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At least 217 records · Page 12Linked to original sources
PubMed2006

Engineered internal noise stochastic resonator in gene network: a model study.

Based on a genetic bistable switch model coupled with a gene oscillator model, we have constructed a mesoscopic stochastic model for the coupled synthetic gene network, and studied how internal noise would influence the oscillation of such a system. We found that the state-to-state transitions can occur if the internal noise is taken into account, and the performance of resulting oscillation can reach a maximum in a certain internal noise level, which indicates the occurrence of internal noise stochastic resonance (SR) and makes the coupled gene network work as a stochastic resonator. The potential role of such an effect on gene expression systems is also discussed.

Biological Clocks↗
PubMed1984

Kinetics of acto-S1 interaction as a guide to a model for the crossbridge cycle.

Recent experiments on the kinetics of the interaction between myosin subfragment 1 (S1) and F-actin in solution are summarized. It is concluded that, at every step of the ATPase cycle, the association between the two proteins takes place in two stages. The equilibrium constant of the second step and thus the affinity of S1 for actin changes from step to step during the enzymatic reaction. It is proposed that the transient kinetic evidence can be interpreted in terms of two different classes of contraction models. The first one, which is widely used at present, identifies particular steps in the enzymatic reaction as directly responsible for the conformational change which represents the power stroke of muscle contraction (direct coupling model). In the second class of model, to which we wish to draw attention, changes in affinity modulated by the enzymatic reaction result in changes in the relative amounts of time spent by parts of the myosin molecule in two different environments. These environments determine whether the molecule exists in the 'long' or 'short' state, and it is the transition between these two which constitutes the power stroke (indirect coupling model).

Actins↗
PubMed1982

Energy coupling to ATP synthesis by the proton-translocating ATPase.

This review summarizes recent work on energy coupling to ATP synthesis by the reversible, proton-translocating ATPase to mitochondria, chloroplasts, and bacteria. In the first sections, this enzyme is distinguished from other ATP-linked ion transport systems, and progress in the biochemical analysis is discussed. There is at present a reasonably consistent idea of the overall structure of the enzyme, and one can begin to assign specific functional roles to individual subunits of the complex. The latter half of the review deals with mechanisms of energy coupling, about which there is clear divergence of opinion. An "indirect coupling" model would allow for the possibility that H+ translocation transmits energy for ATP synthesis by driving the enzyme through a sequence of conformational states, so that H+ translocated need not take part in the chemistry of ATP synthesis. By contrast, a "direct coupling" mechanism would specify that H+ translocated must participate in the chemical reaction by combining with oxygen must participate in the chemical reaction by combining with oxygen from phosphate during the synthetic step. Such discussion is preceded by an outlined of the "proton well," since this idea forms the basis of one direct coupling model. In addition, it is suggested that the idea of a proton (ion) well may be of more general significance to the analysis of ion-coupled transport, because it includes the postulate that mechanistically significant ion binding can occur within the profile of the electric field. A proton (ion) well can be derived from both kinetic and equilibrium treatments, and from mechanistic considerations in fields as distinct as biochemistry and neurophysiology. As a result, it illustrates how further advances in formulating mechanisms of energy coupling might profit by a merger of technique and perspective from areas that have as a common goal an understanding of how large proteins catalyze movements of small molecules across a membrane.

Adenosine Triphosphatases↗
PubMed1991

LV-arterial coupling: interactive model to predict effect of wave reflections on LV energetics.

The interaction between the left ventricle (LV) and the arterial system was simulated using sequential convolution of the flow output generated by a time-varying elastance model of the LV with an impulse response calculated from a 128-element model of the arterial system. The model illustrates the effect of independent changes of components of the arterial load on LV performance and energetics. This report studies the response of the model LV to an increase in arterial resistance, a decrease in arterial compliance, and an increase in discrete vascular reflections. Although arterial resistance exerts the greatest effect on ventricular stroke output, a reduction of arterial compliance or an increase in early reflections resulted in less optimal coupling of the heart to the arteries and less efficient energy utilization by the LV. In addition, the earlier the reflections return, the greater the disturbance of ventricular arterial coupling.

Aging↗
PubMed1971

Independence of the sodium and potassium conductance channels. A kinetic argument.

Tightly coupled models for the sodium and potassium conductance changes, in which the potassium "on" process is intimately related to the sodium "on" and "off" processes, are studied. It is shown that such coupled models are incapable of simultaneously showing the observed effects of conditioning potentials on sodium inactivation and on the translation of the potassium conductance in time. It is concluded that the primary mechanisms for the sodium and potassium channels are probably independent.

Cell Membrane↗
PubMed2002

Electronic security systems and active implantable medical devices.

