Biomedical subjects

Youping Huang

Publications and source records attributed to Youping Huang.

3 recordsLinked to original sources

PubMed2004

Predicting GPCR-G-protein coupling using hidden Markov models.

MOTIVATION: Determining the coupling specificity of G-protein coupled receptors (GPCRs) is important for understanding the biology of this class of pharmacologically important proteins. Currently available in silico methods for predicting GPCR-G-protein coupling specificity have high error rate. METHOD: We introduce a new approach for creating hidden Markov models (HMMs) based on a first guess about the importance of various residues. We call these knowledge restricted HMMs to emphasize the fact that the state space of the HMM is restricted by the application of a priori knowledge. Specifically, we use only those amino acid residues of GPCRs which are likely to interact with G-proteins, namely those that are predicted to be in the intra-cellular loops. Furthermore, we concatenate these predicted loops into one sequence rather than considering them as four disparate units. This reduces the HMM state space by drastically decreasing the sequence length. RESULTS: Our knowledge restricted HMM based method to predict GPCR-G-protein coupling specificity has an error rate of <1%, when applied to a test set of GPCRs with known G-protein coupling specificity. AVAILABILITY: Academic users can get the data set mentioned herein and HMMs from the authors.

Binding Sites↗

PubMed2004

Experimental design on single-time-point high-throughput microsomal stability assay.

An experimental design for a single-time-point microsomal stability assay was evaluated as compared with multiple-time-point studies. Results obtained from single-time-point experiments are in excellent agreement with those from multiple time points. First-order reaction kinetics revealed rapid changes of predicted half-life from percent remaining of the parent compound at the inflection points, suggesting a maximum predictive limit for half-life. Selection of the incubation time in single-time-point assays is important to obtain balanced information for stable and unstable compounds. A short incubation time (e.g., 5 min) is most useful for differentiating between unstable compounds, which is beneficial to direct the synthetic efforts in projects with poor metabolic stability. A long incubation time (e.g., 30 min) is more applicable to a compound series with high metabolic stability. For screening purposes, a moderate incubation time (e.g., 15 min) is recommended to achieve good resolution and a sufficiently high maximum predictive limit for half-life. This study suggests that a single-time-point assay is sufficient for ranking compounds in early drug discovery. It increases throughput and reduces turnaround time and cost.

Animals↗

PubMed2003

A dual luciferase multiplexed high-throughput screening platform for protein-protein interactions.

To study the biology of regulators of G-protein signaling (RGS) proteins and to facilitate the identification of small molecule modulators of RGS proteins, the authors recently developed an advanced yeast 2-hybrid (YTH) assay format for GalphaZ and RGS-Z1. Moreover, they describe the development of a multiplexed luciferase-based assay that has been successfully adapted to screen large numbers of small molecule modulators of protein-protein interactions. They generated and evaluated 2 different luciferase reporter gene systems for YTH interactions, a Gal4 responsive firefly luciferase reporter gene and a Gal4 responsive Renilla luciferase reporter gene. Both the firefly and Renilla luciferase reporter genes demonstrated a 40- to 50-fold increase in luminescence in strains expressing interacting YTH fusion proteins versus negative control strains. Because the firefly and Renilla luciferase proteins have different substrate specificity, the assays were multiplexed. The multiplexed luciferase-based YTH platform adds speed, sensitivity, simplicity, quantification, and efficiency to YTH high-throughput applications and therefore greatly facilitates the identification of small molecule modulators of protein-protein interactions as tools or potential leads for drug discovery efforts.

Dose-Response Relationship, Drug↗