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PubMed2007

SODOCK: swarm optimization for highly flexible protein-ligand docking.

Protein-ligand docking can be formulated as a parameter optimization problem associated with an accurate scoring function, which aims to identify the translation, orientation, and conformation of a docked ligand with the lowest energy. The parameter optimization problem for highly flexible ligands with many rotatable bonds is more difficult than that for less flexible ligands using genetic algorithm (GA)-based approaches, due to the large numbers of parameters and high correlations among these parameters. This investigation presents a novel optimization algorithm SODOCK based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. To improve efficiency and robustness of PSO, an efficient local search strategy is incorporated into SODOCK. The implementation of SODOCK adopts the environment and energy function of AutoDock 3.05. Computer simulation results reveal that SODOCK is superior to the Lamarckian genetic algorithm (LGA) of AutoDock, in terms of convergence performance, robustness, and obtained energy, especially for highly flexible ligands. The results also reveal that PSO is more suitable than the conventional GA in dealing with flexible docking problems with high correlations among parameters. This investigation also compared SODOCK with four state-of-the-art docking methods, namely GOLD 1.2, DOCK 4.0, FlexX 1.8, and LGA of AutoDock 3.05. SODOCK obtained the smallest RMSD in 19 of 37 cases. The average 2.29 A of the 37 RMSD values of SODOCK was better than those of other docking programs, which were all above 3.0 A.

Algorithms↗

PubMed1998

Experimental characterization of APS undulator A at high photon energies (50-200 keV).

The considerable intensity of Advanced Photon Source (APS) undulator A as a source of high-energy X-rays permits the performance of numerous types of experiments that require such photon energies. Measured and calculated properties, in the 50-200 keV range, of the X-ray beam from undulator A, installed in sector 1 of the APS, are presented. The flux spectra observed at various gaps agree well with calculations that incorporate the actual magnetic field within the device and the emittance and energy spread of the stored positrons. The field errors and energy spread cause the X-ray beam to lose undulator radiation properties at high energies, as seen in the smeared-out spectral harmonics and increased beam divergence, giving resemblance to a low-K wiggler source. Owing to the wiggler-like behavior in this photon-energy range, the optimal operating condition for undulator A is in the vicinity of the closed-gap setting, corresponding to a maximum critical energy.

Journal Article↗

PubMed2004

What energy functions can be minimized via graph cuts?

In the last few years, several new algorithms based on graph cuts have been developed to solve energy minimization problems in computer vision. Each of these techniques constructs a graph such that the minimum cut on the graph also minimizes the energy. Yet, because these graph constructions are complex and highly specific to a particular energy function, graph cuts have seen limited application to date. In this paper, we give a characterization of the energy functions that can be minimized by graph cuts. Our results are restricted to functions of binary variables. However, our work generalizes many previous constructions and is easily applicable to vision problems that involve large numbers of labels, such as stereo, motion, image restoration, and scene reconstruction. We give a precise characterization of what energy functions can be minimized using graph cuts, among the energy functions that can be written as a sum of terms containing three or fewer binary variables. We also provide a general-purpose construction to minimize such an energy function. Finally, we give a necessary condition for any energy function of binary variables to be minimized by graph cuts. Researchers who are considering the use of graph cuts to optimize a particular energy function can use our results to determine if this is possible and then follow our construction to create the appropriate graph. A software implementation is freely available.

Algorithms↗

PubMed2003

[The heart in diabetics].

Macrovascular complications in diabetics create a high risk for cardiovascular disease (CVD). Generally, the main risk factors for CVD include age, men's sex, elevated LDL-cholesterol and reduced HDL-cholesterol, elevated fibrinogen, hypertension, smoking, and diabetes mellitus. Clinical manifestation of coronary disease is determined by number, area, and severity of coronary stenoses, myocardial function, and presence of induced ischemia. Routine pharmacological treatment of ISHD concentrates on risk factors and hasn't been yet focused on changes in energy metabolism during ischemic situation which are important factors contributing to ischemic damage. Substances able to optmize energy metabolism of heart muscle offer a very tempting way both for ISHD treatment and for treatment of following cardiovascular complications. Optimal use of energy source in heart muscle can favour heart activity so that comparable amount of contractile work requires less oxygen. The most beneficial way of getting energy for myocardium while low consumption of oxygen is oxidation of glucose. Because of a large amount of free fatty acids (FFAs) in diabetics a more demanding way of oxidation takes place in them, the oxidation of FFAs. Therefore myocardium of a diabetic needs under normal perfusion conditions more oxygen to provide energy. Besides increase in demand of oxygen, FFAs separate glycolysis from glucose oxidation and increase undesirable production of lactate and protons. An ischemic myocardium of a diabetic has primarily bigger demand of oxygen then myocardium of a non-diabetic. Development of cell ischemia, with all the known consequences in forms of lactate acidosis, calcium overload, and depletion of ATP, leads to considerable contractile disorder. Unfavourable position of metabolic activities in myocardium of diabetics and faster and more serious progression of atherosclerosis result in a big risk of CVD in diabetics. Incidence of coronary events in diabetics without history of ISHD is as big as in non-diabetics with history of coronary events.

