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PubMed2003

Docking and electron transfer studies between rubredoxin and rubredoxin:oxygen oxidoreductase.

The interaction and electron transfer (ET) between rubredoxin (Rd) and rubredoxin:oxygen oxidoreductase (ROO) from Desulfovibrio gigas is studied by molecular modelling techniques. Experimental kinetic assays using recombinant proteins show that the Rd reoxidation by ROO displays a bell-shaped dependence on ionic strength, suggesting a non-trivial electrostatic dependence of the interaction between these two proteins. Rigid docking studies reveal a prevalence for Rd to interact, in a very specific way, with the surface of the ROO dimer near its FMN cofactors. The optimization of the lowest energy complexes, using molecular dynamics simulation, shows a very tight interaction between the surface of the two proteins, with a high probability for Rd residues (but not the iron centre directly) to be in direct contact with the FMN cofactors of ROO. Both electrostatics and van der Waals interactions contribute to the final energy of the complex. In these complexes, the major contributions for complex formation are polar interactions between acidic residues of Rd and basic residues of ROO, plus substantial non-polar interactions between different groups. Important residues for this process are identified. ET estimates (using the Pathways model), in the optimized lowest energy complexes, suggest that these configurations are efficient for transferring electrons. The experimental bell-shaped dependence of kinetics on ionic strength is analysed in view of the molecular modelling results, and hypotheses for the molecular basis of this phenomenon are discussed.

Amino Acid Sequence↗

PubMed2005

Optimizing the structures of minimum and transition state on the free energy surface.

Presented here is the application of a scheme for optimizing the structures of minima and transition states on the free energy surface (FES) for a path along a fixed reaction coordinate with the aid of ab initio molecular dynamics (AIMD) simulation. In the direction of the reaction coordinate, the values corresponding to the stationary points were optimized using the quasi-Newton method, in which the gradient of the free energy along the reaction coordinate was obtained by a constraint AIMD method, and the Bofill Hessian update scheme was used. The equilibrium values for the other directions were taken as the corresponding averages in the dynamic simulation. This scheme was applied to several elementary bimolecular addition reactions: (A) BH(3) + H(2)O --> H(2)O.BH(3); (B) BF(3) + NH(3) --> FB(3).NH(3); (C) SO(3) + NH(3) --> O(3)S.NH(3); (D) C(2)H(4) + CCl(2) --> H(4)C(2).CCl(2); (E) Ni(NH(2))(2) + PH(3) --> (NH(2))(2)Ni.PH(3); (F) W(CO)(5) + CO --> W(CO)(6). For reactions A, B, C, and F, no transition state (TS) exists on the potential energy surface (PES). However there is a TS on the FES. This stems from the curvature difference of the PES and -TDeltaS as a function of the reaction coordinate. For all reactions, it is found that the TS shifts toward the complexation product with increasing temperature because of the curvature increase of -TDeltaS. The equilibrium bond distances for the inactive coordinates perpendicular to the reaction coordinate always increase with temperature, which is due to the thermal excitation and anharmonicity of the PES.

Journal Article↗

PubMed2004

Secondary structure prediction of interacting RNA molecules.

Computational tools for prediction of the secondary structure of two or more interacting nucleic acid molecules are useful for understanding mechanisms for ribozyme function, determining the affinity of an oligonucleotide primer to its target, and designing good antisense oligonucleotides, novel ribozymes, DNA code words, or nanostructures. Here, we introduce new algorithms for prediction of the minimum free energy pseudoknot-free secondary structure of two or more nucleic acid molecules, and for prediction of alternative low-energy (sub-optimal) secondary structures for two nucleic acid molecules. We provide a comprehensive analysis of our predictions against secondary structures of interacting RNA molecules drawn from the literature. Analysis of our tools on 17 sequences of up to 200 nucleotides that do not form pseudoknots shows that they have 79% accuracy, on average, for the minimum free energy predictions. When the best of 100 sub-optimal foldings is taken, the average accuracy increases to 91%. The accuracy decreases as the sequences increase in length and as the number of pseudoknots and tertiary interactions increases. Our algorithms extend the free energy minimization algorithm of Zuker and Stiegler for secondary structure prediction, and the sub-optimal folding algorithm by Wuchty et al. Implementations of our algorithms are freely available in the package MultiRNAFold.

