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PubMed2004

Interactions between the PAS and HAMP domains of the Escherichia coli aerotaxis receptor Aer.

The Escherichia coli energy-sensing Aer protein initiates aerotaxis towards environments supporting optimal cellular energy. The Aer sensor is an N-terminal, FAD-binding, PAS domain. The PAS domain is linked by an F1 region to a membrane anchor, and in the C-terminal half of Aer, a HAMP domain links the membrane anchor to the signaling domain. The F1 region, membrane anchor, and HAMP domain are required for FAD binding. Presumably, alterations in the redox potential of FAD induce conformational changes in the PAS domain that are transmitted to the HAMP and C-terminal signaling domains. In this study we used random mutagenesis and intragenic pseudoreversion analysis to examine functional interactions between the HAMP domain and the N-terminal half of Aer. Missense mutations in the HAMP domain clustered in the AS-2 alpha-helix and abolished FAD binding to Aer, as previously reported. Three amino acid replacements in the Aer-PAS domain, S28G, A65V, and A99V, restored FAD binding and aerotaxis to the HAMP mutants. These suppressors are predicted to surround a cleft in the PAS domain that may bind FAD. On the other hand, suppression of an Aer-C253R HAMP mutant was specific to an N34D substitution with a predicted location on the PAS surface, suggesting that residues C253 and N34 interact or are in close proximity. No suppressor mutations were identified in the F1 region or membrane anchor. We propose that functional interactions between the PAS domain and the HAMP AS-2 helix are required for FAD binding and aerotactic signaling by Aer.

Carrier Proteins↗

PubMed2003

The concave-convex procedure.

The concave-convex procedure (CCCP) is a way to construct discrete-time iterative dynamical systems that are guaranteed to decrease global optimization and energy functions monotonically. This procedure can be applied to almost any optimization problem, and many existing algorithms can be interpreted in terms of it. In particular, we prove that all expectation-maximization algorithms and classes of Legendre minimization and variational bounding algorithms can be reexpressed in terms of CCCP. We show that many existing neural network and mean-field theory algorithms are also examples of CCCP. The generalized iterative scaling algorithm and Sinkhorn's algorithm can also be expressed as CCCP by changing variables. CCCP can be used both as a new way to understand, and prove the convergence of, existing optimization algorithms and as a procedure for generating new algorithms.

Algorithms↗

PubMed2001

How to guarantee optimal stability for most representative structures in the Protein Data Bank.

We proposed recently an optimization method to derive energy parameters for simplified models of protein folding. The method is based on the maximization of the thermodynamic average of the overlap between protein native structures and a Boltzmann ensemble of alternative structures. Such a condition enforces protein models whose ground states are most similar to the corresponding native states. We present here an extensive testing of the method for a simple residue-residue contact energy function and for alternative structures generated by threading. The optimized energy function guarantees high stability and a well-correlated energy landscape to most representative structures in the PDB database. Failures in the recognition of the native structure can be attributed to the neglect of interactions between different chains in oligomeric proteins or with cofactors. When these are taken into account, only very few X-ray structures are not recognized. Most of them are short inhibitors or fragments and one is a structure that presents serious inconsistencies. Finally, we discuss the reasons that make NMR structures more difficult to recognizeCopyright 2001 Wiley-Liss, Inc.

Computational Biology↗

PubMed2000

Development of a neural network heating controller for solar buildings.

Artificial neural networks (ANN's) are more and more widely used in energy management processes. ANN's can be very useful in optimizing the energy demand of buildings, especially of those of high thermal inertia. These include the so-called solar buildings. For those buildings, a controller able to forecast not only the energy demand but also the weather conditions can lead to energy savings while maintaining thermal comfort. In this paper, such an ANN controller is proposed. It consists of a meteorological module, forecasting the ambient temperature and solar irradiance, the heating energy switch predictor module and the indoor temperature-defining module. The performance of the controller has been tested both experimentally and in a building thermal simulation environment. The results showed that the use of the proposed controller can lead to 7.5% annual energy savings in the case of a highly insulated passive solar test cell.

Equipment Design↗

PubMedDate not supplied

Radiographic information theory and application to mammography.

