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Orientational sampling and rigid-body minimization in molecular docking.

The biological activities of proteins depend on specific molecular recognition and binding. Computational methods for predicting binding modes can facilitate the discovery and design of ligands and yield information on the factors governing complementarity. The DOCK suite of programs has been applied to several systems; here, the degree of orientational sampling required to reproduce and identify known binding modes, with and without rigid-body energy minimization, is investigated for four complexes. There is a tradeoff between sampling and minimization. The known binding modes can be identified with intensive sampling alone (10,000 to 20,000 orientations generated per system) or with moderate sampling combined with minimization. Optimization improves energies significantly, particularly when steric clashes are present, and brings many orientations closer to the experimentally observed position. Whether or not minimization is performed, however, sampling must be sufficient to find at least one structure in the vicinity of the presumed true binding mode. Hybrid approaches combining docking and minimization are promising and will become more viable with the use of faster algorithms and the judicious selection of fewer orientations for minimization.

Carboxypeptidases↗

Optimized retrograde cerebral perfusion reduces ischemic energy depletion.

It has been reported that retrograde cerebral perfusion (RCP) provides minimal capillary flow; however, the extent to which RCP can provide aerobic metabolic support is unknown. We evaluated whether perfusate composition optimization for RCP would preserve brain energy metabolism during hypothermic circulatory arrest (HCA) at 20 degrees C in rats. Three types of perfusates were prepared: hemoglobin-free saline, rat red blood cells, and artificial blood substitute (liposome-encapsulated hemoglobin); perfusates were made hypertonic, cooled to 20 degrees C, and oxygenated and CO(2) was administered (pH-stat management). Circulatory arrest was induced in 24 pH-stat-ventilated Wistar rats that had been surface cooled to 20 degrees C; 18 were assigned to the RCP group in which one of the three ( n = 6 each) perfusates was administered via the maxillary vein, and 6 received no perfusion. In two similarly surface-cooled rats (controls), brains were excised when the temperature reached 20 degrees C. After 20 min of RCP or HCA, brains were excised and immediately frozen; brain high-energy phosphates, adenosine, and water content were measured. The liposome-encapsulated hemoglobin perfusate preserved levels of brain tissue adenosine triphosphates and energy charge, but not significantly better than rat red blood cells. Both maintained significantly higher levels than perfusion with oxygenated saline or hypothermic circulatory arrest alone ( P = 0.0419-0.0001), under which regimes high-energy phosphates and energy charge declined to similar low values. RCP with hypertonic solution prevented brain edema. RCP with optimized composition perfusate (pH-stat, hypertonic rat red blood cells or liposome-encapsulated hemoglobin) reduced ischemic energy depletion during 20 min of HCA at 20 degrees C in rats.

Adenosine Triphosphate↗

Quantum chemical and molecular mechanics studies on the binding of stereoisomers of the oligopeptide antibiotics amidinomycin and noformycin to the minor groove of B-DNA.

Ab initio calculations (Hartree-Fock) using the 6-31G basis set have been performed on two chiral oligopeptide antitumor antibiotics amidinomycin 5 and noformycin 6. The latter are DNA minor groove binding agents related to the A.T recognizing netropsin 4 and distamycin 3 but, unlike the latter, bear stereocenters (two for 5 and one for 6) that may be expected to affect binding to the B-DNA receptor. Geometry optimized conformations, energies and distribution of electrostatic charges within the molecules were derived. The rotational barrier for bond C3-C6 in 6 was calculated to be ca. 6 kcal.mole-1 and the dipole moment for 6 was 7.69D and for 5 was 5.58D. The ab initio derived parameters of the geometry optimized conformations of the different possible stereoisomeric forms of 5 and 6 were used to interpret their different interactions with the minor groove of DNA at both A.T and G.C sequences and the results were compared with molecular mechanics calculations. The order of binding of the four stereoisomers of 5 at the preferred (A.T)n sequences by both ab initio and molecular mechanics calculations is 1S,3R > RR > RS > SS. The predicted energy differences for complexation with DNA of the other stereoisomers from that of 1S,3R are: RR (4.2%); RS (6.7%) and SS (21.5%). In the case of noformycin the 4R structure binds more effectively than the enantiomer. Considerations of phasing in the computed distances between hydrogen bond donating sites in the DNA-bound antibiotics provide further insight into the binding processes. In the complexes of noformycin 6 the N-N1-N4 and N1-N5 distances (9.05 and 9.15 A respectively for 4R-6 and 9.23 and 9.26 A respectively for 4S-6) are close to the optimum value of 9.1 A for effective binding. In the case of amidinomycin 5 the best agreement with the optimum value occurs with the strongest binding diastereomer 1S,3R (N1-N3 = 8.91, N1-N4 = 9.41 A). The unexpected result, consistent in both ab initio and molecular mechanics treatments, is that, in contrast to the cases of kikumycin 1 and anthelvencin 2, the natural 3S configuration of 5 and 4S of 6 do not confer maximal binding efficiency. This suggests that biogenetic factors in the generation of the oligopeptide antibiotics lead to maximum DNA binding in the cases of kikumycin and anthelvencin but not in the cases of amidinomycin and noformycin.

