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Displacement Based Design, (DBD), Nonlinear Static Pushover Analysis To Verify The Proper Collapse Mechanism Of Structures MAJD NAFEZ ATTAR Director of Department of Civil Engineering. Response Spectrum Method using the UBC-97 design response spectrum. Another method for the polymerization of temperature-sensitive monomers. Using the Spectrum (PerkinElmer) software package and SpectraGryph 1.30. N.; Karakatsani E. K.; Papaspyrides C. Solid state polymerization.
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.): all chaperone-subunit complexes are first recruited to the N-terminal domain (NTD) of the usher and subsequently transferred to two C-terminal domains (CTDs) that form a secondary chaperone-subunit binding platform. DSE occurs when a subunit located at the NTD reacts with the previously assembled subunit located at the CTDs. Indeed, the subunit at the NTD is positioned relative to the subunit at the CTDs in such a way that its Nte is close to the groove of the CTD-bound subunit and thus can “zip-in” into that groove, thereby displacing the chaperone and forming a native Nte-groove subunit-subunit interaction. At this point, the NTD-bound chaperone-subunit complex transfers to the CTDs with a rotation-and-translation motion that results in the extrusion of the pilus, one subunit at a time. The two structures differ in the orientation of donor-strand insertion with respect to the last β strand of the Ig-like pilin fold. In FimAa (PDB: ), the donor strand is inserted in a stable antiparallel fashion, identical to the orientation and register observed in the quaternary structure of the pilus; whereas in FimA (PDB: ) the donor strand is inserted in a less stable parallel arrangement (D). In addition, two structures of FimA in complex with the chaperone FimC were determined by X-ray crystallography (.
(A and B) Top and side views of (A) the type 1 pilus rod (colored dark blue, light blue, and gray) and (B) the P pilus rod (colored dark green, light green, and gray). The top view is shown in both surface and cartoon representation, whereas the side view is shown in surface representation. The last Nte of the top subunit in the surface representation of the top view, which does not undergo DSE with another subunit here, is outlined in black to distinguish it from the Nte of the same color emanating from the subunit below (n−3).
Indicated are the dimensions of the outer and lumen diameters (top view), and the helical parameters of rise (R) and the number of subunits per turn (side view). A black arrow indicates the degree of twist in the pilus by tracing up the front face of the pilus structure. The N-terminal end of the Nte is visible between subunits (dashed red box) and is shorter and oriented differently in the type 1 pilus compared with the previously described “staple” region (residues 1–5) in the P pilus (. (C) A comparison between the Nte peptides complementing the pilin's hydrophobic groove in the type 1 pilus (left) and P pilus (right).
The pilin subunits are shown in surface representation (FimA, light blue; PapA, light green) and the Nte peptide is shown in stick representation (FimA, dark blue; PapA, dark green). The Ntes of the pilin subunits shown in surface representation have been removed for clarity. The bottom panels show the quality of the electron density surrounding the Nte peptides, illustrating the differences at the N terminus. The PapA Nte makes a sharp turn and forms the “staple” region (red dashed ellipse), whereas the FimA Nte lies flat against the FimA subunit.
Residues are labeled and an arrow indicates the overall orientation of the pilins. (C) Left panel: superposition of the two subunits participating in the pilus' main stacking interface (n and n+3) of the cryo-EM-derived model (blue, Nte in red) and the ssNMR/STEM-derived model (gray, Nte in yellow).
The n subunit was aligned and the RMSD value for the alignment of Cα atoms for residues 2–158 is indicated below. Right panel: 90° rotation of the n+3 subunit showing the offset of key β strands and loops in the stacking interface as a result of the differences in twist and rise. The distances between equivalent Cα atoms (F54 and G108) are indicated.), we hypothesized that pili assembled in vivo and in vitro should differ in their kinetic stability against dissociation and unfolding by denaturants, even if they only had slightly different quaternary structures. Shows the guanidinium chloride (GdmCl)-dependent dissociation/unfolding kinetics at pH 2.1 for both pilus preparations, recorded via the decrease in the far-UV circular dichroism (CD) signal at 230 nm.
The results demonstrated that native pili formed in vivo were indeed significantly more stable against dissociation and unfolding than pili assembled in vitro and also differed in the denaturant sensitivity of the rate constant of dissociation/unfolding. Specifically, the extrapolated unfolding rate constants of pili assembled in vivo proved to be 3–4 orders of magnitude smaller compared with the unfolding rates of pili assembled in vitro recorded in the range of 5.8–6.4 M GdmCl. In addition, both pilus preparations proved to be homogeneous, as all unfolding traces could be fitted with a single exponential function (see; and ).

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We conclude that type 1 pili can adopt different quaternary structures and that the mechanism and the conditions of the assembly reaction likely define the specific quaternary structure of the pilus rod. In addition, formation of a specific pilus conformer appears to be irreversible. The differences between the cryo-EM and the ssNMR/STEM structures of type 1 pili might thus indeed result from different quaternary structures. The kinetics of dissociation/unfolding of type 1 pili assembled in vivo (black symbols) or in vitro (red symbols) at pH 2.1 and different GdmCl concentrations were followed via the decrease in the far-UV CD signal of FimA upon unfolding.
All kinetic traces were fully consistent with a single first-order reaction, showing that the pilus preparations were homogeneous and did not consist of mixtures of pili with different stability against unfolding/dissociation. The logarithms of the rate constants of dissociation/unfolding (k obs) were plotted against GdmCl concentration. The results show that pili assembled in vivo are clearly more stable than those assembled in vitro. The differences in the slopes of the GdmCl dependence of k obs indicate a higher solvent accessibility of the transition state of dissociation/unfolding for the pili assembled in vivo. Please refer to for the general architecture of UPEC chaperone-usher pili and for further details about type 1 pilus rod unfolding/dissociation.Discussion. However, as demonstrated for the P pilus, the most important interface is the main stacking interface formed between every n and n+3 subunit (C and A). This interface is responsible for maintaining the quaternary structural integrity of the pilus and also governs the biomechanical properties of reversible uncoiling in response to shear forces such as those experienced in the urinary tract.
Chaperone-usher pili have been the subjects of several studies utilizing force spectroscopy techniques such as optical tweezers or AFM (. Region I is characterized by a linear force versus elongation response and is thought to reflect the elastic stretching of the quaternary rod structure (although not yet breaking it). Region II results in elongation under constant force and represents the sequential opening of the stack-to-stack interactions resulting in rod unwinding. Finally, Region III shows an “s-shaped” force versus elongation response and represents the overstretching of the now linearized rod, still held together by intermolecular DSE interactions. Both regions I and II depend on the interface created by the n and n+3 subunits.
The unwinding of the rod in region II occurs either under steady-state or dynamic conditions depending on the elongation speed applied (.