A theoretical estimate is made for the lowest exposure necessary to record the smallest feature of interest, using various radiographic detecting surfaces and allowing for the probability of making errors to be within certain specified bounds. These calculated exposures are compared with the errors to be within certain specified bounds. These calculated exposures are compared with the actual exposures given in clinical situations in order that the smallest feature of interest can be observed by the practitioner with the same probability of error. A measure of the viewing efficiency of a radiographic process is given by the ratio of these exposures. The application of these concepts to mammography for three different recording media--film, film/screen, and xeroradiography--shows that the minimum entrance exposure necessary for recording information by each receptor varies with the energy of the x-ray beam, and that the optimal photon energy lies in the 21- to 25-keV region. All three methods with their present modes of processing use at most only a few percent of the information they actually intercept. This argues, for example, that if some more efficient method of reading xerographic plates were found, entrance exposures as low as 9 mR per exposure would suffice for a mammogram.

Calcinosis↗

PubMed1989

Assessment of the scatter fraction evaluation methodology using Monte Carlo simulation techniques.

To evaluate scatter fraction and scatter pair spatial distribution, experimental methods are generally used. These methods make use of a line source, placed along the FOV axis, inserted in a cylindrical phantom filled with air or water. The accuracy of these experimental methodologies can be tested by the use of a Monte Carlo method. In fact, the simulation allows the shape of the scatter event projection and the scatter fraction to be defined. An example of this application is the simulation package PETSI (PET SImulation). In this paper the comparison between the predicted scatter fraction and the experimentally evaluated one, obtained using an ECAT III PT 911/02 double ring whole body scanner are presented. PETSI permits additional data to be obtained: a) the true and scatter component of the energy spectrum; b) the spatial distribution, in the FOV plane, of the detected scatter events at different energy thresholds; c) the scatter to total detected events ratio; d) the predicted scatter fraction at both energy thresholds and FOV diameters. This information is very useful for optimizing both energy threshold and FOV size and to improve the accuracy of the currently used methods for the scatter fraction evaluation. Preliminary results of the predicted scatter fraction in a uniform phantom are presented.

Models, Structural↗

PubMed1988

Energy profile of Cs+ in gramicidin A in the presence of water. Problem of the ion selectivity of the channel.

The effect of water present at the mouth and inside the channel of Gramicidin A on the energy profile calculated for a caesium ion is determined. The total optimal interaction energy computed for the system GA-Cs+-(22 waters) leads to an energy profile characterized by a deep minimum at 11 A followed by an entrance energy barrier of 7 Kcal/mol expanding until 9 A from the center. After this point, a second minimum less deep than the previous one is observed, itself followed by a central barrier. The shape of the profile at the entrance is governed by the balance between the progressive desolvation process of the ion and the increase of favorable hydrogen bond interactions implying both the water molecules and GA. The comparison of this energy profile with that obtained in vacuo shows that the presence of water molecules does not modify the pathway of the ion which, owing to its size, is constrained essentially to remain on the channel axis. The comparison Na+ versus Cs+ indicates that although the phenomena involved are globally the same, differences between the two profiles appear due firstly to the difference in the affinity of the two ions for water and secondly to their respective size. This last difference implies that the number of water molecules present in the interior of the channel during the cation progression is reduced roughly by one in the case of caesium. The desolvation barrier computed for Cs+ is half the corresponding value for Na+, a result in agreement with the observed selectivity.

Biological Transport↗

PubMed2003

Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods.

Optimized geometries and total energies of some conformers of alpha- and beta-D-galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of alpha- and beta-D-galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units alpha 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles psi and phi of the glycosidic linkage are considered. In each calculation, at each increment of psi and phi, using a step of 30 degrees from 0 to 330 degrees, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*.

Algorithms↗

PubMed2005

Growth algorithm for finding low energy configurations of simple lattice proteins.

PERM and its new variant nPERMis have been developed to optimize the energy function of protein folding based on HP simple lattice model and were found to outperform all other previous fully blind general purpose algorithms. Using the concept of core-guiding and life-forecasting, we propose a new version of nPERMis, called nPERMh. A major difference with respect to nPERMis is that criteria for further growth of new residue are based on the species of current growing monomer and its position in the HP sequence. Seventeen sequences of length ranging from 46 to 124 residues were tested by nPERMh on the cubic lattice and our algorithm proved very efficient. It should be pointed out that our new version of nPERMis is exclusively designed for conformational search. We hope that similar methods will ultimately be useful for finding native states of more realistic protein models.