Coronary Disease↗

PubMed1994

Is total parenteral nutrition immunosuppressive?

Total parenteral nutrition (TPN) has been a major advance in patient therapeutics, particularly for critically ill patients. Incorrect administration of TPN, however, primarily through excessive use of energy, either as dextrose or lipid, is an underappreciated risk factor that leads to serious complications in nutritional support. Even a modest degree of uncontrolled hyperglycemia induced by TPN appears to increase the risk of infection, usually to a level that can nullify any potential benefit of feeding. Rapid and/or excessive lipid administration can interfere with the reticuloendothelial system function, which may also predispose the patient to serious infection. The goals of nutritional support in the critically ill are to provide ample protein at 1.5 to 2.0 g/kg body weight/day, while limiting calories to approximately the patient's resting energy expenditure, which optimally supports the metabolic response to injury. Repleting the critically ill, malnourished patient with calories in excess of the patient's energy expenditure is not effective, but rather increases the likelihood of an adverse outcome.

Body Weight↗

PubMed1990

Generation of optimum pseudorandom signals for respiratory impedance measurements.

Spontaneous breathing may impair the reliability of forced oscillatory impedance estimates at low frequencies, especially when the oscillatory power is distributed among many frequency values. Since the amplitude of the external forcing is limited to avoid non-linearities, it is suggested that the total energy of a composite electrical signal driving the loudspeaker be maximized at a given amplitude by finding the optimum phase relationships of the signal components, and that the low-frequency components increase in energy at the expense of the less disturbed high-frequency region. In healthy children and adults and in obstructed patients, the coherences and the coefficients of variation of the respiratory system impedance (Zrs) at 2 and 3 Hz were studied in the case of three test signals of 2-15 Hz bandwidth. Signals T1 and T2 had a flat power spectrum, whereas the components of T3 decreased sharply between 2 and 5 Hz; T1 was generated by simple random selection of phase angles, while optimization for maximum energy was done for T2 and T3. Optimization alone (T2) increased the reliability of the Zrs estimates at all frequencies, whereas enhancement of the low-frequency power (T3) resulted in a radical improvement of the estimates at 2 and 3 Hz, without loss in reliability at higher frequencies.

Adult↗

PubMed1988

Strict insulin therapy normalises organ nitrogen contents and the capacity of urea nitrogen synthesis in experimental diabetes in rats.

Rats with experimental diabetes due to streptozotocin (75 mg/kg body weight) and free access to food were divided into two groups. One group (n = 9) was optimally treated with insulin (glucosuria less than 4.0 mmol/24 h), using heat treated very long-acting ultralente insulin. The other group (n = 10) was poorly treated with insulin (glucosuria 20-30 mmol/24 h). The nitrogen balance and energy balance of optimally treated diabetic rats was positive and not different from the control group (n = 6). In the poorly treated diabetic rats the nitrogen balance was reduced whereas the energy balance was not different from that of control rats. After 4 weeks the fasting glucagon was: 50 +/- 21 ng/l (mean +/- SEM) in control rats, 62 +/- 18 ng/l in optimally treated diabetic rats and 249 +/- 58 ng/l in poorly treated diabetic rats (p less than 0.01). The capacity of urea nitrogen synthesis determined during alanine loading was: 9.6 +/- 1.0 mumol/(min 100 g body weight) in control rats, 10.6 +/- 1.7 mumol/(min 100 g body weight) in optimally treated diabetic rats and 17.3 +/- 1.3 mumol/(min 100 g body weight) in poorly treated diabetic rats (p less than 0.01). Nitrogen contents of carcass, heart, intestines, liver, and kidneys as determined by Kjeldahl analyses were identical in control rats and optimally treated diabetic rats.(ABSTRACT TRUNCATED AT 250 WORDS)

Alanine↗

PubMed2001

A new potential toxaphene congener: synthesis, GC/EI-MS study, crystal structure, NMR analysis, and ab initio calculations of 3-endo,5-endo-dichloro-7,7-bis-chloromethyl-4-dichloromethyl-tricyclo[2.2.1.0(2,6)]heptane.

