Optimal foraging in bumblebees: calculation of net rate of energy intake and optimal patch choice.
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Animals↗
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Results for “energy optimization”
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Charge optimization leads to favorable electrostatic binding free energy.
Variational optimization of molecular electrostatic charge distributions is a tool for the study of association reactions of molecules in solution. In principle, this method can be used in drug design and protein folding to analyze and improve molecular interactions and to provide electrostatic templates for molecular design. This optimization problem reduces to an inverse source problem in classical electrostatics, where the sources are determined by a combination of external and self-polarization potentials. In this paper, we show that the electrostatic portion of the free energy of association for electrostatically optimized molecules has an upper bound of zero in many situations of physical interest. That is, variational optimization provides a ligand-charge distribution that contributes favorably to the energetics of binding, even in a strongly polar medium. This stabilizing effect on association reactions is contrary to the usual role of electrostatics in aqueous complexes, in which desolvation effects generally dominate. We also show the existence and nonuniqueness of the variational solution and make a connection to the electrostatic image charge problem.
Biophysical Phenomena↗
An automated method for modeling proteins on known templates using distance geometry.
We present an automated method incorporated into a software package, FOLDER, to fold a protein sequence on a given three-dimensional (3D) template. Starting with the sequence alignment of a family of homologous proteins, tertiary structures are modeled using the known 3D structure of one member of the family as a template. Homologous interatomic distances from the template are used as constraints. For nonhomologous regions in the model protein, the lower and the upper bounds for the interatomic distances are imposed by steric constraints and the globular dimensions of the template, respectively. Distance geometry is used to embed an ensemble of structures consistent with these distance bounds. Structures are selected from this ensemble based on minimal distance error criteria, after a penalty function optimization step. These structures are then refined using energy optimization methods. The method is tested by simulating the alpha-chain of horse hemoglobin using the alpha-chain of human hemoglobin as the template and by comparing the generated models with the crystal structure of the alpha-chain of horse hemoglobin. We also test the packing efficiency of this method by reconstructing the atomic positions of the interior side chains beyond C beta atoms of a protein domain from a known 3D structure. In both test cases, models retain the template constraints and any additionally imposed constraints while the packing of the interior residues is optimized with no short contacts or bond deformations. To demonstrate the use of this method in simulating structures of proteins with nonhomologous disulfides, we construct a model of murine interleukin (IL)-4 using the NMR structure of human IL-4 as the template. The resulting geometry of the nonhomologous disulfide in the model structure for murine IL-4 is consistent with standard disulfide geometry.
Algorithms↗
Structure of viroid replicative intermediates: physico-chemical studies on SP6 transcripts of cloned oligomeric potato spindle tuber viroid.
The structure and structural transitions of transcripts of cloned oligomeric viroid were studied in physico-chemical experiments and stability calculations. Transcripts of (+) and (-) polarity, from unit up to sixfold length, were synthesized from DNA clones of the potato spindle tuber viroid (PSTV) with the SP6 transcription system. Their structural properties were investigated by optical denaturation curves, high performance liquid chromatography (HPLC), electron microscopy, sedimentation-diffusion equilibrium and velocity sedimentation. Secondary structures of the RNAs and theoretical denaturation curves were calculated using an energy optimization program. The secondary structure of lowest free energy for unit length and oligomeric transcripts is a rod-like structure similar to that of the mature circular viroids. When this structure is used as a model for calculations, there is a large degree of agreement between the theoretical and the experimental denaturation curves. At high temperatures, however, (+) strand transcripts exhibited a transition which was more stable than expected from the calculations or than was known from curves of mature viroids. This transition arises from a rearrangement of the central conserved region of viroids to a helical region of 28 stable base pairs either intermolecularly leading to bimolecular complexes, or intramolecularly giving rise to a branched secondary structure. The rearrangement could be detected by electron microscopy, HPLC, and analytical ultracentrifugation. The helical region serves to divide up the oligomeric (+) strand into structural units which may be recognized by cleavage and ligation enzymes which process the oligomeric intermediates to circular mature viroids.
Microscopy, Electron↗
Solvent-amino acid interaction energies in three-dimensional-lattice Monte Carlo simulations of a model 27-mer protein: Folding thermodynamics and kinetics.
Amino acid residue-solvent interactions are required for lattice Monte Carlo simulations of model proteins in water. In this study, we propose an interaction-energy scale that is based on the interaction scale by Miyazawa and Jernigan. It permits systematic variation of the amino acid-solvent interactions by introducing a contrast parameter for the hydrophobicity, C(s), and a mean attraction parameter for the amino acids, omega. Changes in the interaction energies strongly affect many protein properties. We present an optimized energy parameter set for best representing realistic behavior typical for many proteins (fast folding and high cooperativity for single chains). Our optimal parameters feature a much weaker hydrophobicity contrast and mean attraction than does the original interaction scale. The proposed interaction scale is designed for calculating the behavior of proteins in bulk and at interfaces as a function of solvent characteristics, as well as protein size and sequence.
