Biomedical subjects

Yonghui Chen

Publications and source records attributed to Yonghui Chen.

3 recordsLinked to original sources

PubMed2006

SEQOPTICS: a protein sequence clustering system.

BACKGROUND: Protein sequence clustering has been widely used as a part of the analysis of protein structure and function. In most cases single linkage or graph-based clustering algorithms have been applied. OPTICS (Ordering Points To Identify the Clustering Structure) is an attractive approach due to its emphasis on visualization of results and support for interactive work, e.g., in choosing parameters. However, OPTICS has not been used, as far as we know, for protein sequence clustering. RESULTS: In this paper, a system of clustering proteins, SEQOPTICS (SEQuence clustering with OPTICS) is demonstrated. The system is implemented with Smith-Waterman as protein distance measurement and OPTICS at its core to perform protein sequence clustering. SEQOPTICS is tested with four data sets from different data sources. Visualization of the sequence clustering structure is demonstrated as well. CONCLUSION: The system was evaluated by comparison with other existing methods. Analysis of the results demonstrates that SEQOPTICS performs better based on some evaluation criteria including Jaccard coefficient, Precision, and Recall. It is a promising protein sequence clustering method with future possible improvement on parallel computing and other protein distance measurements.

Algorithms↗

PubMed2006

Evolutionarily conserved allosteric network in the Cys loop family of ligand-gated ion channels revealed by statistical covariance analyses.

The Cys loop family of ligand-gated ion channels mediate fast synaptic transmission for communication between neurons. They are allosteric proteins, in which binding of a neurotransmitter to its binding site in the extracellular amino-terminal domain triggers structural changes in distant transmembrane domains to open a channel for ion flow. Although the locations of binding site and channel gating machinery are well defined, the structural basis of the activation pathway coupling binding and channel opening remains to be determined. In this paper, by analyzing amino acid covariance in a multiple sequence alignment, we have identified an energetically interconnected network in the Cys loop family of ligand-gated ion channels. Statistical coupling and correlated mutational analyses along with clustering revealed a highly coupled cluster. Mapping the positions in the cluster onto a three-dimensional structural model demonstrated that these highly coupled positions form an interconnected network linking experimentally identified binding domains through the coupling region to the gating machinery. In addition, these highly coupled positions are also condensed in the transmembrane domains, which are a recent focus for the sites of action of many allosteric modulators. Thus, our results revealed a genetically interconnected network that potentially plays an important role in the allosteric activation and modulation of the Cys loop family of ligand-gated ion channels.

Allosteric Regulation↗

PubMed2002

Desensitization mechanism of GABA receptors revealed by single oocyte binding and receptor function.

Prolonged exposure of most fast neurotransmitter-operated ion channels to agonist drives the receptors into a nonfunctional, or desensitized, state. Despite extensive investigation, desensitization remains a thoroughly characterized, yet poorly understood, process. Part of the difficulty in elucidating the mechanism of desensitization has been an inability to resolve the kinetics of both agonist binding and functional desensitization in the same set of operable receptors. To overcome this limitation, we applied single oocyte 3H-ligand binding and two-electrode voltage clamp to oocytes expressing recombinant alpha1beta2gamma2 GABA receptors. Using this approach, we report several observations fundamental to the mechanism of desensitization. First, we confirm that desensitization reversibly shifts GABA receptors into a high-affinity state. For [3H]GABA binding, the half-maximal binding of the desensitized state was approximately 0.040 microm. Second, we show that, upon agonist removal, this high-affinity state disappears with a time constant of 127 +/- 12 sec (n = 4), similar to the time constant for functional recovery from desensitization of 124 +/- 26 sec (n = 5). [3H]GABA, however, dissociates fourfold faster (tau = 30 +/- 2 sec; n = 3) than functional recovery, indicating that desensitized receptors need not be bound by GABA. These data provide direct evidence for a cyclical model of receptor desensitization.

Animals↗