Anti-Bacterial Agents↗

Analysis of the defibrillation efficacy for 5-ms waveforms.

INTRODUCTION: Empirical studies have shown that biphasic defibrillation waveforms are more efficacious than monophasic waveforms. However, a more systematic approach to waveform development might be more productive. This study tested 147 multiphasic waveforms uniformly sampled from all possible 5-ms waveforms. METHODS AND RESULTS: One hundred ninety-eight guinea pigs (850-1,050 g) received 30 episodes of ventricular fibrillation followed by transthoracic defibrillation. The first 10 shocks were used to determine the ED(50) for a biphasic control. Then, 20 waveforms including 2 controls were tested once at the ED(50). Of the 147 waveforms tested here, 21 waveforms showed equivalent or greater efficacies than the biphasic control, with one being statistically more efficacious (P < 0.05). Two fundamental assumptions were addressed: (1) similarly efficacious waveforms are analytically similar, and (2) a single optimal waveform can be described. The mean percentage of similarly efficacious waveforms with similar shapes was greater than zero in the most efficacious 21 waveforms (P = 0.023), but less efficacious waveforms showed randomly distributed shapes. Cluster analysis revealed that the best waveforms share a major phase containing most of the defibrillation energy. The optimal waveform shape extrapolated from the sample waveforms was a 2.5/1-ms biphasic-type waveform (highest correlation r = 0.701, P < 0.001). CONCLUSION: This work supports the assumption that efficacious waveforms are similarly shaped and the notion that one single optimum exists.

Animals↗

Receiver operating characteristic analysis for the selection of threshold values for detection of capping in powder compression.

The acoustic emission (AE) energy obtained from compressing lactose powder to form pharmaceutical tablets was chosen for condition monitoring of the tablets. The method used was based on the setting of an AE energy decision threshold such that problems of tablet capping and lamination were successfully identified. Capping and lamination are the most common types of problem that can occur in tablets manufacturing using a powder compression process. To assess the performance of a classifier, use was made of a receiver operating characteristic curve (ROC) obtained by plotting the correct detection probability against the false alarm probability based on AE energy distributions for capped and non-capped tablets. The area under the ROC curve, referred to as the AUC, determines the level of competency of the classifier. A value of 0.5 suggests a mere hazarding of guesses whilst a value of 1 indicates correct classification every time. The AE energy approach for tablet capping monitoring gives an AUC value of 0.96, thereby suggesting the possibility of a highly accurate classifier. With the assumption that penalties for false alarm and missed detection are equally severe, using the graphical method of expected penalty cost (EPC), the optimal AE energy decision threshold was established to be 1.2x10(8) units, at which the maximum correct capping detection rate of 95% was achieved. The paper also explains how a decision threshold can be obtained when the two penalties are not equal.

Acoustics↗

A new and improved vitreoretinal erbium:YAG laser scalpel: long-term morphologic characteristics of retinal-choroidal injury.

