IntroductionOne reason I like Blender so much is that you can make nice pictures with it and the only limit is your imagination. One good illuatration of this can be seen here. Below I illustrate the work of my PhD thesis using a couple of images generated using Blender:
The Crystal Structure of ProteinsThis is a representation of the human beta-B1-crystallin magnified about 100,000 times. Crystallin is a protein that is essential for maintaining the transparency of the eye lens by forming a crystalline array. As proteins are infinitely small objects, their structure is most commonly studied by X-ray crystallography in order to obtain atomic resolution. This technique requires a protein to form crystals, such as those growing from the floor in the picture. Thus, this picture illustrates the importance of crystals, which on the one hand allow us to view the macroscopic world with our eyes through beta-B1-crystallin, and on the other hand allow us to visualize atomic details of molecules such as proteins, which are the topic of my thesis.
The Graph representation used in the database 3D ComplexThis image illustrates the "graph" representation of protein complexes used in 3D Complex to classify them and study them. On the left-hand side, the full atomic structures of protein complexes are shown, and their corresponding graphs are displayed on the right hand-side.
Illustration for the PiQSi databasePiQSi relies on symmetry information to describe protein quaternary structure. The image illustrates three types of cyclic symmetry (C2, C3, C4), and three types dihedral symmetry (D2, D3, D4). The central "monomer" has no possible symmetry, as indicated by the abbreviation NPS.
Creation of homo-oligomers from monomeric protein blocsIn my study about the evolution of homo-oligomers, I define the quaternary structure by the symmetry formed by the subunits. Each yellow bloc in the figure represents a protein, and arrows denote transitions between different quaternary structure types that take place during evolution, as well as during the assembly in solution. The formula above each quaternary structure type correspond to the model of homomer evolution developed in a study (currently submitted for publication), which predicts the observed abundances of dihedral complexes, as well as the evolutionary routes taken to make them.
Creation of novel protein complexes from homo-oligomers via gene duplicationThis image illustrates an evolutionary scenario for a homodimer. The homodimer, represented by gold beads, evolves a novel specificity to a protein represented by the orange square. The gene coding for the homodimer then duplicates, and leads to a dimer of paralogous proteins (gold and silver beads). Immediately after duplication, both proteins still bind to the same partner (orange square). However, after divergence, the silver protein looses its specificity towards the orange protein and binds the green polyhedron instead. We will see in this chapter that this scenario of evolution is frequent, and in fact, has led to several important molecular machines such as photosystem I, which is shown in the image.
Complexity of protein-protein interactionsThis image highlights the human protein-protein interaction network characterized by (Stelzl, et al., 2005). The many reflections of the network in surrounding mirrors symbolize the puzzlement of the scientific community in the face of the constantly growing body of information on protein-protein interactions.
The findings of my thesis recapitulated in one Protein Complex: the ProteasomeEvolution of proteasome oligomeric states. In the figure, balls represent protein subunits and edges represent subunit-subunit contacts as calculated in 3D Complex. All subunits in the different protein complexes are made of the same N-terminal nucleophile aminohydrolases domain, suggesting that the proteasome originates form a single ancestral protein. The existence of this domain (1xfg), as a stable and catalytically active unit with a catalytic mechanism similar to that of the proteasome (Isupov, et al., 1996), suggests that the proteasome may have originated from a monomeric protein. A possible evolutionary route leading to the proteasome from this hypothetical monomer is shown and recapitulates evolutionary mechanisms illustrated in two images above.
Animations and moviesI had the animation below in my mind for the 3D Complex web site. It was actually not too tricky to make it concrete: (i) I generated a movie of a rotating protein complex using VMD, then did the same for the corresponding graph (still using VMD). Then I merged the two movies together using Adobe ImageReady, and played with the layer transparency to achieve the effect.
This is my first animation movie using Blender. Below is just an animated gif showing 1/20 frames. The entire movie can be downloaded here. There are 200 frames, it lasts 8 seconds and took 20 hours to compute on my Mac (1.3Ghz)!