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1.
Gemma L. Holliday Syed Asad Rahman Nicholas FurnhamJanet M. Thornton 《Journal of molecular biology》2014
Using a novel method to map and cluster chemical reactions, we have re-examined the chemistry of the ligases [Enzyme Commission (EC) Class 6] and their associated protein families in detail. The type of bond formed by the ligase can be automatically extracted from the equation of the reaction, replicating the EC subclass division. However, this subclass division hides considerable complexities, especially for the C–N forming ligases, which fall into at least three distinct types. The lower levels of the EC classification for ligases are somewhat arbitrary in their definition and add little to understanding their chemistry or evolution. By comparing the multi-domain architecture of the enzymes and using sequence similarity networks, we examined the links between overall reaction and evolution of the ligases. These show that, whilst many enzymes that perform the same overall chemistry group together, both convergent (similar function, different ancestral lineage) and divergent (different function, common ancestor) evolution of function are observed. However, a common theme is that a single conserved domain (often the nucleoside triphosphate binding domain) is combined with ancillary domains that provide the variation in substrate binding and function. 相似文献
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We develop a theoretical model of a clathrin protein lattice on a flexible cell membrane. The clathrin subunit is modeled as a three-legged pinwheel with elastic deformation modes and intersubunit binding interactions. The pinwheels are constrained to lie on the surface of an elastic sheet that opposes bending deformation and is subjected to tension. Through Monte Carlo simulations, we predict the equilibrium phase behavior of clathrin lattices at various levels of tension. High membrane tensions, which correspond to suppressed membrane fluctuations, tend to stabilize large, flat crystalline structures similar to plaques that have been observed in vivo on cell membranes that are adhered to rigid surfaces. Low tensions, on the other hand, give rise to disordered, defect-ridden lattices that behave in a fluidlike manner. The principles of two-dimensional melting theory are applied to our model system to further clarify how high tensions can stabilize crystalline order on flexible membranes. These results demonstrate the importance of environmental physical cues in dictating the collective behavior of self-assembled protein structures. 相似文献
5.
S?ren Brage Kate Westgate Paul W. Franks Oliver Stegle Antony Wright Ulf Ekelund Nicholas J. Wareham 《PloS one》2015,10(9)
Background
Accurate assessment of energy expenditure (EE) is important for the study of energy balance and metabolic disorders. Combined heart rate (HR) and acceleration (ACC) sensing may increase precision of physical activity EE (PAEE) which is the most variable component of total EE (TEE).Objective
To evaluate estimates of EE using ACC and HR data with or without individual calibration against doubly-labelled water (DLW) estimates of EE.Design
23 women and 23 men (22–55 yrs, 48–104 kg, 8–46%body fat) underwent 45-min resting EE (REE) measurement and completed a 20-min treadmill test, an 8-min step test, and a 3-min walk test for individual calibration. ACC and HR were monitored and TEE measured over 14 days using DLW. Diet-induced thermogenesis (DIT) was calculated from food-frequency questionnaire. PAEE (TEE ÷ REE ÷ DIT) and TEE were compared to estimates from ACC and HR using bias, root mean square error (RMSE), and correlation statistics.Results
Mean(SD) measured PAEE and TEE were 66(25) kJ·day-1·kg-1, and 12(2.6) MJ·day-1, respectively. Estimated PAEE from ACC was 54(15) kJ·day-1·kg-1 (p<0.001), with RMSE 24 kJ·day-1·kg-1 and correlation r = 0.52. PAEE estimated from HR and ACC+HR with treadmill calibration were 67(42) and 69(25) kJ·day-1·kg-1 (bias non-significant), with RMSE 34 and 20 kJ·day-1·kg-1 and correlations r = 0.58 and r = 0.67, respectively. Similar results were obtained with step-calibrated and walk-calibrated models, whereas non-calibrated models were less precise (RMSE: 37 and 24 kJ·day-1·kg-1, r = 0.40 and r = 0.55). TEE models also had high validity, with biases <5%, and correlations r = 0.71 (ACC), r = 0.66–0.76 (HR), and r = 0.76–0.83 (ACC+HR).Conclusions
Both accelerometry and heart rate may be used to estimate EE in adult European men and women, with improved precision if combined and if heart rate is individually calibrated. 相似文献6.
