Biomedical subjects

Da-Fu Ding

Publications and source records attributed to Da-Fu Ding.

At least 19 recordsLinked to original sources

PubMed2003

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. The results suggest that the central domain of GFRalpha1 is a crucial determinant for ligand binding. This established a solid basis for further study to find the key amino acid mediating the binding of GDNF and GFRalpha1.

Amino Acid Sequence↗

PubMed2003

[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. Some trace residues had been proved to be important in ligand-receptor binding, especially in rat GFRalpha1, where alanine scanning mutagenesis confirmed that sites N(152)N(153), R(259), S(316)N(317)S(318) and Q(247)D(248)S(249) were critical for GFRalpha1 binding to GDNF or Ret and thus affected the formation of GDNF-GFRalpha1-Ret complex.

Animals↗

PubMed2003

[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. The expression of many genes is regulated by environmental stress. The products of many genes that induced in the environmental stress are involved in metabolism of carbohydrates, structural repairs and even sporulation. Interestingly, it is identified that transcription factors Mcm1 and Dal82 matched their binding sites TT[bond]CC[triple bond]T[double bond]GGAAA and TGAAAAWTTT in cell cycle progression and environmental stress response, respectively. These conclusions agree with the known observations. The results indicate that the approach may be useful for modeling gene networks from microarray data.

Cell Cycle↗

PubMed2003

[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. Benchmarking the novel scorer on a large set of experimental MS/MS spectra, it is demonstrated that PepSearch performs significantly better than the widely used software SEQUEST. The PepSearch software is available at http://compbio.sibsnet.org/projects/pepsearch.

Databases, Protein↗

PubMed2002

[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. Compared with the method of COG (cluster of orthologous groups of proteins), this approach can generally identify the orthologous relationships and accurately predict the genome function.

Animals↗

PubMed2001

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. Besides, some rational explanations were presented for the different inhibitor/substrate specificity of the furin/kexin members by combining the model structures with results of evolutionary tracing. Based on these analyses,an attempt was made to rationally redesign the eglin C by interface engineering with heterogeneous self-consistent ensemble optimization to improve its inhibitory specificity on furin/kex2. With the model complex structures of furin/kex2 and eglin C variants as structural templates, the P(1), P(2) and P(4) of eglin C were redesigned, respectively. The design results show that both furin and kex2 favored basic residues at P(1), P(2) and P(4) in eglin C, in good agreement with the experimental data. The detection of many specific residues in S' part of furin/kexin sequences made possible designing inhibitors with high specific binding to furin and kex2, respectively. As for furin, the best inhibitor designed was eglin C-P(2)'Glu-P(3)'Asp-P(4)'Arg (only these three positions were shown), while the best eglin C variant for kex2 designed was P(2)'Arg-P(3)'Arg-P(4)'Glu. The structures show that furin and kex2 form distinct interactions with these two eglin C variants. Herein, a strategy was proposed that combine homology modeling, evolutionary tracing and rational interface redesign to investigate enzyme-inhibitor interactions and inhibitor engineering. This computational design gives some rational guidance to further experimental inhibitor engineering.

Journal Article↗

PubMed2001

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. Unfortunately, up to now there is not an ideal means to achieve that. This paper proposes a method for domain delineation based on the maximum refolding free energy. The criteria are more or less objective. By using this method, 50 proteins are analyzed. The boundaries for most proteins agree with the data reported in literature. There are a few examples that seem more reasonable, although they are not identical with those in literature.

Journal Article↗

PubMed2001

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. Based on aphysical model, we address a novel treatment with accurate positioning, complement of saturation and correction of interference. Thus the accurate quantificati on of expression can be extracted with remarkably improved reproducibility.

Journal Article↗

PubMed2000

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. A high throughput statistical analysis of SwissProt and TrEMBL protein databases showed that it's enough to identify a protein in database with three sequence tags of four amino acid residues, two sequence tags of five amino acid residues or one sequence tag of eight amino acid residues.

Journal Article↗

PubMed2000

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.elegans and mammals, and were regarded as the components of the"core apoptotic engine". But in fruit fly, Drosophila melanogaster, this network is incomplete. A series of bioinformatic analyses found the lost chains of "core apoptotic engine" by discovering two homologues of BCL2/CED9 and one of EGL1 in fruit fly genome sequences. These findings proved that the "core apoptotic engine" is indeed widely conserved among multicellular organisms and the evolutionary complexity of this network of Drosophila is between that of C.elegans and mammals.

Journal Article↗

PubMed2000

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.abyssi and those of another archaeon, M.jannaschii, revealed that there was no peptide uptake ABC transporter system in M.jannaschii. This may result from their different metabolic types.

Journal Article↗

PubMed1999

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. In the sites found by this study, some sites are corresponding to known cis-acting elements, while others may indicate new ones that can be tested by experiments. The results are helpful to understand more about gene functions, metabolic pathways and genetic networks.

Journal Article↗

PubMed1999

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. When this database is completed, unknown genes can be predicted accurately and quickly by searching it. The pilot study on five families proves that our method is feasible.

Journal Article↗

PubMed1999

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. Total 9 aminoacyl-tRNA synthetases were clustered into CRC2, whereas 4 heat-shock proteins into CRC3. These results indicate with enough proteome expression data and the efficient algorithm, proteome expression profile can provide very important information for genome annotation, while this kind of information is sequence-independent.

Journal Article↗

PubMed1999

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.

Journal Article↗

PubMed1999

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.

Journal Article↗

PubMed1998

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. Compared with GOLD, a program of genetic algorithm, our method has high accuracy, low limit and short computation time.

Journal Article↗

PubMed1998

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.

Journal Article↗