Poliovirus Type-1 Mahoney (PDB ID:2PLV) from Homo sapiens
Created By: K. Sunga
Poliovirus Type-1 Mahoney (PDB ID: 2PLV) is a strain of poliovirus that is known to cause poliomyelitis, or polio (1). Type-1 Poliovirus is an enterovirus that is part of the picornavirus family which includes other viruses such as rhinovirus that can cause diseases such as foot and mouth disease or Hepatitis A (1). The study of poliovirus in general, is biologically significant as poliovirus is easily transmitted among humans, causing infection (8). Upon infection, poliovirus causes poliomyelitis, an inflammation of the grey matter of the spinal cord (8). In most cases of poliomyelitis, symptoms of influenza are usually exhibited, however, in rare cases, poliomyelitis can cause irreversible paralysis of the limbs, the heart, and even the respiratory system (8). Paralysis can occur, because the virus travels through the fecal-oral route (8). Through this route, poliovirus can potentially enter the bloodstream, and in turn infect the central nervous system, thereby infecting the motor neurons of the spinal cord, and thus causing paralysis (8). Because poliovirus, like all viruses, relies on the machinery of the infected cell to continue replication, the structure of the virus is the single most important factor that contributes to the survival of the virus, as shown in this molecular document. Not only will the study of poliovirus contribute to our understanding of poliovirus, but it will also help understand how other viruses of the picornavirus family operate, as their viral structures are closely related to each other. With the knowledge gained by studying the structure of poliovirus, the weaknesses of structurally similar viruses can be further exploited.
The poliovirus virion consists of plus-sense RNA enclosed by capsid proteins that are arranged in a icosahedral-spherical shape (3). The spherical capsid proteins consists of 4 subunits, VP1, VP2, VP3, and VP4 (3). An ExPasy bioinformatics tool was run on the protein to determine some of the chemical properties of the capsid protein. The amino acid sequence for the viral protein totals to 880 residues, with a molecular weight of 97,248 Daltons (4). Chemically, the isoelectric point (pI) of the capsid proteins is 6.1 (4). The virion is known to bind to fatty acid ligands as the virion was able to bind with ligands like myristic acid and sphingosine during ligand binding (7).
Before the development of a mature virion particle, the viral mRNA uses the infected cell’s machinery to translate a polyprotein, P1 (3). The P1 polyprotein is then myristoylated at residue 22 of the N-terminus, and then cleaved by viral proteases 2A and 3CD (3). The proteolytic cleavage and processing of the P1 polyprotein produces the capsid proteins VP1 and VP3, as well as an immature myristoylated capsid protein, VP0 (3). VP0, VP1, and VP3 then form an intermediate, that is assembled into pentamers, which are then further assembled into “empty capsids” with 60 copies of each protein, VP0, VP1, and, VP3 in the empty capsid (3). This structure is known as the provirion (3). Upon assembly of the provirion, the VP0 myristoylated capsid is further processed and is cleaved in an autocatalytic process to produce the capsid proteins VP2, and VP4. The autocatalytic cleaving of the VP0 capsid is due to a Histidine residue at position 195 on the VP2 capsid (3). Before cleavage of VP0, the imidazole side chain of Histidne acts as a base, and activates a water molecule, which then acts as a nucleophile and initiates cleavage of a peptide bond in VP0 to yield the VP2 and VP4, subunits (3). It has been shown that His-195 residue on VP2 has been highly conserved in other picornaviruses, which indicates that this autocatalytic cleavage of the VP0 capsid into the VP2 and VP4 capsid is essential, and largely increases the stability of the virion as a whole (3).
As mentioned, the poliovirus virion has a binding pocket for myristic acid at the Gly-22 of the P1 precursor protein (3). The myristoylation of Gly-22 is known to help direct the assembly of the VP4 subunit during virion assembly, as well as during the entering of a cell membrane (1). After cleavage of the P1 protein, the myristoylated residue ends up being Gly-2 of the VP4 subunit of the virion (1). The myristoylation of the glycine residue on the VP4 subunit is beneficial to the structure as poliovirus as a whole. The myristoylated residue helps mediate interactions between the VP3, and VP4 subunit, as well as shields the hydrophobic Leu-2, and Pro-3 residues of the VP3 subunit (1).
A fully mature virion of poliovirus consists of 60 copies of each of the 4 capsid proteins, VP1, VP2, VP3, and VP4 (1). Subunits VP1, VP2, and VP3, are considered the “core” proteins of the capsid protein, and are all compressed and arranged in a common structural motif which is an 8-stranded anti-parallel β-barrel that is flanked by 2 helices (2). Strands B,I,D and G of the β-barrel form the bottom and front surfaces of the barrel, as well as a large β-sheet (2). The other 4 strands, C, H, E, and F make up the back surface of the β-barrel and form a relatively flat β-sheet (2).
Though the structure of poliovirus is relatively “simple”, and similar to that of the structure of related picornaviruses and plant viruses, the structure of poliovirus has several features that distinguish the virus from other related viral structures (2). The outer surface has 2 prominent features; a set of prominent peaks near the five-fold axis, and a set of broad plateaus around the three-fold axis (2). The prominent peaks near the five-fold axis are caused by a tilt in the VP1 capsid protein, in which the upper surface of the β-barrel forms an upward slope, and creates a peak (2). This peak causes loops of residues 96-104, 245-251, and 142-152 of VP1 to be exposed at the peak (2). The broad plateaus of the three-fold axis are are caused by an outward tilt of the VP2 and VP3 capsid proteins resulting in exposed loops of residues 72 – 75, 240-244 in VP2, and in residues 75-81, 196-206 in VP3 (2). It is said that these broad plateaus on the outer surface are the sites of receptor attachment for viral invasion of the cell (3).
