xaktly | Virology

Viral attachment & entry

The virology pages are organized like this:

Getting into the host cell

In order for a virus to propagate — to make new copies of itself (or really, to trick the host-cell machinery into doing so), it must first get in, and after that, all of the conditions necessary for its replication have to exist. Here are some important terms we use to describe the basic relationships between viruses and potential host cells:

A cell is susceptible to a virus if it has a receptor on its surface that will recognize some part of the virus. Many viruses are not recognized by cells, and thus won't get in. Such cells can't be infected. It's also important to note that while cells display a large variety of receptors on their surfaces, no host cell displays any that evolved just to let a virus in. That's always an accident.

A cell that does not have a receptor that will bind to a virus is called resistant. Many viruses are able to get into, say, respiratory-system cells but not blood cells. The respiratory-system cells are susceptible, and the blood cells are resistant.

A permissive cell is able to replicate the virus once it enters the cell or its genome is injected. A permissive cell need not be susceptible to infection, and will therefore be resistant. Only cells that are susceptible and permissive can be infected and co-opted by viruses for making new copies.

Only cells that are both susceptible and permissive can be used by a virus to copy itself.

In this section we'll need to review the basics of cell membranes and transmembrane proteins to get an idea about the host-cell side of things, then we'll see how viruses co-opt key cellular defenses to get inside. Along the way we'll refresh our memories about aliphatic stretches of protein sequence and the hydrophobic effect.

Cell attachment & entry terms

Susceptible Cell has a receptor that will recognize a part of the virus
Resistant Cell has no receptors that recognize the virus; it is locked out.
Permissive Cell has the necessary molecular machinery to replicate the genome and proteins of the virus so that they can reassemble into new virus particles.

Cell membranes

All cell membranes are made mostly of phospholipids, which consist of a charged phosphate "head group" bound to one or more long aliphatic "tails." Here's a diagram of a common phospholipid, 1-Oleoyl-2-palmitoyl-phosphatidylcholine.

The zigzag lines on the left are a shorthand: each vertex represents a carbon, and we assume that each carbon is bonded to as many hydrogen atoms as possible (the "oleoyl" and "palmitol" parts of the cumbersome name of this lipid just name those two long chains). It's not important for this discussion that you understand the structure or the chemistry of phospholipid molecules, only that you understand that there are two ends, one a charged, water-soluble end and the other an extended aliphatic (or hydrophobic) end that is not soluble in water. We can simplify that diagram like this:

Now a cell membrane consists of a sandwich of phospholipids, aliphatic tails on the inside away from water and phosphate heads on the outside It looks more-or-less like this:

Phospholipid bilayer

This lipid bilayer is the only way that lipids can remain soluble in water. The aliphatic tails are buried in the inside of the membrane (remember the principle "like dissolves like" from chemistry, which we can generalize as "like associates with like"), leaving the charged phosphate groups on the outside, exposed to the aqueous environments inside and outside the cell.

The phosphate or phosphatidyl heads form layers on the outside and inside that are about 15 Å (1.5 nm) thick, while the buried hydrophobic zone is about twice that thickness, for an overall membrane thickness of about 60 Å or 6 nm.

Phospholipid membranes like this can be extensive enough to form sheets that can form closed compartments – cells. One thing to remember is that membranes are held together by weak intermolecular forces, so they're quite flexible and tend to warp and move a lot.

The composition of cell membranes depends on the organism and the type of cell within it. Generally, membranes consist of about 50% lipids and 50% proteins (which we'll cover below). The lipids consist, on average, of

  • 50% phospholipids
  • 2% glycolipids
  • balance: sterols like cholesterol

Cholesterol is a special lipid that looks like this:

One important function of cholesterol in membranes is to add a bit of stiffness where and when needed. The multi-ring structure of cholesterol is planar and stiff compared to the lipid tails of the phospholipids.

Glycolipids are lipid molecules that are capable of having sugars covalently attached, or glycosylated. These sugars and sugar chains can decorate the outside of the cell to identify it to surrounding cells, among other functions.

You can learn more about lipids here.

