Bioinformatics analysis of copalyl diphosphate synthase in Salviae Miltiorrhizae Radix et Rhizoma / 中草药

To provide the useful information for the further study of copalyl diphosphate synthase (CPS) of Salviae Miltiorrhizae Radix et Rhizoma through amino acid (aa) sequences comparison in S. miltiorrhiza and other plants. Bioinformatics analysis methods were used to perform the prediction of composition and physicochemical character, leader peptide, signal peptide, transmembrane domain, hydrophobicity/hydrophilicity, secondary structure, tertiary structure, and functional domain of 18 CPS amino acid sequences in S. miltiorrhiza and other different plants which belong to 16 species and 13 families. Homology analysis and phylogenetic trees of CPS were also carried out. Most CPS proteins contain more than 730 aa. Their molecular weight is approximately 91 610 and the isoelectric point of them is about 5.87, which suggests that CPS is acidic protein. The results of the sequence structure prediction show that CPS has apparent hydrophobic region and hydrophilicity region, no signal peptide, no transmembrane domain, and may probably have chloroplast transit peptide. The main secondary structures of the proteins are α-helix and random coil. Homology analysis reveals that S. miltiorrhiza has the highest homology comparied with Rosmarinus officinalis and Scoparia dulcis. This work provides a systemic sequence analysis of CPS in S. miltiorrhiza and other plants. It will provide the useful information for CPS studies in the future.

Determination of low-energy structures of a small RNA hairpin using Monte Carlo–based techniques.

The energy landscape of RNA is known to be extremely rugged, and hence finding low-energy structures starting from a random structure is a challenging task for any optimization algorithm. In the current work, we have investigated the ability of one Monte Carlo–based optimization algorithm, Temperature Basin Paving, to explore the energy landscape of a small RNA T-loop hairpin. In this method, the history of the simulation is used to increase the probability of states less visited in the simulation. It has been found that using both energy and end-to-end distance as the biasing parameters in the simulation, the partially folded structure of the hairpin starting from random structures could be obtained.

Predicción computacional de estructura terciaria de las proteínas humanas Hsp27, αB-cristalina y HspB8 / Computational prediction of tertiary structure of the human proteins Hsp27, αB-crystalline and HspB8 / Predição computacional da estrutura terciária das proteínas humanas Hsp27, αB-cristalina e HspB8

Objetivo. Realizar predicciones computacionales de estructura de las proteínas humanas Hsp27, αB cristalina y HspB8. Materiales y métodos. La predicción de la estructura secundaria se obtuvo mediante un consenso de los programas de predicción secundaria GOR 4, nnPred, Sspro, APSSP2, JPredict, Porter, Prof, SOPMA, HNN y Psi-Pred. Los modelos de estructura terciaria se elaboraron a partir de fragmentos homólogos de proteínas con estructura terciaria conocida que fueron obtenidos por múltiples alineamientos. Empleando la secuencia primaria se obtuvieron perfiles de antigenicidad de las proteínas nativas y fueron analizados los perfiles de hidrofobicidad, polaridad, flexibilidad, accesibilidad tanto de las proteínas nativas como de las mutadas. Resultados. Las predicciones de estructura secundaria y terciaria de las proteínas estudiadas muestran que en los tres casos, más del 65% son regiones en coil, 20-25% en hoja plegada y menos del 10% en alfa hélice. Los análisis de estructura primaria muestran que al menos uno de los perfiles estudiados, en cada mutación está alterado. Conclusiones. Los análisis comparativos de estructura sugieren que las mutaciones afectan la solubilidad de las proteínas mutadas y con ello su función como chaperonas moleculares.

Objective: To make computational predictions of the structure of the human proteins Hsp27, αB-crystalline and HspB8. Materials and methods. The prediction of the secondary structure was obtained by a consensus of the programs for secondary prediction GOR 4, nnPred, Sspro, APSSP2, JPredict, Porter, Prof, SOPMA, HNN and Psi-Pred. The models of tertiary structure were built from fragments homologous to proteins with tertiary known structure that were obtained by multiple alignments. Using the primary sequence we obtained the antigenicity profiles of native proteins and we analyzed the profiles of hydrophobicity, polarity, flexibility and accessibility of both native and mutant proteins. Results. Predictions of the secondary and tertiary structures of the studied proteins show that in the three cases, more than 65% are coil regions, 20-25% are folded sheet and less than 10% are alpha helix. Analyses of the primary structure show that at least one of the studied profiles in every mutation is altered. Conclusions. The comparative analyses of structure suggest that mutations affect the solubility of the mutated proteins and hence affect their function as molecular chaperones.

Objetivo. Realizar predições computacionais da estrutura das proteínas humanas Hsp27, αB-cristalina e HspB8. Materiais e métodos. A predição da estrutura secundária foi obtida através de um consenso dos programas de predição secundária GOR 4, nnPred, Sspro, APSSP2, JPredict, Porter, Prof, SOPMA, HNN e Psi-Pred. Os modelos de estrutura terciária foram desenvolvidos a partir de fragmentos homólogos de proteínas com estrutura terciária conhecida que foram obtidos por alinhamentos múltiplos. Utilizando a seqüência primária foram obtidos perfis de antigenicidade das proteínas nativas e foram analisados os perfis de hidrofobicidade, polaridade, flexibilidade e acessibilidade, tanto da proteína nativa, como das mutantes. Resultados. As predições de estrutura secundária e terciária das proteínas estudadas mostram que nos três casos, mais de 65% são regiões em coil, 20-25% de folha pregueada e inferior a 10% em alfa-hélice. A análise da estrutura primária mostra que pelo menos um dos perfis estudados, em cada mutação está alterado. Conclusões. A análise comparativa da estrutura sugere que as mutações afetam a solubilidade das proteínas mutantes e, assim, sua função como chaperones moleculares.

Homology Modeling for the Structure of the Soluble Segment of TRAIL / 中国肿瘤生物治疗杂志

Objective: In order to further investigate the structural/functional relationship of TRALL. Methods: We did homology modeling for the extracellular segment of TRAIL, which is from R117 to G281, totally 165 aa residues long. The modeling software is Insight II from MSI/Biosym and the modeling work is based on the three dimensional structure of TNF-?. Results: From the modeling result, it can be seen that the modeled structure of TRAIL contains 10 ?-sheets and homologs for all these sheets could be found in TNF-?. This just confirms with the principle that the structurally con-seived regions within molecules of the same structure family should experience relatively small sequence mutations. In addition, the credibility of the modeled structure is checked by the way of inverse folding from Profile-3D. Conclusion: The result shows modeled structure is generally correct.