Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Feb 23;10(2):e0117499.
doi: 10.1371/journal.pone.0117499. eCollection 2015.

Using common spatial distributions of atoms to relate functionally divergent influenza virus N10 and N11 protein structures to functionally characterized neuraminidase structures, toxin cell entry domains, and non-influenza virus cell entry domains

Arthur Weininger  1 , Susan Weininger  1
Affiliations

Using common spatial distributions of atoms to relate functionally divergent influenza virus N10 and N11 protein structures to functionally characterized neuraminidase structures, toxin cell entry domains, and non-influenza virus cell entry domains

Arthur Weininger et al. PLoS One. .

Abstract

The ability to identify the functional correlates of structural and sequence variation in proteins is a critical capability. We related structures of influenza A N10 and N11 proteins that have no established function to structures of proteins with known function by identifying spatially conserved atoms. We identified atoms with common distributed spatial occupancy in PDB structures of N10 protein, N11 protein, an influenza A neuraminidase, an influenza B neuraminidase, and a bacterial neuraminidase. By superposing these spatially conserved atoms, we aligned the structures and associated molecules. We report spatially and sequence invariant residues in the aligned structures. Spatially invariant residues in the N6 and influenza B neuraminidase active sites were found in previously unidentified spatially equivalent sites in the N10 and N11 proteins. We found the corresponding secondary and tertiary structures of the aligned proteins to be largely identical despite significant sequence divergence. We found structural precedent in known non-neuraminidase structures for residues exhibiting structural and sequence divergence in the aligned structures. In N10 protein, we identified staphylococcal enterotoxin I-like domains. In N11 protein, we identified hepatitis E E2S-like domains, SARS spike protein-like domains, and toxin components shared by alpha-bungarotoxin, staphylococcal enterotoxin I, anthrax lethal factor, clostridium botulinum neurotoxin, and clostridium tetanus toxin. The presence of active site components common to the N6, influenza B, and S. pneumoniae neuraminidases in the N10 and N11 proteins, combined with the absence of apparent neuraminidase function, suggests that the role of neuraminidases in H17N10 and H18N11 emerging influenza A viruses may have changed. The presentation of E2S-like, SARS spike protein-like, or toxin-like domains by the N10 and N11 proteins in these emerging viruses may indicate that H17N10 and H18N11 sialidase-facilitated cell entry has been supplemented or replaced by sialidase-independent receptor binding to an expanded cell population that may include neurons and T-cells.

