Ement) along the fivefold local symmetry axis was performed [22]. Interpretation of

Ement) along the fivefold local symmetry axis was performed [22]. Interpretation of the electron density maps for each solution together with buy LY2409021 monitoring of the Rfree/Rvalue ratio revealed that no preferred orientation can be detected. In further refinement overall anisotropic B-factor and bulk solvent corrections were utilized. Simulated annealing omit 25033180 maps confirmed the correctness of the protein and ligand structures. Water molecules were added chosen by distance criteria and hydrogen bonding geometry and were tested for position in spherical density, reasonable temperature factors, real space R-values, and improvement of the R-factors. The program CHARMM [23] and the effective energy function EEF [24] were employed for flG determinations as described previously [25]Figure 1. The COMPcc channel in complex with fatty acids. (A) The pentameric COMPcc channel is drawn as Ca-backbone superimposed by van der Waals spheres of individual chains that are highlighted by different color schemes. Both N nd C-termini as well as the Q54 ring system (drawn in stick-and ball mode) are labelled. (B) The individual COMPcc – fatty acid complex structures show that one molecule of each fatty acid is bound in the N-terminal Methyl linolenate chemical information cavity of the hydrophobic channel (the C-terminal part of the structure is not hown). The aliphatic side chains of individual knobs-into holes residues (Leu37, Thr40, Leu44, Val47, Leu51 and Gln54) inside of the coiled coil cause 6 regular constrictions to the diameter of the pore, varying in size ?between 2 and 6 A as defined by the van der Waals radii. Individual simulated annealing 2Fo-Fc-omit maps (1.2s contour level) superimposed on: myristic acid (C14:0), palmitic acid (C16:0), stearic acid (C18:0) and oleic acid (C18:1) are drawn in lightblue. Water molecules are not shown for clarity reasons (see in detail Figures 2 and 4, instead). doi:10.1371/journal.pone.0048130.g(C16:0), stearic acid (C18:0) and oleic acid (C18:1). In addition, the binding of these ligands to COMPcc in solution has also been studied with fluorescence spectroscopy. From the binding constants we have deciphered a trend in binding favorability that is determined by length of the aliphatic tail and geometry altered by introduction of a cis-configured double bond. A significant finding of this study is the observation that only fatty acids in an elongated configuration can pass the selectivity filter formed by the ring of five Met33 residues located at the entrance to the hydrophobic channel.Fluorescence spectroscopy of COMPcc-fatty acid complexesSteady-state fluorescence spectra were measured on a Fluorolog-3 Horiba Jobin Yvon spectrofluorometer (Edison, NJ). The sample was held in a 10610 mm quartz cuvette equipped with a continuous stirrer. The data were analyzed with Sigmaplot (Point Richmond, CA) software. The reaction was thermostatically controlled at 25uC by a Jeio-Tech refrigerating bath circulator (Des Plaines, IL). All fluorescence data were collected in 16 PBS buffer, pH 7.4. From the fluorescence enhancement profile of CPA, the fraction of ligand bound protein (f) can be calculated using: f F {F0 F420 {F0 ??Materials and Methods Expression and purification of recombinant COMPccThe coiled-coil domain of rat COMPcc comprising residues 27?72 was prepared as described previously [5]. Purified COMPcc was dialyzed against PBS pH 7.4 and concentrated to 10 mg/mL using an 10 kDa Amicon membrane (Millipore).Crystallization and Data CollectionCrystallizati.Ement) along the fivefold local symmetry axis was performed [22]. Interpretation of the electron density maps for each solution together with monitoring of the Rfree/Rvalue ratio revealed that no preferred orientation can be detected. In further refinement overall anisotropic B-factor and bulk solvent corrections were utilized. Simulated annealing omit 25033180 maps confirmed the correctness of the protein and ligand structures. Water molecules were added chosen by distance criteria and hydrogen bonding geometry and were tested for position in spherical density, reasonable temperature factors, real space R-values, and improvement of the R-factors. The program CHARMM [23] and the effective energy function EEF [24] were employed for flG determinations as described previously [25]Figure 1. The COMPcc channel in complex with fatty acids. (A) The pentameric COMPcc channel is drawn as Ca-backbone superimposed by van der Waals spheres of individual chains that are highlighted by different color schemes. Both N nd C-termini as well as the Q54 ring system (drawn in stick-and ball mode) are labelled. (B) The individual COMPcc – fatty acid complex structures show that one molecule of each fatty acid is bound in the N-terminal cavity of the hydrophobic channel (the C-terminal part of the structure is not hown). The aliphatic side chains of individual knobs-into holes residues (Leu37, Thr40, Leu44, Val47, Leu51 and Gln54) inside of the coiled coil cause 6 regular constrictions to the diameter of the pore, varying in size ?between 2 and 6 A as defined by the van der Waals radii. Individual simulated annealing 2Fo-Fc-omit maps (1.2s contour level) superimposed on: myristic acid (C14:0), palmitic acid (C16:0), stearic acid (C18:0) and oleic acid (C18:1) are drawn in lightblue. Water molecules are not shown for clarity reasons (see in detail Figures 2 and 4, instead). doi:10.1371/journal.pone.0048130.g(C16:0), stearic acid (C18:0) and oleic acid (C18:1). In addition, the binding of these ligands to COMPcc in solution has also been studied with fluorescence spectroscopy. From the binding constants we have deciphered a trend in binding favorability that is determined by length of the aliphatic tail and geometry altered by introduction of a cis-configured double bond. A significant finding of this study is the observation that only fatty acids in an elongated configuration can pass the selectivity filter formed by the ring of five Met33 residues located at the entrance to the hydrophobic channel.Fluorescence spectroscopy of COMPcc-fatty acid complexesSteady-state fluorescence spectra were measured on a Fluorolog-3 Horiba Jobin Yvon spectrofluorometer (Edison, NJ). The sample was held in a 10610 mm quartz cuvette equipped with a continuous stirrer. The data were analyzed with Sigmaplot (Point Richmond, CA) software. The reaction was thermostatically controlled at 25uC by a Jeio-Tech refrigerating bath circulator (Des Plaines, IL). All fluorescence data were collected in 16 PBS buffer, pH 7.4. From the fluorescence enhancement profile of CPA, the fraction of ligand bound protein (f) can be calculated using: f F {F0 F420 {F0 ??Materials and Methods Expression and purification of recombinant COMPccThe coiled-coil domain of rat COMPcc comprising residues 27?72 was prepared as described previously [5]. Purified COMPcc was dialyzed against PBS pH 7.4 and concentrated to 10 mg/mL using an 10 kDa Amicon membrane (Millipore).Crystallization and Data CollectionCrystallizati.

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