1. Structural Basis for Paramyxovirus-Mediated Membrane Fusion
Kent A Baker, Rebecca Ellis Dutch, Robert A Lamb, Theodore S Jardetzky 
Molecular Cell 
Volume 3, Issue 3, Pages (March 1999)
DOI: /S (00)80458-X

2. Figure 1 Structure Determination of the SV5 F1 Core Trimer
(A) Schematic of the paramyxovirus F protein structure. F1 and F2 are formed after proteolytic cleavage of the precursor, Fo, protein. FP and TM refer to the fusion peptide and transmembrane anchor, respectively. HRA and HRB indicate the two heptad repeat regions that are indicated above the sequence in (B). There is only one cysteine in F2, and the residue linkage to F1 is unknown. Based on the notion of an ancestral fusion protein, the most likely residue in F1 to form the disulfide bond is at the end of HRA (C185).
(B) Sequence alignment of the HRA and HRB of the SV5 F protein with that of other paramyxoviruses. NDV, Newcastle disease virus; HRSV, human respiratory syncytial virus. Conserved residues among paramyxoviruses are colored orange, and residues with similar properties (hydrophobic or charged) are colored red. As HRSV is evolutionarily distant from other paramyxoviruses, conserved residues are only indicated if they match the other virus sequences. Letters immediately above the sequence indicate the predicted hydrophobic heptad repeat a and d residues. The predicted heptad is incorrect for residues 175–184, and the observed a and d residues are indicated above the predicted repeat and underlined. Asterisks indicate N-linked carbohydrate sites for the SV5 F protein.
(C) The experimental electron density map contoured at 1.5 σ showing the trimer axis and side chains of the SV5 F1 core.
(D) The final 1.4 Å electron density map showing the extended chain of C1. The map was calculated using phases from the final model, using the omit protocol of CNS (Brünger et al. 1998). The map is contoured at 2 σ.
Molecular Cell 1999 3, DOI: ( /S (00)80458-X)

3. Figure 2 The SV5 F1 Core Trimer Structure
(A) A single N1/C1 heterodimer is shown with the N1 helix colored gray and the C1 peptide colored blue. The observed termini are indicated.
(B) The complete SV5 F1 core trimer is shown colored as in (A), except for the N-terminal residues of C1 (red) that are absent in the shorter C2 peptides (see Figure 1B).
(C) A stutter in the N1 coiled coil. The heptad (3-4) repeat extends from the N terminus of N1 (top) to residue 172. From residue 168, the coiled coil forms a repeat (pentadecatad), resulting in an underwinding of this section of the coiled coil as indicated.
(D) A surface representation of the N1 trimer showing the packing of the C1 peptides into the N1 interhelical groove. The surface is colored by potential, blue for positive and red for negative. Carbon atoms are yellow for the C2 peptide (453–477) and magenta for the C1 peptide residues (440–452). Nitrogen and oxygen atoms are blue and red, respectively. A narrowing and deepening of the N1 interhelical groove is apparent near the base of the trimer, corresponding to the binding pockets for C1 residues L447 and I449.
Molecular Cell 1999 3, DOI: ( /S (00)80458-X)

4. Figure 3
Hydrogen Bond and Buried Ion Interactions Link the SV5 F1 Core Peptides
(A) T147 forms a buried network of H bonds that involve residues S470, N148, and D471. The helices of two N1 chains are shown in gray, and a C1 helix is shown in yellow. N1 and C1 carbon atoms are magenta and yellow, respectively. Nitrogen atoms are colored blue and oxygen atoms red. A surface H bond interaction between residues K146 and Q469 is also shown.
(B) Conserved residues and H bonds between two N1 monomers and the N terminus of C1. The N1 and C1 backbones are colored gray and yellow, respectively. Atoms are colored as in (A). The conserved residues Q169 and N173 form H bonds to the main chain atoms of L447 and I449. N173 forms a bidentate, ring structure with L447. H171 also forms an H bond to P446.
(C) Electron density from the final 1.4 Å omit map, showing the positions of two electron-dense atoms in the trimer core. Electron density is shown looking down the N1 trimer axis near residues N133 and T158 as indicated, contoured at 2 σ.
Molecular Cell 1999 3, DOI: ( /S (00)80458-X)