PubMed Disclaimer

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Structural alignment of N10P and N11P with influenza and bacterial neuraminidases.
Sequences of N6N, N10P, N11P, IBN, and SPN are shown aligned by common spatial occupancy of residues in their superposed structures. Other influenza A sequences are shown aligned by sequence identity to the structurally aligned N6N, N10P, N11P, and INB residues. Structurally invariant residues above the 'SPATIAL' row and spatially corresponding SPN residues below the 'SPATIAL' row are shaded dark blue. If both the N10P and N11P residues are present in the rest of the column above the 'SPATIAL' row, then the corresponding residues are shaded medium blue. If either, but not both, of the N10P or N11P residue are present in the rest of the column above the 'SPATIAL' row, then the corresponding residues are shaded light blue. If the non-N10P, non-N11P residues are identical to each other but do not match either N10P or N11P, then the non-N10P, non-N11P residues are shaded dark grey. If either of the non-N10P/N11P residues match either IBN or N6P but do not match either N10 or N11, then the residue is shaded light grey. If the N10P and N11P residues are identical to each other but do not match any other residue in that column, then the N10P and N11P residues are shaded black. Upside VLR residues, not shaded as above, are shaded yellow, orange, brown, purple, red, green, and light brown, according to position in the protein and this color is also shown in that column in the 'SPATIAL' row. Residues shaded deep teal are residues in protein loops that deviate spatially from structure common to N6N, N10P, N11P, IBN, and SPN. In the 'SPNSEQ' row, "<>" means that there is an insertion of additional residues that are listed after the "<> = " in the 'SPN<>' row(s) directly below the 'SPNSEQ' row. In the 'SPATIAL' row, the symbol: "*" means spatially conserved, "/" means missing, "~" means not spatially conserved; and a number indicates corresponding cysteines in disulfide bridges. Lowercase residues represent residues shown as spheres in Figs. 4–13.
Fig 2
Fig 2. Consensus active site components of N6N, N10P, N11P, and IBN.
Structure ribbon and residue spheres are color-coded at each structurally aligned position as in the 'FIG2COL' row in Fig. 1. Fig. 2A shows structure ribbons representing influenza A N10P [1], N6N [2], N11P [3], and IBN [4]) structures superposed using CNSA118:O, CNSA224:O, and CNSA276:O atoms. Fig. 2B-2F show structure ribbons and residues spheres of N6N (Fig. 2B), N11P (Fig. 2C), IBN (Fig. 2D), and N10P (Fig. 2E-2F). Fig. 2F also shows sialic acid (white spheres) positioned relative to N10P by its superposition onto N6N, which was crystalized with sialic acid in its binding pocket. Fig. 2E and 2F residues side chains in the area of the sialic acid have been repositioned slightly from the crystal structure positions to approximate the positions of the corresponding superposed N6N residues but no other side chain or main chain atoms have been moved.
Fig 3
Fig 3. Loop swapping of CNSR151, CNSR152, and CNSR178.
The structure ribbons of N6N (Fig. 3A), N10P (Fig. 3B), N11P (Fig. 4C), and SPN (Fig. 4D) are shown individually in their superposed positions. N6N residues D151, R152, and W178, shown in Fig. 4A, correspond to: N10P residues E153, R178, and W154, shown in Fig. 4B; N11P residues E151, Q152, and W178, shown in Fig. 4C; and SPN residues D372, R400 and W373, shown in Fig. 4D.
Fig 4
Fig 4. Consensus active site components and Upside VLR domains of N6N, N10P, N11P, IBN, and SPN.
Panel 4A shows structure ribbons representing influenza A N10P [5], N11P [7], N6N [8], IBN [9]), and SPN [20] structures superposed using CNSA118:O, CNSA224:O, and CNSA276:O atoms. Atom spheres shown for each structure are identified by lowercase letters in Fig. 1. Structure ribbons and residue spheres of N10P, N11P, N6N, and IBN are color-coded as in the 'SPATIAL' row in Fig. 1. SPN residues are color coded as in the 'SPNSEQ' and 'SPN<>' rows in Fig. 1. Panel 4B shows substance P-like domains (green and red spheres) in the Upside VLR of N6N. Panel 4C shows E2S-like (green, brown, and orange spheres) and SARSSP-like (purple, red, and yellow spheres) in the Upside VLR of N11P. Panel 4D shows a C-terminal domain common to influenza B viruses (light brown colored spheres) in the Upside VLR of IBN. Panel 4E shows SEI-like domains (orange and yellow spheres) in the Upside VLR of N10P. Panel 4F shows a C-terminal domain common to bacterial viruses (light brown colored spheres) in the Upside VLR of SPN. Medium blue spheres adjacent to the consensus active site region in Panels 4A-4F are CNSR151, CNSR152, and CNSR 178 residues. Sialic acid sticks (colored medium brown) are shown in the consensus active site region of N6N, N10P, N11P, IBN, and SPN (Panel 4A), N6N (Panel 4B), and SPN (Panel 4F).
Fig 5
Fig 5. Downside VLR domains of N6N, N10P, N11P, IBN, and SPN.
