The crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin (PDB ID: 4GXU) is a protein that inhibits receptor binding (rotation). More specifically, it will bind to viruses containing HA residues (1). This is a viral protein associated with the influenza A virus, appearing as a significant part of the virus’ structure Because the influenza A virus impacts humans, this protein can also appear in the immune system of humans (2). In humans, it is known for binding to HA residues. Through these bonds, it is capable of mediating the specificity of receptors. The capability of the crystal structure of antibody 1F1 bound to 1918 influenza hemagglutinin to mediate receptor specificity is an important feature of this protein, and it holds significant consequences in human response to influenza virus. In fact, this feature is one of the reasons that this protein is of significant interest to scientists. It has played important roles in the flu viruses of 1918, 1943, and 1977. Scientists believe in the importance of this protein because it has previously been used in neutralizing flu viruses and therefore holds use in current attempts to neutralize flu viruses (1).
Antibody 1F1 bound to the 1918 influenza virus hemagglutinin was crystallized using a sitting drop vapor diffusion method (2). In this technique, a droplet of the sample is mixed in equilibrium with a crystallization reagent. Water is then removed from the sample, leading to an increased concentration of the sample and the subsequent supersaturation of the sample in the drop (3). Once crystals are formed using the sitting drop technique, the actual structure of the crystal is determined using X-ray diffraction data (1). This technique is based on the elastic scattering of X-rays when in contact with objects with long range order. When rays are reinforced by one another, it provides an adequate method of determining crystal structure (4). In the crystallization methods described above, no ligands in the crystal structure of antibody 1F1 bound to 1918 influenza hemagglutinin are involved.
The molecular weight of crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin is 35916.37 Da (or 35.92 kDa) (5). This protein also possesses an isoelectric point at 7.69 (5). The general structure of the protein is made of four total subunits. These are described as the hemagglutinin HA1 chain, the hemagglutinin HA2 chain, the antibody 1F1 heavy chain, and the antibody 1F1 light chain (2). Each of these four subunits is an important domain of the protein that allow for the determination of specificity of the receptor through individual interactions with the binding site as they each reach its location (1). In spite of this, the main focus of structural analysis and comparison is the hemagglutinin HA1 chain. In this chain, there are 331 total residues. This protein is not, however, fully crystallized as there are four sets of CH1/Cλ domains that were not successfully placed. Even after refinement of the crystallized structure, these domains are still missing (1).
The quaternary structure of the crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin has been determined to be dodecameric, but the chain being focused on (hemagglutinin HA1 chain) possesses only four subunits (subunits) (2). In this chain, there are 331 residues that comprise alpha helices, beta sheets, and 3/10 helices. Throughout the protein structure, there are no random coils. The HA1 chain is comprised of 8% helical structures, including both alpha helices and 3/10 helices. Making up this 8% are four separate helices, composed in total of 28 residues. Beta sheets make up 39% of the secondary structure of the HA1 chain. There are 45 separate beta strands of 132 residues. It is worth noting that in the HA2 chain, helical structures are more abundant than beta sheets: 55% (6 helices, 98 residues) and 14% (9 strands, 25 residues), respectively. Comparing the antibody 1F1 heavy and light chains, it can be seen that these two subunits are relatively similar in their secondary structures. The heavy chain has 5% helical structures, with four helices and twelve residues, while the light chain is made of 6% helical structures, with three helices and fourteen residues. The presence of beta sheets is also comparable: 48% (23 strands, 113 residues) in the heavy chain and 50% (24 strands, 109 residues) in the light chain (secondary structure) (2).
One of the most important functions of the crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin is that it plays a role in human response to influenza viruses. When antibodies are in contact with the protein, they interact with receptor sites on the surface of the hemagglutinin HA chains. On the HA surface are antigenic sites that are unique to certain receptors (1). At these sites, certain antibodies can attach themselves and neutralize the virus. According to Yu et. al. these sites are unique within their own virus, but are similar in function with sites on other similar viruses (6). This is an important feature in the treatment and preparedness of the body for influenza viruses, as the antibodies that bind these receptor sites can not only cross-neutralize multiple viruses, but can be maintained for multiple decades. Specific residues are important in these reactions between virus and antibody. The hemagglutinin HA that was prevalent in the 1918, 1943, and 1977 influenza outbreaks showed specific reactivity to the 1F1 antibodies at residues 190 and 227 (important residues) (1). In the normal crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin, there are no mutations. In the 1918 HA influenza pandemic, however, these two residues were mutated. As a result, these mutations played a large role in the ability of the protein to neutralize the subsequent 1943 and 1977 H1N1 viruses (7).
Comparisons between different proteins are possible through servers such as BLAST and DALI. For proteins, PSI-BLAST allows for highly specific comparisons between two different proteins. Using the amino acid sequence of a single protein, it will provide proteins that are similar in their primary structure. The PSI-BLAST software will not only give similar proteins, but will also return the extent of the similarity between the two sequences. This level of similarity is reported in the E-value: a value of 0.0 indicates that the two proteins are identical, and the larger the E-value the more differences there are between the two sequences (8). Like PSI-BLAST, the DALI Server also provides similar structures to a given protein sequence. The extent of similarity is determined by measurements and comparisons of intramolecular distances. In this case, it is an assigned Z score that designates the significance of the similarities between two proteins. A score greater than 2.0 indicates that the similarity between the structures can be considered significant (9). The 1931 H1 Hemagglutinin in complex with LSTC (PDB ID: 1RVT) presented a Z value of 41.3, indicating that it has a very significant similarity with crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin (8). The E value of Chain A, Hemagglutinin HA1 Chain in the H6N1 Subtype (PDB ID: 4XKD) is 6e-179 (comparison protein). This very small number indicates that there are very few differences in sequence between this protein and the crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin (superposition) (9).
The Hemagglutinin HA1 Chain in the H6N1 subtype is a very similar protein to the crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin, but differences occur between the associated ligands of each (2). The H6N1 subtype structure contains only one associated ligand (NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose) (ligand binding). The crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin also contains this ligand, but it also has the associated beta-D-mannopyranose ligand (2) (other notable ligand). Like the crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin, the H6N1 subtype possesses the L-peptide linking PCA residue. This structure is incredibly specific in its location. Chain A, Hemagglutinin HA1 Chain in H6N1 Subtype only affects humans; it does not actually reside in the virus itself (2). When comparing secondary structures of this subtype with that of the HA1 chain of crystal structure of antibody 1F1 bound to 1918 influenza hemagglutinin, it is determined that their helical composition is the same. There is a slight difference in the percentage of beta strands: the H6N1 subtype possesses 37% beta sheets, while the beta sheet percentage in crystal structure of antibody 1F1 bound to 1918 influenza hemagglutinin is 39% (2).
The crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin is an important protein in both responses to and prevention of influenza viruses. Because this protein is capable of mediating the specificity of receptors of viral proteins and antibodies, it can provide a necessary response to influenza viruses within individuals. The close associations of the crystal structure of antibody 1F1 bound to the 1918 influenza hemagglutinin with proteins in other influenza subtypes indicates that there is the possibility of specificity regulation of these other types as well. Previous research has shown that the receptor sites are able to remember this specificity for decades. It is reasonable to assume from this evidence that the same ability is present in the receptor binding sites of other viral proteins. Future studies of this protein may be done to confirm not only its usefulness in the human immune response to influenza A, but also to other viruses, as well as potential use in the prevention or inoculation against other influenza viruses.