BACKGROUND AND OBJECTIVE: To report a modified erbium:YAG laser scalpel designed to incise tissue more efficiently and safely than other systems reported to date. MATERIALS AND METHODS: An erbium:YAG laser delivery system was built to deliver laser energy in bursts of micropulses with a repetition rate of 1,000 Hz. The laser was coupled to handpieces with tip designs equipped with shields, backstops, and beveled, straight, and flexible fibers. In vivo studies in the rabbit eye were performed to determine damage threshold, optimal pulse energy, and burst frequency required to make incisions in the retina and choroid. The safety profile and directional control provided by the handpieces were tested for consistency. Partial- and full-thickness retinal-choroidal incisions were examined clinically and histologically at various time intervals. RESULTS: The best incisions were obtained at a fluence of 3.5 J/cm2 or greater, a burst repetition rate of 10 to 40 Hz, and 6 micropulses per burst. Retinal damage occurred when incising laser energy was used 500 microm or closer to the retinal surface. Depth of penetration of laser energy did not depend on burst repetition rate. The use of laser endoprobes equipped with shields and backstops provides absolute protection from stray laser energy in aqueous media. The use of flexible beveled fiber tips provides reliable, accurate directional control. Retinal-choroidal incisions and damage resulted in local retinal-choroidal degeneration and adhesion formation. CONCLUSION: The modifications to the erbium:YAG laser scalpel provide a more efficient, versatile, and safe application to vitreoretinal surgery than any system reported to date.

Animals↗

The influence of the rotational energy of a flywheel on the load pulse sum during pedalling on a cycle ergometer.

Employing seven male subjects, the influence of four different ergometer flywheels with the moments of inertia at the crankshaft (J') = 5.5, 10.5, 16.5, and 19.5 kg.m2 on 6-min load pulse sum (LPS), the heart rate integrated over 6-min was investigated. The J' was demonstrated to influence LPS at each of the corresponding rotational energies of the flywheels (75, 144, 226 and 276 J at 50 rev.min-1) in the four work-load steps (50, 100, 150 and 200 W). Between the values J' = 5.5 kg.m2 and 10.5 kg.m2 the LPS decreases, to rise again in the range J' = 10.5 kg.m2-19.5 kg.m2. For equal work-loads the minimum LPS was reached at a J' of 10.5 kg.m2. For the workloads of 100, 150 and 200 W it was possible to show statistically significant differences. The moment of inertia of ergometer flywheels J has a smoothing effect on the fluctuations of the rotational speed which are unavoidable during work on a cycle ergometer. The flywheel stores the leg forces acting on the pedals as rotational energy and opposes any rotational acceleration. If the J used is too small, equalization of the fluctuations of the rotational speed remains unsatisfactory. Flywheels with larger J require larger torques at the crankshaft for acceleration. For the most effective delivery of work to a cycle ergometer, an optimal rotational energy of the flywheel was found. For equal physical work, smaller or larger rotational energies require a larger expenditure of biological energy. A J' = 11 +/- 2 kg.m2 was incorporated into the draft for the German standard DIN 13,405 -- cycle-type ergometers.

Adult↗

Novel and global approach of the complex and interconnected phenomena related to the contact line movement past a solid surface from hydrophobized silica gel.

