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PubMedDate not supplied

Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling.

Structural data of protein-DNA complex show redundancy and flexibility in base-amino acid interactions. To understand the origin of the specificity in protein-DNA recognition, we calculated the interaction free energy, enthalpy, entropy, and minimum energy maps for AT-Asn, GC-Asn, AT-Ser, and GC-Ser by means of a set of ab initio force field with extensive conformational sampling. We found that the most preferable interactions in these pairs are stabilized by hydrogen bonding, and are mainly enthalpy driven. However, minima in the free energy maps are not necessarily the same as those in the minimum energy map or enthalpy maps, due to the entropic effect. The effect of entropy is particularly important in the case of GC-Asn. Experimentally observed structures of base-amino acid interactions are within preferable regions in the calculated free energy maps, where there are many different interaction configurations with similar energy. The full geometry optimization procedure using ab initio molecular orbital method was applied to get the optimal interaction geometries for AT-Asn, GC-Asn, AT-Ser, and GC-Ser. We found that there are various base-amino acid combinations with similar interaction energies. These results suggest that the redundancy and conformational flexibility in the base-amino acid interactions play an important role in the protein-DNA recognition.

Adenine↗
PubMed1991

Alternation of the q-switched Nd:YAG laser and the cw argon laser for tunneling through organic material.

The rapidly alternating combination of Nd:YAG laser power of the optical break-down mode with cw energy of the argon laser ablates tissue. Blood agar provides a standard test medium as tissue substitute and permits to quantify the effect of various laser energy combinations to achieve optimal ablation. High wattage of the Nd:YAG laser provides destructive pressure that creates fissures which act as the light traps of a black body simulator for efficient cw argon laser energy conversion to pressure and kinetic energy. Within the fissure the deposited cw argon laser energy is directed by gradients toward the tissue surface so that deepening troughs or tunnels are formed by expelling tissue debris.

Agar↗
PubMed1992

Raised resting energy expenditure in Parkinson's disease and its relationship to muscle rigidity.

1. Resting energy expenditure was measured, by indirect calorimetry, in 12 patients with Parkinson's disease and in eight healthy age-matched control subjects. In the patients with Parkinson's disease measurements were made in both the untreated state and after an injection of the dopamine agonist apomorphine (treated state). In each state muscle rigidity was recorded. 2. Resting energy expenditure was higher in patients with Parkinson's disease in both the treated and untreated states than in the control subjects. Of the patients with Parkinson's disease, seven showed no difference in resting energy expenditure between the two treatment states, whereas four showed markedly increased resting energy expenditure in the untreated state. The change in resting energy expenditure in the untreated state, as compared with the treated state, was significantly related to the development of muscle rigidity in the untreated state. 3. In Parkinson's disease, even in optimally treated patients, resting energy expenditure is raised and this may contribute to the weight loss seen in this disease. Severe muscle rigidity occurring during untreated periods results in a further increase in resting energy expenditure.

Apomorphine↗
PubMedDate not supplied

[Theoretical study of the structure of adenosine deaminase complexes with adenosine analogues: I. Aza-, deaza- and isomeric azadeazaanalogues of adenosine].

The conformational models of the active site of adenosine deaminase (ADA) and its complexes in the basic state with adenosine and 13 isosteric analogues of the aza, deaza, and azadeaza series were constructed. The optimization of the conformational energy of the active site and the nucleoside bound with it in the complex was achieved in the force field of the whole enzyme (the 1ADD structure was used) within the molecular mechanics model using the AMBER 99 potentials. The stable conformational states of each of the complexes, as well as the optimal conformation of the ADA in the absence of ligand, were determined. It was proved that the conformational state that is close to the structure of the ADA complex with 1-deazaadenosine (1ADD) known from the X-ray study corresponds to one of the local minima of the potential surface. Another, a significantly deeper minimum was determined; it differs from the first minimum by the mutual orientation of side chains of amino acid residues. A similar conformational state is optimal for the ADA active site in the absence of the bound ligand. A qualitative correlation exists between the values of potential energies of the complexes in this conformation and the enzymatic activity of ADA toward the corresponding nucleosides. The dynamics of conformational conversions of the active site after the binding of substrate or its analogues, as well as the possibility of the estimation of the inhibitory properties of nucleosides on the basis of calculations, are discussed.

