#Align peptide backbone in pymol code#

#Align peptide backbone in pymol code#

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. Model was displayed with Pymol.Zoom to the time window, considered for the fitting (0 to 10000 ps). R15, D17, S18, E19 and Q22 residues are shown in licorice showing the DSF common backbone interactions consensus sequence. De novo peptide prediction of Xcm RpfC ( BBa_K3071001) N-terminal receptor (1-22) using PEP-FOLD 3.5. De novo peptide prediction of Xcc RpfC ( BBa_K3071000) N-terminal receptor (1-22) using PEP-FOLD 3.5. Figure 4 shows the prediction of RpfC periplasmic sensor peptide from Xcc and figure 5 shows that of Xcm.įigure 4. We conducted de novo peptide prediction of N-terminal receptor using PEP-FOLD 3.5 RPBS Mobyle platform. 3D models of RpfC periplasmic sensor peptide from Xcc and Xcm musacearum RpfC ( BBa_K3071001) HisKA and HPt domains. campestris RpfC ( BBa_K3071000) and Xanthomononas campestris pv. ClustalW alignment of Xanthomononas campestris pv. RpfG and Clp proteins in the downstream two-component signaling pathway also reveals sequence homology and thus we conclude the compatibility of Xcc as the basis of our system’s design.įigure 3. musacearum RpfC sequence data from recently published genome sequencing data reveals the conserved HisKA and HPt domains and their histidine residues involved in phosphorelay (figure 3). Kinase domain alignmentįurther analysis of Xanthomononas campestris pv. musacearum RpfC ( BBa_K3071001) periplasmic sensor segment. campestris to regulate quorum-sensing and virulence. Fatty acid DSF binds and allosterically activates histidine kinase RpfC of phytopathogenic bacterium Xanthomononas campestris pv. Periplasmic sensor of Xanthomononas campestris pv. Gene cassette organization of Rpf proteins in Xcm from genome sequences further supports their close relatedness, supporting our rationale of using well-studied Xcc DSF signaling pathway as our system design.įigure 1. To investigate whether Xcc signaling cascade can be the basis of our design, we conducted protein alignment of various Xanthomonas species (figure 2), which shows sequence conservation at key DSF binding residues between Xcc and Xcm ( Xanthomononas campestris pv. campestris ( Xcc) RpfC protein functions by DSF binding at the periplasmic sensor as shown in figure 1, where a 22 amino acid sensing sequence participates in DSF interaction. RpfC transmembrane protein is the first component of our two-component detection system. Homology Study Periplasmic peptide alignment