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PubMed2000

Seasonal changes in energy and water use by verdins, Auriparus flaviceps.

We used the doubly labeled water (DLW) method to measure field metabolic rate (FMR) and water turnover during winter and summer in a very small (6.5 g) insectivorous desert passerine bird, the verdin (Auriparus flaviceps). Concurrently, we monitored weather conditions and used time-activity budget data of free-living birds and laboratory data on resting metabolic rate to construct time-activity laboratory (TAL) estimates of daily energy expenditure (DEE ) and to partition the verdins' energy budget into thermoregulatory, activity and basal components. The FMR of adult verdins was 33.6+/-0.9 kJ day(-)(1) (mean +/- s.e.m.; N=14) in winter and 22.8+/-0.45 kJ day(-)(1) (N=7) in summer. FMR correlated negatively with the mean standard operative environmental temperature (T(es)) prevailing during the measurement period. TAL analysis produced DEE estimates that corresponded on average to within -0.9+/-2.4 % of our DLW-measured FMR values (range of individual values -18.3 % to +14.3 %). Metabolic expeditures for cold defense were 19.5+/-2.1 % of DEE in winter (computed assuming substitution of exercise thermogenesis for thermoregulatory costs in active birds). In the summer, thermoregulatory costs amounted to 9.0+/-0.4 % of DEE for keeping warm and 1.0+/-0.1 % of DEE for keeping cool in the heat. Activity costs were 21.0+/-0.5 % of DEE in winter and 17.5+/-0.1 % of DEE in summer. The water efflux of nonbreeding adult verdins was 3.9+/-0.2 ml day(-)(1) (624+/-22 ml kg(-)(1 )day(-)(1)) in summer (N=5) and 3. 4+/-0.2 ml day(-)(1) (498+/-26 ml kg(-)(1 )day(-)(1)) in winter (N=14). The water economy index (WEI; water efflux per unit FMR) of verdins was higher in summer (0.17+/-0.01 ml kJ(-)(1)) than in winter (0.10+/-0.01 ml kJ(-)(1)) and correlated negatively with mean T(es).

Animals↗

PubMed2001

Physiological and biochemical correlates of brood size and energy expenditure in tree swallows.

Intra-population variation in many fitness-related traits (e.g. clutch size) is often attributed to variation in individual parental quality. One possible component of quality is the level at which each individual can expend energy while provisioning dependent young. We used breeding tree swallows (Tachycineta bicolor) to test whether adults with large, natural-sized broods and/or nestlings in good nutritional condition had relatively high daily energy expenditures (DEEs). Adults with high DEEs were predicted to have large internal organs and high metabolic capacities. We first measured the growth rate of nestlings in natural broods of five, six and seven over a 4-day period and then measured parental DEE using doubly labelled water. Adults were then dissected for analyses of body composition and to determine maximum enzyme activities in the pectoral muscle. Although the total mass gain of large broods was greater than that of small broods, parental DEE was independent of brood size. We hypothesize that adults matched their clutch size (and consequently, brood size) to their individual foraging efficiencies. When statistically controlling for the effects of brood size, in one of two years there was a positive correlation between DEE and brood mass. This suggests that among individuals rearing the same-sized broods there were reproductive benefits of a relatively high DEE. There was no correlation between either brood size or DEE and the mass of any internal organ or the metabolic capacity of the pectoral muscle.

Animals↗

PubMed2002

Solvent-dependent mixed complex formation-NMR studies and asymmetric addition reactions of lithioacetonitrile to benzaldehyde mediated by chiral lithium amides.