Algorithms↗

PubMed1992

The distribution of anaerobic energy in 1000 and 4000 metre cycling bouts.

In sprinting events of short duration, performance depends not only on the mean external power output and the frictional losses but also on the distribution of energy over the race. To investigate the optimal distribution of anaerobic energy during cycling the 1000 m time trial and the 4000 m pursuit, we simulated a power equation which contains expressions for the production of aerobic and anaerobic power, for frictional losses and for the rate of change of kinetic energy. Parameters for air- and rolling resistance were derived from the literature and the equations for aerobic and anaerobic power production were based on supra-maximal bicycle ergometer tests. Simulated lap and final times were compared to those realized by the best four athletes during the 1990 World Championships. The mean final times of these athletes of 64.1 s and 272.6 s for the 1000 m and 4000 m respectively were closely approximated by the simulated times of 63.7 s and 281.3 s. The simulations show that performance in the 1000 m race depends to a great extent on a large power output at the onset of the race. Moreover, it is demonstrated that this distance should be cycled in an all out fashion and not with a uniform velocity after the start despite the higher air frictional losses. For the 4000 m pursuit it appears to be more effective to perform a short but powerful start and then continue the race with a constant or only slightly decreasing power output.

Bicycling↗

PubMed2006

Body mass regulation at altitude.

Altitude exposure decreases energy intake and thus induces an energy deficit resulting in the loss of body mass. The energy deficit is worsened when energy expenditure is increased by exercise because the increase is not matched by an increased energy intake. The indicated fuel for the optimal use of the rarefied oxygen at altitude is carbohydrate. For optimal taste and maximizing energy intake, fat is the best. Protein should rather be limited because of its high thermic effect. Intestinal malabsorption probably does not play a role in the energy deficit. Even though the sensation of exertion during climbing at high altitude is intense, the actual energy expenditure is not high.

Altitude↗

PubMed2005

Effects of different energy intakes on nitrogen balance in patients with acute renal failure: a pilot study.

BACKGROUND: Thus far, there have been no controlled studies to examine optimal levels of energy provision in critically ill patients with acute renal failure (ARF) receiving artificial nutrition. METHODS: After a 24 h nitrogen-free regimen (20% dextrose), we assigned during an open-label, AB/BA-crossover-trial, 10 ARF patients receiving both total parenteral nutrition (TPN) and renal replacement therapy (seven males; mean age 72 years, range 60-83; mean APACHE II score 27.1, range 23-34, mechanical ventilation 8/10) to a lower calorie-TPN regimen (30 kcal/kg/day) and to a higher calorie-TPN regimen (40 kcal/kg/day), each for 3 days. Nitrogen intake was 0.25 g/kg/day for both regimens. We estimated nitrogen balance, protein catabolic rate and urea generation rate by urea kinetic methods based on both timed blood samples of serum urea and direct urea quantification from dialysis fluid. RESULTS: Two patients were excluded from the analysis (due to death and serum triglycerides above 5.1 mmol/l, respectively). Compared with the lower calorie-TPN, the higher calorie-TPN regimen did not improve estimated nitrogen balance [+1.55 g/day (95% confidence interval: -0.95 to +4.05, P = 0.18)], protein catabolic rate [-0.10 g/kg/day (-0.33 to +0.14, P = 0.35)], or urea generation rate [-1.3 mg/min (-5.2 to +2.7, P = 0.46)], whereas it increased serum triglycerides [+1.36 mmol/l (+0.53 to +2.19, P = 0.007)], glucose [+1.15 mmol/l (+0.07 to +2.24, P = 0.041)], insulin need [+20.4 U/day (+8.3 to +32.6, P = 0.006)] and nutritional fluid administration [+468 ml/day (+370 to +566, P<0.001)]. CONCLUSIONS: The present study, conducted in a small group of subjects, shows that in critically ill patients with ARF on a nitrogen intake of 0.25 g/kg/day, an energy provision of 40 kcal/kg/day does not improve nitrogen balance estimates compared with a 30 kcal/kg/day intake; instead, it may increase the risk of artificial nutrition-related side-effects.

