Structural comparison of H6 HAs in binding to human receptor analogues.

<p><b>a).</b> GD H6 HA-LSTc complex. GD H6 HA structure is shown in yellow and LSTc is in green. The composite omit 2<i>F</i>_o-<i>F</i>_c electron density map for the receptor is shown at 1σ. The hydrogen bonds detected by LIGPLOT are shown as black dashed lines. <b>b).</b> TW H6 HA-LSTc complex. TW H6 HA structure is shown in blue and LSTc is in green. The composite omit 2<i>F</i>_o-<i>F</i>_c electron density map for the receptor is shown at 1σ. The hydrogen bonds detected by LIGPLOT are shown as black dashed lines. <b>c).</b> Comparison of LSTc interaction with GD (in yellow) and TW (in blue) H6 HAs. The hydrogen bonds different between these two complexes are shown as dashed lines (yellow dashed lines for hydrogen bonds unique to GD H6 HA-LSTc; blue dashed lines for hydrogen bonds unique to TW H6 HA-LSTc). The arrow is to highlight the different sitting positions of the LSTc Sia-1 moiety in the receptor-binding sites of GD and TW H6 HAs. <b>d).</b> Comparison of human receptor analogues in TW H6 HA (in blue) and H2 HA from the pandemic A/Singapore/1/1957(H2N2) virus (PDB code: 2WR7; in green). <b>e).</b> Comparison of human receptor analogues in TW H6 HA (in blue) and H3 HA from the pandemic A/Aichi/2/68(H3N2) virus (PDB code: 2YPG; in grey). <b>f).</b> Comparison of human receptor analogues in TW H6 HA (in blue) and H5 HA from a transmissible mutant of A/Vietnam/1203/2004(H5N1) (PDB code: 4BH3; in red).</p

Amino-acid composition in the receptor-binding site of H6 HA proteins.

<p>Amino-acid composition in the receptor-binding site of H6 HA proteins.</p

Hydrogen bonds between H6 HA proteins and bound receptors.

<p>*Hydrogen atoms were added to the structures by Molprobity [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134576#pone.0134576.ref045" target="_blank">45</a>]. These structures were then used to calculate the hydrogen bonds by LIGPLOT [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134576#pone.0134576.ref044" target="_blank">44</a>] with default parameters.</p><p>Hydrogen bonds between H6 HA proteins and bound receptors.</p

Structural comparison of H6 HAs in binding to avian receptor analogues.

<p><b>a).</b> GD H6 HA-LSTa complex. GD H6 HA structure is shown in yellow and LSTa is in green. The composite omit 2<i>F</i>_o-<i>F</i>_c electron density map for the receptor is shown at 1σ. The hydrogen bonds detected by LIGPLOT are shown as black dashed lines. <b>b).</b> TW H6 HA-LSTa complex. TW H6 HA structure is shown in blue and LSTa is in green. The composite omit 2<i>F</i>_o-<i>F</i>_c electron density map for the receptor is shown at 1σ. The hydrogen bonds detected by LIGPLOT are shown as black dashed lines. <b>c).</b> Comparison of LSTa interaction with GD (in yellow) and TW (in blue) H6 HAs. The hydrogen bonds different between these two complexes are shown as dashed lines (yellow dashed lines for hydrogen bonds unique to GD H6 HA-LSTa; blue dashed lines for hydrogen bonds unique to TW H6 HA-LSTa). Highlighted by arrows are the different sitting positions of the LSTa Sia-1 moiety in the receptor-binding sites of GD and TW H6 HAs. <b>d).</b> Comparison of avian receptor analogues in GD H6 HA (in yellow) with avian H1 HA from A/WDK/JX/12416/2005(H1N1) (PDB code: 3HTP; in green). <b>e).</b> Comparison of avian receptor analogues in GD H6 HA (in yellow) with avian H5 HA from A/Indonesia/5/2005(H5N1) (PDB code: 4K63; in grey). <b>f).</b> Comparison of avian receptor analogues in TW H6 HA (in blue) and H5 HA from an airborne transmissible mutant of A/Indonesia/5/2005(H5N1) (PDB codes: 4K66; in red). <b>g).</b> Comparison of avian receptor analogues in TW H6 HA (in blue) and H5 HA from a transmissible mutant of A/Vietnam/1203/2004(H5N1) (PDB code: 4BH4; in cyan).</p

The overall structures of GD and TW H6 HAs.