Lithioacetonitrile and a chiral lithium amide with an internally coordinating methoxy group form mixed dimers in diethyl ether (DEE) and in tetrahydrofuran (THF) according to NMR studies. Based on the observed (6)Li,(1)H heteronuclear Overhauser effects, in THF lithioacetonitrile is present in a mixed complex with the chiral lithium amide, and this complex has a central N-Li-N-Li core. In DEE, on the other hand, the acetonitrile anion bridges two lithiums of the dimer to form a central six-membered Li-N-C-C-Li-N ring. Gauge individual atomic orbital DFT calculations of the (13)C NMR chemical shifts of the DEE- and THF-solvated mixed dimers show good agreement with those obtained experimentally. Lithioacetonitrile complexed to the chiral lithium amide has been employed in asymmetric addition to benzaldehyde in both DEE and THF. In THF the product, (S)-3-phenyl-3-hydroxy propionitrile, is formed in 55 % ee and in DEE the R enantiomer is formed in 45 % ee. This change in stereoselectivity between solutions in DEE and THF was found to be general among a number of different chiral lithium amides, all with an internal chelating methoxy group.

Acetonitriles↗

PubMed2000

Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design.

Finding the minimum energy amino acid side-chain conformation is a fundamental problem in both homology modeling and protein design. To address this issue, numerous computational algorithms have been proposed. However, there have been few quantitative comparisons between methods and there is very little general understanding of the types of problems that are appropriate for each algorithm. Here, we study four common search techniques: Monte Carlo (MC) and Monte Carlo plus quench (MCQ); genetic algorithms (GA); self-consistent mean field (SCMF); and dead-end elimination (DEE). Both SCMF and DEE are deterministic, and if DEE converges, it is guaranteed that its solution is the global minimum energy conformation (GMEC). This provides a means to compare the accuracy of SCMF and the stochastic methods. For the side-chain placement calculations, we find that DEE rapidly converges to the GMEC in all the test cases. The other algorithms converge on significantly incorrect solutions; the average fraction of incorrect rotamers for SCMF is 0.12, GA 0.09, and MCQ 0.05. For the protein design calculations, design positions are progressively added to the side-chain placement calculation until the time required for DEE diverges sharply. As the complexity of the problem increases, the accuracy of each method is determined so that the results can be extrapolated into the region where DEE is no longer tractable. We find that both SCMF and MCQ perform reasonably well on core calculations (fraction amino acids incorrect is SCMF 0.07, MCQ 0.04), but fail considerably on the boundary (SCMF 0.28, MCQ 0.32) and surface calculations (SCMF 0.37, MCQ 0.44).

Algorithms↗

PubMed2000

Daily energy expenditure of the grey mouse lemur (Microcebus murinus): a small primate that uses torpor.

We aimed to investigate the pattern of utilisation of torpor and its impact on energy budgets in free-living grey mouse lemurs (Microcebus murinus), a small nocturnal primate endemic to Madagascar. We measured daily energy expenditure (DEE) and water turnover using doubly labelled water, and we used temperature-sensitive radio collars to measure skin temperature (Tsk) and home range. Our results showed that male and female mouse lemurs in the wild enter torpor spontaneously over a wide range of ambient temperatures (Ta) during the dry season, but not during the rainy season. Mouse lemurs remained torpid between 1.7-8.9 h with a daily mean of 3.4 h, and their Tsk s fell to a minimum of 18.8 degrees C. Mean home ranges of mouse lemurs which remained normothermic were similar in the rainy and dry season. During the dry season, the mean home range of mouse lemurs showing daily torpor was significantly smaller than that of animals remaining normothermic. The DEE of M. murinus remaining normothermic in the rainy season (122 +/- 65.4 kJ x day(-1)) was about the same of that of normothermic mouse lemurs in the dry season (115.5 +/- 27.3 kJ x day(-1)). During the dry season, the mean DEE of M. murinus that utilised daily torpor was 103.4 +/- 32.7 kJ x day(-1) which is not significantly different from the mean DEE of animals remaining normothermic. We found that the DEE of mouse lemurs using daily torpor was significantly correlated with the mean temperature difference between Tsk and Ta (r2 = 0.37) and with torpor bout length (r2 = 0.46), while none of these factors explained significant amounts of variation in the DEE of the mouse lemurs remaining normothermic. The mean water flux rate of mouse lemurs using daily torpor (13.0 +/- 4.1 ml x day(-1)) was significantly lower than that of mouse lemurs remaining normothermic (19.4 +/- 3.8 ml x day(-1)), suggesting the lemurs conserve water by entering torpor. Thus, this first study on the energy budget of free-ranging M. murinus demonstrates that torpor may not only reflect its impact on the daily energy demands, but involve wider adaptive implications such as water requirements.

