Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain

Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1 ubiquitin-associated (UBA) domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. No experimentally determined molecular structure of this unusual UBA domain is available. We fused the UBA domain to the 1TEL variant of the translocation ETS leukemia protein sterile alpha motif (TELSAM) crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and crystallize at protein concentrations as low as 0.2 mg/mL. Our studies support a mechanism of 1TEL fusion crystallization and show that 1TEL fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.

Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain

Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1-UBA domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. Sequence analysis suggests an unusual architecture for the TNK1 UBA domain, but an experimentally-validated molecular structure is undetermined. To gain insight into TNK1 regulation, we fused the UBA domain to the 1TEL crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. A 1TEL search model enabled solution of the X-ray phases. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and to crystallize at protein concentrations as low as 0.1 mg/mL. Our studies support a mechanism of TELSAM fusion crystallization and show that TELSAM fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.

Prediction and Mechanistic Interpretation of Human Oral Drug Absorption Using MI-QSAR Analysis

Membrane-interaction [MI]-QSAR analysis, which includes descriptors explicitly derived from simulations of solutes [drugs] interacting with phospholipid membrane models, was used to construct QSAR models for human oral intestinal drug absorption. A data set of 188 compounds, which are mainly drugs, was divided into a parent training set of 164 compounds and a test set of 24 compounds. Stable, but not highly fit [R2 = 0.68] MI-QSAR models could be built for all 188 compounds. However, the relatively large number [47] of drugs having 100% absorption, as well as all zwitterionic compounds [11], had to be eliminated from the training set in order to construct a linear five-term oral absorption diffusion model for 106 compounds which was both stable [R2 = 0.82, Q2 = 0.79] and predictive given the test set compounds were predicted with nearly the same average accuracy as the compounds of the training set. Intermolecular membrane-solute descriptors are essential to building good oral absorption models, and these intermolecular descriptors are displaced in model optimizations and intramolecular solute descriptors found in published oral absorption QSAR models. A general form for all of the oral intestinal absorption MI-QSAR models has three classes of descriptors indicative of three thermodynamic processes: (1) solubility and partitioning, (2) membrane-solute interactions, and (3) flexibility of the solute and/or membrane. The intestinal oral absorption MI-QSAR models were compared to MI-QSAR models previously developed for Caco-2 cell permeation and for blood-brain barrier penetration. The MI-QSAR models for all three of these ADME endpoints share several common descriptors, and suggest a common mechanism of transport across all three barriers. A further analysis of these three types of MI-QSAR models has been done to identify descriptor-term differences across these three models, and the corresponding differences in thermodynamic transport behavior of the three barriers.

4D-fingerprints, universal QSAR and QSPR descriptors

An elusive goal in the field of chemoinformatics and molecular modeling has been the generation of a set of descriptors that, once calculated for a molecule, may be used in a wide variety of applications. Since such universal descriptors are generated free from external constraints, they are inherently independent of the data set in which they are employed. The realization of a set of universal descriptors would significantly streamline such chemoinformatics tasks as virtual high-throughout screening (VHTS) and toxicity profiling. The current study reports the derivation and validation of a potential set of universal descriptors, referred to as the 4D-fingerprints. The 4D-fingerprints are derived from the 4D-molecular similarity analysis. To evaluate the applicability of the 4D-fingerprints as universal descriptors, they are used to generate descriptive QSAR models for 5 independent training sets. Each of the training sets has been analyzed previously by several varying QSAR methods, and the results of the models generated using the 4D-fingerprints are compared to the results of the previous QSAR analyses. It was found that the models generated using the 4D-fingerprints are comparable in quality, based on statistical measures of fit and test set prediction, to the previously reported models for the other QSAR methods. This finding is particularly significant considering the 4D-fingerprints are generated independent of external constraints such as alignment, while the QSAR methods used for comparison all require an alignment analysis.

Selective cytotoxicity of azatyrosinamides against ras-transformed NIH 3T3 cells

This study aims to develop novel azatyrosinamide compounds structurally modified from ras-specific antioncogenic azatyrosine. Analogues 4-15 were prepared and their inhibition on the growth of wild-type and ras-transformed NIH 3T3 cell lines was compared. Compound 12 was found to be the most active with IC50 16.5+/-2.2 microM which is 458-fold more potent than that of azatyrosine. The selective toxicity, defined as IC(50 wild-type)/IC(50 ras-transformed) for this compound was 138.5.