Journal Article↗

PubMed1997

Optimization models for the force and energy in competitive running.

In [2] the author has developed an optimization model for the force and energy in competitive running. In this paper the energy processes in the muscle were described by a three-compartment hydraulic model. Here this is reviewed briefly and applied to the current world records in order to determine the key parameters, maximal force, energy reserves and oxygen uptake. These values agree well with those given in the literature and those obtained by other means. The velocity profiles for 100 m sprints are described equally well. The model is then applied to older world records to deduce a relation between the force and energy by linear regression. Finally the fully parameterized model is used to compute the effects of adverse wind and altitude. Inasmuch as there are data available, there is a good agreement.

Biomechanical Phenomena↗

PubMed2006

The 2005 USDA Food Guide Pyramid is associated with more adequate nutrient intakes within energy constraints than the 1992 Pyramid.

The USDA issued the Food Guide Pyramid (FGP) to help Americans choose healthy diets. We examined whether adherence to the 1992 and 2005 FGP was associated with moderate energy and adequate nutrient intakes. We used data for 2138 men and 2213 women > 18 y old, from the 2001-2002 U.S. National Health and Nutrition Examination Survey (NHANES). Quadratic programming was used to generate diets with minimal departure from intakes reported for the NHANES 2001-02. We examined the effect of the number of servings/d of Food Pyramid groups set at 1992 and at 2005 FGP recommendations for 1600, 2200, and 2800 kcal (1 kcal = 4.184 kJ) levels. We calculated energy and nutrients provided by different FGP dietary patterns. Within current U.S. dietary practices, following the 1992 FGP without sodium restriction may provide 200 more kcal than recommended for each energy level. Although it can meet most of old nutrient recommendations (1989), it fails to meet the latest dietary reference intakes, especially for the 1600 kcal level. The 2005 FGP appears to provide less energy and more adequate nutrient intakes, with the exception of vitamin E and potassium for some groups. However, without discretionary energy restriction, Americans are at risk of having excessive energy intake even if they follow the 2005 FGP food serving recommendations. Our analysis suggests that following the 2005 FGP may be associated with lower energy and optimal nutrient intake. Careful restriction of discretionary calories appears necessary for appropriate energy intakes to be maintained.

Animals↗

PubMed1999

Optimal paths in disordered media: scaling of the crossover from self-similar to self-affine behavior.

We study optimal paths in disordered energy landscapes using energy distributions of the type P(log(10) E)=const that lead to the strong disorder limit. If we truncate the distribution, so that P(log(10) E)=const only for E(min) < or =E < or =E(max), and P(log(10) E)=0 otherwise, we obtain a crossover from self-similar (strong disorder) to self-affine (moderate disorder) behavior at a path length l(x). We find that l(x) proportional, variant[log(10)(E(max)/E(min))](kappa), where the exponent kappa has the value kappa=1.60 +/- 0.03 both in d=2 and d=3. We show how the crossover can be understood from the distribution of local energies on the optimal paths.

Journal Article↗

PubMed2002

Folding funnels: the key to robust protein structure prediction.

Natural proteins fold because their free energy landscapes are funneled to their native states. The degree to which a model energy function for protein structure prediction can avoid the multiple minima problem and reliably yield at least low-resolution predictions is also dependent on the topography of the energy landscape. We show that the degree of funneling can be quantitatively expressed in terms of a few averaged properties of the landscape. This allows us to optimize simplified energy functions for protein structure prediction even in the absence of homology information. Here we outline the optimization procedure in the context of associative memory energy functions originally introduced for tertiary structure recognition and demonstrate that even partially funneled landscapes lead to qualitatively correct, low-resolution predictions.

Computational Biology↗

PubMed1991

Biological activity of 3-deazauridine nucleoside analogue: a theoretical study.

The incorporation model of Sanyal et al. has been used to understand the biological activity of the cytostatic compound 3-deazauridine. The interaction energies of various types of binding pattern of the enterant molecule with nucleic acid fragments have been computed. The energy values and the sites of association of the analogous base, obtained by optimization of energy values as well as the sites of association of nucleic acid bases during the transcription process have been compared. The specificity of the binding of the interacting molecule has been discussed, along with the inhibitory effect of 3-deazauridine. They are in agreement with the experimentally observed evidence.

