The early adaptive evolution of calmodulin

Interaction between gene duplication and natural selection in molecular evolution was investigated utilizing a phylogenetic tree constructed by the parsimony procedure from amino acid sequences of 50 calmodulin- family protein members. The 50 sequences, belonging to seven protein lineages related by gene duplication (calmodulin itself, troponin-C, alkali and regulatory light chains of myosin, parvalbumin, intestinal calcium-binding protein, and glial S-100 phenylalanine-rich protein), came from a wide range of eukaryotic taxa and yielded a denser tree (more branch points within each lineage) than in earlier studies. Evidence obtained from the reconstructed pattern of base substitutions and deletions in these ancestral loci suggests that, during the early history of the family, selection acted as a transforming force on expressed genes among the duplicates to encode molecular sites with new or modified functions. In later stages of descent, however, selection was a conserving force that preserved the structures of many coadapted functional sites. Each branch of the family was found to have a unique average tempo of evolutionary change, apparently regulated through functional constraints. Proteins whose functions dictate multiple interaction with several other macromolecules evolved more slowly than those which display fewer protein-protein and protein-ion interactions, e.g., calmodulin and next troponin-C evolved at the slowest average rates, whereas parvalbumin evolved at the fastest. The history of all lineages, however, appears to be characterized by rapid rates of evolutionary change in earlier periods, followed by slower rates in more recent periods. A particularly sharp contrast between such fast and slow rates is found in the evolution of calmodulin, whose rate of change in earlier eukaryotes was manyfold faster than the average rate over the past 1 billion years. In fact, the amino acid replacements in the nascent calmodulin lineage occurred at residue positions that in extant metazoans are largely invariable, lending further support to the Darwinian hypothesis that natural selection is both a creative and a conserving force in molecular evolution.      

A blood based 12-miRNA signature of Alzheimer disease patients

Background

Alzheimer disease (AD) is the most common form of dementia but the identification of reliable, early and non-invasive biomarkers remains a major challenge. We present a novel miRNA-based signature for detecting AD from blood samples.

Results

We apply next-generation sequencing to miRNAs from blood samples of 48 AD patients and 22 unaffected controls, yielding a total of 140 unique mature miRNAs with significantly changed expression levels. Of these, 82 have higher and 58 have lower abundance in AD patient samples. We selected a panel of 12 miRNAs for an RT-qPCR analysis on a larger cohort of 202 samples, comprising not only AD patients and healthy controls but also patients with other CNS illnesses. These included mild cognitive impairment, which is assumed to represent a transitional period before the development of AD, as well as multiple sclerosis, Parkinson disease, major depression, bipolar disorder and schizophrenia. miRNA target enrichment analysis of the selected 12 miRNAs indicates an involvement of miRNAs in nervous system development, neuron projection, neuron projection development and neuron projection morphogenesis. Using this 12-miRNA signature, we differentiate between AD and controls with an accuracy of 93%, a specificity of 95% and a sensitivity of 92%. The differentiation of AD from other neurological diseases is possible with accuracies between 74% and 78%. The differentiation of the other CNS disorders from controls yields even higher accuracies.

Conclusions

The data indicate that deregulated miRNAs in blood might be used as biomarkers in the diagnosis of AD or other neurological diseases.     

The existence of a second allosteric site on the M1 muscarinic acetylcholine receptor and its implications for drug design

Fully flexible docking of KT5720, an allosteric modulator of the muscarinic receptors, was performed on a dynamic model of the M(1) muscarinic acetylcholine receptor. The results confirmed the existence of a second allosteric site, located on the intracellular face of the receptor. These results would be beneficial for the design of modulators of this receptor to be used as an effective alternative against the Alzheimer's disease.     

Homology modeling and flex-ligand docking studies on the guinea pig β2 adrenoceptor: structural and experimental similarities/ differences with the human β2

The trachea of a guinea pig is widely used in drug development assays focused on the treatment of pulmonary diseases. Some of these drugs relax the airways by binding to the guinea pig β₂-adrenoceptor (Gβ₂AR). In this work, the amino acid sequence of the Gβ₂AR was searched to carry out homology modeling, using the Swiss-Model server, with the human β₂AR as the parent template. The Gβ₂AR 3-D structure was structurally and energetically optimized in vacuo using NAMD 2.6 program. The refined 3-D model obtained was used for further study. Molecular docking simulations were performed by testing a set of well-known β₂AR ligands using the AutoDock 3.0.5 program. The results show that the homology model of Gβ₂AR has a 3-D structure very similar to the crystal structure of recently studied human β₂AR. This was also corroborated by identity (94.23%), Ramachandran map, and docking results. The theoretical simulation showed that the ligands bind at sites that are similar to those reported for the human β₂AR. The R-enantiomer ligands showed correlation with in vitro data. We have obtained a Gβ₂AR 3-D model which can be used to carry out computational screening as a complementary tool during the drug design and experimental tests under guinea pig models.     

Design,synthesis and in vitro evaluation of (R)-4-(2-(tert-butylamino)-1-hydroxyethyl)-2-(hydroxymethyl)phenyl hydrogen phenylboronate: A novel salbutamol derivative with high intrinsic efficacy on the β2 adrenoceptor

We tested a set of boron containing arylethanolamine derivatives on the human and guinea pig β₂ adrenoceptor (β₂AR) 3-D structures by docking methodology. The compound with the highest affinity based on docking analysis, (R)-4-(2-(tert-butylamino)-1-hydroxyethyl)-2-(hydroxymethyl)phenyl hydrogen phenylboronate (boronterol) was synthesized, characterized and tested in guinea pig tracheal rings at basal tone and with histamine-induced contractions. Boronterol was at least eightfold more potent than salbutamol as a smooth muscle relaxant drug (judged by the EC₅₀ values) and showed a similar maximal relaxant effect as isoproterenol. ICI118,551 showed competitive antagonism on the relaxing effect of boronterol. These results suggest the β₂AR agonist action of boronterol.     

Homology model and docking studies on porcine β<Subscript>2</Subscript> adrenoceptor: description of two binding sites

The affinity of the classical β₂ adrenoceptor-selective inverse agonist ICI118,551 is notoriously lower for porcine β₂ adrenoceptors (p₂βAR) than for human β₂ adrenoceptors (hβ₂AR) but molecular mechanisms for this difference are still unclear. Homology 3-D models of pβ₂AR can be useful in predicting similarities and differences, which might in turn increase the comparative understanding of ligand interactions with the hβ₂AR. In this work, the pβ₂AR amino acid sequence was used to carry out homology modeling. The selected pβ₂AR 3-D structure was structurally and energetically optimized and used as a model for further theoretical study. The homology model of pβ₂AR has a 3-D structure very similar to the crystal structures of recently studied hβ₂AR. This was also corroborated by sequence identity, RMSD, Ramachandran map, TM-score and docking results. Upon performing molecular docking simulations with the AutoDock4.0.1 program on pβ₂AR, it was found that a set of well-known β₂AR ligands reach two distinct binding sites on pβ₂AR. Whereas one of these sites is similar to that reported on the hβ₂AR crystal structure, the other can explain some important experimental observations. Additionally, the theoretical affinity estimated for ICI118,551 closely agrees with affinities estimated from experimental in vitro data. The experimental differences between the human/porcine β₂ARs in relation to ligand affinity can in part be elucidated by observations in this molecular modeling study.