1.G.4 The Viral Pore-forming Membrane Fusion Protein-4 (VMFP4) Family

Many envelope viruses enter host cells via the endocytotic pathway. The virus is internalized via coated vesicles and transferred to endosomes. Due to the acidic conditions, the envelope of the virus fuses with the endosomal membrane. In Semliki Forest virus (SFV), fusion is mediated by the trimeric type I glycoprotein E1, which is initially complexed with other proteins (i.e., E2 and E3). These dissociate under acidic conditions. E1 has been shown to form pores in both animal cell and E. coli membranes under low pH (pH 6) conditions (Nyfeler et al. 2001). No other viral protein is required for pore formation. E1 (341 aas) is derived from the C-terminal region of the polyprotein of SMV. E1 shows a high degree of sequence identity with homologues from many other viruses.

The 6K proteins of two Alphaviruses, Ross River virus and Barmah Forest virus (derived from polyproteins of about 1250 aas) have been shown to form cation-selective channels in planar lipid bilayers. The purified proteins (of 60 and 58 aas, respectively) gave conductances that varied from 40 to 800 picosiemens, suggesting that they can form channels with a range of oligomeric states (Melton et al. 2002).

The reaction catalyzed by these cation-selective channels is:

ions (in) ⇌ ions (out)



Apellaniz B., Huarte N., Largo E. and Nieva JL. (2014). The three lives of viral fusion peptides. Chem Phys Lipids. 181:40-55.

Elmasri, Z., V. Negi, R.J. Kuhn, and J. Jose. (2022). Requirement of a functional ion channel for Sindbis virus glycoprotein transport, CPV-II formation, and efficient virus budding. PLoS Pathog 18: e1010892.

Gibbons, D.L., M.C. Vaney, A. Roussel, A. Vigouroux, B. Reilly, J. Lepault, M. Kielian, and F.A. Rey. (2004). Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus. Nature 427: 320-325.

Huang, T.C. and W.B. Fischer. (2022). Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach. Biomolecules 12:.

Hyser, J.M. and M.K. Estes. (2015). Pathophysiological Consequences of Calcium-Conducting Viroporins. Annu Rev Virol 2: 473-496.

Melton, J.V., G.D. Ewart, R.C. Weir, P.G. Board, E. Lee, and P.W. Gage. (2002). Alphavirus 6K proteins form ion channels. J. Biol. Chem. 277: 46923-46931.

Nyfeler, S., K. Senn, and C. Kempf. (2001). Expression of Semliki Forest virus E1 protein in Escherichia coli. Low pH-induced pore formation. J. Biol. Chem. 276: 15453-15457.


TC#NameOrganismal TypeExample

The Semliki Forest Virus (SFV) (Class II) Structural polyprotein (1253 aas; E1=816-1253 E2=334-774).  The fusion peptide is residues 895 - 913 (Apellániz et al. 2014). The 6K viroporin transports monovalent cations and Ca2+ (Hyser and Estes 2015). Conformational change and protein-protein interactions of this fusion protein have been considered (Gibbons et al. 2004).

Virus (Flaviviridae)

Structural polyprotein of Semliki Forest Virus (P03315)


The Ross River virus 6K protein.  The class II fusion peptide is residues 896 - 914 (Apellániz et al. 2014).  The 6K protein transports monovalent cations and Ca2+ (Hyser and Estes 2015).

Arbovirus (Togaviridae; alphavirus genus)

6K protein of Ross River Virus (P08491)

1.G.4.1.3The Barmah Forest virus 6K protein (58 aas; present within the viral structural polyprotein (P89946))

Arbovirus (Alphavirus genus)

6K protein of Barmah Forest Virus (P89946)


The Sindbis virus 6K protein (55 aas; present within the structural polyprotein (AAC83379)).  Transports monovalent cations and Ca2+ (Hyser and Estes 2015).


6K protein of Sindbis Virus (Q9YJX7)


Salmonid α-virus 6K protein of 1319 aas and 6 TMSs in a possible 1 + 4 + 1 TMS arrangement (Elmasri et al. 2022).

6K protein of Salmonid virus


Structural polyprotein, E2-6K-E1 region of 923 aas and 5 TMSs in a 4 (central) + 1 (C-terminal) TMS arrangement (Huang and Fischer 2022).

E2-6K-E1 polyproptein of Chikungunya virus (CHIIKV).