Algorithms↗
[Sclerostomy with an erbium YAG laser--the relationship with pulse energy].
PURPOSE: To investigate the optimal pulse energy to do sclerostomy with an erbium YAG laser. MATERIALS AND METHODS: The experiments were performed in enucleated porcine eyes. We changed pulse energy and examined the effects on surrounding tissue. RESULTS: With the increase of pulse energy, the effects of the laser extended to the area surrounding the laser probe. At the threshold energy for doing full-thickness sclerostomy, the total energy was significantly higher than with higher pulse energy. And with pulse energy higher than 2 mJ, the total energy did not show any significant change. Histopathologically, the damaged area around sclerostomy became larger with the increase of pulse energy. CONCLUSION: The optimal energy to do full-thickness sclerostomy with this system seemed to be 2 mJ.
Animals↗
Introduction to respiratory control in skeletal muscle.
It is well known that a linear relationship exists for submaximum exercise intensity and oxygen consumption. Most of the increase in oxygen consumption is by skeletal muscle mitochondria for the purpose of producing enough ATP to match the energy needs of the muscle. The control of mitochondrial ATP production in muscle when workload is varied is a complex process and remains a very active area of research. Thus, the purpose of this symposium is to discuss the factors involved in the coupling between increases in work and increased oxygen consumption by muscle. The program will begin with a consideration of the challenges faced by skeletal muscle when attempting to meet its energy demands and the intracellular strategies that have evolved to optimize energy delivery. Next the major control theories for mitochondrial respiration will be discussed. Finally, experiments will be presented that are designed to determine which of these theories are best suited for specific skeletal muscle fiber types. It is hoped that the information presented will increase our awareness of different energy supply-demand strategies among fiber types and how supply-demand strategies are optimized by endurance training.
Adenosine Triphosphate↗
Energy expenditure in hospitalized patients: implications for nutritional support.
An understanding of energy expenditure in hospitalized patients is necessary to determine optimal energy supply in the care of individuals who require nutritional support. A review was conducted of 19 studies in which resting energy expenditure (REE) had been measured using indirect calorimetry and compared with estimated basal energy expenditure (BEE) from the Harris-Benedict equation. Studies of patients with burns, head injuries, and fever were excluded because REE is known to be increased in these conditions. The studies reported data on 1256 patients with the following diagnoses: postoperative (28%), trauma or sepsis (26%), cancer (18%), pulmonary disease (9%), cardiovascular disease (2%), miscellaneous (9%), and unspecified (6%). The average REE in the 19 studies was 113% of the BEE. The mean +/- SD REE/BEE ratio was higher in 11 studies in which the REE was measured during feeding than in 5 studies in which the measurement was made during fasting (117% +/- 3% vs 105% +/- 4%; P = .047). In those 11 studies, overfeeding may have contributed to higher REE values than otherwise would have been observed. Some evidence indicated that the REE/BEE ratio is higher in more severe illness, but results were inconsistent. Unfortunately, little information is available concerning total energy expenditure, which includes the contribution of physical activity. It appears that most patients can be fed adequately with energy equal to 100% to 120% of estimated BEE. Hypoenergetic feeding may be appropriate in some overweight and obese individuals. Additional research in hospitalized patients on total energy expenditure and on the relationship between severity of illness and energy expenditure is needed.
Basal Metabolism↗
A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field.
A method for optimizing potential-energy functions of proteins is proposed. The method assumes a hierarchical structure of the energy landscape, which means that the energy decreases as the number of native-like elements in a structure increases, being lowest for structures from the native family and highest for structures with no native-like element. A level of the hierarchy is defined as a family of structures with the same number of native-like elements (or degree of native likeness). Optimization of a potential-energy function is aimed at achieving such a hierarchical structure of the energy landscape by forcing appropriate free-energy gaps between hierarchy levels to place their energies in ascending order. This procedure is different from methods developed thus far, in which the energy gap and/or the Z score between the native structure and all non-native structures are maximized, regardless of the degree of native likeness of the non-native structures. The advantage of this approach lies in reducing the number of structures with decreasing energy, which should ensure the searchability of the potential. The method was tested on two proteins, PDB ID codes and, with an off-lattice united-residue force field. For, the search of the conformational space with the use of the conformational space annealing method and the newly optimized potential-energy function found the native structure very quickly, as opposed to the potential-energy functions obtained by former optimization methods. After even incomplete optimization, the force field obtained by using located the native-like structures of two peptides, and betanova (a designed three-stranded beta-sheet peptide), as the lowest-energy conformations, whereas for the 46-residue N-terminal fragment of staphylococcal protein A, the native-like conformation was the second-lowest-energy conformation and had an energy 2 kcal/mol above that of the lowest-energy structure.