Panel 5A shows structure ribbons representing influenza A N10P [5], N11P [7], N6N [8], IBN [9]), and SPN [20] structures superposed using CNSA118:O, CNSA224:O, and CNSA276:O atoms. Atom spheres shown for each structure are identified by lowercase letters in Fig. 1. Structure ribbons and residue spheres of N10P, N11P, N6N, and IBN are color-coded as in the 'SPATIAL' row in Fig. 1. SPN residues are color coded as in the 'SPNSEQ' and 'SPN<>' rows in Fig. 1. Panel 5B shows the Downside VLR loops of N6N (colored magenta, hot pink, cyan, and salmon) in the foreground and the Upside VLR C-terminal light brown spheres also shown in Panel 4B in the background. Panel 5C shows residues found in ABT and SEI (colored magenta, hot pink, cyan, and salmon spheres) on the Downside VLR of N11P in the foreground and the Upside VLR E2S-like and SARSSP-like residues residues also shown in Panel 4C in the background. Panel 5D shows the Downside VLR loops of IBN (colored magenta, hot pink, cyan, and salmon) in the foreground and the Upside VLR C-terminal light brown spheres also shown in Panel 4D in the background. Panel 5E shows the Downside VLR loops of N10P (colored magenta, hot pink, cyan, and salmon) in the foreground and the Upside VLR SEI-like domain orange and yellow spheres also shown in Panel 4E at the top. Panel 5F shows the Downside VLR loops of SPN (colored magenta, hot pink, cyan, and salmon) in the foreground, an extra domain (colored teal) on the right hand side, and the Upside VLR C-terminal light brown spheres also shown in Panel 4F in the background.
Fig 6
Fig 6. SEI domain and corresponding N10P tetramer Upside VLR residues with N11P tetramer reference.
Shown are structure ribbons for SEI monomer (colored white), N10P tetramer (colored grey), and N11P tetramer (colored blue). The SEI monomer and N11P tetramer are unaltered crystal structures. The N10P tetramer was formed by translocating N10P monomers onto N11P monomers in the N11P tetramer. The yellow triangles on the N10P monomers are lines between CNSA118:O, CNSA224:O, and CNSA276:O whose superposition was used to orient N10P monomers into N11P tetramer positions. Residue spheres colored orange represent: SEI residues S31, A32, N33, and Q34; and corresponding N10P Upside VLR residues S139, A140, N141, and Q142. Residue spheres colored yellow represent: SEI residues W51and E53; and corresponding N10P Upside VLR residues W106 and E109.
Fig 7
Fig 7. SEI and N10P Upside VLR residues in common spatial reference orientation.
Shown are structure ribbons for superposed crystal structure SEI monomer (colored white) and N10P monomer (colored grey). Residue spheres colored orange represent: SEI residues S31, A32, N33, and Q34; and corresponding N10P Upside VLR residues S139, A140, N141, and Q142. Residue spheres colored yellow represent: SEI residues W51and E53; and corresponding N10P Upside VLR residues W106 and E109. The SEI monomer shown was superposed onto N11P tetramer Upside VLR residues using the atoms listed in Table 5.
Fig 8
Fig 8. E2S domains, SARSSP domains, and corresponding N11P Upside VLR residues.
Shown are N11P tetramer crystal structure ribbons colored grey, associated calcium atoms are colored cyan, and spheres depicting selected N11P Upside VLR residues colored grey with the following exceptions: in monomers in positions “A”, ”B”, ”C”, and ”D”, Y138 is colored orange, V149 is colored light tangerine and calcium atoms are colored cyan; in monomers in positions “A”, ”C”, and ”D”, ALA428-G433 spheres are colored green, and Y159 is colored brown; and in monomers in positions ”B”, ”C”, and ”D”, G105-G108 are colored yellow, P166-P169 are colored purple, and N401-T403 are colored red. Residues between Y138 and V149 are missing in the crystal structure in monomers in positions “A”, ”B”, and ”D”, and the structure is disjoint. In monomer in position “C”, residue G139 is between residues Y138 and V149 and the crystal structure of this monomer chain is presented as contiguous. Green, brown, and orange spheres correspond to an E2S-like domain. Yellow, purple, and red spheres correspond to a SARS spike protein-like domain.
Fig 9
Fig 9. E2S and N11P Upside VLR residues in common spatial reference orientation.
Shown are two E2S monomers (structure ribbons colored white) and a N11P tetramer (structure ribbons colored grey and associated calcium atoms colored cyan) from crystal structures. One E2S monomer is shown apart from the N11P tetramer and the other E2S monomer is shown with E2S residues superposed onto N11P tetramer Upside VLR residues using the atoms listed in Table 6. N11P Upside VLR residue spheres depict: Y138 colored orange, V149 colored light tangerine, Y158 colored brown, and ALA428-G433 spheres colored green. E2S residue spheres in the stand-alone and superposed monomers depict: Y557 colored orange, Y561 colored brown, and G551-G556 colored green. V149 light tangerine residue spheres in N11P monomers in positions “A”, ”B”, ”C”, and ”D” and arrows in monomers in positions “A” and ”B” are shown as a reference to residues missing between Y138 and V149 in the N11P monomers and have no structural correspondence in E2S. The E2S monomer residues spheres shown are superposed onto N11P residue spheres from two N11P monomers.
Fig 10
Fig 10. SARSSP and N11P Upside VLR residues in common spatial reference orientation.
Shown are two SARSSP monomers (structure ribbons colored white) and a N11P tetramer (structure ribbons colored grey and associated calcium atoms colored cyan) from crystal structures. One SARSSP monomer is shown apart from the N11P tetramer and the other SARSSP monomer is shown with SARSSP residues superposed onto N11P tetramer Upside VLR residues using the atoms listed in Table 7. N11P Upside VLR residue spheres depict: Y138 colored orange, V149 colored light tangerine, G105-G108 colored yellow, P166-P169 colored purple, and N401-T403 colored red. SARSSP residue spheres in the stand-alone and superposed monomers depict: T485-G488 colored yellow, P469-P472 colored purple, and T425-N427 colored red. Y138 orange and V149 light tangerine residue spheres in N11P are shown as a reference to residues missing between Y138 and V149 in the N11P monomers and have no correspondence in the SARSSP monomer.
Fig 11
Fig 11. Corresponding residues in ABT dimer and N11P Downside VLR.
