Periodic Forces Trigger a Complex Mechanical Response in Ubiquitin

Mechanical forces govern physiological processes in all living organisms. Many cellular forces, for example, those generated in cyclic conformational changes of biological machines, have repetitive components. In apparent contrast, little is known about how dynamic protein structures respond to periodic mechanical information. Ubiquitin is a small protein found in all eukaryotes. We developed molecular dynamics simulations to unfold single and multimeric ubiquitins with periodic forces. By using a coarse-grained representation, we were able to model forces with periods about 2 orders of magnitude longer than the protein's relaxation time. We found that even a moderate periodic force weakened the protein and shifted its unfolding pathways in a frequency- and amplitude-dependent manner. A complex dynamic response with secondary structure refolding and an increasing importance of local interactions was revealed. Importantly, repetitive forces with broadly distributed frequencies elicited very similar molecular responses compared to fixed-frequency forces. When testing the influence of pulling geometry on ubiquitin's mechanical stability, it was found that the linkage involved in the mechanical degradation of cellular proteins renders the protein remarkably insensitive to periodic forces. We also devised a complementary kinetic energy landscape model that traces these observations and explains periodic-force, single-molecule measurements. In turn, this analytical model is capable of predicting dynamic protein responses. These results provide new insights into ubiquitin mechanics and a potential mechanical role during protein degradation, as well as first frameworks for dynamic protein stability and the modeling of repetitive mechanical processes.     

Linking intronic polymorphism on the CHD1‐Z gene with fitness correlates in Black‐tailed Godwits Limosa l. limosa

We show that variation in an intronic length polymorphism in the CHD1‐Z gene in Black‐tailed Godwits Limosa l. limosa is associated with fitness correlates. This is the second example of the CHDZ‐1 gene being correlated with fitness, a previous study having established that Moorhens Gallinula chloropus carrying the rare Z* allele have reduced survival. In Godwits, however, carriers of the Z* allele (374 bp) fared better than those with the more frequent Z allele (378 bp) with respect to body mass, plumage ornamentation, reproductive parameters and habitat quality. The Z* allele was found in 14% of 251 adult birds from nature reserves, but was absent from 33 birds breeding in intensively managed agricultural lands. Males and females with the Z* allele had less extensive breeding plumage, and females had a higher body mass, bred earlier and had larger eggs. There were no significant differences in annual survival between birds with and without the Z* allele. DNA isolated from museum skins demonstrated that this polymorphism was present at low frequency in 1929. We speculate that strong asymmetrical overdominance may explain the low frequency of the Z* allele and that genetic linkage to causal genes might be an explanation for the phenotypic correlations. Our findings suggest a degree of cryptic genetic population structuring in the Dutch Godwit population.     

A phylogenomic resolution for the taxonomy of Aegean green lizards

Lacerta pamphylica and Lacerta trilineata are two currently recognized green lizard species with a historically problematic taxonomy. In cases of tangled phylogenies, next-generation sequencing and double-digest restriction-site-associated DNA protocols can provide a wealth of genomic data and resolve difficult taxonomic issues. Here, we generated genome-wide SNPs and mitochondrial sequences, and applied molecular species delimitation approaches to provide a stable taxonomy for the Aegean green lizards. Mitochondrial gene trees, genetic cluster delimitation and population structure analyses converged into recognizing the populations of (a) L. pamphylica, (b) east Aegean islands, Anatolia and Thrace (diplochondrodes lineage), (c) central Aegean islands (citrovittata), and (d) remaining Balkan populations and islands (trilineata), as separate clusters. Phylogenomic analyses revealed a split into two major clades, east and west of the Aegean Barrier, unambiguously showing a sister–clade relationship between pamphylica and diplochondrodes, rendering L. trilineata paraphyletic. Species delimitation models were tested in a Bayesian framework using the genomic SNPs: lumping all populations into a single ‘species’ had the lowest likelihood but the current taxonomy was also outperformed by all other models. All lines of evidence support the Pamphylian green lizard as a valid species; thus, east Aegean L. trilineata should also be considered a distinct species under the name Lacerta diplochondrodes. Finally, evidence from the mitochondrial and nuclear genomes is overwhelmingly in favour of recognizing the morphologically distinct Cycladian green lizards as a distinct species. We propose their elevation to full species under the name Lacerta citrovittata. All remaining insular and continental populations of the Balkan Peninsula represent the species L. trilineata.     