Animals↗

PubMed2004

Anionic carbonato and oxalato cobalt(III) nitrogen mustard complexes.

Synthetic approaches to cobalt(III) complexes [Co(L)(L')2] containing the bidentate dialkylating nitrogen mustard N,N-bis(2-chloroethyl)-1,2-ethanediamine (L = dce) together with anionic ancilliary ligands (L') which are either carbonato (CO3(2-)), oxalato (ox2-), bis(2-hydroxyethyl)dithiocarbamato (bhedtc-), 2-pyridine carboxylato (pico-) or 2-pyrazine carboxylato (pyzc-) were investigated. Synthetic routes were developed using the related amines N,N-diethyl-1,2-ethanediamine (dee) and 1,2-ethanediamine (en). The complexes [Co(CO3)2(L)]- (L = dee 1, dce 2), [Co(ox)2(L)]- (L = dee 3, dce 4), [Co(bhedtc)2(dee)]+ 5, [Co(bhedtc)2(en)]+ 6, mer-[Co(pico)3], mer-[Co(pyzc)]3 7 and [Co(pico)2(dee)]+ 8 were prepared and were characterised by IR, UV-Vis, 1H and 13C[1H] NMR spectroscopy, mass spectrometry and cyclic voltammetry. [Co(bhedtc)2(en)]BPh4 6b and trans(O)-[Co(pico)2(dee)]ClO4 8 were characterised by X-ray crystallography. In vitro biological tests were carried out on complexes 1-4 in order to assess the degree to which coordination of the mustard to cobalt attenuated its cytotoxicity, and the differential toxicity in air vs. nitrogen.

Animals↗

PubMed2003

Resting and daily energy expenditures of free-living field voles are positively correlated but reflect extrinsic rather than intrinsic effects.

Resting metabolic rates at thermoneutral (RMRts) are unexpectedly variable. One explanation is that high RMRts intrinsically potentiate a greater total daily energy expenditure (DEE), but recent work has suggested that DEE is extrinsically defined by the environment, which independently affects RMRt. This extrinsic effect could occur because expenditure is forced upwards in poor habitats or enabled to rise in good habitats. We provide here an intraspecific test for an association between RMRt and DEE that separates intrinsic from extrinsic effects and forcing from enabling effects. We measured the DEE and RMRt of 75 free-living short-tailed field voles at two time points in late winter. Across all sites, there was a positive link between individual variation in RMRt and DEE. This correlation, however, emerged only because of an effect across sites, rather than because of an intrinsic association within sites. We defined site quality from the survivorship of voles at the sites and the time at which they commenced breeding in spring. The associations between DEE/RMRt and site quality suggested that in February voles in poorer sites had higher energy demands, indicating that DEE was forced upwards, but in March the opposite was true, with higher demands in good sites, indicating that high expenditure was enabled. These data show that daily energy demands are extrinsically defined, with a link to RMRt that is secondary or independent. Both forcing and enabling effects of the environment may pertain at different times of year.

Animals↗

PubMed2004

Optimal body size and energy expenditure during winter: why are voles smaller in declining populations?

Winter is energetically challenging for small herbivores because of greater energy requirements for thermogenesis at a time when little energy is available. We formulated a model predicting optimal wintering body size, accounting for the scaling of both energy expenditure and assimilation to body size, and the trade-off between survival benefits of a large size and avoiding survival costs of foraging. The model predicts that if the energy cost of maintaining a given body mass differs between environments, animals should be smaller in the more demanding environments, and there should be a negative correlation between body mass and daily energy expenditure (DEE) across environments. In contrast, if animals adjust their energy intake according to variation in survival costs of foraging, there should be a positive correlation between body mass and DEE. Decreasing temperature always increases equilibrium DEE, but optimal body mass may either increase or decrease in colder climates depending on the exact effects of temperature on mass-specific survival and energy demands. Measuring DEE with doubly labeled water on wintering Microtus agrestis at four field sites, we found that DEE was highest at the sites where voles were smallest despite a positive correlation between DEE and body mass within sites. This suggests that variation in wintering body mass between sites was due to variation in food quality/availability and not adjustments in foraging activity to varying risks of predation.