<p><b>a).</b> One monomer of GD H6 HA (in yellow color) with the glycans (in stick model). The receptor-binding site (RBS) is labeled. <b>b).</b> One monomer of TW H6 HA (in blue color) with the glycans (in stick model). <b>c).</b> Superposition of the monomers of GD (in yellow color) and TW (in blue color) H6 HAs. <b>d).</b> Comparison of the receptor-binding sites of GD (in yellow) and TW (in blue) H6 HAs. Highlighted are the residues at or surrounding the receptor-binding site. All residues are in H3 HA numbering. <b>e).</b> Comparison of the receptor-binding sites of GD (in yellow) and TW (in blue) H6 HAs with H1 HA from A/Brevig Mission/1/1918(H1N1) (PDB code: 2WRG; in magenta), H2 HA from A/Singapore/1/1957(H2N2) (PDB code: 2WR7; in orange), H3 HA from A/Aichi/2/68(H3N2) (PDB code: 2YPG; in green), H5 HA from an airborne transmissible mutant of A/Indonesia/5/2005(H5N1) (PDB code: 4K67; in cyan), H7 HA from A/Anhui/1/2013(H7N9) (PDB code: 4BSB; in purple), H9 HA from A/swine/Hong Kong/9/1998(H9N2) (PDB code: 1JSI; in grey), H10 HA from A/Jiangxi/Donghu/346/2013(H10N8) (PDB code: 4QY2; in forest), and H13 HA from A/gull/Maryland/704/1977(H13N6) (PDB code: 4KPS; in pink). The strictly conserved residues among all these HAs within the receptor-binding sites, Y98, W153, H183 and Y195, are shown. Also shown are the main chains of HA₁ 133 that display different configurations among these structures.</p

Structural Basis of Actin Filament Nucleation by Tandem W Domains

Spontaneous nucleation of actin is very inefficient in cells. To overcome this barrier, cells have evolved a set of actin filament nucleators to promote rapid nucleation and polymerization in response to specific stimuli. However, the molecular mechanism of actin nucleation remains poorly understood. This is hindered largely by the fact that actin nucleus, once formed, rapidly polymerizes into filament, thus making it impossible to capture stable multisubunit actin nucleus. Here, we report an effective double-mutant strategy to stabilize actin nucleus by preventing further polymerization. Employing this strategy, we solved the crystal structure of AMPPNP-actin in complex with the first two tandem W domains of Cordon-bleu (Cobl), a potent actin filament nucleator. Further sequence comparison and functional studies suggest that the nucleation mechanism of Cobl is probably shared by the p53 cofactor JMY, but not Spire. Moreover, the double-mutant strategy opens the way for atomic mechanistic study of actin nucleation and polymerization

Microsecond hydrophobic collapse in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein

Using small-angle X-ray scattering combined with a continuous-flow mixing device, we monitored the microsecond compaction dynamics in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein. A significant collapse of the radius of gyration from 30 A to 23.2 A occurs within 300 micros after the initiation of refolding by a urea dilution jump. The subsequent folding after the major chain collapse occurs on a considerably longer time-scale. The protein folding trajectories constructed by comparing the development of the compactness and the secondary structure suggest that the specific hydrophobic collapse model rather than the framework model better explains the experimental observations. The folding trajectory of this alpha/beta-type protein is located between those of alpha-helical and beta-sheet proteins, suggesting that native structure determines the folding landscape

Microsecond barrier-limited chain collapse observed by time-resolved FRET and SAXS

It is generally held that random-coil polypeptide chains undergo a barrier-less continuous collapse when the solvent conditions are changed to favor the fully folded native conformation. We test this hypothesis by probing intramolecular distance distributions during folding in one of the paradigms of folding reactions, that of cytochrome c. The Trp59-to-heme distance was probed by time-resolved Forster resonance energy transfer in the microsecond time range of refolding. Contrary to expectation, a state with a Trp59-heme distance close to that of the guanidinium hydrochloride (GdnHCl) denatured state is present after ~27 mus of folding. A concomitant decrease in the population of this state and an increase in the population of a compact high-FRET (Forster resonance energy transfer) state (efficiency \u3e 90%) show that the collapse is barrier limited. Small-angle X-ray scattering (SAXS) measurements over a similar time range show that the radius of gyration under native favoring conditions is comparable to that of the GdnHCl denatured unfolded state. An independent comprehensive global thermodynamic analysis reveals that marginally stable partially folded structures are also present in the nominally unfolded GdnHCl denatured state. These observations suggest that specifically collapsed intermediate structures with low stability in rapid equilibrium with the unfolded state may contribute to the apparent chain contraction observed in previous fluorescence studies using steady-state detection. In the absence of significant dynamic averaging of marginally stable partially folded states and with the use of probes sensitive to distance distributions, barrier-limited chain contraction is observed upon transfer of the GdnHCl denatured state ensemble to native-like conditions