Shown are two ABT dimers (structure ribbons colored white with dark blue spheres representing disulfide bridges) and a N11P tetramer (structure ribbons colored grey and with dark blue spheres representing disulfide bridges) from the crystal structures. One ABT dimer is shown apart from the N11P tetramer and the other ABT dimer is shown at an angle that is 90 degrees rotated from the first dimer in position “B”, i.e. positioned with the ABT dimer superposed onto and substituting for the N11P monomer in position “B” in the tetramer. Atoms used to superpose the ABT dimer into the position that would be occupied by the N11P “B” monomer are listed in Table 8. N11P Downside VLR residue spheres in monomer positions “A”, “C”, and “D” depicting: G88-L91 colored magenta, C92 colored plum, S125-E128 colored hot pink, D185-F187 colored cyan, and Y413A-S415 colored salmon. Corresponding ABT residue spheres in the two dimers depicting: G19-L22 colored magenta, C23 colored plum, S61-K64 colored hot pink, D29-F31 colored cyan, and Y54-E56 colored tan. N11P monomers in the “A” and “D” positions are shown in the crystal structure positions. In the N11P monomer in the “C” position, the Y413A-S415 residues (colored salmon) have been rotated into the same position relative to G19-L22 (colored magenta) and D29-F31 (colored cyan) as in corresponding residues of ABT crystal structure dimer (shown in the “B” position) in order to illustrate that small movements of the mobile N11P Downside VLR residues can produce nearly identical relative residue presentation to ABT.
Fig 12
Fig 12. N11P Downside VLR residues and corresponding SEI, ABT, ALF, CBN, and TTX residues.
Shown are grey structure ribbons depicting: N11P monomer (panel A), SEI monomer (panel B), ABT dimer (panel C), ALF monomer (panel D), CBN monomer (panel E), and TTX monomer (panel F). Corresponding residue spheres in each panel are identified and colored according to Table 9.
Fig 13
Fig 13. Reoriented Substance P residues and corresponding N6N Upside VLR residues.
Shown are a crystal structure N6N tetramer (structure ribbons colored grey), a crystal structure substance P apart from the N6N tetramer, and a model-built substance P monomer superposed on a monomer in the N6N tetramer. The model built structure coordinates are given as a PDB file, “WSUBP.pdb”, available as supporting information S2 File. The atoms used to map WSUBP.pdb onto the N6N monomer are given in Table 10. The model building consisted of reorienting the first 3 residues of substance P, R365-K367 (colored green), to exactly match the corresponding N6N residues, R438-K440 (colored green), and leaving the rest of the structure as in the crystal structure. N11P residues, Q 407 and N408 (colored red), correspond to substance P residues, Q369 and Q370 (colored red).
Fig 14
Fig 14. Interatomic distance population standard deviations for selected N6N, N10P, N11P, IBN, and SPN atoms.
Shown are the standard deviations of the interatomic distances for specific main chain oxygens of N6N, N10P, N11P, IBN, and SPN residues; these oxygens were selected if the Table 2 row for their associated residue does not contain cysteines, prolines, or missing residues. The standard deviations colored in cyan correspond to the minimal standard deviation of the distances between the CNSA118:O, CNSA224:O, and CNSA276:O atoms. The standard deviations colored in green correspond to the minimal standard deviation of the distances between the CNSA185:O atom and each of the CNSA224:O and CNSA276:O atoms. The CNSA118:O, CNSA224:O, CNSA276:O, and CNSA185:O atoms form a tetrahedron. Values under 3.00 are colored and, unless colored cyan or green as above, default to yellow.
Fig 15
Fig 15. Overlapping CNSA118:O, CNSA224:O, CNSA276:O, and CNSA185:O atom tetrahedrons.
Shown are the superposed CNSA118:O, CNSA224:O, CNSA276:O, and CNSA185:O atoms from N6N, N10P, N11P, IBN, and SPN. The CNSA118:O, CNSA224:O, and CNSA276:O atoms are colored cyan. The CNSA185:O atoms are colored green. The CNSA118:O, CNSA224:O, CNSA276:O, and CNSA185:O atoms form a tetrahedron. Also shown are yellow lines drawn between the N6N CNSA118:O, CNSA224:O, CNSA276:O, and CNSA185:O atoms. The combined superposed substrates and inhibitors from the superposed structures are shown as grey sticks.
Fig 16
Fig 16. CNSA118:O, CNSA224:O, CNSA276:O, and CNSA185:O atom tetrahedrons in N6N, N10P, N11P, IBN, and SPN.
Panel A shows the superposed N6N, N10P, N11P, IBN, and SPN structure ribbons colored grey, the CNSA118:O, CNSA224:O, and CNSA276:O atoms colored cyan, the CNSA185:O atoms colored green, and the lines between N6N CNSA118:O, CNSA224:O, CNSA276:O, and CNSA185:O atoms colored yellow. Panels B-E show individual N6N, N10P, N11P, IBN, and SPN structures. In Panels B-E, the structure ribbons are colored grey, the corresponding CNSA118:O, CNSA224:O, and CNSA276:O atoms are colored cyan, the corresponding CNSA185:O atoms are colored green, and actual or superposed lines between N6N CNSA118:O, CNSA224:O, CNSA276:O, and CNSA185:O atoms are colored yellow (forming a tetrahedron).
Fig 17
Fig 17. Interatomic distance population standard deviations for selected N10P and SEI atoms.
Shown are the standard deviations of the interatomic distances for N10P residue atoms in W106 and E109 and the interatomic distances SEI residue atoms in W51 and E53. The standard deviations shown in magenta correspond to the minimal standard deviations less than 0.1. The standard deviations shown in yellow correspond to the minimal standard deviations less than 0.2. The TRP and GLU residues in the N10P and SEI proteins are in the same relative spatial orientation indicated by a large cluster of low interatomic distance standard deviations despite the fact that these residues are separated by two amino acids in N10P and one amino acid in SEI.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

