![]() ![]() We selected key residues at the pore of each aquaporin tetramer. What is the advantage to allow the water permeation in a single-file fashion? How would you describe the water passage through each one of these paths? How many water pathways can you identify? Also fraphical representations can be hidden/shown for more clarity. In the VMD Main window, press play, adjusting the speed, orientation and zoom. Replace "resname SOL and within 4 of protein" by "protein and resid 62 64 180 183" Look at the protein with pymolįor "Selected Atoms" choose "resname SOL and within 4 of protein" Select "PDB Format" and save the file in the Desktop directory. Download the structure, by clicking on the "Download Files" button at the right side. Please go to the protein data bank, search the structure with PDB code 2B6O. We will consider aquaporin-0, the most abundant protein in our eye lense. We will consider an aquaporin, a class of membrane proteins which facilitate the permeation of water and other solutes through biological lipid bilayers in response to osmotic pressure. Now, we will setup an MD simulation of a membrane protein. What change in conformation (area per lipid and thickness), ordering, and dynamics (diffusion coefficient) is expected if the temperature is reduced?Ĭ. What is the origin of the discrepancies between the simulation and the experimental value? How does the estimated value compares with the experimental diffusion coefficient for this lipid at 320 K (D exp~1.5x10 -7 cm 2/s)? The slope of this curve is related to the diffusion coefficient. Which type of diffusive behavior do the lipids display at that given time scale (sub-diffusive, diffusive or super-diffusive)?. Use the zoom button at the up-left xmgrace menu for this purpose. The copyright for this article belongs to the Authors.Zoom to the time window, considered for the fitting (0 to 10000 ps). iPBAvizu enables to generate iPBA alignments, create and interactively explore structural superimposition, and assess the quality of the protein alignments. Conclusions: iPBAvizu is an implementation of iPBA within the well-known and widely used PyMOL software. To facilitate the usage of iPBA, we designed and implemented iPBAvizu, a plugin for PyMOL that allows users to run iPBA in an easy way and analyse protein superimpositions. Our approach, iPBA, has shown to perform better than other available tools in benchmark tests. We improved the procedure with a specific two-step search: (i) very similar regions are selected using very high weights and aligned, and (ii) the alignment is completed (if possible) with less stringent parameters. Proteins are described using PB from which we have previously developed a sequence alignment procedure based on dynamic programming with a dedicated PB Substitution Matrix. Results: We used Protein blocks (PB), a widely used SA consisting of 16 prototypes, each representing a conformation of the pentapeptide skeleton defined in terms of dihedral angles. The interest of a SA is to translate into 1D sequences into the 3D structures. a library of 3D local protein prototypes able to approximate protein backbone. Our methodology is based on the use of a Structural Alphabet (SA), i.e. Multiple approaches have been developed to perform such task and are often based on structural superimposition deduced from sequence alignment, which does not take into account structural features. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure superimposition analysis. Background: Protein 3D structure is the support of its function. ![]()
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