Parainfluenza Virus 5F Protein

By: Andrew Braith, Andrew Hipp, Rob Hlavacek, and Ben Krage

Java version

HTML 5 version (does not require Java; downloads and moves slowly)

I. Introduction

Parainfluenza 5F protein catalyzes the entry of the viral into the cell. The F protein undergoes refolding during this process, which leads to differing conformations when it is in the pre- and post- transitional states. The parainfluenza virus is similar to other paramyxovirides, (enveloped viruses) which include: mumps, measles, sendai, Newcastle, and the human respiratory sincytial virus. The parainfluenza 5F protein consists of a globular head attached to a trimeric coiled-coil stalk formed by the C-terminal of the HRB region.  This exact form of the virus shown in this tutorial is that of the pre-conformational state in which the stalk sits above the viral membrane.   The pdb file shown does not contain the membrane domain

For more information see Biochemistry Online: Chapter 5C - Model Binding Systems

II. General Structure

Wireframe
Cartoon
Cartoon displays the cartoon configuration of three subunits. 

Cartoon
Cartoon displays the specific secondary structures gold being the beta sheet and pink being the alpha helix. 

Subunit
F-GCNt (Fusion Peptide)
Fusion Peptide: the peptide is sandwiched between the DIII of its own subunit and the DII of another subunit. 

Domain I
Domain II
Domain I and II: during the conformational change domains I and II reposition as rigid molecules.  At the C-terminus of domain II, an extended linker to HRB, wraps around the trimer to where the stalk begins. 

Domain III
Domain III: this domain acts as a scaffold for the folding of HRA and subsequently preventing it from forming a helix in the post-conformational state. 

Backbone
Hydrogen Bonds as the Head engages the HRB Stalk
The residues S443 and D448 of each subunit make hydrogen bonds to the D445 residue of the same subunit and the S342 of the neighboring subunit.  

Spacefill: Subunits
The protein contains three separate subunits each of which contains three distinct domains.  

Solvent accessible surface: dots
Disulfide Bonds
Disulfide Bonds

The bonds are indicated by the yellow lines.  The wireframe structures indicate the location of cystine residues.

The next surface displays are solid and require calculations with some time delays

solvent excluded molecular surface (solid 1.4 A) - surface at contact with sphere (molecular)
Map of electrostatic potential
Character: the electron density for the HRB linker is weaker as compared to the HRB stalk, suggesting that the region has a greater degree of flexibility. The red indicates a larger negative charge density while the more blue, the more positive charge density.

Works Cited:
Hsien-Sheng Yin, Xiaolin Wen, Reay G. Paterson, Robert A. Lamb, and Theodore S. Jardetzy.  "Structure of the parainfluenza virus 5 F protein in its metastable, prefusion conformation."  Nature.  Volume 439, January 2006, (38-44).