pFlexAna Web Server: Example Results

E6AP and WWP1 Ubiquitin Ligases

Parameters:

The crystal structures of the E6AP and WWp1 ubiquitin ligases display a striking example of domain rearrangement. Our method finds six core regions structural similarity between the proteins and successfully clusters them into two domains. The actual results can be viewed on this page. One alignment from each cluster is shown below.

References:

  1. Huang et. al. (1999) Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade. Science 286: 1321-1326
  2. Verdecia et. al. (2003) Conformational Flexibility Underlies Ubiquitin Ligation Mediated by the WWP1 HECT domain E3 Ligase Mol. Cell 11: 249-259

Alignment of Cro Proteins

Parameters:

A secondary structure switch from two folded helices to a hairpin is visualized by pFlexAna.

References:

  1. Newlove et. al. (2004) Secondary Structure Switching in Cro Protein Evolution. Structure 12: 569-581.

Conformational motion in transglutaminase

Parameters:

A recent structure of a transglutaminase (PDB:2q3z) shows an open structure with an accessible active site, considerably different from all previous structures of proteins in the transglutaminase family. Using pFlexAna to analyze the conformational differences seen between the open structure and a homologous protein from sea bream (PDB:1g0d) yields 10 regions of structural similarity, which are successfully clustered into the two independently moving domains. The results page can be viewed here. The images generated by the largest fragments in each cluster are shown below.

References:

  1. Pinkas et. al. (2007) Transglutaminase 2 Undergoes a Large Conformational Change upon Activation . PLoS Biol 5(12): e327
  2. Noguchi et. al. (2001) Crystal structure of red sea bream transglutaminase. J.Biol.Chem. 276: 12055-12059

Conformational changes between TFIIB and gamma-herpesvirus cyclin

Parameters:

The structure of TFIIB core domain (code 1TFB in the PDB) and the structure of gamma-herpesvirus cyclin (chain D of 1F5Q in the PDB) display a significant domain-level alignment, detectable by pFlexAna using small or large values of sigma. The following figure shows this alignment with 1TFB in orange, 1F5Q in blue, and the fragments of highest similarity in red/green.

In addition, when using higher values of sigma, pFlexAna can also detect another large region of structural similarity, aligned in the following figure. To perceive the magnitude of the difference between the orientations of the domains in the different aligments, note that TFIIB (blue) appears is in the same orientation in the first two figures, and only the cyclin (orange) placement is different.

To get a less cluttered view of the weaker alignment, pFlexAna was run on a subset of the amino acids (residues 224-297 and 165-241 of the respective proteins), to generate the following alignment.

References:

  1. Card et. al. (2000) Crystal structure of a gamma-herpesvirus cyclin-cdk complex. EMBO Journal 19(12): 2877-2888.
  2. Hayashi et al. (1998) Human General Transcription Factor TFIIB: Conformational Variability and Interaction with VP16 Activation Domain. Biochemistry 37: 7941-7951.
NUS School of Computing