A least-squares error minimization approach in the determination of ferric ion diffusion coefficient of Fricke-infused dosimeter gels

A least-squares error minimization approach was adopted to assess ferric ion diffusion coefficient of Fricke-agarose gels. Ferric ion diffusion process was modeled as a Gaussian-shaped degradation kernel operating on an initial concentration distribution. Diffusion coefficient was iteratively determined by minimizing the error function defined as the difference between the theoretically calculated and the experimentally measured dose distributions. A rapid MR image-based differential gel dosimetry technique that time resolves the evolution of the ferric ion diffusion process minimizes smearing of the dose distribution. Our results showed that for a Fricke-agarose gel contained 1 mM ammonium ferrous sulfate, 1% agarose, 1 mM sodium chloride, and 50 mM sulfuric acid, its ferric ion diffusion coefficient is (1.59 +/- 0.28) x 10(-2) cm2 h(-1) at room temperature. This value falls within the 1.00-2.00 x 10(-2) cm2 h(-1) range previously reported under varying gelling ingredients and concentrations. This method allows a quick, nondestructive evaluation of the ferric ion diffusion coefficient that can be used in conjunction with the in situ gel dosimetry experiment to provide a practical diffusion characterization of the dosimeter gel.

The role of dose distribution gradient in the observed ferric ion diffusion time scale in MRI-Fricke-infused gel dosimetry

Ferric ion diffusion is a detrimental factor in MRI-Fricke-infused gel dosimetry. In this study, a novel approach involving MR image subtraction and a fast image-based dosimetry technique to study ferric ion diffusion effects is presented. The fast image-based approach allows studying dose profile degradation within minutes post-irradiation. The relationship between the rate of dose profile deterioration and dose distribution gradients can be elucidated with the improved imaging temporal resolution also. Our results showed that for a dose distribution with gradient 4 Gy/mm or higher, ferric ion diffusion causes apparent dose profile degradation in 0.5-1 h post-irradiation. For a gradual dose gradient change of 2.1 Gy/mm or smaller, dose profile degradation appears insignificant for a two-hour elapsed diffusion time. These observations agree well with the theoretical analysis of a square dependence between dose profile degradation and dose distribution gradient. Because all stereotactic radiosurgery procedures produce steep dose distributions and because the ideal "snapshot" of MR scanning cannot be achieved, knowledge of the ferric ion diffusion time scale is important in experimental designs in order to avoid potential measurement errors in MRI-Fricke-agarose gel dosimetry.

Seminal plasma zinc levels and sperm motion characteristics in infertile samples

BACKGROUND

Zinc (Zn) in seminal plasma stabilizes the cell membrane and nuclear chromatin of spermatozoa. It may also have an antibacterial function. However, extremely high concentrations of Zn (10 to 100 x the normal range) may inhibit sperm motility and the function of the mannose receptor on the sperm head. In this study, we analyzed the correlation between Zn levels in seminal plasma and the characteristics of semen as measured by conventional and computer aided sperm analysis (CASA).

METHODS

One hundred fifteen infertile couples were recruited for conventional semen analysis and CASA from December 1995 through January 1996, and Zn levels in semen samples were determined by flame atomic absorption spectroscopy (AAS).

RESULTS

A good correlation in a positive direction (r = 0.73, p = 0.0001) was noted between the total amount of Zn per ejaculate and the Zn concentration. The Zn concentration in seminal plasma was negatively correlated with the seminal pH (r = -0.35, p = 0.0081). There was no significant correlation between the total amount of Zn per ejaculate and sperm characteristics, including sperm count, motility (% sperm count), progressive motility (% motility), rapid motility (% motility), average path velocity (VAP, microns/s), straight-line velocity (VSL, microns/s), curvilinear velocity (VCL, microns/s), amplitude of lateral head displacement (ALH, microns), beat/cross frequency (BCF, beats/s), straightness (STR), and linearity (LIN). There was also no significant correlation between the Zn concentration in seminal plasma and the above sperm characteristics.

CONCLUSION

The characteristics of semen as determined by conventional semen analysis or CASA bore no correlation with total seminal Zn amount or Zn concentrations in the ejaculates. Routine determination of the Zn concentration in seminal plasma offers no advantages in infertility work-ups.

Carcinosarcoma of the renal pelvis: a case report with immunohistochemical study

The clinicopathologic feature of one carcinosarcoma of the renal pelvis is reported. The tumor occurred in a 51-year-old woman with a long standing history of renal calculi. The epithelial component was consistent with squamous cell carcinoma, whereas the sarcomatous component was composed of pleomorphic spindle cells. The immunohistochemical studies demonstrated obvious epithelial and mesenchymal reactivity respectively. The tumor progressed rapidly with widespread metastases and the patient died one month after operation.