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Results for “Functional potential”

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PubMed1985

Potential energy functions and the role of the conformational entropy of clonidine-like imidazolidines in determining their affinity for alpha-adrenergic receptors.

Energy as a function of the ring interplanar torsional angle was calculated for 12 2-(phenylimino)imidazolidines by the method of perturbation configuration interaction using localized orbitals. The potential energy functions indicate that the molecules may assume any conformation within rather broad limits. The functions were used in calculating the gas phase and solution conformational entropies. The latter were used as the independent variable in regression analysis to derive equations connecting the conformational entropy with pKi (pKi = -log Ki) for [3H]clonidine displacement (literature data). As a comparison, correlations between pKi and several other parameters (modified neglect of diatomic overlap-computed highest occupied and lowest unoccupied molecular orbital energies and dipole moments; pKa; log P; substituent steric parameters) were sought. Correlation coefficients C greater than 0.6 were obtained with the conformational entropy (-0.77), and the ortho steric parameters (-0.71). The correlation with the conformational entropy was not markedly improved by adding other parameters in multiple regression analysis. This result is discussed in terms of the contribution to the ligand-receptor complexation free energy arising from the conformational restriction of the ligands upon binding to the receptor.

Animals↗

PubMed1975

Well-posed inverse spectral problems.

It is known that if complete spectral data are provided, the potential function in a Sturm-Liouville operator is uniquely determined almost everywhere. If two such operators have spectra that differ in a finite number of eigenvalues, then the corresponding potential functions will no longer be the same. However, as is demonstrated when the nonidentical eigenvalues are almost equal, then the corresponding potential functions will also be nearly equal almost everywhere. Furthermore, if an operator and its spectrum are given and the potential is presumably known and if a second operator is defined in such a way such that its eigenvalues agree with the eigenvalues of the first operator except for a finite set, then the potential corresponding to the second operator can be explicitly found by solving a set of nonlinear ordinary differential equations. Lastly, it is shown that the procedures discussed here and the Gelfand-Levitan procedures are significantly different, and in fact that the Gelfand-Levitan procedure is almost certainly not well posed.

Journal Article↗

PubMed2006

A general perturbation approach for equation of state development: applications to simple fluids, ab initio potentials, and fullerenes.

A new perturbation scheme based on the Barker-Henderson perturbation theory [J. Chem. Phys. 47, 4714 (1967)] is proposed to predict the thermodynamic properties of spherical molecules. Accurate predictions of second virial coefficients and vapor-liquid coexistence properties are obtained for a large variety of potential functions (square well, Yukawa, Sutherland, Lennard-Jones, Buckingham, Girifalco). New Gibbs ensemble Monte Carlo simulations of the generalized exp-m Buckingham potential are reported. An extension of the perturbation approach to mixtures is proposed, and excellent predictions of vapor-liquid equilibria are obtained for Lennard-Jones mixtures. The perturbation scheme can be applied to complex potential functions fitted to ab initio data to predict the properties of real molecules such as neon. The new approach can also be used as an auxiliary tool in molecular simulation studies, to efficiently optimize an intermolecular potential on macroscopic properties or match force fields based on different potential functions.

Journal Article↗

PubMed2005

DFT-based chemical reactivity indices in the Hartree-Fock method. II. Fukui function, chemical potential, and hardness.

A derivation of the density-functional-theory- (DFT) based reactivity indices in the ensemble unrestricted Hartree-Fock (eUHF) method is presented. The comparison between the properties of the reactivity indices evaluated in one and two sets of spin-orbital approach of the eUHF and hyper-unrestricted Hartree-Fock (UHF) methods are shown. All approaches give similar Fukui function irrespective of methodology used, but significantly differ for the global indices, containing important chemical information, and so their interpretation in terms of DFT- based indices can be questionable. The calculation scheme for the indices using the first- and second-order coupled perturbed eHF equations is proposed. A method for the identification of the spinorbitals involved in the change of the total number of electrons is included. The illustrative examples (water and hydrogen cyanide) show that the ground-state (GS) properties of the (Z +/- 1)-electron systems can be predicted from the GS properties of the Z-electron systems with an accuracy comparable with the UHF calculations. The relaxation effect, important for the HCN system in which a change in the symmetry of the highest-occupied spin-orbital occurs, is effectively predicted.

