Mapping Central α‑Helix Linker Mediated Conformational Transition Pathway of Calmodulin via Simple Computational Approach

The effects of intrinsic structural flexibility of calmodulin protein on the mechanism of its allosteric conformational transition are investigated in this article. Using a novel in silico approach, the conformational transition pathways of intact calmodulin as well as the isolated N- and C- terminal domains are identified and energetically characterized. It is observed that the central α-helix linker amplifies the structural flexibility of intact Ca²⁺-free calmodulin, which might facilitate the transition of the two domains. As a result, the global conformational transition of Ca²⁺-free calmodulin is initiated by the barrierless transition of two domains and proceeds through the barrier associated unwinding and bending of the central α-helix linker. The binding of Ca²⁺ cations to calmodulin further increases the structural flexibility of the C-terminal domain and results in a downhill transition pathway of which all regions transit in a concerted manner. On the other hand, the separation of the N- and C-terminal domains from calmodulin protein loses the mediating function of central α-helix linker, leading to more difficult conformational transitions of both domains. The present study provides novel insights into the correlation of the integrity of protein, the structural flexibility, and the mechanism of conformational transition of proteinlike calmodulin

MicroRNAs activate gene transcription epigenetically as an enhancer trigger

<p>MicroRNAs (miRNAs) are small non-coding RNAs that function as negative gene expression regulators. Emerging evidence shows that, except for function in the cytoplasm, miRNAs are also present in the nucleus. However, the functional significance of nuclear miRNAs remains largely undetermined. By screening miRNA database, we have identified a subset of miRNA that functions as enhancer regulators. Here, we found a set of miRNAs show gene-activation function. We focused on miR-24-1 and found that this miRNA unconventionally activates gene transcription by targeting enhancers. Consistently, the activation was completely abolished when the enhancer sequence was deleted by TALEN. Furthermore, we found that miR-24-1 activates enhancer RNA (eRNA) expression, alters histone modification, and increases the enrichment of p300 and RNA Pol II at the enhancer locus. Our results demonstrate a novel mechanism of miRNA as an enhancer trigger.</p

Summary of alignment and variation calling using SOAP3-dp and BWA with different parameters and datasets.

<p>Summary of alignment and variation calling using SOAP3-dp and BWA with different parameters and datasets.</p

Benchmarking using real reads.

<p>Benchmarking using real reads.</p

Alignment time consumption of using GPU card “GTX680” and previous generation GPU card “Tesla C2070” respectively.

<p>Alignment time consumption of using GPU card “GTX680” and previous generation GPU card “Tesla C2070” respectively.</p

The length distribution of Indels identified by SOAP3-dp and BWA respectively using full set of 100 bp paired-end YH sample reads.

<p><b>a.</b> Indels smaller than or equal to 20 bp, <b>b.</b> larger than 20 bp.</p

Comparison on 16 sets of programs and parameters using 100 bp paired-end simulated reads.

<p>Comparison on 16 sets of programs and parameters using 100 bp paired-end simulated reads.</p

Alignment workflow.

<p>For each read (paired-end specifically, single-end is only with step 1 and step 3), the alignment would be decided in at most three steps. In step 1, SOAP3-dp aligns both ends of a read-pair to the reference genome by using GPU version 2way-BWT algorithm (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065632#s4" target="_blank">Methods</a>). Pairs with only one end aligned proceed to step 2 for a GPU accelerated dynamic programming (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065632#s4" target="_blank">Methods</a>) alignment at candidate regions inferred from the aligned end. Pairs with both ends unaligned in step 1 and those ends failed in step 2 proceed to step 3 to perform a more comprehensive alignment across the whole genome until all seed hits (substrings from the read) are examined or until a sufficient number of alignments are examined.</p

The accumulated number of incorrectly aligned reads categorized at different mapping quality scores by the five aligners.

<p>The accumulated number of incorrectly aligned reads categorized at different mapping quality scores by the five aligners.</p