A new potential toxaphene congener 3-endo,5-endo-dichloro-7,7-bis-chloromethyl-4-dichloromethyl-tricyclo[2.2.1.0(2,6)]heptane 2 has been isolated from reaction mixture obtained by the chlorination of 2-exo, 10,10-trichlorobornane 1. The X-ray structural analysis of 2 revealed an unusual tricyclic structure, where the two chlorine atoms occupying endo-positions are in close spatial proximity with each other and near to the neighbouring CHCl2 group. Further, it revealed that the symmetry of the molecule is distorted. The 1H and 13C NMR spectra of 2 have been assigned by means of 1H, 1H double-quantum filtered correlation spectroscopy (DQF COSY), PFG 1H, 13C HMQC (pulsed field gradient heteronuclear multiple-quantum coherence), 1H, 13C heteronuclear multiple bond correlation (HMBC) experiments, and computer aided 1H NMR spectral analysis. The asymmetry of 2 is also discernible on the 1H NMR parameters. In addition, gas chromatographic (GC) properties and electron impact (EI) mass spectrum of 2 has been studied. Ab initio Hartree-Fock (HF) method with the basis set 6-31G(d) has been used for the optimization of the equilibrium geometry and calculation of total energy for 2. The optimized geometry is in good agreement with the crystal structure. According to the rotation energy profile calculated at the HF/6-31G(d) level, rotation of the chloromethyl and dichloromethyl groups are highly unlikely at the room temperature.

Environmental Pollutants↗

PubMed2005

Microbial fuel cells: novel biotechnology for energy generation.

Microbial fuel cells (MFCs) provide new opportunities for the sustainable production of energy from biodegradable, reduced compounds. MFCs function on different carbohydrates but also on complex substrates present in wastewaters. As yet there is limited information available about the energy metabolism and nature of the bacteria using the anode as electron acceptor; few electron transfer mechanisms have been established unequivocally. To optimize and develop energy production by MFCs fully this knowledge is essential. Depending on the operational parameters of the MFC, different metabolic pathways are used by the bacteria. This determines the selection and performance of specific organisms. Here we discuss how bacteria use an anode as an electron acceptor and to what extent they generate electrical output. The MFC technology is evaluated relative to current alternatives for energy generation.

Biodegradation, Environmental↗

PubMed2003

TOUCHSTONE II: a new approach to ab initio protein structure prediction.

We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting C(alpha) atoms, with attached C(beta) atoms and side-chain centers of mass. The model force field includes various short-range and long-range knowledge-based potentials derived from a statistical analysis of the regularities of protein structures. The combination of these energy terms is optimized through the maximization of correlation for 30 x 60,000 decoys between the root mean square deviation (RMSD) to native and energies, as well as the energy gap between native and the decoy ensemble. To accelerate the conformational search, a newly developed parallel hyperbolic sampling algorithm with a composite movement set is used in the Monte Carlo simulation processes. We exploit this strategy to successfully fold 41/100 small proteins (36 approximately 120 residues) with predicted structures having a RMSD from native below 6.5 A in the top five cluster centroids. To fold larger-size proteins as well as to improve the folding yield of small proteins, we incorporate into the basic force field side-chain contact predictions from our threading program PROSPECTOR where homologous proteins were excluded from the data base. With these threading-based restraints, the program can fold 83/125 test proteins (36 approximately 174 residues) with structures having a RMSD to native below 6.5 A in the top five cluster centroids. This shows the significant improvement of folding by using predicted tertiary restraints, especially when the accuracy of side-chain contact prediction is >20%. For native fold selection, we introduce quantities dependent on the cluster density and the combination of energy and free energy, which show a higher discriminative power to select the native structure than the previously used cluster energy or cluster size, and which can be used in native structure identification in blind simulations. These procedures are readily automated and are being implemented on a genomic scale.

Algorithms↗

PubMed2006

Design, synthesis, and conformational dynamics of a gated molecular basket.