Animals↗

PubMed1999

Variations and determinants of energy expenditure as measured by whole-body indirect calorimetry during puberty and adolescence.

BACKGROUND: Adolescence is characterized by rapid anatomic, physiologic, and behavioral alterations expected to induce changes in metabolic rate. OBJECTIVE: The aim of the present study was to investigate variations in daily energy expenditure (DEE) and its main components during adolescence and to quantify their significant determinants. DESIGN: Eighty-three children and adolescents (44 boys and 39 girls aged 10-16 y) participated in this cross-sectional study. Tanner stages ranged from 1 to 5. Body composition was assessed by both the skinfold-thickness method and bioimpedance analysis. Energy expenditure (EE) was determined continuously over 24 h by using 2 whole-body calorimeters. The subjects followed a standardized activity program that included four 15-min periods of exercise on a cycle ergometer. RESULTS: Body composition, DEE, sleeping EE (SEE), resting EE, and EE during meals, miscellaneous activities, and physical exercise varied significantly with sex and stage of puberty. The DEE of boys and girls averaged 8.22 and 7.60 MJ in prepubertal children, 11.35 and 9.10 MJ in pubertal children, and 11.73 and 9.68 MJ in postpubertal adolescents, respectively. The significant determinants of DEE and SEE, respectively, were fat-free mass (r2 = 0.842 and 0.826), sex (r2 = 0.017 and 0.022), and season (r2 = 0.021 and 0.011). Stage of puberty and fat mass were not significant factors. DEE and SEE adjusted for fat-free mass were on average 5% higher in boys than in girls and 6% higher in spring than in autumn. CONCLUSIONS: The DEE of adolescents measured under standardized conditions varied with sex, body composition, and season, but not with stage of puberty. These variables could be predicted accurately from fat-free mass, sex, and season.

Adolescent↗

PubMed2006

Individually variable energy management strategies in relation to energetic costs of egg production.

Marked interindividual variation in metabolic rate suggests considerable complexity in energy management strategies, but attempts to further our understanding of the relationship between resting metabolic rate (RMR), daily energy expenditure (DEE), and reproductive effort have been hampered by the complexity of studying this system in the field. Here, we describe energy management strategies in a captive-breeding system, using Zebra Finches (Taeniopygia guttata), to demonstrate the high level of complexity and interindividual variability in energy expenditure, food intake, locomotor activity, and reproductive effort. In particular, we investigated whether the increase in RMR associated with egg production is additive, resulting in higher DEE and a need for elevated food intake, or whether this cost is compensated by reduced expenditure in nonreproductive components of the energy budget. We found high levels of intra-individual variation in energy expenditure associated with egg production in female Zebra Finches, e.g., comparing nonbreeding stage with the one-egg stage, change in RMR varied from 4.0% and 41.3%, and change in DEE varied from -33.3% to +46.4%. This variation was systematically related to aspects of locomotor activity and reproductive effort. Females with the largest increase in RMR during egg production decreased locomotor activity the most but still had increased DEE at the one-egg stage, and females with high DEE at the one-egg stage produced larger clutches. Our study suggests that females minimize increases in DEE during egg production through behavioral energy reallocation (reduced locomotor activity) but that individuals differ in their use of this strategy, which, in turn, is related to the absolute level of reproductive investment. This suggests a very complex, individually variable system of energy management to meet the demands of egg production.

Animals↗

PubMed2001

Quantitative cross-species extrapolation in noncancer risk assessment.