Adenosine↗
PubMed2004

Noninvasive inductive stent heating: alternative approach to prevent instent restenosis?

RATIONALE AND OBJECTIVES: To test noninvasive inductive heating of implanted vascular stents as an alternative approach for reduction or prevention of neointimal hyperplasia. METHODS: Calorimetric pretests were performed to get an orientation on the different parameters of influence for inductive heating of stents. The field strength was set to a maximum of 90 kA/m within a frequency range from 80 kHz to 320 kHz. The electromagnetic field was emitted by a custom-made water-cooled copper winding antenna. A flow model for stent heating was set up to assess the increase in temperature of an expanded 316L stainless steel stent with typical coronary stent dimensions of 3.5 mm diameter and 14.5 mm in length, and in a second setup with 4.5 mm diameter and 13 mm in length, respectively. The stent was located in a bioartificial artery, simulated by a fibrinogen matrix with a defined number of vital cells. The system was exposed to a pulsating perfusion and to an electromagnetic field of 200 kHz over a period of 20 minutes and in a second setup to an electromagnetic field of 300 kHz and increasing intensity up to maximum power-output. Afterward, the artificial vessel was sliced and examined by fluorescence microscopy to evaluate the number and location of damaged cells. RESULTS: The calorimetric tests show an exponential correlation of energy uptake in the stent with an increase in frequency and a constant generator output. At a frequency of 80 kHz, the power uptake accounts for 0.1 W (250 kHz 1.0 W; 320 kHz 1.9 W, respectively). The flow tests confirmed feasibility to elevate the stent temperature from 37 degrees C body temperature to 44 degrees C at 200 kHz within 55 seconds. The temperature increase of the fluid passing the heated vessel region was only marginal (maximum of 0.5 degrees C). Cell necrosis after 20 minutes of treatment was not observed. In a second set-up with 4.5 mm stent diameter, a frequency of 300 kHz and with maximum power output, the stent temperature was increased to 80 degrees C and there was extensive necrosis area around the stent. Treatment time and stent temperature were optimized in further tests. CONCLUSION: Selective noninvasive energy transfer to coronary stainless steel stents by inductive heating is possible within a wide range of power. By thermal conduction, vital cells close to the stent struts can be affected. The frequency of 200 kHz turned out to be favorable. There is still room for further optimization of energy dosage with regard to material and stent design, to induce controlled cell death. The method has potential to serve as an alternative approach for prevention of instent restenosis.

Calorimetry↗
PubMed2006

How to prevent 'half-bastard' progeny? or An alternative for three-parent babies: two-parent babies through transplantation of sperm mitochondria.

Body development and activity depend on the level of internal energy generation. Therefore, unaffected, optimally active mitochondria are indispensable in a healthy and vital body. A mutation in the DNA of the semi-autonomous mitochondria (mtDNA) may cause an inheritable insufficiency that is due to decreased energy generation needed for adequate development. Sperm mitochondria will not enter the egg cell during fusion of male and female gametocytes. Since women with mutated mtDNA will increasingly know and realize the effect of such mutation in their own body, they will more often ask for treatment to stop the effect of such inconvenient mutation in their progeny. Thus far, solutions for this problem were thought to be: (i) nucleus transplantation just after fertilization into a nucleus-free egg cell of a second healthy woman and later (ii) transplantation of healthy mitochondria from a second woman into the egg cell before fertilization. Although both transplantations create babies with three, instead of two-parents that have contributed to the genetic content, in case of the newer mitochondria transplantation technique the part of the second woman is somewhat more reduced, but still clearly present. Thus, assisted-reproduction techniques that mix egg cell mitochondria from two women may create not only 'three-parents' babies, but also fears for 'three-parents' babies, since this handling may create non-scientific problems, especially regarding emotional, ethical, religious and juridical aspects of life. Transplantation of healthy sperm mitochondria of the partner into the egg cell with insufficient mitochondria is thought to be the best solution for this problem, since it may create a 'two-parents' instead of a 'three-parents' baby. This only implies that at the moment of (successful) transplantation the biological dogma is broken that mitochondria are maternally inherited: the mitochondria of the maternal line of the woman will have been substituted by the mitochondria of the maternal line of the man.

