Representation of protein structures

I am currently putting together my 3D animatic/rough cut. I got pretty hung up on the depiction of proteins and things so I just wanted to log my research and thoughts:

Molecular weights to get a sense of scale...

NGF: 32.8 kDa x 2 = 75.6 (ProtParam, homo sapiens) 73 kDa | ref 1 (rat, high molecular weight form)

TrkA: 87.5 kDa x 2= 175  (ProtParam, homo sapiens) 140 kDa | 87.73 kDa ref 2

TRPV1: 94.9 kDa (ProtParam, homo sapiens) 85-90 kDa | ref 1

ASIC: ~59.2 kDa (ProtParam, homo sapiens ASIC4)

Nav: ~227.9 kDa (ProtParam, homo sapiens)

More visual references:

TrkA: binding domain available

. 2IFG (extracellular domain w/ NGF)

. 1HE7 (second Ig-like domain w/ NGF)

. 1WWW (Ig-like domain only? w/ NGF)

. Dimerization depends on alteration of Ig-like domain | ref

. General info on Wiki ;)

"The extracellular domain of TrkA is composed of two cysteine-rich motifs that are separated by three leucine-rich motifs; these are followed by two Ig-like motifs... There is a single short transmemrbrane spanning region that is followed by the juxtamembrane region. Beyond the juxtamembrane region is the catalytic domain that contains the conserved tyrosine residues..." (Nicol and Vasko 2007)

TRPV1: full structure available (also refer to refs from Geraldine)

. ref 1 (full structure, basket-like region)

. ref 2 (schematic representation)

. ref 3 (tetrameric structure, schematic)

. ankyrin repeats in PDB

. David Goodsell's schematic representations

Suggestions from Prof. Nick Woolridge:

. Represent unknown portions very schematically (e.g. cylinder)

. Use cinematic methods: only show known portion in composition (I think this will be difficult though since the cell membrane will be embedded with TrkA. But it might be a good idea to "zoom in" when the hero NGF binds to the TrkA receptor to show the full structure, but then pull back to a more schematic representation for the rest of the story.)

. David Goodsell's article: Getting the most of the Protein Data Bank (Goodsell discusses this issue, and suggests assembling as much as you can from the PDB and using schematic representations for unknown portions.)

Times like these I really wish I had a degree molecular in biology! I will be asking for one of my colleagues with a PhD in molecular bio for assistance in building up trkA shortly. :)

But for now, I will focus on getting my camera movements right and finish laying out all my shots. I get caught up in details way too easily...

Possible solution?

surface model based on 2IFG (extracellular segment of human TrkA in complex with nerve growth factor)