Identification and categorization of horizontally transferred genes in prokaryotic genomes.

Horizontal gene transfer (HGT), a process through which genomes acquire genetic materials from distantly related organisms, is believed to be one of the major forces in prokaryotic genome evolution. However, systematic investigation is still scarce to clarify two basic issues about HGT: (1) what types of genes are transferred; and (2) what influence HGT events over the organization and evolution of biological pathways. Genome-scale investigations of these two issues will advance the systematical understanding of HGT in the context of prokaryotic genome evolution.

Searching for potential drug targets in two-component and phosphorelay signal-transduction systems using three-dimensional cluster analysis.

Two-component and phosphorelay signal transduction systems are central components in the virulence and antimicrobial resistance responses of a number of bacterial and fungal pathogens; in some cases, these systems are essential for bacterial growth and viability. Herein, we analyze in detail the conserved surface residue clusters in the phosphotransferase domain of histidine kinases and the regulatory domain of response regulators by using complex structure-based three-dimensional cluster analysis. We also investigate the protein-protein interactions that these residue clusters participate in.

Rational redesign of inhibitors of furin/kexin processing proteases by electrostatic mutations.

Aim: To model the three-dimensional structure and investigate the interaction mechanism of the proprotein convertase furin/kexin and their inhibitors (eglin c mutants).

Methods: The three-dimensional complex structures of furin/kexin with its inhibitors, eglin c mutants, were generated by modeller program using the newly published X-ray crystallographical structures of mouse furin and yeast kexin as templates. The electrostatic interaction energy of each complex was calculated and the results were compared with the experimentally determined inhibition constants to find the correlation between them.

Identification of the key amino acids of glial cell line-derived neurotrophic factor family receptor alpha1 involved in its biological function.

Glial cell line-derived neurotrophic factor (GDNF) plays a critical role in neurodevelopment and survival of midbrain dopaminergic and spinal motor neurons in vitro and in vivo. The biological actions of GDNF are mediated by a two-receptor complex consisting of a glycosylphosphatidylinositol-linked cell surface molecule, the GDNF family receptor alpha1 (GFRalpha1), and receptor protein tyrosine kinase Ret. Although structural analysis of GDNF has been extensively examined, less is known about the structural basis of GFRalpha1 function.

[A novel approach for peptide identification by tandem mass spectrometry].

High throughput scoring algorithms that are used to find the match of a tandem mass spectrum to a predicted mass spectrum of a peptide within a database have been applied in shotgun proteomics. However, these algorithms could produce a significant number of incorrect peptide identifications. Here a novel approach was developed to scoring tandem mass spectra against a peptide database, in which fragment ion probabilities, number of enzymatic termini of candidate peptides, matching quality and match pattern between experimental and theoretical spectrum were considered.

[Estimating coarse gene networks from yeast gene expression time series].

Gene networks is the collection of gene-gene regulatory relations at the expression level. In this study, a combined approach of the linear transcriptional modeling, identification of promoter elements and gene co-expression clustering is developed to decipher yeast gene networks from expression time series. The cell must reorganize the genomic expression to programs required for growth and survival in each environment.

[Deducing functional epitopes for GDNF proteins and its specific GFRalpha co-receptors using phylogenetic approach].

Glial cell line-derived neurotrophic factor (GDNF) has received much attention as potential therapeutic agent for the treatment of neurodegenerative diseases. It will be very important to discover the molecular mechanism of this factor and its specific GFRalpha co-receptor. Based on the principle of molecular evolution that site-specific functional importance is relevant to the pressure it undergoes under natural selection, evolutionary trace method was used to identify the functional epitopes in GDNF and GFRalpha families.

A structure-function analysis of glial cell-line-derived neurotrophic factor receptor alpha1.

The GFRalpha1 cDNA was amplified by RT-PCR from fetal rat hippocampus. The soluble recombinant GFRalpha1 and its mutants were obtained from an Escherichia coli expression system. The biological activity of soluble GFRalpha1 and its mutants were evaluated in PC12 cells.

An Assembly Algorithm for DNA Sequence with Repeats.

A program for assembling DNA fragments using a new approach has been developed. In the program, a filter and a sequence alignment are used to identify the true overlap between the two fragments. Then the fragments in repeat copies are put into a repeat contig and the others are put into nonrepeat contigs.

Predicting Binding Free Energy for Protein Complexes.

A novel empirical free energy function and a computationally more effect algorithm are applied to 21 protein complexes to predict the free energies of binding. Compared with the other works what have done in literature, better agreement between the predicted and measured binding free energies is obtained. The predicted values, are typically within 1.

Design of Protein Cores by Screening Combinatorial Sequence Library.

We have developed a new method, heterogeneous self-consistent ensemble optimization (hetero-SCEO), to select appropriate hydrophobic cores of proteins. It has been tested with five kinds of proteins: lambda-repressor, phage 434 CRO protein, interleukin-4, thioredoxin and ubiquitin. The results show that the method can be used for the de novo desigh of the hydrophobic cores of proteins.

Flexible Docking of Proteins and "Drug-like" Ligands.

By using "tabu search" algorithm and Gehlhaar potential function, a new approach is presented for flexible docking of protein and its "drug-like" ligand has been developed. Computational test for this method with a set of 100 complexes has been performed, which indicated that the deviation of 89% of the predicted complex conformation was less than 0.25 nm.

Modeling and Analysis of Structures of Phospholipase A(2)'s from Venom of Agkistrodon haly Pallas.

