The energetics of off-rotamer protein side-chain conformations

Non-rotameric ("off-rotamer") conformations are commonly observed for the side-chains of protein crystal structures. This study examines whether such conformations are real or artifactual by comparing the energetics of on and off-rotamer side-chain conformations calculated with the CHARMM energy function. Energy-based predictions of side-chain orientation are carried out by rigid-geometry mapping in the presence of the fixed protein environment for 1709 non-polar side-chains in 24 proteins for which high-resolution (2.0 A or better) structures are available. For on-rotamer conformations, 97.6 % are correctly predicted; i.e. they correspond to the absolute minima of their local side-chain energy maps (generally to within 10 degrees or less). By contrast, for the observed off-rotamer side-chain conformations, 63.8 % are predicted correctly. This difference is statistically significant (P<0.001) and suggests that while most of the observed off-rotamer conformations are real, many of the erroneously predicted ones are likely to be artifacts of the X-ray refinements. Probabilities for off-rotamer conformations of the non-polar side-chains are calculated to be 5.0-6.1 % by adaptive umbrella-sampled molecular dynamics trajectories of individual amino acid residues in vacuum and in the presence of an average protein or aqueous dielectric environment. These results correspond closely to the 5.7 % off-rotamer fraction predicted by the rigid-geometry mapping studies. Since these values are about one-half of the 10.2 % off-rotamer fraction observed in the X-ray structures, they support the conclusion that many of the latter are artifacts. In both the rigid-geometry mapping and the molecular dynamics studies, the discrepancies between the predicted and observed fractions of off-rotamer conformations are largest for leucine residues (approximately 6 % versus 16.6 %). The simulations for the isolated amino acid residues indicate that the real off-rotamer frequency of 5-6 % is consistent with the internal side-chain and local side-chain-backbone energetics and does not originate from shifts due to the protein. The present results suggest that energy-based rotation maps can be used to find side-chain positional artifacts that appear in crystal structures based on refinements in the 2 A resolution range.     

Exploring strategies for protein trapping in Drosophila

The use of fluorescent protein tags has had a huge impact on cell biological studies in virtually every experimental system. Incorporation of coding sequence for fluorescent proteins such as green fluorescent protein (GFP) into genes at their endogenous chromosomal position is especially useful for generating GFP-fusion proteins that provide accurate cellular and subcellular expression data. We tested modifications of a transposon-based protein trap screening procedure in Drosophila to optimize the rate of recovering useful protein traps and their analysis. Transposons carrying the GFP-coding sequence flanked by splice acceptor and donor sequences were mobilized, and new insertions that resulted in production of GFP were captured using an automated embryo sorter. Individual stocks were established, GFP expression was analyzed during oogenesis, and insertion sites were determined by sequencing genomic DNA flanking the insertions. The resulting collection includes lines with protein traps in which GFP was spliced into mRNAs and embedded within endogenous proteins or enhancer traps in which GFP expression depended on splicing into transposon-derived RNA. We report a total of 335 genes associated with protein or enhancer traps and a web-accessible database for viewing molecular information and expression data for these genes.     

Annexin A1 Induces Skeletal Muscle Cell Migration Acting through Formyl Peptide Receptors

Annexin A1 (ANXA1, lipocortin-1) is a glucocorticoid-regulated 37-kDa protein, so called since its main property is to bind (i.e. to annex) to cellular membranes in a Ca²⁺-dependent manner. Although ANXA1 has predominantly been studied in the context of immune responses and cancer, the protein can affect a larger variety of biological phenomena, including cell proliferation and migration. Our previous results show that endogenous ANXA1 positively modulates myoblast cell differentiation by promoting migration of satellite cells and, consequently, skeletal muscle differentiation. In this work, we have evaluated the hypothesis that ANXA1 is able to exert effects on myoblast cell migration acting through formyl peptide receptors (FPRs) following changes in its subcellular localization as in other cell types and tissues. The analysis of the subcellular localization of ANXA1 in C2C12 myoblasts during myogenic differentiation showed an interesting increase of extracellular ANXA1 starting from the initial phases of skeletal muscle cell differentiation. The investigation of intracellular Ca²⁺ perturbation following exogenous administration of the ANXA1 N-terminal derived peptide Ac2-26 established the engagement of the FPRs which expression in C2C12 cells was assessed by qualitative PCR. Wound healing assay experiments showed that Ac2-26 peptide is able to increase migration of C2C12 skeletal muscle cells and to induce cell surface translocation and secretion of ANXA1. Our results suggest a role for ANXA1 as a highly versatile component in the signaling chains triggered by the proper calcium perturbation that takes place during active migration and differentiation or membrane repair since the protein is strongly redistributed onto the plasma membranes after an rapid increase of intracellular levels of Ca²⁺. These properties indicate that ANXA1 may be involved in a novel repair mechanism for skeletal muscle and may have therapeutic implications with respect to the development of ANXA1 mimetics.     

