Biomedical subjects

Chao Tang

Publications and source records attributed to Chao Tang.

At least 19 recordsLinked to original sources

PubMed2006

Robustness and modular design of the Drosophila segment polarity network.

Biomolecular networks have to perform their functions robustly. A robust function may have preferences in the topological structures of the underlying network. We carried out an exhaustive computational analysis on network topologies in relation to a patterning function in Drosophila embryogenesis. We found that whereas the vast majority of topologies can either not perform the required function or only do so very fragilely, a small fraction of topologies emerges as particularly robust for the function. The topology adopted by Drosophila, that of the segment polarity network, is a top ranking one among all topologies with no direct autoregulation. Furthermore, we found that all robust topologies are modular-each being a combination of three kinds of modules. These modules can be traced back to three subfunctions of the patterning function, and their combinations provide a combinatorial variability for the robust topologies. Our results suggest that the requirement of functional robustness drastically reduces the choices of viable topology to a limited set of modular combinations among which nature optimizes its choice under evolutionary and other biological constraints.

Animals↗

PubMed2006

Dynamic studies of scaffold-dependent mating pathway in yeast.

The mating pathway in Saccharomyces cerevisiae is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and the mitogen-activated protein kinase (MAPK) cascade. According to current understanding of the mating pathway, we construct a system of ordinary differential equations to describe the process. Our model is consistent with a wide range of experiments, indicating that it captures some main characteristics of the signal transduction along the pathway. Investigation with the model reveals that the shuttling of the scaffold protein and the dephosphorylation of kinases involved in the MAPK cascade cooperate to regulate the response upon pheromone induction and to help preserve the fidelity of the mating signaling. We explored factors affecting the dose-response curves of this pathway and found that both negative feedback and concentrations of the proteins involved in the MAPK cascade play crucial roles. Contrary to some other MAPK systems where signaling sensitivity is being amplified successively along the cascade, here the mating signal is transmitted through the cascade in an almost linear fashion.

Biophysics↗

PubMed2006

Facile synthesis of complicated 9,9-diarylfluorenes based on BF3.Et2O-mediated Friedel-Crafts reaction.

[reaction: see text] BF3.OEt2-mediated Friedel-Crafts reaction of 9-phenyl-fluoren-9-ol with electron-rich aromatic substrates to prepare a new family of complicated 9,9-diarylfluorenes is described. The 9,9-diarylfluorenes tethered with various functional substituents, e.g., bulky spiro units, hole-transporting moieties, and fluorescent dyes, will be promising building blocks for the construction of optoelectronic materials.

Journal Article↗

PubMed2006

Unexpected one-pot method to synthesize spiro[fluorene-9,9'-xanthene] building blocks for blue-light-emitting materials.

[reaction: see text] An unexpected one-pot synthetic approach toward spiro[fluorene-9,9'-xanthene] (SFX) under excessive MeSO(3)H conditions has been developed. The key step involves a thermodynamically controlled cyclization reaction. Blue-light-emitting materials based on SFX building blocks that exhibit high thermal stability have also been synthesized.

Journal Article↗

PubMed2006

Novel h-shaped persistent architecture based on a dispiro building block system.

[structure: see text] A novel dispiro building block, dispiro[fluorene-9,5'(7'H)-diindeno[2,1-b:1',2'-d]thiophene-7',9' '-fluorene], and its two derivatives, TBP-DSFDITF and TDOF-DSFDITF, were designed and synthesized. Because of the rigidity and orthogonality of the spiro structure, TBP-DSFDITF exhibits a well-defined H-shaped architecture, which consists of two ter(biphenyls) as the arms of the H-shape and 3,4-diphenylthiophene as the rung, connecting via completely rigid dispiro linkages with two sp(3) carbon atoms.

Journal Article↗

PubMed2005

Gibbs sampling and helix-cap motifs.

Protein backbones have characteristic secondary structures, including alpha-helices and beta-sheets. Which structure is adopted locally is strongly biased by the local amino acid sequence of the protein. Accurate (probabilistic) mappings from sequence to structure are valuable for both secondary-structure prediction and protein design. For the case of alpha-helix caps, we test whether the information content of the sequence-structure mapping can be self-consistently improved by using a relaxed definition of the structure. We derive helix-cap sequence motifs using database helix assignments for proteins of known structure. These motifs are refined using Gibbs sampling in competition with a null motif. Then Gibbs sampling is repeated, allowing for frameshifts of +/-1 amino acid residue, in order to find sequence motifs of higher total information content. All helix-cap motifs were found to have good generalization capability, as judged by training on a small set of non-redundant proteins and testing on a larger set. For overall prediction purposes, frameshift motifs using all training examples yielded the best results. Frameshift motifs using a fraction of all training examples performed best in terms of true positives among top predictions. However, motifs without frameshifts also performed well, despite a roughly one-third lower total information content.

Algorithms↗

PubMed2005

Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant.