In the inner surface of the virion, another distinct feature occurs due to an interaction of the VP3 and VP4 subunits at their respective NH2 termini (2). At the inner surface near the five-fold axis, 5 subunits of VP3 form a 5-stranded twisted parallel β sheet which is surrounded by 2-stranded anti-paralell β-sheets of the VP4 capsid at its NH2 terminus (2). This structure is known as a β-annulus (2). Although some plant viruses are known to have a β-annulus, the β-annulus is still a distinguishing feature of the structure of poliovirus (2).
Another feature of type 1 poliovirus Mahoney is the creation of a hydrophobic pocket (3). At the base of the broad plateaus on the outer surface of the virion, is a hydrophobic pocket formed by the VP1 capsid protein (3). The hydrophobic pocket is usually then filled with some sort of fatty acid ligand, know as a pocket factor (3). The pocket factor is usually a sphingolipid, or a mixture of short fatty acid chains (3). The hydrophobic pocket is known to be the site of binding for capsid antiviral agents, which prevent the virion to undergo conformation changes; a necessary process needed for the invasion of a cell (3).
One of the most important roles of the capsid protein is the ability to undergo conformational changes. It is proposed that the Ability to undergo conformational changes Is essential in how the virus invades the cell (3, Refer to image on image tab for lifecycle). When the broad plateaus of the outer surface of poliovirus bind to the poliovirus receptor (PVR) on a target cell, poliovirus forms an initial binding complex with the receptor (3). After the formation of the initial binding complex, at a physiological temperature, the initial binding complex undergoes an irreversible conformational change into an intermediate known as an A particle (3). The A-particle is hydrophobic, and disrupts the cell membrane and in turn forms a pore in which the viral RNA can travel through (3). The conformational changes that poliovirus undergoes through in cell invasion is important due to the fact that upon binding, the PVR receptor acts as a catalyst which decreases the activation energy of the virion and causes the necessary conformational changes (3).
A Position-specific-iterated basic local alignment search tool (PSI-BLAST) was conducted to compare if there were any homologous primary amino acid sequences to type-1 poliovirus. One homolog that was found was type-2 poliovirus, another strain of the virus (5). The primary sequences between these two types had an E-value of 0.0, and had 88% identical primary sequences, suggesting that very few residues differed, and that structure was overall conserved (5). A DALI analysis was then conducted to determine if there were any secondary and tertiary homologs similar to type-1 poliovirus Mahoney (6). It was found that the poliovirus type-3 strain was a very close homolog in that it had a Z score of 29.0, and had an 81% match to poliovirus type 1 Mahoney, meaning that the secondary and tertiary structures between the two types of poliovirus are relatively similar (6).
In comparing and contrasting the type-1 poliovirus and the type-3 poliovirus, though both these types are mostly similar in their secondary and tertiary structures, the small differences in structure contribute to notable physiological differences between the two strain of poliovirus. Structurally, in the core of the subunits, both types of poliovirus are highly conserved between another, due to the nature of the recurring β-barrel motif (1). On the other hand the outer loops of the structure have differences, in that type-3 poliovirus is less constrained than type-1 poliovirus, due to the side-chains of the amino acids (1). These less constrained outer loops of type-3 poliovirus contribute to the more dynamic nature of the virion as a whole, with respect to processes such as assembly, and infection (1).
Another difference between the two types of poliovirus occurs at the VP1 subunit at a specific loop (1). In type-1 poliovirus, at residues 95, 97, and 102 is a proline, serine and a aspartate respectively(1). In type-3 poliovirus at the same residues 95, 97, and 102, substitutions occur where there is a glutamate, proline and a glutamine respectively(1). These substitutions, result in the a major difference of loop conformation in this area of subunit VP1, which ultimately result in a larger and more exposed loop in type-3 poliovirus, than in type-1 poliovirus (1). The difference in loop confirmation and exposure ultimately results in a difference of antigen specificity and immunodominance between the two types of poliovirus (1).
Perhaps the most minute difference in structure between the two viruses causes one of most distinguishing features between the two viruses. In subunit VP3 at the turn of a β-barrel intersects with the turn of a helix, ultimately trapping 3 water molecules (1). In type-3 poliovirus at this intersection exists phenylalanine at residue 91, where as a serine occurs at this same position in type-1 poliovirus (1). In type- poliovirus the side-chain of Ser-91 points inward to the pocket, and creates a hydrogen bond with one of the trapped water molecules (1). However, in type-3 poliovirus, the side chain of Phe-91 point outward, due to aromatic ring, and ultimately causes the entire side chain to be solvated by the water molecules (1). Solvation of the side chain is energetically unfavorable, and is thought to have cause an increased temperature-sensitivity in type-3 poliovirus, which can be exploited at specific times during the viral life cycle (1).
As shown with the comparison between type-1 poliovirus and type-3 poliovirus, even though the structures quite similar to each other, small diffrences in the amino acid sequences can account for major phsyiological effects to the virus as a whole. Such consequences resulted in compromised sensitivity to temperature, a different type of antigen specificity, or even a more dynamic protein. By studying the proteins of viruses with similar viral proteins, a better understanding of the virus as a whole can be obtained.