Non-sequential protein structure alignment by conformational space annealing and local refinement.

Protein structure alignment is an important tool for studying evolutionary biology and protein modeling. A tool which intensively searches for the globally optimal non-sequential alignments is rarely found. We propose ALIGN-CSA which shows improvement in scores, such as DALI-score, SP-score, SO-score and TM-score over the benchmark set including 286 cases. We performed benchmarking of existing popular alignment scoring functions, where the dependence of the search algorithm was effectively eliminated by using ALIGN-CSA. For the benchmarking, we set the minimum block size to 4 to prevent much fragmented alignments where the biological relevance of small alignment blocks is hard to interpret. With this condition, globally optimal alignments were searched by ALIGN-CSA using the four scoring functions listed above, and TM-score is found to be the most effective in generating alignments with longer match lengths and smaller RMSD values. However, DALI-score is the most effective in generating alignments similar to the manually curated reference alignments, which implies that DALI-score is more biologically relevant score. Due to the high demand on computational resources of ALIGN-CSA, we also propose a relatively fast local refinement method, which can control the minimum block size and whether to allow the reverse alignment. ALIGN-CSA can be used to obtain much improved alignment at the cost of relatively more extensive computation. For faster alignment, we propose a refinement protocol that improves the score of a given alignment obtained by various external tools. All programs are available from http://lee.kias.re.kr

Exploring the Folding Mechanism of Small Proteins GB1 and LB1

The computational atomistic description of the folding reactions of the B1 domains, GB1 and LB1, of protein G and protein L, respectively, is an important challenge in current protein folding studies. Although the two proteins have overall very similar backbone structures (β-hairpin-α-helix-β-hairpin), their apparent folding behaviors observed experimentally were remarkably different. LB1 folds in a two-state manner with the single-exponential kinetics, whereas GB1 folds in a more complex manner with an early stage intermediate that may exist on the folding pathway. Here, we used a new method of all-atom molecular dynamics simulations to investigate the folding mechanisms of GB1 and LB1. With the Lorentzian energy term derived from the native structure, we successfully observed frequent folding and unfolding events in the simulations at a high temperature (414 K for GB1 or 393 K for LB1) for both the proteins. Three and two transition-state structures were predicted for the GB1 and LB1 folding, respectively, at the high temperature. Two of the three transition-state structures of GB1 have a better formed second β-hairpin. One of the LB1 transition states has a better formed first hairpin, and the other has both hairpins equally formed. The structural features of these transition states are in good agreement with experimental transition-state analysis. At 300 K, more complex folding processes were observed in the simulations for both the proteins. Several intermediate structures were predicted for the two proteins, which led to the conclusion that both the proteins folded through similar mechanisms. However, the intermediate state accumulated in a sufficient amount only in the GB1 folding, which led to the double-exponential feature of its folding kinetics. On the other hand, the LB1 folding kinetics were well fitted by a single-exponential function. These results are fully consistent with those previously observed experimentally

Ghrelin enhances the proliferating effect of thyroid stimulating hormone in FRTL-5 thyroid cells

Ghrelin regulates cell proliferation through the growth hormone secretagogue receptor (GHS-R). We confirmed the expression of GHS-R in FRTL-5 thyroid cells and investigated the effects of ghrelin in thyrocytes using FRTL-5 cells. Ghrelin increased intracellular calcium levels but not intracellular cyclic AMP levels. Ghrelin activated Erk within 2min, then activated Akt and STAT3. Erk phosphorylation was inhibited by the calcium inhibitor cyclopiazonic acid (CPA). Ghrelin alone did not stimulate FRTL-5 cell proliferation but enhanced the effects of thyroid stimulating hormone (TSH). Pretreatment with TSH potentiates the growth effects of ghrelin in thyroid cells, and p66Shc, a growth factor receptor adaptor protein, might mediate these synergistic effects. Ghrelin phosphorylated TSH-induced p66Shc, which was inhibited by CPA. Ghrelin did not affect the proliferation of ARO cells, which showed no increased expression of p66Shc after TSH treatment. Thus, ghrelin-induced intracellular calcium signaling enhanced the TSH-induced proliferation of thyrocytes, possibly mediated by the p66Shc pathway

Assessment of network module identification across complex diseases

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