Trypsin and chymotrypsin are both serine proteases with high sequence and structural similarities, but with different substrate specificity. Previous experiments have demonstrated the critical role of the two loops outside the binding pocket in controlling the specificity of the two enzymes. To understand the mechanism of such a control of specificity by distant loops, we have used the Gaussian network model to study the dynamic properties of trypsin and chymotrypsin and the roles played by the two loops. A clustering method was introduced to analyze the correlated motions of residues. We have found that trypsin and chymotrypsin have distinct dynamic signatures in the two loop regions, which are in turn highly correlated with motions of certain residues in the binding pockets. Interestingly, replacing the two loops of trypsin with those of chymotrypsin changes the motion style of trypsin to chymotrypsin-like, whereas the same experimental replacement was shown necessary to make trypsin have chymotrypsin's enzyme specificity and activity. These results suggest that the cooperative motions of the two loops and the substrate-binding sites contribute to the activity and substrate specificity of trypsin and chymotrypsin.

Amino Acid Sequence↗

PubMed2005

[Influence of hypoxia on leptin and leptin receptor gene expression of C57BL/6J mice].

OBJECTIVE: To investigate the influence of hypoxia on leptin and leptin receptor gene expression of C57BL/6J mice. METHODS: C57BL/6J mice, exposed to hypoxia in the man-made auto pressure and hypoxia control cabin (XQ-I), were divided into 3 groups: the normal control group, 24 h hypoxia group and 48 h hypoxia group. Reverse transcription-polymerase chain reaction (RT-PCR) was used to measure the mRNA levels of leptin and leptin receptor. RESULTS: (1) Compared with the normal control group (0.508 +/- 0.207), the leptin mRNA level of 24 h hypoxia group (0.903 +/- 0.190) and 48 h hypoxia group (0.856 +/- 0.336) were up-regulated markedly (all < 0.05); (2) Compared with the normal control group (Ra 0.630, Rb 0.258 +/- 0.049, Rc 0.133), the Ra, Rb, Rc mRNA levels of 24 h hypoxia group (Ra 0.724, Rb 0.381 +/- 0.038, Rc 0.299) and 48 h hypoxia group (Ra 0.700, Rb 0.345 +/- 0.042, Rc 0.292) were up-regulated to different degrees. CONCLUSIONS: As an independent factor, hypoxia can stimulate increased expression of leptin, leptin receptor Ra, Rb, Rc mRNA. It is suggested that leptin play an important role in positive regulation of respiratory function.

Adipose Tissue↗

PubMed2004

Flexibility of beta-sheets: principal component analysis of database protein structures.

Protein folds are built primarily from the packing together of two types of structures: alpha-helices and beta-sheets. Neither structure is rigid, and the flexibility of helices and sheets is often important in determining the final fold (e.g., coiled coils and beta-barrels). Recent work has quantified the flexibility of alpha-helices using a principal component analysis (PCA) of database helical structures (J. Mol. Bio. 2003, 327, pp. 229-237). Here, we extend the analysis to beta-sheet flexibility using PCA on a database of beta-sheet structures. For sheets of varying dimension and geometry, we find two dominant modes of flexibility: twist and bend. The distributions of amplitudes for these modes are found to be Gaussian and independent, suggesting that the PCA twist and bend modes can be identified as the soft elastic normal modes of sheets. We consider the scaling of mode eigenvalues with sheet size and find that parallel beta-sheets are more rigid than antiparallel sheets over the entire range studied. Finally, we discuss the application of our PCA results to modeling and design of beta-sheet proteins.

Databases, Protein↗

PubMed2004

The yeast cell-cycle network is robustly designed.

The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle regulatory network of the budding yeast. With the use of a simple dynamical model, it was demonstrated that the cell-cycle network is extremely stable and robust for its function. The biological stationary state, the G1 state, is a global attractor of the dynamics. The biological pathway, the cell-cycle sequence of protein states, is a globally attracting trajectory of the dynamics. These properties are largely preserved with respect to small perturbations to the network. These results suggest that cellular regulatory networks are robustly designed for their functions.

Cell Cycle↗

PubMed2004

Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins.

Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tend to occur at the surface of a folded protein. By analyzing the known protein structures, we quantify the degree to which the hydrophobicity sequence of a protein correlates with its pattern of surface exposure. We have assessed the statistical significance of this correlation for several hydrophobicity scales in the literature, and find that the computed correlations are significant but far from optimal. We show that this less than optimal correlation arises primarily from the large degree of mutations that naturally occurring proteins can tolerate. Lesser effects are due in part to forces other than hydrophobicity, and we quantify this by analyzing the surface-exposure distributions of all amino acids. Lastly, we show that our database findings are consistent with those found from an off-lattice hydrophobic-polar model of protein folding.

Algorithms↗

PubMed2004

Simulation and analysis of in vitro DNA evolution.