3-Deazauridine↗

PubMed2006

Quadratic string method for determining the minimum-energy path based on multiobjective optimization.

Based on a multiobjective optimization framework, we develop a new quadratic string method for finding the minimum-energy path. In the method, each point on the minimum-energy path is minimized by integration in the descent direction perpendicular to path. Each local integration is done on a quadratic surface approximated by a damped Broyden-Fletcher-Goldfarb-Shanno updated Hessian, allowing the algorithm to take many steps between energy and gradient calls. The integration is performed with an adaptive step-size solver, which is restricted in length to the trust radius of the approximate Hessian. The full algorithm is shown to be capable of practical superlinear convergence, in contrast to the linear convergence of other methods. The method also eliminates the need for predetermining such parameters as step size and spring constants, and is applicable to reactions with multiple barriers. The effectiveness of this method is demonstrated for the Muller-Brown potential, a seven-atom Lennard-Jones cluster, and the enolation of acetaldehyde to vinyl alcohol.

Acetaldehyde↗

PubMed2002

Energy landscape paving for X-ray structure determination of organic molecules.

The efficiency of a recently proposed novel global optimization method, energy landscape paving (ELP), is evaluated with regard to the problem of crystal structure determination from simulated X-ray diffraction data comprising integrated diffraction intensities. The new approach has been tested using the example of 9-(methylamino)-1H-phenalen-1-one 1,4-dioxan-2-y1 hydroperoxide solvate (C14H11NO.C4H8O4). The results indicate that, for this example, ELP outperforms standard techniques such as simulated annealing.

Journal Article↗

PubMed2002

Serial measurements of energy expenditure in critically ill children: useful in optimizing nutritional therapy?

OBJECTIVES: To determine the variation in total daily energy expenditure (TDEE) and respiratory quotient (RQ) in mechanically ventilated children and examine the relation to daily and cumulative energy balance toward optimizing nutritional therapy. METHODS: Serial measurements of TDEE and RQ were performed in 18 patients (median age 16 months) with an indirect calorimeter during admission (total 69 TDEE measurements). Daily caloric intake was recorded, and after determination of the amount of carbohydrates and fat a RQ of these macronutrients (RQ(macr)) was obtained. Daily 24-h urine was analyzed for urinary nitrogen excretion. RESULTS: There was a great variability in the median serial TDEE between children (40-64 kcal/kg), while the variation within individual children was small; the mean intraindividual coefficient of variation (CV) in daily measurements of TDEE was less than 10% in 15 of the 18 children (83%). On the last day of measurement 8 children with a positive cumulative energy balance (+98 kcal/kg) had a significantly higher RQ than 10 with a negative cumulative energy balance (-24 kcal/kg, 0.89 vs. 0.84). From the difference between RQ and RQ(macr) the optimal caloric intake was determined as 1.4x TDEE, divided into 60% carbohydrates and 40% fat. From the median nitrogen excretion of 33 samples (300 mg/kg per day, range 60-708) optimal daily protein intake was calculated as 1.9 g/kg (range 0.4-4.4). CONCLUSIONS: For most children a single measurement of TDEE gave a good insight in the daily energy needs. RQ is strongly affected by the ratio energy intake/TDEE and by the cumulative energy balance. Optimal caloric intake was found to be 1.4x TDEE with a daily protein intake of 1.9 g/kg.

Child, Preschool↗

PubMed1996

Optimization of conformal electron beam therapy using energy- and fluence-modulated beams.

Fluence modulation of multiple electron beams of various energies has been used to optimize the delivered dose distribution during electron beam radiation therapy. By maximizing the probability of achieving tumor control without causing severe complications electron beam fluence profiles have been optimized for superficial target volumes. It is possible to use several equiportal fluence-modulated electron beams to modify the energy deposition with depth in a controlled manner making it possible to use the technique as an alternative to bolus. The technique was tested in two representative phantom geometries and in three clinical patient geometries using a set of five and two different energies. The local maxima in dose for the plans with five energies were typically lower than with the conventional or advanced bolus techniques. The principles for how the technique could be carried out in the future with a fourth generation radiotherapy accelerator are also indicated.

Electrons↗