Whistle characteristics of common dolphins (Delphinus sp.) in the Hauraki Gulf,New Zealand

Quantifying the vocal repertoire of a species is critical for subsequent analysis of signal functionality, geographic variation, and social relevance. However, the vocalizations of free‐ranging common dolphins (Delphinus sp.) have not previously been described from New Zealand waters. We present the first quantitative analysis of whistle characteristics to be undertaken on the New Zealand population. Acoustic data were collected in the Hauraki Gulf, North Island from 28 independent dolphin group encounters. A total of 11,715 whistles were collected from 105.1 min of recordings. Seven whistle contours were identified containing 29 subtypes. Vocalizations spanned from 3.2 to 23 kHz, with most whistles occurring between 11 and 13 kHz. Whistle duration ranged from 0.01 to 4.00 s (mean ± SD; 0.27 ± 0.32). Of the 2,663 whistles analyzed, 82% have previously been identified within U.K. populations. An additional six contours, apparently unique to New Zealand Delphinus were also identified. Data presented here offer a first insight into the whistle characteristics of New Zealand Delphinus. Comparisons with previously studied populations reveal marked differences in the whistle frequency and modulation of the New Zealand population. Interpopulation differences suggest behavior and the local environment likely play a role in shaping the vocal repertoire of this species.     

Subtractive and differential hybridization molecular analyses of <Emphasis Type="Italic">Ceratitis capitata</Emphasis> XX/XY versus XX embryos to search for male-specific early transcribed genes

The agricultural pest Ceratitis capitata, also known as the Mediterranean fruit fly or Medfly, is a fruit crop pest of very high economic relevance in different continents. The strategy to separate Ceratitis males from females (sexing) in mass rearing facilities is a useful step before the sterilization and release of male-only flies in Sterile Insect Technique control programs (SIT). The identification of genes having early embryonic male-specific expression, including Y-linked genes, such as the Maleness factor, could help to design novel and improved methods of sexing in combination with transgenesis, aiming to confer conditional female-specific lethality or female-to-male sexual reversal.We used a combination of Suppression Subtractive Hybrydization (SSH), Mirror Orientation Selection (MOS) and differential screening hybridization (DSH) techniques to approach the problem of isolating corresponding mRNAs expressed in XX/XY embryos versus XX-only embryos during a narrow developmental window (8-10 hours after egg laying, AEL ). Here we describe a novel strategy we have conceived to obtain relatively large amounts of XX-only embryos staged at 8-10 h AEL and so to extract few micrograms of polyA+ required to apply the complex technical procedure. The combination of these 3 techniques led to the identification of a Y-linked putative gene, CcGm2, sharing high sequence identity to a paralogous gene, CcGm1, localized either on an autosome or on the X chromosome.We propose that CcGm2 is a first interesting putative Y-linked gene which could play a role in sex determination. The function exterted by this gene should be investigated by novel genetic tools, such as CRISPR-CAS9, which will permit to target only the Y-linked paralogue, avoiding to interfere with the autosomal or X-linked paralogue function.     

Comparison of twitch potentiation in the gastrocnemius of young and elderly men

The capacity for twitch potentiation in the gastrocnemius muscle was determined following maximal voluntary contractions (MVC) in 11 elderly (means +/- SD; 66.9 +/- 5.3 years) and 12 young (25.7 +/- 3.8 years) men. Potentiation was observed by applying selective stimulation to the muscle belly, 2 s after a 5 s MVC. With this procedure, both groups showed significant (P less than 0.05) increases in twitch tension in the gastrocnemius (ratios of potentiated twitch to baseline were means = 1.68 +/- 0.40 for young vs means = 1.40 +/- 0.20 for the elderly, P less than 0.001). Time to peak tension of the twitch decreased from means = 101.5 +/- 17.9 ms to means = 88.0 +/- 15.8 ms in the young men following potentiation; the respective values for the older men were 136.7 +/- 17.9 ms and 133.1 +/- 28.6 ms. These changes resulted in a greater rate of tension development in the potentiated state. The elderly gastrocnemius thus showed qualitatively similar changes in the isometric twitch following potentiation, but reduced and prolonged responses in comparison to young adults. Slowed muscle contraction and reduced capacity for potentiation may be physiological correlates of the reported morphological changes in aged skeletal muscle.     

Longitudinal changes in aerobic power in older men and women.