We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic simulations of evolution starting from a single DNA sequence. Varying the evolution parameters reveals three different regimes characterized by distinct evolutionary behaviors, and for each regime we find analytical estimates which agree well with simulation results. We also study how the details of the DNA-protein interaction affect the evolution.

DNA↗

PubMed2003

Ideal observer analysis of the development of spatial contrast sensitivity in macaque monkeys.

To explore the factors limiting the development of visual sensitivity, we constructed an ideal observer model for the infant macaque visual system. We made measurements of retinal morphology in infant and adult macaque monkeys, and used the data in combination with published optical data to formulate the model. We compared the ideal observer's ability to detect low-contrast gratings presented either in isolation or in spatiotemporal noise with behavioral data obtained under matched conditions. The ideal observer showed some improvement in visual performance up to the age of 4 weeks, but little change thereafter. Behavioral data show extensive changes over the ages 5-50 wk, after the ideal observer's performance has become asymptotic. We conclude that the development of visual sensitivity in infant monkeys is not limited by changes in the front-end factors captured by the ideal observer model, at least after the age of 5 weeks. Using noise masking, we also estimated the variability of neural processing in comparison with the photon noise-limited ideal. We found that both additive and multiplicative components of this variability are elevated in infant monkeys, and improve (though not to ideal levels) during development. We believe that these changes all reflect maturation of visual processing in cortical circuits, and that no aspect of visual performance in the regime we studied is limited by the properties of the retina and photoreceptors, either in infant or in adult animals.

Animals↗

PubMed2003

Statistical mechanics of RNA folding: importance of alphabet size.

We construct a base-stacking model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four- or six-letter alphabets. With only two kinds of bases, most sequences have many alternative folding configurations and are consequently thermally unstable. Stable ground states are found only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.

Base Composition↗

PubMed2003

Flexibility of alpha-helices: results of a statistical analysis of database protein structures.

Alpha-helices stand out as common and relatively invariant secondary structural elements of proteins. However, alpha-helices are not rigid bodies and their deformations can be significant in protein function (e.g. coiled coils). To quantify the flexibility of alpha-helices we have performed a structural principal-component analysis of helices of different lengths from a representative set of protein folds in the Protein Data Bank. We find three dominant modes of flexibility: two degenerate bend modes and one twist mode. The data are consistent with independent Gaussian distributions for each mode. The mode eigenvalues, which measure flexibility, follow simple scaling forms as a function of helix length. The dominant bend and twist modes and their harmonics are reproduced by a simple spring model, which incorporates hydrogen-bonding and excluded volume. As an application, we examine the amount of bend and twist in helices making up all coiled-coil proteins in SCOP. Incorporation of alpha-helix flexibility into structure refinement and design is discussed.

Databases, Protein↗

PubMed2002

Designability of protein structures: a lattice-model study using the Miyazawa-Jernigan matrix.

We study the designability of all compact 3 x 3 x 3 and 6 x 6 lattice-protein structures using the Miyazawa-Jernigan (MJ) matrix. The designability of a structure is the number of sequences that design the structure, i.e., sequences that have that structure as their unique lowest-energy state. Previous studies of hydrophobic-polar (HP) models showed a wide distribution of structure designabilities. Recently, questions were raised concerning the use of a two-letter (HP) code in such studies. Here, we calculate designabilities using all 20 amino acids, with empirically determined interaction potentials (MJ matrix) and compare with HP model results. We find good qualitative agreement between the two models. In particular, highly designable structures in the HP model are also highly designable in the MJ model-and vice versa-with the associated sequences having enhanced thermodynamic stability.

Amino Acids↗

PubMed2002

Designability of alpha-helical proteins.

A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested on structures composed of four alpha-helices connected by short turns. All such natural four-helix bundles that are connected by short turns seen in nature are reproduced to closer than 3.6 A per residue within the ensemble. Because structures with no natural counterpart may be targets for ab initio structure design, the designability of each structure in the ensemble-defined as the number of sequences with that structure as their lowest-energy state-is evaluated using a hydrophobic energy. For the case of four alpha-helices, a small set of highly designable structures emerges, most of which have an analog among the known four-helix fold families; however, several packings and topologies with no analogs in protein database are identified.

Amino Acid Sequence↗

PubMed2002

Emergence of highly designable protein-backbone conformations in an off-lattice model.

Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally suitable for design. Rather, certain structures are distinguished by unusually high designability: the number of amino acid sequences for which they represent the unique lowest energy state; sequences associated with such structures possess both robustness to mutation and thermodynamic stability. Here we report that highly designable backbone conformations also emerge in a realistic off-lattice model. The highly designable conformations of a chain of 23 amino acids are identified and found to be remarkably insensitive to model parameters. Although some of these conformations correspond closely to known natural protein folds, such as the zinc finger and the helix-turn-helix motifs, others do not resemble known folds and may be candidates for novel fold design.

Amino Acid Motifs↗