venerdì 11 settembre 2009

PROTEIN EXPRESSIONS Study N.1 (VIDEO)



This 3'30'' video represents the first graphical result of the two major aspects of our research: protein motion and visual representation. The main program used is Blender, an open source 3D animation and special effects package, which we have equipped with other scripts. We also make large use of other scientific (VMD, Swiss-PDBviewer with Gromos43B1, Chimera, Reduce – MolProbity, PDB2PQR, PyMLP.py, APBS, and several home made scripts and programs) and graphical programs (Blender, Maya Autodesk, The Gimp, Djv_view, ImageMagick).
It shows a short trip to the interior of a cell, starting inside a small capillary vase. After navigating the vein, we meet some white cells, and we take a close look at one of them. We see the surface from a distance, so that we can observe the membrane dynamics, with no specific object clearly distinguished. We than 'land' on the surface and first see some glycolipids up close; when we look around we get a view of a membrane raft, with a crowd of many proteins, all in constant motion. One very erratic protein is a channel (protein that allow potassium ions to get out of the cell), into which we fall to get inside the cell.
Once inside we see Calmodulin, a very flexible small protein that we observe for a while before travelling along a microtubule, towards a place where Calcium waves are pulsing. Here our favourite protein is hit by Calcium and undergoes a major conformational change. This is shown from different perspectives, until we quickly move towards the periplasmic region of the cell, where the contractile ring is operating to split the cell in two at the time of cell division.
For a more detailed explanation of the scientific and the graphical aspects of the video, scene by scene, download this file.
See the video (Flash Player required)

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