Transport & transmembrane proteins

Membranes separate the inside of a cell from the outside or extracellular world. They contain and protect the contents and control what gets in and out. There must be some transport of nutrients, gases and other molecules, even large proteins, across the membrane in order for the cell to function. In general, the hydrophobic region of a cell membrane is inhospitable to most ions and organic molecules, so transport through the membrane has to be through other means than simple diffusion. There are four principal ways that atoms and molecules (including large things like proteins and viruses) transit the membrane:

  • Simple diffusion
  • Transmembrane channels & transporters
  • Endocytosis
  • Exocytosis

We won't be very concerned with simple diffusion here because it's not important for viral entry. Diffusion is usually osmosis, movement of a substance across a membrane due to a force caused by an imbalance of a substance, like an ion, on either side of the membrane.

Transmembrane channels & transporters

Transmembrane channels are formed from proteins that have a hydrophobic part that penetrates the membrane, forming a "tube" of sorts. Channels allow for diffusion of atoms or molecules, and are often selective for just one type of molecule. For example, the aquaporin channel allows water to transit the membrane by diffusion. Transporters are through (trans)-membrane proteins that bind to a specific molecule or protein, then undergo some sort of conformational change to allow it into the cell. These proteins are important for viral entry.


Endocytosis is the process of engulfing a membrane-enclosed substance, which might be a protein or an enveloped virus, by merging the two membranes. Here is an illustration of how it works:

A protein (illustrated here) or other substance binds to a receptor on the surface and is engulfed or invaginated into the cell membrane. The membrane-surrounding the protein is pinched off leaving a vesicle. Sometimes this process is accompanied by construction of a cage around the vesicle made of the protein clathrin. It's important to note that the protein is not actually inside the cell at this point. It's still a membrane away from being in the cell cytoplasm. Other steps are required for its release, and those depend on what's in the vesicle.

⚡ Energy: We ought to note here that endocytosis doesn't happen for free; it takes energy on the part of the cell for any kind of active transport across the membrane.

Endocytosis can also occur when the substance entering the cell is itself already enclosed by a membrane, such as an enveloped virus. This requires fusion of the two membranes.


You can think of exocytosis as movement of a substance in the other direction, from inside the cell to the outside. This kind of outward flow of matter from the cell generally first involves evelopment in a membrane, usually derived from the membrane of the Golgi apparatus of the cell. Newly-constructed progeny viruses are sometimes exported from an infected cell in this way.

As an example of the binding of a ligand to a cellular receptor, consider the ACE2 receptor (green) below. In normal cell function, this receptor specifically recognizes an enzyme (a protein) called angiotensin-converting enzyme (ACE). Accidentally, the ACE2 receptor also recognizes a part of the "spike" protein of the SARS-CoV-2 virus, the virus that causes the respiratory disease COVID-19, and that's what's shown bound to the receptor here. The binding contacts between the two proteins are in the yellow-highlighted region.

The spike protein of the SARS-CoV-2 virus bound to the ACE-2 receptor of a human epithelial cell

Signal receptors

Some transmembrane proteins are signal receptors. They are there to recognize a specific ligand, but not let it in, or to be chemically modified by some enzyme. Ether event can lead to some structural change in the part of that transmembrane protein on the inside of the cell, thus triggering some intracellular process. In this way, cells can receive communications from outside and change what's going on inside the cell (like manufacturing a certain protein) accordingly.

  Transmembrane domains

Below is a schematic diagram of a few kinds of transmembrane domains of membrane proteins, the part of the protein that anchors the receptor to the membrane. The transmembrane parts of receptors have to consist of stretches of aliphatic amino acids (more below) in order to pass through the aliphatic tail section of the phospholipid membrane bilayer.

The figure below shows some of the protein motifs that penetrate a cell membrane and anchor a cell receptor. They can consist of a single aliphatic region that folds into an α-helix, two or more (sometimes 7 or 8) helices that form a bundle, and sometimes a structure called a β-barrel, made of strands of protein that fold into beta-sheets that then form a barrel-like structure.

  Aliphatic amino acids

Of the twenty naturally-occuring amino acids, here are the six aliphatic ones. Notice that their side chains (green) are neither polar nor charged. The principle "like dissolves like" tells us that these side chains aren't so soluble in water. Longer stretches of such amino acids tend to become buried in "like" hydrophobic substances such as the long hydrophobic chains of lipids, detergents or oils. In proteins, they tend to be "buried" in the interior the folded protein, away from the water molecules that must surround it.