Acute Kidney Injury↗

PubMed1991

A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison.

This article describes the latest version of an RNA folding algorithm that predicts both optimal and suboptimal solutions based on free energy minimization. A number of RNA's with known structures deduced from comparative sequence analysis are folded to test program performance. The group of solutions obtained for each molecule is analysed to determine how many of the known helixes occur in the optimal solution and in the best suboptimal solution. In most cases, a structure about 80% correct is found with a free energy within 2% of the predicted lowest free energy structure.

Algorithms↗

PubMed2003

Structure optimization in an off-lattice protein model.

We study an off-lattice protein toy model with two species of monomers interacting through modified Lennard-Jones interactions. Low energy configurations are optimized using the pruned-enriched-Rosenbluth method (PERM), hitherto employed to native state searches only for off-lattice models. For two dimensions we found states with lower energy than previously proposed putative ground states for all chain lengths >/=13. This indicates that PERM has the potential to produce native states also for more realistic protein models. For d=3, where no published ground states exist, we present some putative lowest energy states for future comparison with other methods.

Journal Article↗

PubMed2006

Global potential energy minima of C60(H2O)n clusters.

Likely candidates for the global potential energy minima of C60(H2O)n clusters with n < or = 21 are found using basin-hopping global optimization. The potential energy surfaces are constructed using the TIP4P intermolecular potential for the water molecules, a Lennard-Jones water-fullerene potential, and a water-fullerene polarization potential, which depends on the first few nonvanishing C60 multipole polarizabilities. This combination produces a rather hydrophobic water-fullerene interaction. As a consequence, the water component of the lowest C60(H2O)n minima is quite closely related to low-lying minima of the corresponding TIP4P (H2O)n clusters. In most cases, the geometrical substructure of the water molecules in the C60(H2O)n global minimum coincides with that of the corresponding free water cluster. Exceptions occur when the interaction with C60 induces a change in geometry. This qualitative picture does not change significantly if we use the TIP3P model for the water-water interaction. Structures such as C60@(H2O)60, in which the water molecules surround the C60 fullerene, correspond to local minima with much higher potential energies. For such a structure to become the global minimum, the magnitude of the water-fullerene interaction must be increased to an unphysical value.

Journal Article↗

PubMed1992

Phantom studies of triple photon absorptiometry and bone mineral measurement at a hip prosthesis.

The feasibility of using triple photon absorptiometry (TPA) for the measurement of bone mineral mass about a hip prosthesis was examined. A theoretical expression describing the variance of TPA measurements was verified using a triple photon source and phantom materials which simulate the soft tissue-bone mineral-metal prosthesis system. The expression for the variance was used to determine an optimized set of photon energies. It was shown that a precision of 3% could be obtained for reasonable measurement times using this optimized set of energies, and that TPA should be a feasible approach for measurement of bone mineral about a hip prosthesis.

Absorptiometry, Photon↗

PubMedDate not supplied

[Optimal relationship between average conformational entropy and average energy of interactions between residues for fast protein folding].

Based on the known experimental data and using the theoretical modeling of protein folding, we demonstrate that there exists an optimal relationship between the average conformational entropy and the average energy of contacts per residue, that is an entropy capacity, for fast protein folding. Statistical analysis of conformational entropy and the number of contacts per residue for 5829 protein structures from four general structural classes (all-alpha, all-beta, +/-/beta, alpha+beta) demonstrates that each class of proteins has its own class-specific average number of contacts and average conformational entropy per residue. These class-specific features determine the folding rates: a proteins are the fastest folding proteins, then follow beta and alpha+beta proteins, and finally alpha/beta proteins are the slowest ones.

Databases, Protein↗

PubMed2002

Side-chain modeling with an optimized scoring function.