Changes in Prokaryote and Eukaryote Assemblages Along a Gradient of Hydrocarbon Contamination in Groundwater

Groundwater biota are particularly sensitive to environmental perturbations such as groundwater contamination. The diversity of prokaryotic and eukaryotic biota has been examined along a gradient of chlorinated hydrocarbon (CHC) contamination in the Botany Sands, an urban coastal sand-bed aquifer (Sydney, Australia). Molecular techniques were used to analyze the richness and composition of prokaryote and eukaryote assemblages using 16S and 18S rDNA, respectively. Taxon richness did not change significantly along the gradient for either prokaryotes or eukaryotes; however, significant shifts in assemblage composition were evident for both groups. Assemblage changes were most strongly correlated with concentrations of the major CHC, cis-1,2-dichloroethene, but the concentrations of a number of the contaminants were also correlated, making it difficult to infer if effects were due to any particular contaminant. The presence of cis-1,2-dichloroethene and other secondary ethenes suggests in situ breakdown of the primary CHCs via natural attenuation. The current focus of management of the Botany aquifer is to stop the contaminant plume reaching the adjoining estuary. This approach is clearly justified given the changes evident in the microbial assemblages in the groundwater, which are a likely consequence of the contamination.     

Radiation damage in the bulk and at the surface

The UK environmental e-science initiative supports the development and modification of simulation tools used to study radiation damage effects. We discuss the development and modification to the DL_POLY molecular dynamics (MD) code. Using the newly developed tools, we study the effects of radiation damage related to the safe encapsulation of highly radioactive materials, including nuclear waste. We address the possible differences between the radiation damage in the bulk and at the surface of a material, and perform MD simulations of energetic events in zircon structure. We find that in the case of readily amorphizable material, the formation of a stable alternative covalent network reduces the possible effect of the surface on the damaged structure.     

Substrate-enzyme interactions and catalytic mechanism in phospholipase C: a molecular modeling study using the GRID program.

Based on the high-resolution X-ray crystallographic structure of phospholipase C from Bacillus cereus, the orientation of the phosphatidylcholine substrate in the active site of the enzyme is proposed. The proposal is based on extensive calculations using the GRID program and molecular mechanics geometry relaxations. The substrate model has been constructed by successively placing phosphate, choline and diacylglycerol moieties in the positions indicated from GRID calculations. On the basis of the resulting orientation of a complete phosphatidylcholine molecule, we propose a mechanism for the hydrolysis of the substrate.     

Modeling of substrate and inhibitor binding to phospholipase A2.

Molecular graphics and molecular mechanics techniques have been used to study the mode of ligand binding and mechanism of action of the enzyme phospholipase A2. A substrate-enzyme complex was constructed based on the crystal structure of the apoenzyme. The complex was minimized to relieve initial strain, and the structural and energetic features of the resultant complex analyzed in detail, at the molecular and residue level. The minimized complex was then used as a basis for examining the action of the enzyme on modified substrates, binding of inhibitors to the enzyme, and possible reaction intermediate complexes. The model is compatible with the suggested mechanism of hydrolysis and with experimental data about stereoselectivity, efficiency of hydrolysis of modified substrates, and inhibitor potency. In conclusion, the model can be used as a tool in evaluating new ligands as possible substrates and in the rational design of inhibitors, for the therapeutic treatment of diseases such as rheumatoid arthritis, atherosclerosis, and asthma.     

Evolution of exceptional species richness among lineages of fleshy-fruited Myrtaceae

MethodsBayesian phylogenetic analyses of plastid and nuclear DNA sequences were used to estimate intertribal relationships and lineage divergence times in Myrtaceae. Focusing on the fleshy-fruited tribes, a variety of statistical approaches were used to assess diversification rates and diversification rate shifts across the family.ConclusionsFleshy fruits have evolved independently in Syzygieae and Myrteae, and this is accompanied by exceptional diversification rate shifts in both instances, suggesting that the evolution of fleshy fruits is a key innovation for rainforest Myrtaceae. Noting the scale dependency of this hypothesis, more complex explanations may be required to explain diversification rate shifts occurring within the fleshy-fruited tribes, and the suggested phylogenetic hypothesis provides an appropriate framework for this undertaking.     

NaV1.2 EFL domain allosterically enhances Ca2+ binding to sites I and II of WT and pathogenic calmodulin mutants bound to the channel CTD

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