Female↗
PubMed2002

Prediction of internal standards in reversed-phase liquid chromatography. II. Selectivity optimization and internal standard prediction for the quantitation of estradiol and levonorgestrel in a transdermal drug delivery formulation based on the linear solvation energy relationships.

This paper describes the results of selectivity optimization and internal standard prediction for the quantitation of estradiol and levonorgestrel in transdermal patches by reversed-phase liquid chromatography (RPLC) based on the linear solvation energy relationships (LSERs). The patch samples are prepared by swelling with acetonitrile (ACN) and the separation is performed by Zorbax Eclipse XDB ODS columns. A proper retention range is first determined with a binary mobile phase of ACN and water based on the general resolution equation. The interference to estradiol from a levonorgestrel impurity is then eliminated by a ternary mobile phase of acetonitrile-methanol-water with a composition predicted by LSERs. When the resolution is optimized and the "open window" in the chromatogram for an internal standard is selected, LSERs are used to predict the candidate compounds to be evaluated as the internal standard. The approach described in this study can be used, in general, to considerably improve the efficiency of RPLC method development, particularly for neutral samples. Finally, the LSER approach for the selectivity optimization is compared with a statistical response surface methodology (RSM) based on a central composite design (CCD) in terms of the effectiveness and number of experiments. It is concluded that, although the predicted mobile phase composition to achieve the desired selectivity is about the same, the LSER approach is more efficient and fewer experiments are required.

Chromatography, Liquid↗
PubMed2006

Towards an understanding of the molecular mechanism of solvation of drug molecules: a thermodynamic approach by crystal lattice energy, sublimation, and solubility exemplified by hydroxybenzoic acids.

Temperature dependencies of saturated vapor pressure and heat capacities for the 2-, 3-, and 4-hydroxybenzoic acids were measured and thermodynamic functions of sublimation calculated (2-hydroxybenzoic acid: DeltaG(sub) (298) = 38.5 kJ/mol; DeltaH(sub) (298) = 96.6 +/- 0.8 kJ/mol; DeltaS(sub) (298) = 191 +/- 3 J/mol . K; 3-hydroxybenzoic acid: DeltaG(sub) (298) = 50.6 kJ/mol; DeltaH(sub) (298) = 105.2 +/- 0.8 kJ/mol; DeltaS(sub) (298) = 180 +/- 2 J/mol . K; 4-hydroxybenzoic acid: DeltaG(sub) (298) = 55.0 kJ/mol; DeltaH(sub) (298) = 113.3 +/- 0.7 kJ/mol; DeltaS(sub) (298) = 193 +/- 2 J/mol . K). Analysis of crystal lattice packing energies based on geometry optimization of the molecules in the crystal using diffraction data and the program Dmol(3) was carried out. The energetic contributions of van der Waals, Coulombic, and hydrogen bond terms to the total packing energy were analyzed. The fraction of hydrogen bond energy in the packing energy increases as: 3-hydroxybenzoic (29.7%) < 2-hydroxybenzoic (34.7%) < 4-hydroxybenzoic acid (42.0%). Enthalpies of evaporation were estimated from enthalpies of sublimation and fusion. Temperature dependencies of the solubility in n-octanol and n-hexane were measured. The thermodynamic functions of solubility and solvation processes were deduced. Specific and nonspecific solvation terms were distinguished using the transfer from the "inert" n-hexane to the other solvents. The transfer of the molecules from water to n-octanol is enthalpy driven process.