Journal Article↗

PubMedDate not supplied

[Effect of pH on the potential-dependent functioning of staphylococcal toxin channels in phosphatidylcholine bilayer].

Potential-dependence of staphylococcal toxin channels at neutral pH is poorly expressed and increases with the medium acidation. It is shown that the value of the translocating charge is practically unchanged, whereas the energy parameters of this process vary essentially. The data obtained indicate the asymmetrical disposition of ionogenic channel groups determining its behaviour in the electric field.

Bacterial Toxins↗

PubMed2005

Second language interferes with word production in fluent bilinguals: brain potential and functional imaging evidence.

Bilingual individuals need effective mechanisms to prevent interference between their languages. Using event-related brain potentials (ERPs) and functional magnetic resonance imaging (fMRI), we present evidence for interference of phonological information from the nontarget language in German-Spanish bilinguals. A tacit picture-naming task was used in which bilinguals and monolinguals had to make speeded responses based on the first letter of the picture's name in the target language. In one condition, subjects were required to respond when the name began with a vowel and to withhold a response if it started with a consonant. Stimuli had been selected such that in half of the trials, the names in both languages necessitated the same response, whereas in the other half, responses were different for the two languages. For the bilinguals, the language in which the stimuli had to be named was changed after each block. Bilinguals showed phonological interference compared with monolingual performance, which was evident in their performance, ERPs, and fMRI patterns. Nonlanguagespecific brain areas such as the left middle prefrontal cortex were found to be crucial for the control of interference.

Adult↗

PubMed2004

Motor protein with nonequilibrium potential: Its thermodynamics and efficiency.

A nonequilibrium potential function is introduced for a motor protein modeled by a rectified Brownian motion. This result provides a concrete case for a class of nonequilibrium systems in steady state with dissipation which possess a potential function. The potential micro is a natural generalization of the chemical potential for isothermal chemical species and micro=const if and only if the system is in an equilibrium. The steady-state flux J proportional, variant - nabla micro, and the total heat dissipation h(d) equals a surface integral integral microJ.dS, representing the energy input. In terms of micro and h(d) the thermodynamic energy conservation in the mesoscopic stochastic system can be rigorously established and various types of motor efficiency are elucidated.

Adenosine Diphosphate↗

PubMed2026

Integrated electronic nose, GC-MS, and metagenomic analyses reveal volatile flavor and microbial community differences in heap-fermented grains of Jiangxiangxing Baijiu across different fermentation degrees.

The fermentation degree of heap-fermented grains in Jiangxiangxing Baijiu production is a critical factor influencing base Baijiu quality. However, conventional assessment methods largely rely on empirical experience and therefore suffer from limited objectivity and accuracy. In this study, integrated volatile profiling and metagenomic approaches were employed to investigate volatile characteristics and microbial functional potential differentiation in fermented grains with different fermentation degrees (under-fermented, normally fermented, and over-fermented). Significant differences in physicochemical properties were observed among fermentation degrees, particularly in acidity and reducing sugar content. Electronic nose analysis revealed distinct sensor response patterns among different fermentation degrees, indicating differences in overall volatile odor fingerprint patterns. A total of 81 volatile compounds were identified by HS-SPME-GC-MS, with aldehydes, ketones, and pyrazines showing pronounced variations among fermentation degrees, and acetaldehyde exhibiting strong discriminatory potential. LEfSe analysis identified 18 microbial taxa as potential biomarkers associated with different fermentation degrees, including Pichia kudriavzevii, Lentibacillus daiqui, and Acetobacter pasteurianus. Correlation analysis revealed significant positive associations between acetaldehyde levels and Acetobacter abundance. Furthermore, KEGG, CAZy, and eggNOG analyses revealed differentiated functional potentials among fermentation degrees, providing insights into the potential metabolic basis associated with flavor differentiation. Overall, these findings highlight that fermentation degree differentiation is closely associated with coordinated changes in physicochemical conditions, microbial communities, and functional potentials, providing ecological insights into flavor differentiation and theoretical support for objective fermentation degree evaluation and quality control of Jiangxiangxing Baijiu production.