A procedure has been developed to extrapolate dose-effect findings across species and quantify some of the associated uncertainty via traditional statistical methods. The relationship between dose-effect curves which are known in two species can be described by a k-parameter dose equivalence equation (DEE). When a DEE is determined for as many agents of a given "family" as are known, a k-dimensional distribution of DEE parameters would obtain. When an actual extrapolation is to be made for a new agent of the same family which has not been (or cannot be) tested in the species to which results are to be extrapolated, the best estimate of the parameters of the new DEE would be some measure of central tendency and the best estimate of the uncertainty would be the variance/covariance of the k-dimensional distribution of DEE parameters. The method of extrapolation seeks to compliment the mechanistic knowledge or be a substitute for mechanistic methods in the large majority of cases where such understanding is lacking.

Dose-Response Relationship, Drug↗

PubMed1985

Influenza virus infection in mice after exposure to coal dust and diesel engine emissions.

Influenza virus infection initiated after aerosol exposure of CD-1, white Swiss mice for durations of 1, 3, and 6 months to respirable particulates maintained at 2 mg/m3 of either coal dust (CD), diesel engine emissions (DEE), a combination of both (CD/DEE), or to filtered air (control) was studied. The course of infection in mice previously exposed for 1 month to various particulates did not differ appreciably among the four animal groups with respect to mortality, virus growth in lungs, interferon levels, or hemagglutinin antibody response. In mice exposed for 3 and 6 months to different particulates, the mortality response was similar among all animal groups. However, the percentage of animals showing lung consolidation was significantly higher in the 3-month groups exposed to DEE (96.5%) and CD/DEE (97%) than in the control (61.2%); in the 6-month groups, the percentages were twice that of the control for both DEE- and CD/DEE-exposed animals. Complementing these observations of both 3- and 6-month-exposed animals was the higher virus growth levels attained in the DEE and CD/DEE animals with concomitant depressed interferon levels which were the inverse of findings noted in the control group. Hemagglutinin-antibody levels in particulate-exposed animals, especially at the 6-month interval, were fourfold less than the control. Histopathologic examination of lungs revealed no qualitative differences in the inflammatory response at any one specified time interval of exposure to influenza virus among the control and particulate-exposed animal groups. However, there were differences in severity of reaction in relation to the particulate component of the exposures. Focal macular collections of pigment-laden macrophages were seen only in DEE and CD/DEE but not in CD animals after 3- and 6-month exposures. The findings of this study indicated that the severity of influenza virus infection is more pronounced in mice exposed to diesel engine emissions than in control animals and it is not appreciably accentuated by coal dust.

Animals↗

PubMed2005

Negative dipole potentials of uncharged langmuir monolayers due to fluorination of the hydrophilic heads.

The dipole potential, affecting the structure, functions, and interactions of biomembranes, lipid bilayers, and Langmuir monolayers, is positive toward the hydrocarbon moieties. We show that uncharged Langmuir monolayers of docosyl trifluoroethyl ether (DFEE) exhibit large negative dipole potentials, while the nonfluorinated docosyl ethyl ether (DEE) forms films with positive dipole potentials. Comparison of the Delta V values for these ethers with those of the previously studied(37-39) monolayers of trifluoroethyl ester (TFEB) and ethyl ester of behenic acid (EB) shows that the reversal of the sign of Delta V causes the same change Delta(Delta V) = -706 +/- 16 mV due to fluorination of heads. The Delta V values of both TFEB and EB films differ by -122 +/- 16 mV from those of DFEE and DEE monolayers, respectively, with the same density. Such quantitative coincidence points to a common mechanism of reversal of the sign of the dipole potential for the ether and ester films despite the different structure of their heads. The mechanical properties and phase behaviors of these monolayers show that both fluorinated heads are less hydrated, suggesting that the change of the sign of Delta V could, at least partially, be related to different hydration water structure. The same negative contribution of the carbonyl bond in both TFEB and EB films contrasts with the generally accepted positive contribution of the C(delta+)=O(delta-) bond in condensed Langmuir monolayers of fatty acids, their alcohol esters, glycerides, and phospholipids but concurs with the theoretical analysis of Delta V of stearic acid monolayers. Both results question the literature values of the molecular dipole moments of these substances calculated via summation of bonds and atomic group contributions. Mixed monolayers of DFEE and DEE show smooth monotonic variation of Delta V from +450 to -235 mV, indicating a way for adjustment of the sign and magnitude of the dipole potential at the membrane-water boundary and regulation of such membrane behaviors as binding and translocation rate of hydrophobic ions and ion-carriers, adsorption and penetration of amphiphilic peptides, polarization of hydration water, and short-range repulsion. The interaction of the hydrophobic ions tetraphenylboron TPhB- and tetraphenylphosphonium TPhP+ with DFEE and DEE monolayers qualitatively follows the theory of binding of such ions to lipid bilayers, but the shifts Delta(Delta V) from the values obtained on water are much smaller than those for DPPC monolayers. This difference seems to be due to the solid (polycrystalline) character of the DFEE and DEE films that hampers the penetration of TPhB- and TPhP+ in the monolayers and reduces the attractive interaction with the hydrophobic moiety. This conclusion orients the future synthesis of amphiphiles with fluorinated heads to those which could form liquid-expanded Langmuir monolayers.