1-Octanol↗
PubMed2006

Towards an understanding of the molecular mechanism of solvation of drug molecules: a thermodynamic approach by crystal lattice energy, sublimation, and solubility exemplified by paracetamol, acetanilide, and phenacetin.

Temperature dependencies of saturated vapor pressure for the monoclinic modification of paracetamol (acetaminophen), acetanilide, and phenacetin (acetophenetidin) were measured and thermodynamic functions of sublimation calculated (paracetamol: DeltaGsub298=60.0 kJ/mol; DeltaHsub298=117.9+/-0.7 kJ/mol; DeltaSsub298=190+/-2 J/mol.K; acetanilide: DeltaGsub298=40.5 kJ/mol; DeltaHsub298=99.8+/-0.8 kJ/mol; DeltaSsub298=197+/-2 J/mol.K; phenacetin: DeltaGsub298=52.3 kJ/mol; DeltaHsub298=121.8+/-0.7 kJ/mol; DeltaSsub298=226+/-2 J/mol.K). Analysis of packing energies based on geometry optimization of molecules in the crystal lattices using diffraction data and the program Dmol3 was carried out. Parameters analyzed were: (a) energetic contribution of van der Waals forces and hydrogen bonding to the total packing energy; (b) contributions of fragments of the molecules to the packing energy. The fraction of hydrogen bond energy in the packing energy increases as: phenacetin (17.5%)<acetanilide (20.4%)<paracetamol (34.0%). Enthalpies of evaporation were estimated from enthalpies of sublimation and fusion. Activity coefficients of the drugs in n-octanol were calculated from cryoscopic data and by estimation of dilution enthalpy obtained from solubility and calorimetric experiments (for infinite dissolution). Solubility temperature dependencies in n-octanol and n-hexane were measured. The thermodynamic functions of solubility and solvation processes were deduced. Specific and nonspecific solvation terms were distinguished using the transfer from the "inert" n-hexane to the other solvents. The transfer of the molecules from water to n-octanol is enthalpy driven for paracetamol; for acetanilide and phenacetin, entropy driven.

1-Octanol↗
PubMed1997

5-iodonaphthyl-1-azide labeling of plasma membrane proteins adjacent to specific sites via energy transfer.

We have examined conditions optimal for 5-iodonaphthyl-1-azide (INA4) labeling of membrane proteins proximal to known membrane sites. Membrane-bound INA can be indirectly activated by energy transfer from visible chromophores. We demonstrate that the efficiency of this sensitized activation is enhanced by use of triplet-forming chromophores such as eosin and by deoxygenation. Variation of sensitized activation efficiency with INA concentration indicates that the critical distance for eosin-INA energy transfer in solution is 8-14 A. We suggest that photosensitization occurs through triplet exchange and present an improved labeling protocol based on these findings. This protocol was used to examine whether different accessory proteins are associated with isolated and crosslinked Type I Fc epsilon receptors on 2H3 rat basophilic leukemia cells. 2H3 cells were incubated with eosin-conjugated IgE and irradiated at 514 nm yielding [125I]INA derivatized peptides at 53, 38, 34, and 29 kDa. Crosslinking IgE with mouse anti-rat IgE prior to irradiation labeled three additional proteins at 60, 54, and 43 kDa. These results demonstrate the utility of sensitized INA labeling in characterizing protein-protein interactions in membranes of intact cells and indicate the importance of considering photophysical factors when selecting sensitizers and reaction conditions. We discuss estimation of the size of the membrane region surrounding a sensitizing chromophore within which INA labeling of membrane proteins occurs.

Animals↗
PubMed1993

Contributions of nuclear medicine to the therapy of malignant tumors.