We have modeled three-dimensional structures of basic-acidic hybrid phospholipase A(2)-II and neutral phospholipase A(2) from venom of snake Agkistrodon halys Pallas, based on the known structures of basic and acidic phospholipase A(2)'s from the same source. We have compared these structures of phospholipase A(2)'s, explained the results of fluorescent spectrum study on the phospholipase A(2)'s and calculated the electrostatic potential maps on the catalytic active site. We suggest that the electrostatic potential around the catalytic active site of PLA(2) containing a calcium ion favors the binding of the PLA(2) to its substrate with negative charge.

Engineering Novel Functional Proteins Grafting Active Sites into Natural Scaffolds.

Engineering novel small functional proteins by grafting active sites into small but stable proteins is an efficient protein design method. Combining heterogeneous self-consistent ensemble optimization (hetero-SCEO) with 3D-motif search tool, we developed a system to accomplish such method. It is tested by transferring zinc-binding site of carbonic anhydrase form B to charybdotoxin and its efficiency is demonstrated.

The Feasibility of Using Proteome Expression Profile for Genome Annotation.

By investigating into the expression data from ECO2DBASE (Edition 6),the feasibility of using proteome expression profile for genome annotation was tested. Based on our newly developed CRC (cellular role cluster) method,79 proteins extracted from ECO2DBASE were clustered into 4 CRCs. Function related proteins tend to be clustered into same CRC.

An Evolutionary Trace Method for Functional Prediction of Genomes.

It is essential for functional genomics to develop an accurate and efficient functional prediction method of genomes. Here, a new method is suggested, that is based on the fact that ortholog-specific motif is an evolutionary trace, in which the functional prediction of genomics is carried out. First, orthologous sets in a family were constructed using evolutionary analysis then functional motifs for each orthologous set were found out and a database consisted of these motifs was built.

The Relationship between Yeast Coexpressed Gene Clusters and Their Upstream cis-acting Elements.

DNA microarrays bring biology a new approach to study functions of genes and genomes from their expression pattern on a genomic scale. With its fully sequenced genome and newly published expression patterns available, budding yeast (Saccharomyces cerevisiae) was chosen to carry out an investigation of the relationship between gene 5' upstream cis-acting elements and expression patterns using bioinformatic tools. Results show that genes in the same cluster share common cis-acting element candidates and can be regulated by same transfactors.

Reconstruction of ABC Transporter Pathways of Archaea and Comparison of Their Genomes.

Reconstruction and comparison of metabolic pathway and regulatory network is an advanced task in genome function prediction. In this study, many bioinformatic tools were employed to reconstruct all ABC transporter pathways and predict their functional features of an archaeon, Pyrococcus abyssi, on genome scale. The comparison between ABC transporter pathways of P.

Conservation and Evolution of the "Core Apoptotic Engine" Lesson from the Genome Comparison of Drosophila.

Genome comparison is the main approach to deduce regulatory network from genome sequence. Apoptotic network is one kind of typical regulatory networks. EGL1, CED3, CED4, CED9 and their homologous proteins play essential roles in apoptosis of C.

De Novo Interpretation of MS/MS Spectra and Protein Identification via Database Searching.

Peptide sequencing via tandem mass spectrometry(MS/MS)is one of the most powerful tools in proteomics to identify proteins. A new algorithm was developed for de novo interpretation of MS/MS spectra using graph theory and dynamic alignment between real spectra and theoretical spectra. The trustworthy peptides from de novo interpretation were used in protein identification via database searching.

The Spot Fitting and Expression Quantification for the Nylon Filter cDNA Microarray.

High-density cDNA microarray is important in monitoring large scalegenomic expression profile. With radiolabeled cDNA sample, nylon filter cDNA microarrays have high sensitivity and wide linear range of hybridization signals, so it can be employed to detect many important low-abundance cDNAs. However, the nylon filter tends to be randomly contaminated, and the array spots are prone to dispersion and saturation, resulting in inaccurate expression value.

Delineation of Continuous Domains in Proteins by Differences of Free Energy.

Domain is a protein architecture under proteins' tertiary structure,which can be identified in most of proteins. Different combinations of domains lead to the formation of diverse tertiary structures with diverse function for proteins. The delineation of domains for a protein is important not only conceptually but also practically.

Rational Redesign of Inhibitors of Furin/kexin Processing Proteases.

Furin/kexin processing proteases catalyze the proteolysis of large protein precursors involved in many biological processes, such as zymogen activation, peptide hormone synthesis, viral protein processing and receptor maturation, making them potential targets for therapeutic agents. Herein, homology modeling and weighted evolutionary tracing were combined to investigate the interactionmechanism of furin/kex2 with eglin C mutants. The model structures showed that there were many acidic residues in the furin (kex2) binding interface, contributing to specificity for multiple basic residues of their corresponding substrates or inhibitors.

[A evolutionary approach to identification of orthologous relationship across proteomes].

How to identify the true orthologous and paralogous relationships among protein families is still a key problem in genome annotation and comparative protemics. Here, a evolutionary approach to ascertainment of the orthologous relationships across the genomes is developed. Forty-four cases of protein families are used in the test for the evolutionary approach.

Detecting Repetitive DNA in Eukaryotes.

A detection software of repetitive elements, especially for Alu is designed according to the theory of the correspondence analysis. The results obtained on the test set of 38 gene sequences showed that the true-negative is about 5.8% and false-positive is about 4.