In this work a generalized hydrodynamic theory for water flow into a mesoporous matrix from hydrophobized silica gel is suggested. Although we examine a fluid dynamics problem, the motion of the water-gas-solid contact line past a hydrophobized silica gel surface, motivation for such research derives from the investigation of a novel principle of mechanical energy dissipation, called surface dissipation, and its attached machine element, named a colloidal damper (CD). Similar to a hydraulic damper, this absorber has a cylinder-piston structure, but oil is replaced by a colloid consisting of a mesoporous matrix and a lyophobic liquid. Here, the mesoporous matrix is from silica gel modified by linear chains of alkyldimethylchlorosilanes and water is the associated lyophobic liquid. Mainly, the colloidal damper energy loss can be explained by the dynamic contact angle hysteresis in advancing (liquid displaces gas) and receding motion (gas displaces liquid); such hysteresis occurs due to the geometrical and chemical heterogeneities of the solid surface. Although this new kind of dissipation could be attractive for many applications, the subject remains almost unexplored in the scientific literature. Many different, complex, and interconnected aspects are related to this subject: capillary hydrodynamics, slippage effect, contact angle hysteresis, estimation of dissipated energy, thickness optimization of the grafted layer on the surface of the mesoporous matrix, etc. For this reason, a novel and global approach to all the complex and interconnected phenomena related to the contact line movement past a solid surface from hydrophobized silica gel is proposed. Our approach has a modest experimental basis but this is compensated for with rich references to other experimental and theoretical work oriented to the study of surface phenomena in such systems. We tried to sort the existing results and to find the right place for each in building our global view of the problem. This work is structured as follows. The measurement technique of the hysteresis loop is described. From experimental data one calculates the dissipated energy versus length of the grafted molecule on the silica gel surface. These results are justified by flow analysis. Generalized hydrodynamic theory means here that the basic structure of the Navier-Stokes equations is kept, but in order to include the relation between macroscopic flow and molecular interactions, slip is allowed on the solid wall. The nanopillar architecture of the silica gel hydrophobic coating is described. Concepts of slip and contact angle hysteresis are detailed and their connection is revealed. During adsorption, water penetrates the pore space by maintaining contact with the top of the coating molecules (region of -CH(3) groups); after that, water is forced into and partially or totally fills the space between molecules (region of -CH(2) groups). In such circumstances, at the release of the external pressure, desorption occurs. An original energetic-barriers approach is proposed to understand the filling of the nanosize canals which occur in the hydrophobic grafted layer. Employing this energetic-barriers approach, one finds the optimum length of the grafted molecule which maximizes the dissipated energy of the CD reversible cycle. Such results are useful for the appropriate design of ultrahydrophobic surfaces in general, and for the optimal design of a hydrophobic coating of a mesoporous matrix destined for CD use.

Journal Article↗

Active leg stiffness and energy stored in the muscles during maximal counter movement jump in the aged.

The purpose of this study was to examine the effects of age on active leg stiffness adjustment, electromyogram (EMG) activities and energy stored during eccentric and concentric phases in performing a maximal functional task involving stretch-shorten cycle. Ten young (24.3+/-2 years) and 10 old (68.6+/-5 years) healthy male subjects were filmed during maximal performance of counter movement jump (CMJ) and squat jump (SJ) on force plate. Integrated EMG (IEMG), ground reaction force (GRF), active leg stiffness, energy stored/returned and active work done by the muscles were compared between two groups on eccentric (ECC) and concentric (CON) phases of CMJ. The GRF, leg stiffness and energy stored in ECC and GRF, IEMG, energy returned and active work in CON were less in the elderly (p<0.05). These results demonstrate that the neuromuscular function of adjusting active stiffness, storing elastic energy and optimizing the performance may decrease with age during CMJ.

Adult↗

[Quantum chemistry study on fluorescence spectra of four flavonoid compounds].

The semi-empirical method PHF/PM3 of quantum chemistry was used for studying the fluorescence spectra of four flavonoid compounds. Firstly, the geometries of these four compounds were optimized by energy gradient method. The results show that in these four copmounds, the two six-membered rings on the left are in the same plane, but these are different torsion angles between this plane and the benzene-ring plane on the right. Secondly, vibrational analyses were performed for the four optimized configurations. There is no imaginary frequency in vibrational analyses. This indicates that the optimized configurations are essentially reasonable. Finally, on this basis, the electronic spectra were calculated by CIS method. All the calculated results are basically consistent with experimental values.

Flavonoids↗

Physiological interactions between diet and exercise in the etiology and prevention of ischaemic heart disease.

Modern eating habits and sedentary life-style interact to promote atherosclerosis and increase risk of ischemic heart disease (IHD). Apparent sites of interaction affecting severity of coronary atherosclerosis are body weight, blood lipid-lipoproteins, blood pressure, glucose-insulin dynamics, and platelet aggregation. In addition the conditioning effects of physical activity on the heart and adrenergic system reduce myocardial oxygen and coronary blood flow requirements, and raise the threshold for ischemia and ventricular dysrhythmias in the presence of existing coronary atherosclerosis. Dietary recommendations to reduce risk factors for IHD are to decrease intake of total and saturated fat, cholesterol, and sodium, increase intake of complex carbohydrates of plant origin and polyunsaturated fatty acids from vegetable oils and fish, adjust energy intake to maintain or achieve desirable body weight, and keep alcoholic consumption low. Epidemiologic evidence also suggests that risk of IHD can be further reduced with 30 to 60 minutes/day of even light or moderate intensity physical activity, including working around the home and yard, walking, exercise or sports. An optimal daily energy expenditure for IHD prevention appears to be between 150 and 300 kcal/day.