Modeling side-chain conformations on a fixed protein backbone has a wide application in structure prediction and molecular design. Each effort in this field requires decisions about a rotamer set, scoring function, and search strategy. We have developed a new and simple scoring function, which operates on side-chain rotamers and consists of the following energy terms: contact surface, volume overlap, backbone dependency, electrostatic interactions, and desolvation energy. The weights of these energy terms were optimized to achieve the minimal average root mean square (rms) deviation between the lowest energy rotamer and real side-chain conformation on a training set of high-resolution protein structures. In the course of optimization, for every residue, its side chain was replaced by varying rotamers, whereas conformations for all other residues were kept as they appeared in the crystal structure. We obtained prediction accuracy of 90.4% for chi(1), 78.3% for chi(1 + 2), and 1.18 A overall rms deviation. Furthermore, the derived scoring function combined with a Monte Carlo search algorithm was used to place all side chains onto a protein backbone simultaneously. The average prediction accuracy was 87.9% for chi(1), 73.2% for chi(1 + 2), and 1.34 A rms deviation for 30 protein structures. Our approach was compared with available side-chain construction methods and showed improvement over the best among them: 4.4% for chi(1), 4.7% for chi(1 + 2), and 0.21 A for rms deviation. We hypothesize that the scoring function instead of the search strategy is the main obstacle in side-chain modeling. Additionally, we show that a more detailed rotamer library is expected to increase chi(1 + 2) prediction accuracy but may have little effect on chi(1) prediction accuracy.

Algorithms↗

PubMed2005

Energy cost of infection burden: an approach to understanding the dynamics of host-pathogen interactions.

A mathematical model of long-term immune defense against infection was used to estimate the energy involved in the principal processes of immune resistance during periods of health and infection. From these values, an optimal level of energy was determined for immune response depending on infection burden. The present findings suggest that weak but prevalent pathogens lead to latent or chronic infection, whereas more virulent but less prevalent pathogens result in acute infection. This energy-based approach offers insight into the mechanisms of immune system adaptation leading to the development of chronic infectious diseases and immune deficiencies.

Acute Disease↗

PubMed2004

Power gain exhibited by motile mechanosensory neurons in Drosophila ears.

In insects and vertebrates alike, hearing is assisted by the motility of mechanosensory cells. Much like pushing a swing augments its swing, this cellular motility is thought to actively augment vibrations inside the ear, thus amplifying the ear's mechanical input. Power gain is the hallmark of such active amplification, yet whether and how much energy motile mechanosensory cells contribute within intact auditory systems has remained uncertain. Here, we assess the mechanical energy provided by motile mechanosensory neurons in the antennal hearing organs of Drosophila melanogaster by analyzing the fluctuations of the sound receiver to which these neurons connect. By using dead WT flies and live mutants (tilB(2), btv(5P1), and nompA(2)) with defective neurons as a background, we show that the intact, motile neurons do exhibit power gain. In WT flies, the neurons lift the receiver's mean total energy by 19 zJ, which corresponds to 4.6 times the energy of the receiver's Brownian motion. Larger energy contributions (200 zJ) associate with self-sustained oscillations, suggesting that the neurons adjust their energy expenditure to optimize the receiver's sensitivity to sound. We conclude that motile mechanosensory cells provide active amplification; in Drosophila, mechanical energy contributed by these cells boosts the vibrations that enter the ear.

Animals↗

PubMed2005

High-throughput screening of low molecular weight NS3-NS4A protease inhibitors using a fluorescence resonance energy transfer substrate.

Hepatitis C virus (HCV) NS3-NS4A protease is an attractive target for anti-HCV agents because of its important role in replication. An optimized fluorescence resonance energy transfer (FRET) substrate for NS3-NS4A protease, based on the sequence of the NS5A-5B cleavage site, was designed and synthesized. High-throughput screening of in-house compound libraries was performed using a FRET substrate FS10 (MOCAcDKIVPC-SMSYK-Dnp) and MBP-NS3-NS4A fusion protein. Several hit compounds were found, including YZ-9577 (2-oxido-1,2,5-oxadiazole-3,4-diyl) bis (phenylmethanone) with potent inhibitory activity (IC50=1.6 microM) and good selectivity against other human serine proteases.

Antiviral Agents↗

PubMed2006

An ab initio periodic study of acidic chabazite as a candidate for dihydrogen storage.