Fermentation↗

PubMed2006

Localizing sites of activation in primary visual cortex using visual-evoked potentials and functional magnetic resonance imaging.

This study compared retinotopic map identification in primary visual cortex (V1) using: (i) functional magnetic resonance imaging (fMRI) and (ii) visual evoked potentials (VEPs) coupled with dipole source localization (DSL). A multielectrode array was used to record VEPs while subjects viewed a flickering dartboard pattern modulated by a 16-bit m-sequence. The stimulus preferentially activates V1. Using a common time function DSL algorithm, the primary source of each stimulus patch was found independent of the fMRI. The VEP/DSL and fMRI localization data for each subject were aligned by a rigid translation and rotation. The average distance between VEP and corresponding fMRI sources was 10.8 mm +/- 3.8 mm. To assess the significance of the results, fMRI and DSL solutions were scrambled so the comparisons were no longer for corresponding patches. The average distance between the noncorresponding data sets was 17.2 mm for 50 million scrambles. The probability of the scrambled data yielding a better fit than the real data was p < 10(-7). The combination of multielectrode recording, multiinput visual stimulation and common time function DSL analysis can provide a detailed retinotopic map of visual cortex that has high correspondence with independent fMRI localization analysis on the same subject.

Brain Mapping↗

PubMed2004

Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library.

Accurate prediction of the placement and comformations of protein side chains given only the backbone trace has a wide range of uses in protein design, structure prediction, and functional analysis. Prediction has most often relied on discrete rotamer libraries so that rapid fitness of side-chain rotamers can be assessed against some scoring function. Scoring functions are generally based on experimental parameters from small-molecule studies or empirical parameters based on determined protein structures. Here, we describe the NCN algorithm for predicting the placement of side chains. A predominantly first-principles approach was taken to develop the potential energy function incorporating van der Waals and electrostatics based on the OPLS parameters, and a hydrogen bonding term. The only empirical knowledge used is the frequency of rotameric states from the PDB. The rotamer library includes nearly 50,000 rotamers, and is the most extensive discrete library used to date. Although the computational time tends to be longer than most other algorithms, the overall accuracy exceeds all algorithms in the literature when placing rotamers on an accurate backbone trace. Considering only the most buried residues, 80% of the total residues tested, the placement accuracy reaches 92% for chi(1), and 83% for chi(1 + 2), and an overall RMS deviation of 1 A. Additionally, we show that if information is available to restrict chi(1) to one rotamer well, then this algorithm can generate structures with an average RMS deviation of 1.0 A for all heavy side-chains atoms and a corresponding overall chi(1 + 2) accuracy of 85.0%.

Algorithms↗

PubMed1985

Frequency and surface phenotype of human T lymphocytes producing interleukin 2. Analysis by limiting dilution and cell cloning.

In this study we have determined the frequency and distribution of interleukin 2 (IL2)-producing cells and their precursors (IL2-P) in the two major subsets of human T cells. The two subsets were identified on the basis of their reactivity (or lack thereof) with anti-T4 or anti-T8 monoclonal antibodies. T4+T8- and T4-T8+ cells were first isolated from peripheral blood T cell populations by positive or negative selection using the fluorescence-activated cell sorter, and then analyzed for total IL2-P and cytolytic T lymphocyte precursor (CTL-P) frequencies using a limiting dilution microculture system which allows clonal growth of every T cell. The results indicated that 50-60% of peripheral blood T cells consisted of IL2-P. In the T4+T8- subset (which represents 60-65% of all T cells) about 75% of the cells were IL2-P, whereas about 15% of T4-T8+ cells exhibited this functional potential. In contrast, about 3% and greater than 95% of T4+T8- and T4-T8+ cells, respectively, were CTL-P. Thus, these data provide direct evidence that there is no absolute correlation between the surface phenotype and the functional potential of human peripheral blood T cells. Moreover, it is evident from this frequency analysis that a significant proportion of T4-T8+ cells have a dual functional potential. IL2-P and CTL-P frequencies were also determined in T cell populations which had been activated in allogeneic mixed lymphocyte culture. The IL2-P frequencies in total T, T4+T8- and T4-T8+ MLC populations were 30, 45 and 10%, respectively. Comparative analysis of IL2 production and CTL activity at the clonal level confirmed that up to 20% of alloreactive CTL with the T4-T8+ surface phenotype were able to produce IL2 upon specific stimulation. This dual functional capacity was also observed among T4+T8- CTL.