Blood Coagulation↗

Lanthanides to quantum dots resonance energy transfer in time-resolved fluoro-immunoassays and luminescence microscopy.

A time-resolved fluoro-immunoassay (TR-FIA) format is presented based on resonance energy transfer from visible emitting lanthanide complexes of europium and terbium, as energy donors, to semiconductor CdSe/ZnS core/shell nanocrystals (quantum dots, QD), as energy acceptors. The spatial proximity of the donor-acceptor pairs is obtained through the biological recognition process of biotin, coated at the surface of the dots (Biot-QD), and streptavidin labeled with the lanthanide markers (Ln-strep). The energy transfer phenomenon is evident from simultaneous lanthanide emission quenching and QD emission sensitization with a 1000-fold increase of the QD luminescence decay time reaching the hundred mus regime. Delayed emission detection allows for quantification of the recognition process and demonstrated a nearly quantitative association of the biotins to streptavidin with sensitivity limits reaching 1.2 pM of QD. Spectral characterization permits calculation of the energy transfer parameters. Extremely large Förster radii (R(0)) values were obtained for Tb (104 A) and Eu (96 A) as a result of the relevant spectral overlap of donor emission and acceptor absorption. Special attention was paid to interactions with the varying constituents of the buffer for sensitivity and transfer efficiency optimization. The energy transfer phenomenon was also monitored by time-resolved luminescence microscopy experiments. At elevated concentration (>10(-)(5) M), Tb-strep precipitated in the form of pellets with long-lived green luminescence, whereas addition of Biot-QD led to red emitting pellets, with long excited-state decay times. The Ln-QD donor-acceptor hybrids appear as highly sensitive analytical tools both for TR-FIA and time-resolved luminescence microscopy experiments.

Journal Article↗

Interaction of scanning probes with semiconductor nanocrystals; physical mechanism and basis for near-field optical imaging.

We investigate the modification of photoluminescence (PL) from single semiconductor nanocrystal quantum dots (NCs) in the proximity of metal and semiconducting atomic force microscope (AFM) tips. The presence of the tip alters the radiative decay rate of an emitter via interference and opens efficient nonradiative decay channels via energy transfer to the tip material. These effects cause quenching (or enhancement) of the emitter's PL intensity as a function of its distance from the interacting tip. We take advantage of this highly distance-dependent effect to realize a contrast mechanism for high-resolution optical imaging. AFM tips are optimized as energy acceptors by chemical functionalization with InAs NCs to achieve optical resolution down to 30 nm. The presented experimental scheme offers high-resolution optical information while maintaining the benefits of traditional AFM imaging. We directly measure the PL intensity of single NCs as a function of the tip distance. Our results are in good agreement with calculations made by a classical theoretical model describing an oscillating dipole interacting with a planar mirror.

Journal Article↗

[Cardiotropic characteristics of mildronat].

The paper summarizes the literature data and the authors' own investigations on cardiotropic and clinical-pharmacological properties of Mildronat. The medication normalizes energy metabolism, optimizes the functions of the heart, and improves the health state of patients with angina pectoris and cardiac insufficiency.

Cardiovascular Agents↗

Electrical energy changes conductivity and determines optimal electrotransformation frequency in gram-negative bacteria.

In many bacterial electrotransformation protocols, pulse time is related to the time constant for a capacitor discharging across a sample of fixed resistance. Using an electroporator which controls pulse time independently of the capacitor time constant, we found that the resistance of bacterial suspensions fluctuates widely during capacitor discharge. With three gram-negative species of bacteria, electrotransformation frequency and survival could be more simply related to the electrical energy delivered in each pulse than to component parameters, such as initial field strength, capacitance, and pulse time. In each case, the number of transformants per survivor increased exponentially and leveled off when more than 0.5 to 1.0 J of electrical energy was delivered. An inverse log-linear relationship between survival and energy delivered was also observed for all three species.