Chemical Phenomena↗

PubMed2006

Degenerate electron exchange reaction of n-alkane radical cations in solution.

The degenerate electron exchange (DEE) reaction involving radical cations (RCs) of n-nonane, n-dodecane, and n-hexadecane in n-hexane solution was studied over the temperature range 253-313 K using the method of time-resolved magnetic field effect in recombination fluorescence of spin-correlated radical ion pairs. In the dilute solutions the rate constant of DEE was found to be 200 times slower than the diffusion limit. Using n-nonane as an example, we showed that two reasons are responsible for the low value of the RC self-exchange rate: (1) conformational variability of molecules and RCs and (2) the activation barrier of DEE reaction. The calculations of the reaction enthalpy performed by the B3LYP/6-31G(d) method indicated that electron transfer can be effective only upon collision of RC with a neutral molecule either in the all-trans conformation or in the conformation differing from the latter by rotation of the end ethyl fragment. The activation barrier of the DEE reaction was estimated using the reorganization energy of the internal degrees of freedom calculated at the B3LYP level and was found to be about 6 kcal/mol. A possible influence of the interaction between RC and a neutral molecule in an encounter complex on DEE rate constant is also discussed.

Journal Article↗

PubMedDate not supplied

Contributing factors and variability of energy expenditure in non-obese, obese, and post-obese adolescents.

Energy expenditure (EE) is a major determinant of energy balance and body composition. The objectives of this paper were to review the contributing factors of the main components of daily EE (DEE) and the inter-individual variability in these components in non-obese (NOb), obese (Ob), and post-obese (POb) adolescents. Body composition especially fat-free mass (FFM), is the major determinant of the basal metabolic rate which contributes 50-70% of DEE, whereas fat mass (FM) is a significant factor only in obese subjects. Physical activity is the second main variation factor of DEE, whereas growth, the thermic effect of food, and thermoregulation are generally of marginal importance. The energy costs and EE associated with various sedentary and physical activities were assessed in NOb, Ob and POb subjects both in standardised and in free-living conditions. The interindividual variability of DEE is high, even after adjustment for body composition, mainly because of great differences in time devoted to the various physical activities. DEE and EE associated with sleep and sedentary activities are significantly higher in Ob than in NOb, but not after adjustment for FFM. On the contrary, EE associated with physical activities is not significantly different between Ob and NOb adolescents, but 61% lower in Ob subjects after adjustment for body composition. Multidisciplinary weight-reduction programmes including moderate energy restriction and physical training result in great FM loss, maintenance of FFM, improvement of physical capacities, but reductions in organ and tissue metabolic rate and in EE associated with the various sedentary and physical activities, which may favour body weight regain in the less active POb subjects.

Adolescent↗

PubMed1982

Alterations in tissue glutathione and angiotensin converting enzyme due to inhalation of diesel engine exhaust.