Radionuclides are applied in oncology for diagnosis and therapy. The former demands gamma--emitting radionuclides for labeling specific substrates for localizing malignant tissue and for analyzing tumor metabolism in vivo. Here, positron emission tomography (PET) may register in vivo the metabolism, for example, of glucose, amino acids, and receptors and of potentially useful cytotoxic agents. The advantage of the positron emitting radionuclides of carbon, nitrogen and fluorine is the labeling of substrates without changing substrate specificity within the metabolic reaction chain; also, substrate concentration in situ may be quantified. With regard to therapy radionuclides that emit beta- and alpha-particles or decay by electron capture with the Auger effect, are administered in ionic form or with tumor seeking substrates. Examples are radioiodine for treating thyroid malignancy and radiophosphorus for myeloproliferative diseases. Organically bound radionuclides are given as labeled ligands for specific receptors, such as meta-iodo-benzylguanidine (MIBG) for treating the catecholamine producing tumors phaeochromocytoma and neuroblastoma and labeled monoclonal antibodies for tumors specific receptors. Highly localized energy depositions come from Auger emitters such as 125I and by the neutron capture therapy, where boron-10 in the tumor cell is exposed to thermal neutrons for initiating the B10 (n; alpha) Li7 reaction, especially for treating neuro- and glioblastoma and melanoma. Endogenous radiotherapy with radionuclides rely on the success of delivering a proper amount of energy into individual tumor cells with optimal protection of normal tissue. The inevitable heterogeneity of energy deposition events from such approaches demands careful dosimetric assessment for which the classical methods of dosimetry for percutaneous radiotherapy are not applicable.

Alpha Particles↗
PubMed2006

Computational studies on the photophysical properties and NMR fluxionality of the tetranuclear copper(I) complexes [Cu4(mu-dppm)4(mu4-E)]2+ (E = PPh and S).

Density functional theory (DFT) calculations at the hybrid Perdew, Burke, and Ernzerhof functional level were performed to study the electronic structures of the ground and excited states of the luminescent tetranuclear copper(I) complexes [Cu4(mu-dppm)4(mu4-E)]2+ [E = PPh (1) and S (2)] by using model complexes [Cu4(mu-H2PCH2PH2)4(mu4-E)]2+ [E = PPh (1a) and S (2a)]. The time-dependent DFT method at the same level associated with the conductor-like polarizable continuum model was used to study the nature of the low-energy transitions in their electronic absorption spectra. The results indicate that the lowest energy absorptions of both 1 and 2 are attributed to ligand-to-metal charge-transfer (LMCT) (E --> Cu4) with mixing of metal-cluster-centered (MCC) (3d --> 4s/3d --> 4p) singlet-singlet transitions. The geometry optimizations on the lowest energy triplet state reveal that the emissive states of both complexes involve a considerable structural distortion in which they are derived predominantly from an admixture of 3LMCT (E --> Cu4) and 3MCC (3d --> 4p) origin. In addition to the photophysical properties, the fluxional behavior of 2 observed from the NMR studies but not that of 1 was investigated. It is found that the fluxionality in 2 involves the shuttling of the sulfido ligand through the rectangular Cu4 core.

Journal Article↗
PubMed2005

Particle selection and beam collimation system for laser-accelerated proton beam therapy.

In a laser-accelerated proton therapy system, the initial protons have broad energy and angular distributions, which are not suitable for direct therapeutic applications. A compact particle selection and collimation device is needed to deliver small pencil beams of protons with desired energy spectra. In this work, we characterize a superconducting magnet system that produces a desired magnetic field configuration to spread the protons with different energies and emitting angles for particle selection. Four magnets are set side by side along the beam axis; each is made of NbTi wires which carry a current density of approximately 10(5) A/cm2 at 4.2 K, and produces a magnetic field of approximately 4.4 T in the corresponding region. Collimation is applied to both the entrance and the exit of the particle selection system to generate a desired proton pencil beam. In the middle of the magnet system, where the magnetic field is close to zero, a particle selection collimator allows only the protons with desired energies to pass through for therapy. Simulations of proton transport in the presence of the magnetic field show that the selected protons have successfully refocused on the beam axis after passing through the magnetic field with the optimal magnet system. The energy spread for any given characteristic proton energy has been obtained. It is shown that the energy spread is a function of the magnetic field strength and collimator size and reaches the full width at half maximum of 25 MeV for 230 MeV protons. Dose distributions have also been calculated with the GEANT3 Monte Carlo code to study the dosimetric properties of the laser-accelerated proton beams for radiation therapy applications.