A theoretical B3LYP study, adopting a polarized double-zeta quality Gaussian basis set, was performed to characterize acidic chabazite by using the periodic CRYSTAL03 program. Different Si/Al loadings (1/1, 3/1, 5/1, and 11/1) were considered, and for each of them the most stable aluminum distribution and location of the acidic proton, needed as charge balancer, were identified. With the optimal structures, the energy of formation and the anharmonic O-H stretching frequency were calculated with the latter being in good agreement with the experimental data. The B3LYP optimal position of H2 physisorbed at the acidic Brönsted sites of chabazite (Si/Al = 11/1 and 5/1) brings about an interaction energy definitely smaller than that derived from infrared spectroscopy, because of the known deficiencies of this functional to cope with dispersive interactions. The latter was included by means of an ONIOM-like procedure that combines periodic B3LYP energy with results at the MP2 level on selected clusters cut out of the chabazite framework. Adsorption of two H2 molecules for Si/Al = 5/1 chabazite showed a complete independence of each Brönsted site, and neither through-space nor intrastructure polarization effects are present. Within the periodic B3LYP approach shifts in both O-H and H-H anharmonic frequencies were also computed and compared with unperturbed values and with the available experimental results.

Journal Article↗

PubMed2006

Dual-energy cardiac imaging: an image quality and dose comparison for a flat-panel detector and x-ray image intensifier.

This study presents a comparison of dual-energy imaging with an x-ray image intensifier and flat-panel detector for cardiac imaging. It also investigates if the wide dynamic range of the flat-panel detector can improve dual-energy image quality while reducing patient dose. Experimental contrast-to-noise (CNR) measurements were carried out in addition to simulation studies. Patient entrance exposure and system tube loading were also recorded. The studied contrast objects were calcium and iodine. System performance was quantified with a figure-of-merit (FOM) defined as the image CNR(2) over patient entrance exposure. The range of thickness studied was from 10 to 30 cm of Lucite (PMMA). Detector dose was initially set to 140 nGy (16 microR)/frame. The high-energy 120 kVp beam was filtered by an additional 0.8 mm silver filter. Keeping the same filament current, the kVp for the low-energy beam was adjusted as a function of thickness until 140 nGy was achieved. System performance was found to be similar for both systems, with the x-ray image intensifier performing better at lower thicknesses and the flat-panel detector performing better at higher thicknesses. This requirement of fixed detector entrance exposure was then relaxed and the kVp for the low-energy beam was allowed to vary while the mAs of the x-ray tube remained fixed to study changes in dual-energy image quality, patient dose and FOM with the flat-panel detector. It was found that as the kVp for the low-energy beam was reduced, system performance would rise until reaching a maximum while simultaneously lowering patient exposure. Suggested recommendations for optimal dual-energy imaging implementation are also provided.

Bone and Bones↗

PubMed2005

Meal-feeding studies in mice: effects of diet on blood lipids and energy expenditure.

To identify optimal study-design conditions to investigate lipid metabolism, male, C57BL/6J mice (age, 59 +/- 3 days) were allotted to eight groups, with six animals per group that were stratified by three factors: diet type (high fat [HF]: 60% of energy from fat versus that of a standard rodent diet, 14% fat, fed for 7 weeks), feeding regimen (ad libitum [ad lib] versus meal fed), and metabolic state (data collected in fasted or fed states). Serum free fatty acids (FFA) and triacylglycerols (TAG) concentrations, and energy expenditure (EE) were assessed. Mice gained 0.30 +/- 0.11 g of body weight/day when allowed ad lib access to HF diet, similar weight when meal-fed the HF or ad lib-fed the standard diet (0.10 +/- 0.03 g/day), and no weight when meal-fed the standard diet (0.01 +/- 0.02 g/day). Fed-state TAG concentration was 88 to 100% higher (P < 0.02) than that of the fasted state, except when animals were ad lib-fed the HF diet. When the standard diet was meal fed, FFA concentration was 30% higher in the fasted compared with the fed state (P = 0.003). Mice had 33% higher postprandial EE when either diet was meal fed (P = 0.01). Mice adapted to meal feeding developed transitions in metabolism consistent with known physiologic changes that occur from fasting to feeding. When fed the standard diet, a 6-h per day meal-feeding regimen was restrictive for normal growth. These data support use of a meal-feeding regimen when HF diets are used and research is focused on metabolic differences between fasted and fed states. This protocol allows study of the metabolic effects of an HF diet without the confounding effects of over-consumption of food and excess body weight gain.

Animal Nutritional Physiological Phenomena↗