Journal Article↗

Osteoarthritis: an example of phenoptosis through autonomic dysfunction?

Phenoptosis, the programmed death of organisms akin to cellular apoptosis, constitutes a type of Darwinian selection that enhances inclusive fitness. It provides a means by which senescent and pre-senescent members can self-terminate if they have incurred sufficient cumulative stress such that their continued survival detracts from inclusive fitness. Sepsis, vascular disease, menopause, cancer, and aging all represent examples of phenoptosis at work. We previously proposed that feed-forward autonomic dysfunction fundamentally drives phenoptosis in all its guises. Accordingly, we now postulate that osteoarthritis defines a type of biomechanical phenoptosis, mediated by feed-forward autonomic dysfunction, and manifested through joint destruction associated with fitness disadvantages. Biomechanical capability plays a significant role in evolutionary fitness, and sustained joint insults such as immobility or undue biomechanical stress may serve as proxies for inferior fitness. By both hindering an individual's ability to compete for energy and increasing that individual's vulnerability to predation, feed-forward joint destruction may facilitate adaptive phenoptosis among impaired or senile members. Empirical data suggests that contrary to common belief, heavy joint use does not necessarily cause osteoarthritis, whereas immobility and neuropathy can predispose to the condition. From a Darwinian perspective, another process mediated by sympathetic activity, the alarm cry of attacked prey, simultaneously promotes the escape of kin while attracting predators and scavengers. By effectively enabling the martyrdom of biomechanically-challenged individuals, osteoarthritis may serve to optimize system energy efficiency in a similar fashion. This framework may generalize to other situations where regenerative capacity dissipates in conjunction with maturation, typically leading to fibrosis. By allowing environmental pressure to sort the phenotypes, imperfect repair mechanisms may accelerate adaptation and optimize long-term inclusive fitness for all individuals. As the basis of competition shifts from biomechanical to cognitive skills, and as novel triggers for physical stress emerge, osteoarthritis may now represent a modern maladaptation.

Apoptosis↗

Protein and energy requirements in healthy and ill paediatric patients.

A reappraisal of available data, together with new studies, suggests that normal infants' energy and protein requirements might be substantially lower than previously estimated. For example, the safe level of protein intake would amount to only 10 g per day during the first 2 years of life and to about 12 g per day during the third. This has direct consequences for the management of malnourished children, particularly for defining an optimal protein:energy ratio. A reduced food intake has long been accepted as the main cause of malnutrition. However, evidence has accumulated suggesting that metabolic dysregulation may also play a part. This is particularly true for proteins. Net protein deposition in the growing child results from protein synthesis rates being higher than protein breakdown. However, this setting can be disrupted by a significant increase in protein breakdown in response to cytokines. This mechanism, which is found in acute as well as in chronic inflammatory processes, may lead to severe protein malnutrition and is not always amenable to nutritional support.

Adolescent↗

Calculations on crystal packing of a flexible molecule, Leu-enkephalin.

Crystal packing calculations have been carried out on a substantial number of conformations of Leu-enkephalin; namely, those obtained both from crystal structures and from energy minimizations on isolated molecules, and with and without waters of crystallization. The known crystal structures represent the most energetically stable packings found. The conformations of the enkephalin molecules in the crystal are not the most stable for an isolated molecule; i.e. intermolecular interactions force the isolated molecule to change conformation in order to achieve a small packing volume and an optimal packing energy in the crystal. It is found that the packing energy of an enkephalin molecule is a reasonably smooth function of its molecular volume in the unit cell, if structures with intermolecular hydrogen bonding are excluded, and is substantially independent of other details of the molecular conformation or of the crystal packing. Hydrogen bonding provides additional stabilization of the crystal structure, and would likely permit crystallization of the system if it is sufficiently dense. Solvent molecules further stabilize the structure when they can also provide intermolecular hydrogen bonds.

Chemical Phenomena↗