Category Archives: Papers

Visualization software for molecular assemblies by Thomas Goddard and Thomas Ferrin

Recently, among articles “in press” from Current Opinion in Structural Biology I found a paper by Thomas Goddard and Thomas Ferrin about software for visualization of large molecular assemblies. Even if the focus of this paper is not preparation of publication quality pictures, software cited there sounds familiar: Chimera, Pymol, VMD, Qutemol. The authors mention also VISION, which is a visual programming environment capable of presenting molecular data. Molecular Graphics Lab of Scripps Research Institute that works on the VISION has some other interesting tools, including PMV – Python Molecular Viewer, which I hope to cover some other time.

Anyway, this paper actually reminded me of something. I did mention that new version of Chimera can produce input for Povray, but I did not realize that it’s not the only change in this version. After upgrading to the current version I found out that it has also several “presets” of settings suitable for on-screen viewing or producing the figure. That makes preparation of the figure much faster and if you still don’t like the results you get good starting points for some tweaking.

Test image from Chimera

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Posted by on September 1, 2007 in Papers, Visualization


Structure of molecular needle

After yesterday’s post it’s no secret anymore that I’m interested (among other things) in oligomeric prokaryotic proteins. I often browse recent additions at PDB and see if there’s a new, exciting and pretty (symmetric) structure deposited. A week ago a picture similar to this below drew my attention.

PDB 2v6l

This nice ring of helices is a model of the molecular needle of type III secretion system (T3SS). This system is used by many bacterial species during an infection: attaching to the host cell is followed by a insertion of a needle into the host cell and transporting effector proteins directly into that cell. The model here is a combination of the crystal structure of the single subunit and 3D reconstruction of the needle from electron microscopy.

I believe that next years will bring more full atom models of important cell structures. It can be seen directly from the publications: certain research groups are solving structures of missing elements of the large protein complexes, one by one. The model above is for sure a one step closer to having the whole T3SS, including cytoplasmic, transmembrane and extracellular parts at a atomic resolution.

The paper about this model was published last year in PNAS (free access) by Janet E. Deane and Pietro Roversi et al. The model is deposited in the PDB as 2V6L. PubMed ID for the abstract is: 16888041.


Posted by on August 8, 2007 in Papers, Proteins, Secretion system