Viral entry

In order for a virus to enter a cell, it must first be "recognized" by that cell. That means it has to bind to something on the cell surface (to be susceptible). That means some transmembrane protein like a receptor, but it can also mean a sialic acid, often the capping sugar on a glycoprotein, or some other moeity on the cell surface.

What's important to remember is that host cells don't produce receptors that allow viruses to bind and enter. When a viral protein binds to a receptor, it's an accident of molecular geometry.

Binding a receptor is not enough for viral entry, however. A non-enveloped virus must somehow trigger endocytosis, and an enveloped virus must trigger membrane fusion. The latter requires excluding water molecules from the interface between membranes, which requires a fair bit of energy. Viral fusion proteins are often "spring loaded" to achieve this purpose.

Now let's go through a couple of examples of viral entry into host cells to give you some of the basic ideas.

Example 1 — influenzavirus

First let's have a look at the overall structure of the influenza virus using this schematic diagram. We won't consider the genome here. The outer capsid, consisting of the matrix protein called M is surrounded by a membrane. Anchored to the membrane are two main proteins. We'll only worry about the red one here, which is hemagluttin (HA). HA recognizes (binds to) sialic acids on the surface of the host cell. Sialic acid is always the last of what can be a chain of several sugars that bind to or "decorate" glycoproteins on the host-cell surface.

The HA on the viral surface is actually a trimer of three HA proteins (monomers). Here are ribbon diagrams of the monomer and trimer.

Each HA monomer is actually in two pieces due to a cleavage performed by a host-cell protease. The two pieces stick together. The part labeled HA1 has a common type of fold and is referred to as a globular domain. It is responsible for binding to sialic acids on glycoproteins on the host cell surface, triggering endocytosis of the virus particle. The HA2 part carries the fusion peptide, shown in red. The fusion peptide is not soluble, and must therefore be "hidden" on the interior of the HA2 fold, and in the interior of the trimer. Trimers are anchored to the viral membrane at the bottom of the images by hydrophobic anchoring peptides.

We will return to the details of the HA molecule later, but for now, let's look at a cartoon version of the events leading to the membrane fusion that lets the flu virus out of endosomes and into the cell cytoplasm.

Membrane fusion

This series of cartoons is a very stylized picture of the sequence of events that leads to fusion of viral and endosomal membranes. In this figure, the virus, with its hemagluttinin (HA) proteins bound to its membrane (bottom) approaches the endosomal membrane (top). The HA trimer is shown as a set of three blue domains attached to three red domains, to which the fusion peptide is attached and initially buried.

The endosomal membrane contains proton pumps which move protons to the interior and thus reduce the pH of that environment. This triggers a dramatic structural change in HA. The well-structured blue section reorganizes to uncover membrane-insertion peptides previously hidden in the interior of the HA trimer. These can extend and insert into the host-cell membrane.

After the insertion, the blue polypeptide chains reorganize in a "hairpin" maneuver, in which they associate closely to the red domains – almost in a zippering motion – pulling the two insertion points closer together and excluding the water molecules between the two membranes.

Research has shown that, on average, it takes about three HA trimers working this way to pull the membranes close enough to fuse, and that the process happens on a timescale of a few tens of seconds.

When the membranes are close enough, they fuse in a two-step process. The innermost phospholipid layer fuses first, then the outermost layer fuses ...

... to form a pore, a passage through which the contents of the influenzavirus can exit the endosome and enter the cytoplasm of the host cell.

Now lets take another look at this process, this time looking at the precise structural rearrangements of the HA protein.

Molecular details

Pre-fusion hemagluttinin

For clarity, a monomer of HAprotein is shown here. Trimers of HA decorate the icosahedral influenza virus, a membrane-coated ss -RNA virus, as little spikes. The short bit of protein labeled C2 is a hydrophibic stretch that anchors each HA to the viral membrane – three anchors per trimer.

Another hydrophobic stretch, labeled as the fusion peptide (and labeled )N2 in the figure) is "buried" inside the protein beneath the α-helix that is colored green. If it were not buried toward the interior of the protein, the virus would not likely be soluble, something it definitely needs to be in order for the virus particle to be as soluble as it needs to be in order to find its host.