Antigens, Surface↗

PubMed2005

Delta9-tetrahydrocannabinol and endogenous cannabinoid anandamide directly potentiate the function of glycine receptors.

Anandamide (AEA) and delta9-tetrahydrocannabinol (THC) are endogenous and exogenous ligands, respectively, for cannabinoid receptors. Whereas most of the pharmacological actions of cannabinoids are mediated by CB1 receptors, there is also evidence that these compounds can produce effects that are not mediated by the activation of identified cannabinoid receptors. Here, we report that THC and AEA, in a CB1 receptor-independent manner, cause a significant potentiation of the amplitudes of glycine-activated currents (I(Gly)) in acutely isolated neurons from rat ventral tegmental area (VTA) and in Xenopus laevis oocytes expressing human homomeric (alpha1) and heteromeric (alpha1beta1) subunits of glycine receptors (GlyRs). The potentiation of I(Gly) by THC and AEA is concentration-dependent, with respective EC50 values of 86 +/- 9 and 319 +/- 31 nM for alpha1 homomeric receptors, 73 +/- 8 and 318 +/- 24 nM for alpha1beta1 heteromeric receptors, and 115 +/- 13 and 230 +/- 29 nM for native GlyRs in VTA neurons. The effects of THC and AEA are selective for I(Gly), because GABA-activated current in VTA neurons or in X. laevis oocytes expressing alpha2beta3gamma2 GABA(A) receptor subunits were unaffected by these compounds. The maximal potentiation by THC and AEA was observed at the lowest concentration of glycine; with increasing concentrations of glycine, the potentiation significantly decreased. The site for THC and AEA seems to be distinct from that of the alcohol and volatile anesthetics. The results indicate that THC and AEA, in pharmacologically relevant concentrations, directly potentiate the function of GlyRs through an allosteric mechanism.

Animals↗

PubMed1997

Empirical potentials and functions for protein folding and binding.

Simplified models and empirical potentials are being increasingly used for the analysis of proteins, frequently augmenting or replacing molecular mechanics approaches. Recent folding simulations have employed potentials that, in addition to terms assuring proper polypeptide geometry, include only two noncovalent effects-hydrogen bonding and hydrophobicity, with extremely simple approximations to the latter. The potentials that have been used in the free-energy ranking of protein-ligand complexes have generally been more involved. These potentials have more detailed solvation models and account for both local (hydrophobic and polar) solute-solvent phenomena and long range electrostatic solvation effects. The models of solvation that have been used most frequently are surface area related atomic parameters, knowledge-based models extracted from protein-structure data, and continum electrostatics with an additional area-related parameter. The knowledge-based approaches to solvation, although convenient and accurate enough, are suspect of double counting certain free-energy terms.

Databases, Factual↗

PubMed2000

A mezoscopic model of nucleic acids. Part 2. An effective potential energy function for DNA.

In this study we present an effective Potential of Mean Force (PMF) designed for Lagrangian and Quaternion Molecular Dynamics (LQMD) of DNA. The DNA model is built from pseudoatoms as well as rigid and pseudo-elastic bodies described by a limited number of selected Cartesian and internal degrees of freedom. Phosphate groups, deoxyribose rings and nucleic acid bases are represented by pseudoparticles, some of them with internal degrees of freedom. PMF is defined as the sum of effective bonded and long-range potentials. The potentials were fitted to numerical free energy surfaces. Over 50 free energy surfaces, each depending on a conformational variable (pseudobond length, angle or dihedral angle) and the pseudorotation phase of the nearest neighbour deoxribose ring, were computed. The numerical free energy surfaces were obtained from probability distributions derived from a 1.5 ns conventional, microscopic MD simulation of the d(GpC)9 double helical DNA molecule. An umbrella sampling method was used to simulate transitions between the A and B DNA forms, and PMF reproduces these transitions.