  • Bat-Borne Influenza A Viruses: An Awakening.
    Ciminski K, Schwemmle M. Ciminski K, et al. Cold Spring Harb Perspect Med. 2021 Feb 1;11(2):a038612. doi: 10.1101/cshperspect.a038612. Cold Spring Harb Perspect Med. 2021. PMID: 31871229 Free PMC article. Review.

References

    1. Chan MCW, Chan RWY, Chan LLY, Mok CKP, Hui KPY, et al. (2013) Tropism and innate host responses of a novel influenza A H7N9 virus: an analysis of ex-vivo and in-vitro cultures of the human respiratory track. Lancet Respir. Med. 1(7):534–542. Available: 10.1016/S2213-2600(13)70138-3 10.1016/S2213-2600(13)70138-3 - DOI - DOI - PMC - PubMed
    1. Wibawa H, Bingham J, Nuradji H, Lowther S, Payne J, et al. (2014) Experimentally Infected Domestic Ducks Show Efficient Transmission of Indonesian H5N1 Highly Pathogenic Avian Influenza Virus, but Lack Persistent Viral Shedding. PloS One 9(1):e83417 Available: 10.1371/journal.pone.0083417 10.1371/journal.pone.0083417 - DOI - DOI - PMC - PubMed
    1. Nishikawa T, Shimizu K, Tanaka T, Kuroda K, Takayama T, et al. (2012) Bacterial Neuraminidase Rescues Influenza A Replication from Inhibition by a Neuraminidase Inhibitor. PloS One 7(9):e45371 Available: 10.1371/journal.pone.0045371 10.1371/journal.pone.0045371 - DOI - DOI - PMC - PubMed
    1. Schrauwen EJA, Bestebroer TM, Rimmelzwaan GF, Osterhaus ADME, Fouchier RAM, et al. (2013) Reassortment between Avian H5N1 and Human Influenza Viruses Is Mainly Restricted to the Matrix and Neuraminidase Gene Segments. PloS One 8(3):e59889 Available: 10.1371/journal.pone.0059889 10.1371/journal.pone.0059889 - DOI - DOI - PMC - PubMed
    1. Protein Data Bank ID: 4FVK. Available: http://www.rcsb.org/pdb/explore/explore.do?structureId=4FVK Li Q, Sun XM, Li ZX, Liu Y, Vavricka CJ, et al. (2012) Structural and functional characterization of neuraminidase-like molecule N10 derived from bat influenza A virus. Proc. Natl. Acad. Sci. USA. 109:18897–18902. Available: 10.1073/pnas.1211037109 10.1073/pnas.1211037109 - DOI - DOI - PMC - PubMed

Grants and funding

The authors received no specific funding for this work.

LinkOut - more resources