Rosemary V. Sampogna

Environmental effects on the protonation states of active site residues in bacteriorhodopsin

Finite difference solutions of the Poisson-Boltzmann equation are used to calculate the pKa values of the functionally important ionizable groups in bacteriorhodopsin. There are strong charge-charge interactions between the residues in the binding site leading to the possibility of complex titration behavior. Structured water molecules, if they exist in the binding site, can have significant effects on the calculated pKa by strongly stabilizing ionized species. The ionization states of the Schiff base and Asp-85 are found to be strongly coupled. Small environmental changes, which might occur as a consequence of trans-cis isomerization, are capable of causing large shifts in the relative pKa values of these two groups. This provides an explanation for the protonation of Asp-85 and the deprotonation of the Schiff base in the M state of bacteriorhodopsin. The different behavior of Asp-85 and Asp-212 is discussed in this regard.

Electrostatic coupling between retinal isomerization and the ionization state of Glu-204: a general mechanism for proton release in bacteriorhodopsin.

The pKa values of ionizable groups that lie between the active site region of bacteriorhodopsin (bR) and the extracellular surface of the protein are reported. Glu-204 is found to have an elevated pKa in the resting state of bR, suggesting that it corresponds to the proton-releasing group in bR. Its elevated pKa is predicted to be due in part to strong repulsive interactions with Glu-9. Following trans-cis isomerization of the retinal chromophore and the transfer of a proton to Asp-85, polar groups on the protein are able to interact more strongly with the ionized state of Glu-204, leading to a substantial reduction of its pKa. This suggests a general mechanism for proton release in which isomerization and subsequent charge separation initially produce a new electrostatic balance in the active site of bR. Here it is proposed that those events in turn drives a conformational change in the protein in which the ionized state of Glu-204 can be stabilized through interactions with groups that were previously inaccessible. Whether these groups should be identified with polar moieties in the protein, bound waters, or Arg-82 is an important mechanistic question whose elucidation will require further study.

Developmental Programming of Branching Morphogenesis in the Kidney

The kidney developmental program encodes the intricate branching and organization of approximately 1 million functional units (nephrons). Branching regulation is poorly understood, as is the source of a 10-fold variation in nephron number. Notably, low nephron count increases the risk for developing hypertension and renal failure. To better understand the source of this variation, we analyzed the complete gestational trajectory of mouse kidney development. We constructed a computerized architectural map of the branching process throughout fetal life and found that organogenesis is composed of two distinct developmental phases, each with stage-specific rate and morphologic parameters. The early phase is characterized by a rapid acceleration in branching rate and by branching divisions that repeat with relatively reproducible morphology. The latter phase, however, is notable for a significantly decreased yet constant branching rate and the presence of nonstereotyped branching events that generate progressive variability in tree morphology until birth. Our map identifies and quantitates the contribution of four developmental mechanisms that guide organogenesis: growth, patterning, branching rate, and nephron induction. When applied to organs that developed under conditions of malnutrition or in the setting of growth factor mutation, our normative map provided an essential link between kidney architecture and the fundamental morphogenetic mechanisms that guide development. This morphogenetic map is expected to find widespread applications and help identify modifiable targets to prevent developmental programming of common diseases.

A Unifying Theory of Branching Morphogenesis

Summary The morphogenesis of branched organs remains a subject of abiding interest. Although much is known about the underlying signaling pathways, it remains unclear how macroscopic features of branched organs, including their size, network topology, and spatial patterning, are encoded. Here, we show that, in mouse mammary gland, kidney, and human prostate, these features can be explained quantitatively within a single unifying framework of branching and annihilating random walks. Based on quantitative analyses of large-scale organ reconstructions and proliferation kinetics measurements, we propose that morphogenesis follows from the proliferative activity of equipotent tips that stochastically branch and randomly explore their environment but compete neutrally for space, becoming proliferatively inactive when in proximity with neighboring ducts. These results show that complex branched epithelial structures develop as a self-organized process, reliant upon a strikingly simple but generic rule, without recourse to a rigid and deterministic sequence of genetically programmed events.

A Subpopulation of Label-Retaining Cells of the Kidney Papilla Regenerates Injured Kidney Medullary Tubules

Summary To determine whether adult kidney papillary label-retaining cells (pLRCs) are specialized precursors, we analyzed their transcription profile. Among genes overexpressed in pLRCs, we selected candidate genes to perform qPCR and immunodetection of their encoded proteins. We found that Zfyve27, which encodes protrudin, identified a subpopulation of pLRCs. With Zfyve27-CreERT2 transgenic and reporter mice we generated bitransgenic animals and performed cell-lineage analysis. Post tamoxifen, Zfyve27-CreERT2 marked cells preferentially located in the upper part of the papilla. These cells were low cycling and did not generate progeny even after long-term observation, thus they did not appear to contribute to kidney homeostasis. However, after kidney injury, but only if severe, they activated a program of proliferation, migration, and morphogenesis generating multiple and long tubular segments. Remarkably these regenerated tubules were located preferentially in the kidney medulla, indicating that repair of injury in the kidney is regionally specified. These results suggest that different parts of the kidney have different progenitor cell pools.

