Numerical framework to model temporally resolved multi-stage dynamic systems.

Numerical modeling of steroid hormone signaling presents an exciting challenge involving spatiotemporal coordination of multiple events. Ligand binding in cytoplasm triggers dissociation and/or association of coregulators which subsequently regulate DNA binding and transcriptional activity in nucleus. In order to develop a comprehensive multi-stage model, it is imperative to follow not only the transcriptional outcomes but also the intermediate protein complexes. Accordingly, we developed a software toolkit for simulating complex biochemical pathways as a set of non-linear differential equations in LabVIEW (Laboratory Virtual Instrumentation and Engineering Workbench, National Instruments, Austin, TX) environment. The toolkit is visual, highly modular, loosely coupled with the rest of LabVIEW, scalable and extensible. The toolkit can be used to develop and validate biochemical models and estimate model parameters from existing experimental data. We illustrate the application of the toolkit for simulation of steroid hormone response in cells, and demonstrate how the toolkit can be employed for other biological and chemical systems as well. The software module presented here can be used stand-alone as well as built into data collection and analysis applications.

Guanidinium chloride-induced spectral perturbations of 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid confound interpretation of data on molten globule states.

We describe limitations in the use of 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) to examine unfolding intermediates associated with guanidinium chloride (GuHCl)-induced protein denaturation. Several studies have used alterations in fluorescence emission of bis-ANS to quantify the population of "molten globule" states. Our findings indicate that the observed changes in bis-ANS spectroscopic properties could originate from the interactions of bis-ANS and GuHCl and the aggregation of the dye at higher GuHCl concentrations. We posit that in the absence of additional complementary structural or spectroscopic measurements, the use of bis-ANS emission alone to monitor protein conformations can be misleading.

Role of the androgen receptor CAG repeat polymorphism in prostate cancer, and spinal and bulbar muscular atrophy.

Androgens are involved in the development of several tissues, including prostate, skeletal muscle, bone marrow, hair follicles, and brain. Most of the biological effects of the androgens are mediated through an intracellular transcription factor, the androgen receptor (AR) at the level of gene regulation. Several types of mutations in the AR gene have been linked to endocrine dysfunctions. The expansion of CAG codon repeat, coding for a polyglutamine (PolyQ) tract in the N-terminal domain is one such mutation. The polyQ chain length impacts AR's ability to interact with critical coregulators, which in turn modulates its transcriptional efficacy. Pathologic manifestations of variations in polyQ chain length have been associated with prostate cancer susceptibility, and the Spinal and Bulbar Muscular Atrophy (SBMA), a neurodegenerative disease. In this review article, we discuss multiple aspects of the role of polyQ chain length in the actions of the AR, their importance in prostate cancer development and progression, and SBMA with an aim to understand the underlying mechanisms involved in these diseases, which can be targeted for future therapeutic approaches.