). Retrieved 11/13, 2015, from http://proteopedia.org/wiki/index.php/Influenza_hemagglutinin

Avian Influenza Neuraminidase.(2014). Retrieved 11/13, 2015, from http://proteopedia.org/wiki/index.php/Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza

Hemagglutinin. (2015). Retrieved 11/14, 2015, from http://proteopedia.org/wiki/index.php/Hemagglutinin

Pinto, L., & Lamb, R. (2006). The M2 proton channels of a A and B viruses. The Journal of Biological Chemistry, 281(14), 8997.

Racaniello, V. (2009). Release of influenza viral RNAs into cells. Retrieved 11/14, 2015, from http://www.virology.ws/2009/05/06/release-of-influenza-viral-rnas-into-cells/

Ruigrok, R. W. H., Barge, A., Durrer, P., Brunner, J., Ma, K., & Whittaker, G. R. (1999). Membrane interaction of influenza virus M1 protein. Virology, 267(2), 289-298. doi:http://dx.doi.org/10.1006/viro.1999.0134

Shors, T. (2013). Infulenza viruses. Understanding Viruses (2nd ed., pp. 345-290). Burlington, MA: Jones & Bartlett Learning.

Wilson, I., Skehel, J., & Wiley, D. (1981). Structure of the hemagglutinin membrane glycoprotein of influenza virus at 3 A resolution. Nature, 289(5796), 366.

Thoennes, S., Li, Z., Lee, B., Langley, W. A., Skehel, J. J., Russell, R. J., et al. (2008). Analysis of residues near the fusion peptide in the influenza hemagglutinin structure for roles in triggering membrane fusion. Virology,370(2), 403-414. doi:http://dx.doi.org/10.1016/j.virol.2007.08.035

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