Fascin Structure
Fascin structure and domains
The Fascin protein is comprised of 8 repeats of the Fascin-like domain in total. It is made of two identical subgroups, each of which contains 4 Fascin-like domains linked together. The 2 subgroups are linked back to back slightly off-centre. The Fascin-like domain's tertiary structure adopts a beta-trefoil fold pattern with an internal threefold repeat. Secondary structure is predominantly Beta-sheet and random coil (loop) with small regions of alpha-helix. Structural similarity with several unrelated proteins is evident (eg. FGF).
Layout of primary and secondary sequences with domain annotations. (Finn et. al. 2006, Kabsch et. al. 1983, Murzin et. al. 2005)
'Front' view showing secondary structure of Fascin.
'Front' view of Fascin protein with each Fascin domain coloured. Red, Blue, Green and Yellow segments represent one subgroup while Aqua, Magenta, White and Orange represent the other. Grey colouration represents conserved residues found in sequence allignment.
'Back' view of Fascin protein. Same colouration as above.
Structual allignments
A Dali database search returned several hundred similar structures to Fascin 1. The first page of results can be seen below. Unfortunately none of the structurally similar molecules were actin binding so could not help with actin binding regions. The molecule 1ijt (Fibroblast Growth Factor - FGF) was alligned with Fascin to show structural similarity (even though they are functionally very different and only contain 9% sequence identity). Structurally FGF has much more Beta sheet secondarty structure, but as said before they are still quite similar.
Dali output showing first 33 structurally similar protein results.
Pymol allignment of Fascin 1 (green) and FGF (aqua)
Similarity is between FGF and the Fascin domain (not the molecule).
Cleft/Pocket analysis
Pockets and clefts in the molecular surface of Fascin were analysed using the online service CASTp (Dundas J et. al. 2006). Three major pockets corresponding to the beleived actin binding sites for Fascin are shown with both a front and back view. Conserved regions from 'across species' multiple sequence allignment are outlined in the sequence window. Note how many of the residues involved in the pocket are from these conserved regions.
Putative actin binding pocket regions on Fascin 'front view'.
Putative actin binding pocket regions on Fascin 'back view'.
Electrostatic surface model
Using the online PDB2PQR resource in conjunction with the APBS feature in pymol an electrostatic surface model for Fascin was generated. Regions corresponding to our putative actin binding sites were circled. Note the positively charged regions encapsulating a negatively charged centre.
Front view of electrostatic surface model. Putative actin binding site 1 (front) circled in green.
Back view of electrostatic surface model. Putative actin binding site 2 (back) circled in green.
Hydrophobicity Plot
Plot showing the hydrophobicity of fascin-1 protein and second plot showing hydrophilicty plot which acts as a peptide property calculator. From these results we can overall state that this protein overall is hydrophobic.
Important molecular regions
References
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-W667 (2004).
Finn R.D., Mistry J., Schuster-Böckler B., Griffiths-Jones S., Hollich V., Lassmann T., Moxon S., Marshall M., Khanna A., Durbin R., Eddy S.R., Sonnhammer E.L., Bateman A. Pfam: clans, web tools and services. Nucleic Acids Res 2006 Jan
Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, and Liang J 2006, CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated resiudes,Nucleic Acid Research, 34:W116-W118.
Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983 Dec
Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res. 37(D)205-10.
Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995 Apr
