Structure Based Study of CA SPASE-3 and D-Arginine Dehydrogenase

Caspases are important players in programmed cell death. Normal activities of caspases are critical for the cell life cycle and dysfunction of caspases may lead to the development of cancer and neurodegenerative diseases. They have become a popular target for drug design against abnormal cell death. In this study, the recognition of P5 position in substrates by caspase-3, -6 and -7 has been investigated by kinetics, modeling and crystallography. Crystal structures of caspase-3 and -7 in complexes with substrate analog inhibitor Ac-LDESD-CHO have been determined at resolutions of 1.61 and 2.45 Å, respectively, while a model of caspase-6/LDESD is constructed. Enzymatic study and structural analysis have revealed that Caspase-3 and -6 recognize P5 in pentapeptides, while caspase-7 lacks P5-binding residues. D-arginine dehydrogenase catalyzes the flavin-dependent oxidative deamination of D-amino acids to the corresponding imino acids and ammonia. The X-ray crystal structures of DADH and its complexes with several imino acids were determined at 1.03-1.30 Å resolution. The DADH crystal structure comprises a product-free conformation and a product-bound conformation. A flexible loop near the active site forms an “active site lid” and may play an essential role in substrate recognition. The DADH Glu87 forms an ionic interaction with the side chain of iminoarginine, suggesting its importance for DADH preference of positively charged D-amino acids. Comparison of the kinetic data of DADH activity on different D-amino acids and the crystal structures demonstrated that this enzyme is characterized by relatively broad substrate specificity, being able to oxidize positively charged and large hydrophobic D-amino acids bound within a flask-like cavity. Understanding biology at the system level has gained much more attention recently due to the rapid development in genome sequencing and high-throughput measurements. Current simulation methods include deterministic method and stochastic method. Both have their own advantages and disadvantages. Our group has developed a deterministic-stochastic crossover algorithm for simulating biochemical networks. Simulation studies have been performed on biological systems like auto-regulatory gene network and glycolysis system. The new system retains the high efficiency of deterministic method while still reflects the random fluctuations at lower concentration

Accurate Inference of Local Phased Ancestry of Modern Admixed Populations

Population stratification is a growing concern in genetic-association studies. Averaged ancestry at the genome level (global ancestry) is insufficient for detecting the population substructures and correcting population stratifications in association studies. Local and phase stratification are needed for human genetic studies, but current technologies cannot be applied on the entire genome data due to various technical caveats. Here we developed a novel approach (aMAP, ancestry of Modern Admixed Populations) for inferring local phased ancestry. It took about 3 seconds on a desktop computer to finish a local ancestry analysis for each human genome with 1.4-million SNPs. This method also exhibits the scalability to larger datasets with respect to the number of SNPs, the number of samples, and the size of reference panels. It can detect the lack of the proxy of reference panels. The accuracy was 99.4%. The aMAP software has a capacity for analyzing 6-way admixed individuals. As the biomedical community continues to expand its efforts to increase the representation of diverse populations, and as the number of large whole-genome sequence datasets continues to grow rapidly, there is an increasing demand on rapid and accurate local ancestry analysis in genetics, pharmacogenomics, population genetics, and clinical diagnosis

MiRNAs Associated Polymorphisms in the 3'UTR of MET Promote the Risk of Non-Small Cell Lung Cancer

Background/Aims: MET can act as an oncogene and its signaling server has essential roles in regulating tumorigenesis. Polymorphisms in MET have been reported to be associated with poor prognosis in human cancer, but an association with the risk of human non-small-cell lung cancer (NSCLC) has not been found so far. In this study rs41281081 and rs76322625, located in the 3'UTR of MET, were selected to evaluate their relationship with the risk of NSCLC among the Chinese population. Methods: A questionnaire, SNaPshot genotype assay, real time PCR assay, cell transfection and the dual luciferase reporter assay were used. Single-nucleotide polymorphisms (SNPs) of rs41281081 and rs76322625 in the 3' untranslated region (UTR) of MET was involved as a risk factor in the occurrence of NSCLC. Results: SNP rs41281081 could be regulated by miR-335 and rs76322625 could be regulated by miR-1026 to cause an up-regulation of MET in patients with NSCLC. Furthermore, the carriers of the GA and AA genotypes in rs41281081, and the CU and UU genotypes in rs76322625 presented with poor cell differentiation and large tumor size, as well as a high probability of metastasis. Conclusion: Our findings have shown that the SNPs rs41281081 and rs76322625 in MET 3ʹUTR, through disruption of the regulatory role of miR-335 and miR-1026 in MET expression, may act as promoting factors in the pathogenesis of NSCLC