Body Burden↗
PubMed2001

Electron fluence correction factors for various materials in clinical electron beams.

Relative to solid water, electron fluence correction factors at the depth of dose maximum in bone, lung, aluminum, and copper for nominal electron beam energies of 9 MeV and 15 MeV of the Clinac 18 accelerator have been determined experimentally and by Monte Carlo calculation. Thermoluminescent dosimeters were used to measure depth doses in these materials. The measured relative dose at dmax in the various materials versus that of solid water, when irradiated with the same number of monitor units, has been used to calculate the ratio of electron fluence for the various materials to that of solid water. The beams of the Clinac 18 were fully characterized using the EGS4/BEAM system. EGSnrc with the relativistic spin option turned on was used to optimize the primary electron energy at the exit window, and to calculate depth doses in the five phantom materials using the optimized phase-space data. Normalizing all depth doses to the dose maximum in solid water stopping power ratio corrected, measured depth doses and calculated depth doses differ by less than +/- 1% at the depth of dose maximum and by less than 4% elsewhere. Monte Carlo calculated ratios of doses in each material to dose in LiF were used to convert the TLD measurements at the dose maximum into dose at the center of the TLD in the phantom material. Fluence perturbation correction factors for a LiF TLD at the depth of dose maximum deduced from these calculations amount to less than 1% for 0.15 mm thick TLDs in low Z materials and are between 1% and 3% for TLDs in Al and Cu phantoms. Electron fluence ratios of the studied materials relative to solid water vary between 0.83+/-0.01 and 1.55+/-0.02 for materials varying in density from 0.27 g/cm3 (lung) to 8.96 g/cm3 (Cu). The difference in electron fluence ratios derived from measurements and calculations ranges from -1.6% to +0.2% at 9 MeV and from -1.9% to +0.2% at 15 MeV and is not significant at the 1sigma level. Excluding the data for Cu, electron fluence correction factors for open electron beams are approximately proportional to the electron density of the phantom material and only weakly dependent on electron beam energy.

Electrons↗
PubMed2006

Feature-specific structured imaging.

We present a feature-specific imaging system based on the use of structured light. Feature measurements are obtained by projecting spatially structured illumination onto an object and collecting all the reflected light onto a single photodetector. Principal component features are used to define the illumination patterns. The optimal linear minimum mean-square error (LMMSE) operator is used to generate object estimates from the measured features. We study the optimal allocation of illumination energy into each feature measurement in the presence of additive white Gaussian detector noise and optical blur. We demonstrate that this new imaging approach reduces imager complexity and provides improved image quality in high noise environments. Compared to the optimal LMMSE postprocessing of a conventional image, feature-specific structured imaging provides a 38% rms error reduction and requires 400 times fewer measurements for a noise standard deviation of sigma = 2 x 10(-3). Experimental results validate these theoretical predictions.

Algorithms↗
PubMedDate not supplied

[Attainment of an energy minimum by a protein chain does not require a complete sorting of conformations: a computerized experiment and phenomenological theory].

We investigate how a protein chain achieves the lowest energy state by Monte Carlo simulation using a simple beta-sheet protein model. We show the existence of an optimal temperature range where the energy minimum is found quickly without any exhaustive sorting of the chain conformations even for random sequences. This optimal temperature range is determined by the critical temperature characteristic for the onset of freezing-out of a few lowest-energy chain folds. A simple phenomenological model is presented to account for this behavior of the protein chain.

Computer Simulation↗