Algorithms↗
Optimization characteristics of walking with and without a load on the trunk of the body.
Previous work showed that subjects naturally adopt a walking speed which optimizes energy cost of locomotion and stability of stride; however, no studies have examined whether these criteria are affected by carrying an external load. The purpose of this study was to compare optimization characteristics during loaded or unloaded walking. Energy cost and stride characteristics were measured for 10 subjects with and without a load on the trunk of the body of 10% of the body weight during 4 sessions. The first 2 sessions represent free walking at 2.5, 3, 3.5, 4, 4.5, and 5 km x hr.(-1). The last sessions represent free vs forced walking at constant speed (preferred frequency and +/- 10 PF and +/-20% of preferred frequency). Results show an effect of load on energy cost of walking but no effect on the optimal speed for stability. Furthermore, when carrying a load the subject does not adopt systematically the speed that minimizes physiological cost. Our findings suggest the necessity to consider this effect to prevent gait disturbance and maintain the health benefits of walking.
Adaptation, Physiological↗
Use of binding energy in catalysis: optimization of rate in a multistep reaction.
The role of binding energy in optimizing the overall rate of catalysis by the tyrosyl-tRNA synthetase from Bacillus stearothermophilus has been investigated by measuring the rate constants for transfer of tyrosine from engineered mutants to tRNA. The residues chosen for mutation are those that were previously identified as binding tyrosyl adenylate and contributing to the rate constant for its formation. It was previously found that tighter binding of the tyrosyl adenylate was accompanied by an increase in the rate constant for its formation. A new linear free energy relationship is presented that links the two. We now find that the rate constant for transfer of Tyr from Tyr-AMP to tRNA decreases with increasing stability of the E.Tyr-AMP complex on mutation of Thr-51. Position 51 is the one that is found to be the most variable of the binding-site residues among the enzymes from different species. The tightness of binding of the intermediate is thus a compromise, since stabilizing the intermediate speeds up the first step but slows down the second. The rate constants for activation and transfer by wild-type enzymes are very similar, which is optimal for the rate of the overall reaction. Those for the mutants diverge so that the rate of overall catalysis is lower.
Adenosine Monophosphate↗
The electrostatically driven Monte Carlo method: application to conformational analysis of decaglycine.
The Electrostatically Driven Monte Carlo (EDMC) method was applied in a study of a decamer of glycine whose conformational behavior is described by the Empirical Conformational Energy Program for Peptides (ECEPP/2) potential energy model. When free neutral end groups were used, it was found that conformations that were not alpha-helical had significantly lower potential energies than fully alpha-helical ones. However, when the N- and C-termini were blocked by acetyl and methyl amide groups, respectively, the number of unsatisfied hydrogen-bond donors and acceptors at the helix termini was diminished from 8 to 6; in this case, the possibility of forming two additional alpha-helical hydrogen bonds was an important enough factor in making the alpha-helical conformation the one with the lowest energy. The EDMC method was used as a global energy optimizer since it does not often become trapped in high-energy local minima.
Electrochemistry↗
Prescription, precision, and decision in treatment planning.
The goal of radiotherapy is to eradicate a tumor without causing severe damage to healthy tissues. Various published experiences have lead to the conclusion that an overall precision of +/- 5% on the absorbed doses, at any point in the patient, is required to meet this goal. Clear definitions of the method for specifying the absorbed dose and dose homogeneity throughout the target volume are essential, to facilitate communication, to improve the knowledge of dose-effect relations and to establish the necessary criteria for the optimization of treatment plans. Determination of the optimal energy is one of the most controversial problems in treatment plan optimization. It is clearly related to the criteria selected. A brief review of some criteria is proposed according to the tumor site. Computers may provide three-dimensional dose calculations for treatment conditions for which manual calculations are not feasible. Because the random errors are very small, computer calculations are often considered as exact although large risks of error are associated with each step of the calculation. The reduction of the overall uncertainty to the stated level of +/- 5% requires a constant effort from both radiotherapists and physicists at each step of treatment planning from basic definitions to dose distribution calculations.
Humans↗
3D-Lattice Monte Carlo simulations of model proteins. Size effects on folding thermodynamics and kinetics.