We have developed a synthesis and examined the conformational behavior and recognition properties of dynamic molecular containers 1-3. As follows from the 1H NMR dilution, diffusion NMR, and vapor pressure osmometry measurements, compound 1 has a low affinity for intermolecular aggregation and is mostly present in monomeric form in dilute chloroform solutions. Inspecting the O-H chemical shift resonances of 1, 3, and model compound 4 as a function of temperature afforded the deltadelta/deltaT coefficients of 17.0, 17.3, and 4.7 ppb K(-1), respectively. In combination with the results from variable temperature 1H NMR and IR measurements, the existence of conformers of 1 and 3 in equilibrium, each having a different extent of hydrogen bonding, was confirmed. Molecular mechanics calculations suggested 1a as the most favorable conformation, with three additional conformers, 1b, 1c, and 1d, populating local energy minima. Further optimization of each of the four conformers using semiempirical PM3 and ab initio (HF/6-31G) methods allowed a determination of their relative free energies and the corresponding Boltzmann population distributions which were heavily weighted toward 1a. A computed composite IR spectrum of a fraction-weighted mixture of the conformers of 1 reproduced the experimentally observed IR spectrum in its structural features, leading to a conclusion that conformer 1a indeed dominates the equilibrium. The egg-shaped cavity of 1 (136.6 angstroms3) is complementary in size, shape, and electrostatic potential to chloroform (74.9 angstroms3). A single-crystal X-ray study of 2 revealed a disordered chloroform molecule positioned inside the cavitand along its C3 axis.

Journal Article↗

PubMed2002

The cell membrane and the struggle for life of lactic acid bacteria.

The major life-threatening event for lactic acid bacteria (LAB) in their natural environment is the depletion of their energy sources and LAB can survive such conditions only for a short period of time. During periods of starvation LAB can exploit optimally the potential energy sources in their environment usually by applying proton motive force generating membrane transport systems. These systems include in addition to the proton translocating F0F1-ATPase: a respiratory chain when hemin is present in the medium, electrogenic solute uptake and excretion systems, electrogenic lactate/proton symport and precursor/product exchange systems. Most of these metabolic energy-generating systems offer as additional bonus the prevention of a lethal decrease of the internal and external pH. LAB have limited biosynthetic capacities and rely heavily on the presence of essential components such as sources of amino acids in their environment. The uptake of amino acids requires a major fraction of the available metabolic energy of LAB. The metabolic energy cost of amino acid uptake can be reduced drastically by accumulating oligopeptides instead of the individual amino acids and by proton motive force-generating efflux of excessively accumulated amino acids. Other life-threatening conditions that LAB encounter in their environment are rapid changes in the osmolality and the exposure to cytotoxic compounds, including antibiotics. LAB respond to osmotic upshock or downshock by accumulating or releasing rapidly osmolytes such as glycine-betaine. The life-threatening presence of cytotoxic compounds, including antibiotics, is effectively counteracted by powerful drug extruding multidrug resistance systems. The number and variety of defense mechanisms in LAB is surprisingly high. Most defense mechanisms operate in the cytoplasmic membrane to control the internal environment and the energetic status of LAB. Annotation of the functions of the genes in the genomes of LAB will undoubtedly reveal additional defense mechanisms.

Biological Transport↗

PubMed2005

Valence electron energy-loss spectroscopy in monochromated scanning transmission electron microscopy.

With the development of monochromators for (scanning) transmission electron microscopes, valence electron energy-loss spectroscopy (VEELS) is developing into a unique technique to study the band structure and optical properties of nanoscale materials. This article discusses practical aspects of spatially resolved VEELS performed in scanning transmission mode and the alignments necessary to achieve the current optimum performance of approximately 0.15 eV energy resolution with an electron probe size of approximately 1 nm. In particular, a collection of basic concepts concerning the acquisition process, the optimization of the energy resolution, the spatial resolution and the data processing are provided. A brief study of planar defects in a Y(1)Ba(2)Cu(3)O(7-)(delta) high-temperature superconductor illustrates these concepts and shows what kind of information can be accessed by VEELS.

Journal Article↗

PubMed2001

Altered energy metabolism in anorexia nervosa.

Optimal nutritional rehabilitation of anorexia nervosa requires more information concerning actual energy and substrate requirements. To this end, indirect calorimetry was performed in female patients (n=34, age 20.9+/-1.2 yr, body mass index [BMI] 15.6+/-0.2 kg/m(2); mean+/-SEM) soon after commencement of refeeding and at the time of discharge from hospital (n=18, BMI 19.0+/-0.3 kg/m(2)). Healthy female controls (n=18, age 24.6+/-1.3 yr, BMI 21.6+/-0.6 kg/m(2)) were also tested. Resting energy expenditure (REE) and respiratory quotient (RQ) were measured in the fasting state, followed by diet-induced thermogenesis (DIT) and RQ over a 4 h period following a 100 g oral glucose load. Compared with post-refeeding patients and controls, pre-refeeding patients had a high basal RQ and a low REE, with a paradoxically higher DIT (13.2+/-0.9% of REE vs. 8.3+/-1.2% and 8.6+/-0.9% in post-refeeding patients and controls, respectively). RQ values in pre-refeeding patients exceeded unity following the glucose load, probably reflecting net lipogenesis, whereas in the post-refeeding patients, post-glucose RQ was similar to that of controls, suggesting premature curtailment of lipogenesis. These data demonstrate energy wasting in emaciated patients with anorexia nervosa. Biological repair processes could account for disproportionate energy loss early in refeeding and there may be some later impediment to full restoration of fat stores.

