Cold-active enzymes studied by comparative molecular dynamics simulation

Enzymes from cold-adapted species are significantly more active at low temperatures, even those close to zero Celsius, but the rationale of this adaptation is complex and relatively poorly understood. It is commonly stated that there is a relationship between the flexibility of an enzyme and its catalytic activity at low temperature. This paper gives the results of a study using molecular dynamics simulations performed for five pairs of enzymes, each pair comprising a cold-active enzyme plus its mesophilic or thermophilic counterpart. The enzyme pairs included α-amylase, citrate synthase, malate dehydrogenase, alkaline protease and xylanase. Numerous sites with elevated flexibility were observed in all enzymes; however, differences in flexibilities were not striking. Nevertheless, amino acid residues common in both enzymes of a pair (not present in insertions of a structure alignment) are generally more flexible in the cold-active enzymes. The further application of principle component analysis to the protein dynamics revealed that there are differences in the rate and/or extent of opening and closing of the active sites. The results indicate that protein dynamics play an important role in catalytic processes where structural rearrangements, such as those required for active site access by substrate, are involved. They also support the notion that cold adaptation may have evolved by selective changes in regions of enzyme structure rather than in global change to the whole protein. Figure Collective motions in C^α atoms of the active site of cold-active xylanase Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

N-demethylation of p-chloro-N-methylaniline catalyzed by subcellular fractions from the avocado pear (Persea americana)

Subcellular fractions from the avocado pear ( Persea americana) catalyzed formation of p-chloroaniline from p-chloro-N-methylaniline. Fractions prepared by centrifugation of avocado homogenates at 20, 000g for 20 min formed p-chloroaniline (2900 +/- 500 pmol min-1 mg protein-1) with an NADPH-generating system. p-Chloroaniline formation required reduced pyridine nucleotide (NADPH was 6-7 times more effective than NADH) and O2. N-Demethylation was inhibited by CO (55% inhibition at CO:O2 = 1) and was not inhibited by CN. Cytochrome P-450 was detected in the 20, 000g pellet at levels of 300-380 pmol/mg protein. This particulate preparation was also active in catalyzing the NADPH-dependent epoxidation of the chlorinated cyclodiene aldrin. Improvements to a colorimetric procedure for measuring p-chloroaniline increased the sensitivity of the procedure fourfold, and allowed use of samples containing high amounts of lipid. Avocado pear is suitable tissue for further studies on the oxidation of foreign compounds by higher plants.     

Analysis of stable states in global savannas: is the CART pulling the horse?

Multiple stable states, bifurcations and thresholds are fashionable concepts in the ecological literature, a recognition that complex ecosystems may at times exhibit the interesting dynamic behaviours predicted by relatively simple biomathematical models. Recently, several papers in Global Ecology and Biogeography, Proceedings of the National Academy of Sciences USA, Science and elsewhere have attempted to quantify the prevalence of alternate stable states in the savannas of Africa, Australia and South America, and the tundra–taiga–grassland transitions of the circum‐boreal region using satellite‐derived woody canopy cover. While we agree with the logic that basins of attraction can be inferred from the relative frequencies of ecosystem states observed in space and time, we caution that the statistical methodologies underlying the satellite product used in these studies may confound our ability to infer the presence of multiple stable states. We demonstrate this point using a uniformly distributed ‘pseudo‐tree cover’ database for Africa that we use to retrace the steps involved in creation of the satellite tree‐cover product and subsequent analysis. We show how classification and regression tree (CART)‐based products may impose discontinuities in satellite tree‐cover estimates even when such discontinuities are not present in reality. As regional and global remote sensing and geospatial data become more easily accessible for ecological studies, we recommend careful consideration of how error distributions in remote sensing products may interact with the data needs and theoretical expectations of the ecological process under study.     