Recently, we devised an energy scale to vary systematically amino-acid residue-solvent interactions for Monte Carlo simulations of lattice-model proteins in water. For 27-mer proteins, the folding behavior varies appreciably with the choice of interaction parameters. We now perform similar simulations with 64-mers to study the size dependence of the optimal energy parameter set for representing realistic behavior typical of many real proteins (i.e. fast folding and high cooperativity for single chains). We find that 64-mers are considerably more stable and more cooperative compared to 27-mers. The optimal interfacial-interaction-energy parameter set, however, is relatively size independent.
Amino Acid Sequence↗
Energy imbalance and prostate cancer.
In this review, the emerging evidence that excessive energy intake relative to energy expenditure increases the risk of prostate cancer is discussed. The adverse effects of energy imbalance can be inferred from an experimental study demonstrating reduced prostate tumor growth, lower circulating concentrations of insulin-like growth factor-I and decreased expression of vascular endothelial growth factor with energy restriction in transplantable tumor models. The effects of energy restriction on factors mediating greater proliferation relative to apoptosis and angiogenesis suggest that energy imbalance may act late in the carcinogenic pathway. Energy intake also has been evaluated in relation to prostate cancer risk in 23 analytic epidemiologic studies. Among studies reporting effect estimates, 8 of 14 case-control studies support a direct association [top versus bottom quantile, OR(summary) = 1.3; 95% confidence interval (CI), 1.1-1.4], but none of four cohort studies do (RR(summary) = 1.0; 95% CI, 0.8-1.2). The four case-control studies that evaluated advanced disease suggest a higher risk with higher energy intake (OR(summary) = 1.6; 95% CI, 1.2-2.0). However, none of these studies considered the balance of energy intake with body size and physical activity, the major determinants of variability in energy demand. Numerous research questions remain to be addressed, including, Which biological pathways are adversely affected by energy imbalance? Does energy imbalance act early or late in prostate carcinogenesis? What is the optimal energy balance for minimizing risk of clinically important prostate cancer? Evidence is beginning to show that energy intake in excess of expenditure may affect prostate carcinogenesis and, in particular, risk of advanced disease.
Animals↗
Beam collimation with polycapillary x-ray optics for high contrast high resolution monochromatic imaging.
Monochromatic imaging can provide better contrast and resolution than conventional broadband radiography. In broadband systems, low energy photons do not contribute to the image, but are merely absorbed, while high energy photons produce scattering that degrades the image. By tuning to the optimal energy, one can eliminate undesirable lower and higher energies. Monochromatization is achieved by diffraction from a single crystal. A crystal oriented to diffract at a particular energy, in this case the characteristic line energy, diffracts only those photons within a narrow range of angles. The resultant beam from a divergent source is nearly parallel, but not very intense. To increase the intensity, collimation was performed with polycapillary x-ray optics, which can collect radiation from a divergent source and redirect it into a quasi parallel beam. Contrast and resolution measurements were performed with diffracting crystals with both high and low angular acceptance. Testing was first done at 8 keV with an intense copper rotating anode x-ray source, then 17.5 keV measurements were made with a low power molybdenum source. At 8 keV, subject contrast was a factor of five higher than for the polychromatic case. At 17.5 keV, monochromatic contrast was two times greater than the conventional polychromatic contrast. The subject contrasts measured at both energies were in good agreement with theory. An additional factor of two increase in contrast, for a total gain of four, is expected at 17.5 keV from the removal of scatter. Scatter might be simply removed using an air gap, which does not degrade resolution with a parallel beam.
Algorithms↗
Packing and recognition of protein structural elements: a new approach applied to the 4-helix bundle of myohemerythrin.
We present a novel search strategy for determining the optimal packing of protein secondary structure elements. The approach is based on conformational energy optimization using a predetermined set of side chain rotamers and appropriate methods for sampling the conformational space of peptide fragments having fixed backbone geometries. An application to the 4-helix bundle of myohemerythrin is presented. It is shown that the conformations of the amino acid side chains are largely determined at the level of helix pairs and that superposition of these results can be used to construct the full bundle. The final solution obtained, taking into account restrictions due to the lateral amphiphilicity of the helices, differs from the native structure by only a 20 degrees rotation of a single helix.
Amino Acid Sequence↗
Energy and variance optimization of many-body wave functions.
We present a simple, robust, and efficient method for varying the parameters in a many-body wave function to optimize the expectation value of the energy. The effectiveness of the method is demonstrated by optimizing the parameters in flexible Jastrow factors that include 3-body electron-electron-nucleus correlation terms for the NO2 and decapentaene (C10H12) molecules. The basic idea is to add terms to the straightforward expression for the Hessian of the energy that have zero expectation value, but that cancel much of the statistical fluctuations for a finite Monte Carlo sample. The method is compared to what is currently the most popular method for optimizing many-body wave functions, namely, minimization of the variance of the local energy. The most efficient wave function is obtained by optimizing a linear combination of the energy and the variance.
Journal Article↗