Taking a bite: endocytosis in the maintenance of the slit diaphragm

In the kidney, the slit diaphragm joins adjacent podocytes, forming an epithelial barrier that filters plasma into the urinary space, yet retains blood cells and proteins within the circulation. In this issue of the JCI, Soda et al. have identified clathrin-mediated endocytosis as a central mechanism by which the function and structural integrity of the slit diaphragm are maintained.

Detection of unrecognized urinothorax with renal scintigraphy

A 50-year-old man presented with severe dyspnea 3 weeks following right-sided percutaneous nephrolithotomy. Chest computed tomography revealed a large pleural effusion (Figure 1). The pleural fluid creatinine was 10.5 mg/100 ml and pleural fluid to serum protein and creatinine ratios were 0.19 and 2.5, respectively, suggesting the presence of urinothorax. The absence of obstruction on renal ultrasound excluded surgical intervention. Persistent symptomatic pleural effusion prompted technetium-99m-mercaptoacetyltriglycine-3 scintigraphy. Tracer extravasation into the right thorax revealed an unrecognized retroperitoneal-pleural tract (Figure 2). Ureteropyelography revealed infundibular stenosis, which was corrected surgically, with resolution of the pleural effusion. Urinothorax is a rare cause of transudative pleural effusion characterized by a pleural fluid to serum creatinine ratio 41. Although the history and fluid analysis suggested persistent urinothorax, intervention was delayed due to lack of evidence of obstructive uropathy. Technetium-99m scintigraphy uncovered the urinothorax and facilitated its definitive resolution. http://www.kidney-international.org n e p h r o l o g y i m a g e

Salt and Pepper Distribution of Cell Types in the Collecting Duct

Many epithelial organs, such as the kidney, gastrointestinal tract, skin, lung, and brain, are segmented such that each region has its characteristic cell type. Close examination of these segments reveals that they are homogenous and contain only one epithelial cell type. With a bit of training, it

Protocadherin cis-dimer architecture and recognition unit diversity

Significance Pcdhs are cell surface homophilic recognition proteins expressed stochastically to assign individual identities to each neuron. These individual identities ensure repulsion between neurites from the same cell and ensure that neurites from different cells do not repel. However, it is difficult to understand how only ∼60 Pcdh isoforms can provide sufficient diversity for the billions of neurons in vertebrate nervous systems. Here, we report the crystal structure of a Pcdh cis-dimer through which individual Pcdh isoforms associate to form diverse bivalent recognition units. The structure reveals asymmetry in the cis-dimer interaction and suggests restrictions on isoform combinations compatible with cis-dimerization. These findings provide a framework to understand Pcdh cis-dimerization and the compositions of functional repertoires of Pcdh recognition units. Clustered protocadherins (Pcdhs) mediate numerous neural patterning functions, including neuronal self-recognition and non–self-discrimination to direct self-avoidance among vertebrate neurons. Individual neurons stochastically express a subset of Pcdh isoforms, which assemble to form a stochastic repertoire of cis-dimers. We describe the structure of a PcdhγB7 cis-homodimer, which includes the membrane-proximal extracellular cadherin domains EC5 and EC6. The structure is asymmetric with one molecule contributing interface surface from both EC5 and EC6, and the other only from EC6. Structural and sequence analyses suggest that all Pcdh isoforms will dimerize through this interface. Site-directed mutants at this interface interfere with both Pcdh cis-dimerization and cell surface transport. The structure explains the known restrictions of cis-interactions of some Pcdh isoforms, including α-Pcdhs, which cannot form homodimers. The asymmetry of the interface approximately doubles the size of the recognition repertoire, and restrictions on cis-interactions among Pcdh isoforms define the limits of the Pcdh recognition unit repertoire.

Clustered protocadherin molecular assembly and implications for neuronal self-avoidance

Kerry Marie Goodman1, Rotem Rubinstein2, Julia Brasch1, Seetha Mannepalli1, Fabiana Bahna3, Hanbin Dan4, Tom Maniatis1, Barry Honig5, Lawrence Shapiro1 1Dept. Of Biochemistry And Molecular Biophysics, Columbia University, New York, United States, 2Dept. of Systems Biology and Center for Computational Biology, Columbia University, New York, United States, 3Dept. of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, United States, 4Dept. of Medicine, Columbia University, New York, United States, 5Dept. of Biochemistry and Molecular Biophysics, Dept. of Systems Biology and Center for Computational Biology, Dept. of Medicine, Howard Hughes Medical Institute, Columbia University, New York, United States E-mail: kg2518@columbia.edu