Do musicians with perfect pitch have more autism traits than musicians without perfect pitch? An empirical study

Perfect pitch, also known as absolute pitch (AP), refers to the rare ability to identify or produce a musical tone correctly without the benefit of an external reference. AP is often considered to reflect musical giftedness, but it has also been associated with certain disabilities due to increased prevalence of AP in individuals with sensory and developmental disorders. Here, we determine whether individual autistic traits are present in people with AP. We quantified subclinical levels of autism traits using the Autism-Spectrum Quotient (AQ) in three matched groups of subjects: 16 musicians with AP (APs), 18 musicians without AP (non-APs), and 16 non-musicians. In addition, we measured AP ability by a pitch identification test with sine wave tones and piano tones. We found a significantly higher degree of autism traits in APs than in non-APs and non-musicians, and autism scores were significantly correlated with pitch identification scores (r = .46, p = .003). However, our results showed that APs did not differ from non-APs on diagnostically crucial social and communicative domain scores and their total AQ scores were well below clinical thresholds for autism. Group differences emerged on the imagination and attention switching subscales of the AQ. Thus, whilst these findings do link AP with autism, they also show that AP ability is most strongly associated with personality traits that vary widely within the normal population.     

Improving model construction of profile HMMs for remote homology detection through structural alignment

Background  

Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance.     

Planar cell polarity proteins differentially regulate extracellular matrix organization and assembly during zebrafish gastrulation

Zebrafish gastrulation cell movements occur in the context of dynamic changes in extracellular matrix (ECM) organization and require the concerted action of planar cell polarity (PCP) proteins that regulate cell elongation and mediolateral alignment. Data obtained using Xenopus laevis gastrulae have shown that integrin–fibronectin interactions underlie the formation of polarized cell protrusions necessary for PCP and have implicated PCP proteins themselves as regulators of ECM. By contrast, the relationship between establishment of PCP and ECM assembly/remodeling during zebrafish gastrulation is unclear. We previously showed that zebrafish embryos carrying a null mutation in the four-pass transmembrane PCP protein vang-like 2 (vangl2) exhibit increased matrix metalloproteinase activity and decreased immunolabeling of fibronectin. These data implicated for the first time a core PCP protein in the regulation of pericellular proteolysis of ECM substrates and raised the question of whether other zebrafish PCP proteins also impact ECM organization. In Drosophila melanogaster, the cytoplasmic PCP protein Prickle binds Van Gogh and regulates its function. Here we report that similar to vangl2, loss of zebrafish prickle1a decreases fibronectin protein levels in gastrula embryos. We further show that Prickle1a physically binds Vangl2 and regulates both the subcellular distribution and total protein level of Vangl2. These data suggest that the ability of Prickle1a to impact fibronectin organization is at least partly due to effects on Vangl2. In contrast to loss of either Vangl2 or Prickle1a function, we find that glypican4 (a Wnt co-receptor) and frizzled7 mutant gastrula embryos with disrupted non-canonical Wnt signaling exhibit the opposite phenotype, namely increased fibronectin assembly. Our data show that glypican4 mutants do not have decreased proteolysis of ECM substrates, but instead have increased cell surface cadherin protein expression and increased intercellular adhesion. These data indicate that Wnt/Glypican4/Frizzled signaling regulates ECM assembly through effects on cadherin-mediated cell cohesion. Together, our results demonstrate that zebrafish Vangl2/Prickle1a and non-canonical Wnt/Frizzled signaling have opposing effects on ECM organization underlying PCP and gastrulation cell movements.     

The role of intravascular ultrasound imaging in vascular brachytherapy

Intracoronary brachytherapy has recently emerged as a new therapy to prevent restenosis. Initial experimental work was achieved in animal models and the results were assessed by histomorphometry. Initial clinical trials used angiography to guide dosimetry and to assess efficacy. Intravascular ultrasound (IVUS) permits tomographic examination of the vessel wall, elucidating the true morphology of the lumen and transmural components, which cannot be investigated on the lumenogram obtained by angiography. This paper reviews the use of IVUS in the clinical studies of brachytherapy conducted to date. IVUS allows clinicians to make a thorough assessment of the remodeling of the vessel and appears to have a major role to play in facilitating understanding of the underlying mechanisms of action in this emerging field. The authors propose that state-of-the-art IVUS techniques should be employed to further knowledge of the mechanisms of action of brachytherapy in atherosclerotic human coronary arteries.