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1.
J Biol Phys ; 36(2): 145-59, 2010 Mar.
Article in English | MEDLINE | ID: mdl-19728123

ABSTRACT

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

2.
J Theor Biol ; 261(1): 93-9, 2009 Nov 07.
Article in English | MEDLINE | ID: mdl-19643109

ABSTRACT

For RNA secondary structure prediction, it is an important issue that how to deal with co-transcriptional folding during the RNA synthesis in the cell. On one hand, co-transcriptional folding, leads to the correct final structure of the whole RNA molecule. On the other hand, it may form the recognition sites for the progress of the transcription. Considering the hurdles in the experimental determination of RNA folding structures, we proposed a so-called "dynamic extended folding simulation" approach. We used two human pre-mRNA samples, the first functional alpha-gene HBZ and the fifth beta-gene HBB, to "display" the co-transcriptional folding images in detail. The modeling process starts from the prediction of a 30-nucleotide (nt) sequence, then in each update 30 nts was extended, say, 1-30, 1-60, 1-90, 1-120,..., 1-1651 nts (for HBB, 1-1606 nts). We selected the RNAstructure program to predict the folding secondary structures of all the segments. We defined "hairpin" as the unit of the secondary structure and analyzed the states of such unit during the sequential dynamic extended folding processes. We found that some hairpins are "conserved", i.e., after its appearance, it always is there in the followed foldings. Some hairpins present partially in the folding segments, and some hairpins appear for only once or twice. This phenomenon vividly depicts the generation and adjusting of the temporal structural units during the co-transcriptional folding process. It is these "hairpins" that support the thermodynamically stable structure at the end of the RNA synthesis. They may also play a role in RNA splicing process and even in the folding structure of the synthesized protein.


Subject(s)
MicroRNAs/genetics , Models, Genetic , Humans , Nucleic Acid Conformation , RNA, Messenger/genetics , RNA, Small Interfering/genetics , Transcription, Genetic
3.
Wei Sheng Wu Xue Bao ; 46(6): 895-9, 2006 Dec.
Article in Chinese | MEDLINE | ID: mdl-17302150

ABSTRACT

Escherichia coli has been regarded as a model organism in the study of codon usage bias. Most studies in this organism regarding this topic have focused their mind on translation efficiency (translation speed and translation precision) . However, some genes with low codon usage bias and high expression can not be explained by translation efficiency. And some evidence of local RNA secondary structure in coding region of Escherichia coli genes have been given. All of these need explanation from a new point of view. The genomic sequence of Escherichia coli K-12 MG 1655 was obtained from GenBank. Several parameter (Nc, CAI, GC, GC3s) of 4199 genes on codon usage bias were computed. Folding tendency of mRNA coding region was represented by its average energy of 50 nucleotides. And then, relationship among mRNA coding region length, folding tendency and codon usage bias in Escherichia coli were studied. It is argued that though translation efficiency is a primary cause that shapes the codon usage bias of highly expressed genes in Escherichia coli, mRNA coding region length and folding tendency are also unneglectable factor for codon usage bias and weakening of bias. In addition, biological significance of folding tendency in mRNA coding regions was discussed.


Subject(s)
Codon , Escherichia coli/genetics , RNA, Bacterial/chemistry , RNA, Messenger/chemistry
4.
Article in Chinese | MEDLINE | ID: mdl-12545230

ABSTRACT

Based on the statistical analysis of 119 human and 92 E. coli proteins it was found that for both human and E. coli, the mRNA sequences consisting of tri-codon and tetra-codon with high translation speed preferably code for alpha helices more than for coils. For beta strand, the preference/avoidance oscillates with the translation speed. Moreover, the non-homogeneous usages of tri-codon and tetra-codon with different translation speeds in a given secondary structure have also been found. These results cannot be simply explained by the effect of stochastic fluctuation.


Subject(s)
Protein Biosynthesis/genetics , Protein Structure, Secondary , Codon/genetics , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Humans , Models, Genetic , Proteins/chemistry , Proteins/genetics , RNA, Messenger/genetics
5.
J Mol Graph Model ; 21(1): 1-2, 2002 Aug.
Article in English | MEDLINE | ID: mdl-12413025

ABSTRACT

The function of a RNA molecule relies on the underlying physical mechanisms and geometric properties in terms of secondary or tertiary structure, in which one of the most important properties is topological connectivity. RNAStudio, available at http://rnastudio.51.net, brings the convenience of Windows to the representation of RNA folding topology including the sections mentioned below.


Subject(s)
Nucleic Acid Conformation , RNA/chemistry , Software , Internet
6.
J Mol Model ; 8(7): 217-22, 2002 Jul.
Article in English | MEDLINE | ID: mdl-12192431

ABSTRACT

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by homology modeling and 1 ns restrained molecular dynamics (MD) simulation. In one only C113-C190 forms a disulfide bond (SS model); in another the potential C32-C277 disulfide bond was formed (2SS model). Analysis of the structures and averaged displacements of Calpha atoms of the N-terminal residues shows that the main differences between the SS and 2SS models lie in a region D25YDYGAPCHKFD36; in the extracellular part of the 2SS model the accessible surfaces of N12, F23, Y26, Y28 and F35 are obviously raised and a more stable H-bond net is formed. The potential energy of the 2SS-water assembly finally fluctuated around -43,020 kJ x mol(-1), which is about 302 kJ x mol(-1) lower than that of the SS-water assembly. All these results suggest that the 2SS model is more favorable. The CCR2b genes of 17 primates were sequenced and four CCR2b models for primates Ateles paniscus (A. pan), Hylobates leucogyneus(H. leu), Papio cynocephalus (P. cyn) and Trachypithecus francoist ( T. fra) were generated based on the 2SS model. A comparison of hCCR2b with primate CCR2b also supports the importance of the region D25YDYGAPCHKFD36. Electrostatic potential maps of human and primate CCR2b all display the dipolar characteristics of CCR2b with the negative pole located in the extracellular part and a strong positive pole in the cytoplasmic part. Based on the CCR2b model, we suggest that the main functional residues fall in the D25YDYGAPCHKFD36 region, and the negative electrostatic feature is a non-specific, but necessary, factor for ligands or gp120/CD4 binding.


Subject(s)
Receptors, Chemokine/chemistry , Amino Acid Sequence , Animals , Computer Simulation , Conserved Sequence , Humans , Models, Molecular , Molecular Sequence Data , Peptide Fragments/chemistry , Primates , Protein Structure, Secondary , Receptors, CCR2 , Sequence Alignment , Sequence Homology, Amino Acid , Static Electricity
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