Kinetic folding mechanism of PDZ2 from PTP-BL

PDZ domains represent a large family of protein-interaction modules associated with a variety of unrelated proteins with different functions. We report a complete characterization of the kinetic folding mechanism of a fluorescent variant of PDZ2 from PTP-BL, investigated under a variety of different experimental conditions. For this purpose, we engineered a fluorescent variant of this protein Y43W (called pseudo-wild-type, pWT43). The results suggest the presence of a high-energy intermediate in the folding of PDZ2, as revealed by a pronounced non-linear dependence of the unfolding rate constant on denaturant concentration. Such an intermediate may or may not be detectable depending on the experimental conditions, giving rise to apparent two-state folding under stabilizing conditions (e.g. in the presence of sodium sulfate). Interestingly, even under these conditions, three-state folding can be restored by selectively destabilizing the native-like rate-limiting barrier by one specific mutation (V44A). Finally, we show that data taken on pWT43 under different experimental conditions (e.g. different pH values from 2.1 to 8.0 or in the presence of a stabilizing salt) and also data on a site-directed conservative mutant can be rationalized in terms of a simple reaction scheme involving a single set of intermediates and transition states.     

Aberrant protein expression in plasma and kidney tissue during experimental obstructive nephropathy

Kidney failure is a major health problem worldwide. Patients with end-stage renal disease require intensive medical support by dialysis or kidney transplantation. Current methods for diagnosis of kidney disease are either invasive or insensitive, and renal function may decline by as much as 50% before it can be detected using current techniques. The goal of this study was, therefore, to identify biomarkers of kidney disease (associated with renal fibrosis) that can be used for the development of a non-invasive clinical test for early disease detection. We utilized two protein-profiling technologies (SELDI-TOF MS and 2-D) to screen the plasma and kidney proteome for aberrantly expressed proteins in an experimental mouse model of unilateral uretric obstruction, which mimics the pathology of human renal disease. Several differentially regulated proteins were detected at the plasma level of day-3-obstructed animals, which included serum amyloid A1, fibrinogen α, haptoglobin precursor protein, haptoglobin and major urinary proteins 11 and 8. Differentially expressed proteins detected at the tissue level included ras-like activator protein 2, haptoglobin precursor protein, malate dehydrogenase, α enolase and murine urinary protein (all p<0.05 versus controls). Immunohistochemistry was used to confirm the up-regulation of fibrinogen. Interestingly, these proteins are largely separated into four major classes: (i) acute-phase reactants (ii) cell-signaling molecules (iii) molecules involved in cell growth and metabolism and (iv) urinary proteins. These results provide new insights into the pathology of obstructive nephropathy and may facilitate the development of specific assay(s) to detect and monitor renal fibrosis.     

Exact spread function for a pulsed collimated beam in a medium with small-angle scattering

A solution has been obtained for the spatial and temporal distribution function for a pulsed fully collimated beam propagating through a homogeneous medium with Gaussian small-angle scattering. The solution was obtained first by separation of the general problem into two plane problems, which results in a partial differential equation in three variables. A Fourier transform on two projected variables (one angular and one spatial) and a Laplace transform on the projected temporal variable yielded a set of nonlinear differential equations, which were solved. A recursion relation for the moments of the distribution function was also obtained, and the software MATHEMATICA was used to evaluate these moments to high orders. The contractions on certain variables are also presented; they correspond to the solutions of less-general problems contained in the main problem. A change in the definition of the time-delay produces a remarkable change in the structure of the equations. These solutions should be quite useful for lidar studies in atmospheric and oceanic optics, x-ray and radio-wave scattering in the atmosphere and interstellar medium, and in medical physics.     

Effect of inhomogeneous turbulence on imaging through turbulent layers

An analysis of the effect of inhomeogeneous turbulence on the point-spread function for imaging through a turbulent layer has been performed. The formulation retains the concept of the modulation-transfer function that has been used in the past for homogeneous turbulence layers, but the integration now depends on more than just the separation distance ρ in the plane of the aperture. An example is chosen in which the rms optical path difference increases by a factor of 3.51 from one side of the aperture to the other in the flow direction. It was found that the results were insensitive to the angle between the separation-distance vector ρ and the flow direction. Surprisingly it was found that the detailed resultswere within a few percent of those obtained with constant-turbulence parameters evaluated at the center line of the aperture.