Adolescent↗

PubMed2000

A method for parameter optimization in computational biology.

Models in computational biology, such as those used in binding, docking, and folding, are often empirical and have adjustable parameters. Because few of these models are yet fully predictive, the problem may be nonoptimal choices of parameters. We describe an algorithm called ENPOP (energy function parameter optimization) that improves-and sometimes optimizes-the parameters for any given model and for any given search strategy that identifies the stable state of that model. ENPOP iteratively adjusts the parameters simultaneously to move the model global minimum energy conformation for each of m different molecules as close as possible to the true native conformations, based on some appropriate measure of structural error. A proof of principle is given for two very different test problems. The first involves three different two-dimensional model protein molecules having 12 to 37 monomers and four parameters in common. The parameters converge to the values used to design the model native structures. The second problem involves nine bumpy landscapes, each having between 4 and 12 degrees of freedom. For the three adjustable parameters, the globally optimal values are known in advance. ENPOP converges quickly to the correct parameter set.

Algorithms↗

PubMed1996

High-performance liquid chromatography/continuous-flow liquid secondary ion mass spectrometry of flavonoid glycosides in leguminous plant extracts.

A method for the identification of flavonoid glycosides utilizing continuous-flow liquid secondary ion mass spectrometry (CF-LSIMS) is presented. Minimum detectable quantities (MDQs) were determined for three model flavonoid glycosides (rutin, naringin and esculin) by both positive ion direct insertion probe (DIP)-LSIMS (1.6 nmol, 1.7 nmol and 730 pmol, respectively) and positive ion CF-LSIMS (330 pmol, 340 pmol and 290 pmol, respectively). Optimization of CF-LSIMS instrumental parameters was performed using the model compound rutin. Parameters optimized included mobile phase composition, glycerol concentration, mobile phase flow rate, ion source temperature, acceleration lens potential (amplitude and polarity) and Cs+ primary ion energy. Final instrumental optimization yielded an MDQ of 1.0 ng (1.6 pmol) for rutin by flow-injection CF-LSIMS. The optimization parameters were utilized in the identification of flavonoid glucosides in alfalfa (Medicago sativa L) and chickpea (Cicer arietinum) extracts by high-performance liquid chromatogrphy/CF-LSIMS. The results support the controversial identification of a major extract component as formononetin-7-O-glucoside-6"-malonate as opposed to afrormosin-7-O-glucoside-6"-malonate.

Chromatography, High Pressure Liquid↗

PubMed1996

Improved design of stable and fast-folding model proteins.

BACKGROUND: A number of approaches to design stable and fast-folding sequences for model polypeptide chains have been based on the premise that optimization of the relative energy of the native conformation (or Z-score) is sufficient to yield stable and fast-folding sequences. Although this approach has been successful, for longer chains it often yielded sequences that failed to fold cooperatively, instead having multidomain folding behavior. RESULTS: We show that one of the factors determining single-domain or multidomain folding behavior is the dispersion of energies of native contacts. So, we study folding of sequences optimized to have the same native conformation as a global energy minimum but having different dispersion of native contact energies. Our results suggest that under conditions at which native conformation is stable, the best-folding proteins are those that have smaller heterogeneity of native contact energies. For them, the folding transition is all-or-none. On the other hand, proteins with greater heterogeneity of native contact energies have more gradual multidomain folding transition and fold into stable native conformation much slower than those proteins with small dispersion of native contact energies.

Amino Acid Sequence↗

PubMedDate not supplied

Determination of effective energies in CT calibration.

The effective energy of a polychromatic beam for a Computed Tomography (CT) scanner can be measured directly only with difficulty. However, a linear relationship exists between the measured CT numbers and corresponding attenuation coefficients of known materials at the effective energy of the x-ray beam. The effective energy can then be determined by searching all energies for the best linear correlation between the CT numbers and the attenuation coefficients. This can be performed by two methods: graphically, by means of choosing visually the straightest of the fitted lines or, mathematically, by maximizing the correlation coefficient. The energy corresponding to the optimal fit is therefore selected as the effective energy. The latter method was implemented by computer and demonstrated by scanning the AAPM phantom, which contained known materials, and determining the effective energies and the relationship between the linear attenuation coefficients and CT numbers for three commercial units.

Tomography, X-Ray Computed↗