Geoffry Fordyce Michael R. McGowan Allan Lisle Tracy Muller Jack Allen Christian Duff Richard G. Holroyd Nicholas J. Corbet Brian M. Burns 《Theriogenology》2014
Normal range for scrotal circumference in Australian beef bulls was established using more than 300,000 measurements of breed, management group, age, liveweight, and scrotal circumference. The data used were derived from Australian bull breeders and two large research projects in northern Australia. Most bulls were within 250 to 750 kg liveweight and 300 to 750 days of age. The differences between breeds and variances within breeds were higher when scrotal circumference was predicted from age rather than liveweight, because of variance in growth rates. The average standard deviation for predicted scrotal circumference from liveweight and age was 25 and 30 mm, respectively. Scrotal circumference by liveweight relationships have a similar pattern across all breeds, except in Waygu, with a 50 to 70 mm range in average scrotal circumference at liveweights between 250 and 750 kg. Temperate breed bulls tended to have higher scrotal circumference at the same liveweight than tropically adapted breeds. Five groupings of common beef breeds in Australian were identified, within which there were similar predictions of scrotal circumference from liveweight. It was concluded that liveweight and breed are required to identify whether scrotal circumference is within normal range for Australian beef bulls that experience a wide range of nutritional conditions. 相似文献
7.
In a previous study, nonlinear autoregressive (NLAR) models applied to ictal electroencephalogram (EEG) recordings in six
patients revealed nonlinear signal interactions that correlated with seizure type and clinical diagnosis. Here we interpret
these models from a theoretical viewpoint. Extended models with multiple nonlinear terms are employed to demonstrate the independence
of nonlinear dynamical interactions identified in the ‘NLAR fingerprint’ of patients with 3/s seizure discharges. Analysis
of the role of periodicity in the EEG signal reveals that the fingerprints reflect the dynamics not only of the periodic discharge
itself, but also of the fluctuations of each cycle about an average waveform. A stability analysis is used to make qualitative
inferences concerning the network properties of the ictal generators. Finally, the NLAR fingerprint is analyzed in the context
of Volterra-Weiner theory.
Received: 6 April 1994/Accepted in revised form: 18 November 1994 相似文献
8.
J Z Wang C V Rojas J H Zhou L S Schwartz H Nicholas E P Hoffman 《Biochemical and biophysical research communications》1992,182(2):794-801
The amino acid sequence of the sodium channel alpha subunit from adult human skeletal muscle has been deduced by cross-species PCR-mediated cloning and sequencing of the cDNA. The protein consists of 1836 amino acid residues. The amino acid sequence shows 93% identity to the alpha subunit from rat adult skeletal muscle and 70% identity to the alpha subunit from other mammalian tissues. A 500 kb YAC clone containing the complete coding sequence and two overlapping lambda clones covering 68% of the cDNA were used to estimate the gene size at 35 kb. The YAC clone proved crucial for gene structure studies as the high conservation between ion channel genes made hybridization studies with total genomic DNA difficult. Our results provide valuable information for the study of periodic paralysis and paramyotonia congenita, two inherited neurological disorders which are caused by point mutations within this gene. 相似文献
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SUMMARY Understanding the relationship between egg size, development time, and juvenile size is critical to explaining patterns of life-history evolution in marine invertebrates. Currently there is conflicting information about the effects of changes in egg size on the life histories of echinoid echinoderms. We sought to resolve this conflict by manipulating egg size and food level during the development of two planktotrophic echinoid echinoderms: the green sea urchin, Strongylocentrotus droebachiensis and the sand dollar, Echinarachnius parma . Based on comparative datasets, we predicted that decreasing food availability and egg size would increase development time and reduce juvenile size. To test our prediction, blastomere separations were performed in both species at the two-cell stage to reduce egg volume by 50%, producing whole- and half-size larvae that were reared to metamorphosis under high or low food levels. Upon settlement, age at metamorphosis, juvenile size, spine number, and spine length were measured. As predicted, reducing egg size and food availability significantly increased age at metamorphosis and reduced juvenile quality. Along with previous egg size manipulations in other echinoids, this study suggests that the relationship between egg size, development time, and juvenile size is strongly dependent upon the initial size of the egg. 相似文献