Quantitative changes in reduced glutathione (GSH) and angiotensin converting enzyme (ACE) of lung and extrapulmonary tissues were determined following exposure of laboratory animals to diesel engine exhaust (DEE). Exposure of male rats and guinea pigs to DEE containing 750 micrograms particulates per cubic meter for 12 wk did not cause any changes in GSH levels of lung, liver, and heart compared to control values. Rats were then exposed for various time periods to 6 mg/m3 DEE. Two weeks of exposure produced statistically significant increases of 21 and 7% in GSH levels of lung and liver, respectively, but not change in the heart. Following 4 wk of exposure, lung showed a 14% increase and heart an 11% increase in GSH level. Furthermore, rats exposed for 4 wk to DEE did not show any particular susceptibility toward the GSH-depleting effect of acetaminophen as compared to controls. A significant depletion (15%) of hepatic GSH was observed after 8 wk of exposure, while lung was still showing an increase of 18% in GSH and heart was unaffected. Time-dependent increases of 18 and 33% in serum ACE activity were noted after 4 and 8 wk of exposure. Pulmonary ACE activity did not decrease until after 8 wk, and then to a small extent (7%). The observed increases in GSH may have been related to the presence of NO2 in the DEE. On the other hand, the depletion of hepatic GSH suggests production of electrophilic compounds due to an induction of metabolic activity of liver. The change in serum ACE activity may be due to time-requiring perturbations in the pulmonary endothelial cells.

Animals↗

PubMed2006

Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design.

MOTIVATION: Structure-based protein redesign can help engineer proteins with desired novel function. Improving computational efficiency while still maintaining the accuracy of the design predictions has been a major goal for protein design algorithms. The combinatorial nature of protein design results both from allowing residue mutations and from the incorporation of protein side-chain flexibility. Under the assumption that a single conformation can model protein folding and binding, the goal of many algorithms is the identification of the Global Minimum Energy Conformation (GMEC). A dominant theorem for the identification of the GMEC is Dead-End Elimination (DEE). DEE-based algorithms have proven capable of eliminating the majority of candidate conformations, while guaranteeing that only rotamers not belonging to the GMEC are pruned. However, when the protein design process incorporates rotameric energy minimization, DEE is no longer provably-accurate. Hence, with energy minimization, the minimized-DEE (MinDEE) criterion must be used instead. RESULTS: In this paper, we present provably-accurate improvements to both the DEE and MinDEE criteria. We show that our novel enhancements result in a speedup of up to a factor of more than 1000 when applied in redesign for three different proteins: Gramicidin Synthetase A, plastocyanin, and protein G. AVAILABILITY: Contact authors for source code.

Algorithms↗

PubMed2005

Metabolic adjustments to increasing foraging costs of starlings in a closed economy.

Knowledge of the physiological consequences of variation in food availability may be essential for understanding behavioural and life history responses to such variation. To study the physiological consequences of food availability animals are generally subjected to caloric restriction or starvation, thereby reducing the upper limit to the energy budget. The relevance of this approach to free-living animals is questionable, however, because under natural conditions low food availability often results in higher foraging costs, and everything else remaining equal this results in a higher energy budget. We manipulated food availability by varying the foraging costs and studied effects on daily energy expenditure (DEE) and energy allocation of captive starlings Sturnus vulgaris. Birds in a closed economy earned their food by flying between two perches 5 m apart. The probability of a reward was set at three different levels, thereby creating a 'poor', 'intermediate' and 'rich' environment. Compared with the rich environment, birds flew 4 times more (2.3 h per day) in the poor environment, and increased DEE by 43% to 220 kJ day-1 (3.7xBMR), within the range of free-living parents rearing young. To our knowledge this is the first study to show an increase in DEE with decreasing food availability. Body mass, basal metabolic rate (BMR) and pectoral muscle size were reduced in the poor environment. Nocturnal energy expenditure was further reduced by reaching BMR earlier in the night. Calculations show that the energy demands in the poor environment could not be met with the flight costs of 20.5 W that we measured previously in a rich environment. Flight costs derived indirectly from the energy budget were lower, at 17.5 W, probably due to lower body mass. By reducing body mass by 20%, and economising during sleep, the birds achieved savings of 37% in their DEE. Without these savings, a DEE substantially higher than measured in free-living parents rearing young would be required to remain in energy balance. Surprisingly little data exist to verify whether free-living animals use the same tactics to survive periods with low food availability.

Animals↗