The purpose of this study was to describe the longitudinal (10 yr) decline in aerobic power [maximal O(2) uptake (Vo(2 max))] and anaerobic threshold [ventilatory threshold (T(Ve))] of older adults living independently in the community. Ten years after initial testing, 62 subjects (34 men, mean age 73.5 +/- 6.4 yr; 28 women, 72.1 +/- 5.3 yr) achieved Vo(2 max) criteria during treadmill walking tests to the limit of tolerance, with T(Ve) determined in a subset of 45. Vo(2 max) in men showed a rate of decline of -0.43 ml.kg(-1).min(-1).yr(-1), and the decline in Vo(2 max) was consequent to a lowered maximal heart rate with no change in the maximum O(2) pulse. The women showed a slower rate of decline of Vo(2 max) of -0.19.ml.kg(-1).min(-1).yr(-1) (P < 0.05), again with a lowered HR(max) and unchanged O(2) pulse. In this sample, lean body mass was not changed over the 10-yr period. Changes in Vo(2 max) were not significantly related to physical activity scores. T(Ve) showed a nonsignificant decline in both men and women. Groupings of young-old (65-72 yr at follow-up) vs. old-old (73-90 yr at follow-up) were examined. In men, there were no differences in the rate of Vo(2 max) decline. The young-old women showed a significant decline in Vo(2 max), whereas old-old women, initially at a Vo(2 max) of 19.4 +/- 3.1 ml.kg(-1).min(-1), showed no loss in Vo(2 max). The longitudinal data, vs. cross-sectional analysis, showed a greater decline for men but similar estimates of the rates of change in women. Thus the 10-yr longitudinal study of the cohort of community-dwelling older adults who remained healthy, ambulatory, and independent showed a 14% decline in Vo(2 max) in men, and a smaller decline of 7% in women, with the oldest women showing little change over the 10-yr period.     

An efficient probabilistic methodology for incorporating uncertainty in body segment parameters and anatomical landmarks in joint loadings estimated from inverse dynamics

Inverse dynamics is a standard approach for estimating joint loadings in the lower extremity from kinematic and ground reaction data for use in clinical and research gait studies. Variability in estimating body segment parameters and uncertainty in defining anatomical landmarks have the potential to impact predicted joint loading. This study demonstrates the application of efficient probabilistic methods to quantify the effect of uncertainty in these parameters and landmarks on joint loading in an inverse-dynamics model, and identifies the relative importance of the parameters and landmarks to the predicted joint loading. The inverse-dynamics analysis used a benchmark data set of lower-extremity kinematics and ground reaction data during the stance phase of gait to predict the three-dimensional intersegmental forces and moments. The probabilistic analysis predicted the 1-99 percentile ranges of intersegmental forces and moments at the hip, knee, and ankle. Variabilities, in forces and moments of up to 56% and 156% of the mean values were predicted based on coefficients of variation less than 0.20 for the body segment parameters and standard deviations of 2 mm for the anatomical landmarks. Sensitivity factors identified the important parameters for the specific joint and component directions. Anatomical landmarks affected moments to a larger extent than body segment parameters. Additionally, for forces, anatomical landmarks had a larger effect than body segment parameters, with the exception of segment masses, which were important to the proximal-distal joint forces. The probabilistic modeling approach predicted the range of possible joint loading, which has implications in gait studies, clinical assessments, and implant design evaluations.     

The effects of [Arg14, Lys15] nociceptin/orphanin FQ, a highly potent agonist of the NOP receptor, on in vitro and in vivo gastrointestinal functions

Nociceptin/orphanin FQ (N/OFQ) administered into the lateral left cerebral ventricle of rats has been reported to inhibit in vivo gut motor and secretory functions. Recently, a novel N/OFQ analog, [Arg14, Lys15] N/OFQ, was synthesized and demonstrated to behave as a highly potent agonist at the human recombinant N/OFQ peptide (NOP) receptors and to produce long-lasting effects in vivo in mice compared with the natural ligand N/OFQ. In the present study, the pharmacological profile of [Arg14, Lys15] N/OFQ was further evaluated and compared with that of N/OFQ in vitro on guinea pig exocrine pancreas and in vivo on gastric emptying, colonic propulsion and gastric acid secretion in rats. [Arg14, Lys15] N/OFQ and N/OFQ significantly decreased the KCl-evoked amylase secretion from isolated pancreatic lobules of the guinea pig. In in vivo experiments, [Arg14, Lys15] N/OFQ mimicked the effects of N/OFQ, inducing, after intracerebroventricular injection, a delay (up to 70%) in the gastric emptying of a phenol red meal, an increase (about 40 times) of the mean bead colonic expulsion time and a decrease (up to 90%) of gastric acid secretion in water loaded rats after 90 min pylorus ligature. In all these assays, [Arg14, Lys15] N/OFQ was more effective than N/OFQ, and its effective doses were at least 10-fold lower than N/OFQ effective doses. The highly selective NOP receptor antagonist, UFP-101, decreased the efficacy of [Arg14, Lys15] N/OFQ in in vitro and in vivo assays above reported. These findings: (a) show that pancreatic NOP receptors mediate an in vitro inhibitory effect on stimulated guinea pig amylase secretion; (b) confirm that the stimulation of central NOP receptors exerts an inhibitory control on gastric emptying, colonic motility and gastric secretion in rats and (c) put in evidence that [Arg14, Lys15] N/OFQ, being more potent and effective than the natural ligand N/OFQ, represents a new pharmacological tool for the study of the physiological and pharmacological roles mediated by the N/OFQ-NOP receptor system.