Algorithms↗

PubMed2002

Functions and potential applications of glycolipid biosurfactants--from energy-saving materials to gene delivery carriers.

Biosurfactants (BS) produced by various microorganisms show unique properties (e.g., mild production conditions, lower toxicity, higher biodegradability and environmental compatibility) compared to their chemical counterparts. The numerous advantages of BS have prompted applications not only in the food, cosmetic, and pharmaceutical industries but in environmental protection and energy-saving technology as well. Glycolipid BS are the most promising, due to high productivity from renewable resources and versatile biochemical properties. Mannosylerythritol lipids (MEL), which are glycolipid BS produced by a yeast Candida antarctrica, exhibit not only excellent interfacial properties but also remarkable differentiation-inducing activities against human leukemia cells. MEL also show a potential anti-agglomeration effect on ice particles in ice slurry used for cold thermal storage. Recently, the cationic liposome bearing MEL has been demonstrated to increase dramatically the efficiency of gene transfection into mammalian cells. These features of BS should broaden its applications in new advanced technologies. The current status of research and development on glycolipid BS, especially their function and potential applications, is discussed.

Journal Article↗

PubMed2006

Fluorescence and ultraviolet absorption spectra and structure of coumaran and its ring-puckering potential energy function in the S1(pi,pi*) excited state.

The fluorescence excitation (jet cooled), single vibrational level fluorescence, and the ultraviolet absorption spectra of coumaran associated with its S1(pi,pi*) electronic excited state have been recorded and analyzed. The assignment of more than 70 transitions has allowed a detailed energy map of both the S0 and S1 states of the ring-puckering (nu45) vibration to be determined in the excited states of nine other vibrations, including the ring-flapping (nu43) and ring-twisting (nu44) vibrations. Despite some interaction with nu43 and nu44, a one-dimensional potential energy function for the ring puckering very nicely predicts the experimentally determined energy level spacings. In the S1(pi,pi*) state coumaran is quasiplanar with a barrier to planarity of 34 cm(-1) and with energy minima at puckering angles of +/-14 degrees. The corresponding ground state (S0) values are 154 cm(-1) and +/-25 degrees . As is the case with the related molecules indan, phthalan, and 1,3-benzodioxole, the angle strain in the five-membered ring increases upon the pi-->pi* transition within the benzene ring and this increases the rigidity of the attached ring. Theoretical calculations predict the expected increases of the carbon-carbon bond lengths of the benzene ring in S1, and they predict a barrier of 21 cm(-1) for this state. The bond length increases at the bridgehead carbon-carbon bond upon electron excitation to the S1(pi,pi*) state give rise to angle changes which result in greater angle strain and a nearly planar molecule.

Journal Article↗

PubMed2004

Teaching computers to fold proteins.

A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages which are estimated by (generalized ensemble) Monte Carlo. We test the learning algorithm on a Lennard-Jones (LJ) force field with a torsional angle degrees-of-freedom and a single-atom side-chain. In a test with 24 peptides of known structure, none folded correctly with the initial potential functions, but two-thirds came within 3 A to their native fold after optimizing the potential functions.

Algorithms↗

PubMed1999

Sperm dysfunction in subfertile patients with varicocele and marginal semen analysis.

A comparative analysis of potentially functional spermatozoa per ejaculate, progressive motility, hypo-osmotic swelling test, acrosome integrity and sperm viability (24 and 48 h) was carried out in a group of 40 subfertile patients with varicocele and marginal semen analysis and 40 fertile subjects, in order to identify subclinical abnormalities that may explain subfertility. Patients with varicocele had lower numbers of potentially functional spermatozoa per ejaculate, progressive motility, acrosome and membrane integrity and sperm viability. These abnormalities were not related to the grade of varicocele, testicular volume or serum FSH concentration. A positive correlation between the hypo-osmotic swelling test and progressive motility (r = 0.71) and between potentially functional spermatozoa and the hypo-osmotic swelling test (r = 0.69) was found in patients with varicocele. These data suggest that some of the deleterious effects produced by the varicocele might be related to sperm migration and viability in the female genital tract and others to sperm-zona interaction and/or sperm-egg fusion.

Adult↗