Notice also that the orange stretch of protein between amino acids 58 and 75 is relatively disordered. That is, it's not an α-helix or β-strand.

Hemagluttinin undergoes a dramatic rearrangement when it is taken into cells in endosomes. Cellular endosomes pump protons into the interior of the endosome and some bind to basic amino acids in HA, causing a dramatic structural rearrangement. The next figure shows that rearrangement.

Fusion-competent hemagluttinin

When the pH drops, HA goes through a dramatic conformational change, revealing the fusion peptide and pairing it with the anchoring peptide. Notice that the long helix projecting the fusion peptide is composed of the original yellow and red helices, plus a newly-rearranged orange helix.

From this conformation, the fusion peptide can insert into the host-cell's endosomal membrane, triggering another conformational change that brings the viral and host membranes together (by excluding water molecules) closely enough that they can fuse.

Notice that the HA1 globular domain, which initiates the cell-entry process by recognizing a sialic acid on the cell surface, is pretty much pushed out of the way during this process.

The animation below presents a pretty good picture of how the fusion works.

Example 2 — HIV

Here is a schematic view of the HIV virus, a single-stranded RNA retrovirus. It is an envoloped virus that displays a few trimers of a pair of proteins called gp41 (the stalk) and gp120, the binding spike.

Because HIV is a retrovirus, it also carries key enzymes that ensure that its genome can be copied and inserted into the host-cell DNA.

The animation below shows the essential process of viral membrane fusion with the host cell. For clarity, the gp120 part of the envelope protein isn't shown. The process begins with gp120 binding to a receptor on the cell surface called CD4. This initiates a structural rearrangement that allows the buried fusion peptides of gp41 to be exposed to the membrane and insert there.

After insertion of the membrane peptides, the three proteins re-bundle their helices, reducing the distance between the viral and cell membranes, and excluding water, to the point where the membranes fuse and contents of the virus can be spilled into the cytoplasm of the host cell.



A pathogen is a virus, bacterium or other microorganism that can cause disease in a host organism. Not all viruses or microorganisms are pathogens.



An aliphatic molecule is composed mostly of extended carbon and hydrogen chains, not rings. Aliphatic molecules generally have few or no charged or polar subunits.



Literally (from Greek words), hydrophobic means water (hydro) fearing (phobic). Hydrophobic compounds are not soluble in water and are not by wetted by water solutions (think about water beading on a piece of glass). Contrast these to hydrophilic compounds (water loving), which dissolve easily in water.



Literally hydro = water, phobic = fearing → water-fearing. Oily, fatty or waxy substances that do not dissolve in water are hydrophobic. The floating of oil on top of water is an example of the hydrophobic effect.



An aqueous solution is one in which the solvent is water (root = "aqua"). Typically, but not always, aqueous solutions are ionic salts dissolved in water.


solute / solvent

A solute is the thing that is dissolved in a solvent. For example, when we dissolve sodium chloride (NaCl) in water, the ions Na+ and Cl- are solutes and water is the solvent.

Solutes can be charged or not charged, polar or non-polar, and solvents can be polar or nonpolar. Solutes can also be gases. For example, carbon dioxide (CO2) and oxygen (O2) can dissolve in water.



Osmosis is a spontaneous movement of a substance across a semi-permeable membrane. It occurs when there is a concentration difference of that substance on either side of the membrane. The greater the difference, the greater the osmotic force or osmotic pressure driving the two sides toward the same (equilibrium) concentration.



To propagate in this context is to move forward and to spread out.

It can also mean to spread an idea or rumor, or to continue a plant or animal gene line in breeding.



Moeity is a word for a generic constituent part of a whole, in context. If we're talking about polymers, a moeity is one of the building blocks that make up the larger polymer. In DNA, each nucleotide-phosphate is a moeity. If we're talking about condominium units, a moeity might be one condo in the complex, and so on.



Glycoproteins are proteins to which sugars are attached after translation of the polypeptide chains. The proces of adding sugar molecules, often in chains of several sugars (oligosaccharides), is called glycosylation. Often membrane-bound proteins are glycosylated for the purpose of displaying sugars function in cell-to-cell interactions.

The terminal sugar in an oligosaccharide chain is often sialic acid.

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