5. Figure 4
Structural Implications for the Ends of the F Protein Structure
(A) Comparison of the two N1/C1 heterodimers in the asymmetric unit. The N1/C1 heterodimers are colored by temperature factor, with blue corresponding to low, white to intermediate, and red to high temperature factors. Note the periodicity in the temperature factor for the C1 helix and the increase in disorder at the C-terminal end of N1 and the N-terminal end of C1.
(B) Conserved residues of the fusion peptide form one face of an α helix that aligns with the SV5 F1 coiled-coil core. A two-dimensional representation of an α helix is shown, with residues conserved in paramyxoviruses indicated in yellow. The N terminus of the fusion peptide is residue 103 (top right). Residues 122–124 (TAA) form an α helix in the SV5 F1 core trimer crystal structure, indicated by a white background and dashed line. A123 is the first observed residue in the interior of the N1 coiled coil. The helical face of the fusion peptide that aligns with the interior of the coiled coil of the SV5 F1 core structure is highlighted in blue.
Molecular Cell 1999 3, DOI: ( /S (00)80458-X)

6. Figure 5
Residues between the C1 Helix and the Transmembrane Domain Are Not Required for Membrane Fusion
(A) Sequences of C-terminal linker amino acids to the transmembrane anchor and deletion mutants.
(B) Fusion assays of mutants. Lipid mixing with cells expressing wt F and linker region deletion mutant proteins. RBCs labeled with R18 were bound to CV-1 cells coexpressing SV5 HN and either wt F or Δ2–Δ8 proteins at 4°C, and fusion was triggered by shifting incubation to 37°C. The distribution of dye was monitored at different time periods (as indicated) by confocal microscopy as described in Experimental Procedures.
Molecular Cell 1999 3, DOI: ( /S (00)80458-X)

7. Figure 6 Virus Fusion Proteins and Models for Membrane Fusion
(A) Comparison of the SV5 F1 core trimer to other viral fusion protein structures. The proteins under comparison include the low-pH-induced influenza virus HA, tBHA2 (Bullough et al. 1994), HIV gp41 (Chan et al. 1997), MMLV Env-TM protein (Fass et al. 1996), and Ebola virus Gp2 (Weissenhorn et al. 1998b). The interior coiled coil is gray, and the exterior polypeptide is blue. Top and side views are shown for each molecule.
(B) A model of virus-mediated membrane fusion, based on studies of the influenza virus HA and HIV gp41 crystal structures (Bullough et al. 1994; Weissenhorn et al. 1997, Weissenhorn et al. 1998b; Chan and Kim 1998). This model includes two conformational transitions of the fusion protein, the insertion of the fusion peptide into the target membrane, followed by refolding and juxtaposition of the target and viral bilayers. Flexible linkers between the protein and the two membranes allow the coiled coil to reorient with its long axis parallel to the membrane surface. Membrane fusion may occur during or after the conformational rearrangements by an unknown mechanism.
(C) A model for paramyxovirus-mediated membrane fusion. Conformational events potentially analogous to those observed for influenza virus HA are thought to lead to the insertion of the fusion peptide into the target membrane. In contrast to the fusion model shown in (B), the structural and biochemical evidence suggest that flexible tethers to the two lipid bilayers are not required for membrane fusion. Flexibility and the close approach of the two membranes could instead be promoted by the intervening ∼250 amino acids between the N- and C-terminal heptad repeats. This model would predict that the free energy associated with conformational rearrangements of the fusion protein could be directly coupled to the fusion of the two membranes.
Molecular Cell 1999 3, DOI: ( /S (00)80458-X)