How do active implantable medical devices react in the presence of strong magnetic fields in the frequency range between extremely low frequency (ELF) to radiofrequency (RF) as they are emitted by electronic security systems (ESS)? There are three different sorts of ESSs: electronic article surveillance (EAS) devices, metal detector (MDS) devices, and radiofrequency identification (RFID) systems. Common to all is the production of magnetic fields. There is an abundance of literature concerning interference by ESS gates with respect to if there is an influence possible and if such an influence can bear a risk for the AIMD wearers. However, there has been no attempt to study the physical mechanism nor to develop a model of how and under which conditions magnetic fields can influence pacemakers and defibrillators and how they could be disarmed by technological means. It is too often assumed that interference of AIMD with ESS is inevitable. Exogenous signals of similar intensity and rhythm to heart signals can be misinterpreted and, thus, confuse the implant. Important for the interference coupling mechanism is the differentiation between a "unipolar" and a "bipolar" system. With respect to magnetic fields, the left side implanted pacemaker is the most unfavorable case as the lead forms approximately a semicircular area of maximum 225 cm2 into which a voltage can be induced. This assumption yields an interference coupling model that can be expressed by simple mathematics. The worst-case conditions for induced interference voltages are a coupling area of 225 cm2 that is representative for a large human, a homogeneous magnetic field perpendicular to the area formed by the lead, and a unipolar ventricular pacemaker system that is implanted on the left side of the thorax and has the highest interference sensitivity. In bipolar systems the fields must be 17 times larger when compared to a unipolar system to have the same effect. The magnetic field for interfering with ICDs must be 1.7 stronger than that of the most sensitive unipolar pacemaker. The lowest interference thresholds measured over the last 10 years in the low frequency range (16 2/3 Hz-24 kHz) together with thresholds > 24 kHz that were supplied by the CETECOM study are listed. Both sets of data together with the coupling model, allow for judging which fields of ESSs could influence AIMDs. From measurements at gate antennas, it is possible to derive a "maximum allowed field" curve over the whole frequency range, below which no interference will occur. Comparison of data from literature with these maximum allowed fields confirm the correctness of the calculations. Thus, it is possible to predict interference situations in gates if the magnetic field is known. If all future pacemakers were to have the immunity against interference of the better 50% of today's pacemakers, the magnetic field ceiling values could be at least four times higher. The same is true if the ventricular sensitivity is routinely set at 7 mV. Pacemaker manufacturers should consider filter improvement with modern technology, but gate manufacturers should not claim the privilege of being out of bounds.

Defibrillators, Implantable↗
PubMed2003

Plausible interaction of an alpha-fetoprotein cyclopeptide with the G-protein-coupled receptor model GPR30: docking study by molecular dynamics simulated annealing.

In this manuscript, the procedure of molecular dynamics simulated annealing is applied to locate a probable receptor and binding site of a cyclicpeptide that inhibits estrogen-stimulated proliferation of breast cancer. The hydrophilic cyclopeptide EMTOVNOGQ (O = 4-hydroxyproline), derived from alpha-fetoprotein, is an inhibitor of estrogen-stimulated proliferation of human breast cancer. This peptide has been shown to act through a mechanism different from that of estrogen; however, its receptor is unknown. We report computer experiments that suggest that this peptide may execute its actions by interacting with GPR30, a G-protein-coupled receptor. The subject of this work is the simulation, by molecular dynamics simulated annealing, of the interaction of cyclopeptide EMTOVNOGQ with receptor GPR30 protein. A conformational analysis of the cyclopeptide was undertaken and the final structure was docked on several sites of the GPR30 3D model. Our results show that the cyclopeptide interacts on the pocket located between TM6 and TM7 transmembrane helices of the G-protein, triggering a slight conformational change in the secondary structure of the receptor in the complex. Based on differences in accessible surface areas between GPR30 and its ligand, the residues in the interaction zone were identified. The cyclopeptide is stabilized in the active site by forming a network of hydrogen bonds between Glu, Thr, (1)Pro(OH) and GLn residues of the ligand and Arg-259, Cys-271, Asn-316, Asn-320 and Tyr-324 of the G-protein. Moreover, the study of the electrostatic surface potential on the GPR30 receptor shows that the active site is more positively charged than the other sites. Our modeling indicates a plausible interaction of the cyclopeptide with the seven transmembrane GPR30 protein. This may have profound implications for the treatment of breast cancer.

Amino Acid Sequence↗
PubMed2006

Cap- and initiator tRNA-dependent initiation of TYMV polyprotein synthesis by ribosomes: evaluation of the Trojan horse model for TYMV RNA translation.

Turnip yellow mosaic virus (TYMV) RNA directs the translation of two overlapping open reading frames. Competing models have been previously published to explain ribosome access to the downstream polyprotein cistron. The Trojan horse model, based on cell-free experiments, proposes noncanonical cap-independent initiation in which the 3'-terminal tRNA-like structure (TLS) functionally replaces initiator tRNA, and the valine bound to the TLS becomes cis-incorporated into viral protein. The initiation coupling model, based on in vivo expression and ribosome toe-printing studies, proposes a variation of canonical leaky scanning. Here, we have re-examined the wheat germ extract experiments that led to the Trojan horse model, incorporating a variety of controls. We report that (1) translation in vitro from the polyprotein AUG of TYMV RNA is unchanged after removal of the 3' TLS but is stimulated by the presence of a 5'-cap; (2) the presence of free cap analog or edeine (which interferes with initiation at the ribosomal P site and its tRNA(i) (Met) involvement) inhibits translation from the polyprotein AUG; (3) the toe-prints of immediately post-initiation ribosomes on TYMV RNA are similar with and without an intact TLS; and (4) significant deacylation of valyl-TYMV RNA in wheat germ extract can complicate the detection of cis-incorporation. These results favor the initiation coupling model.

Amino Acid Sequence↗
PubMed1990

Voltage-dependent gating of Shaker A-type potassium channels in Drosophila muscle.

The voltage-dependent gating mechanism of A1-type potassium channels coded for by the Shaker locus of Drosophila was studied using macroscopic and single-channel recording techniques on embryonic myotubes in primary culture. From a kinetic analysis of data from single A1 channels, we have concluded that all of the molecular transitions after first opening, including the inactivation transition, are voltage independent and therefore not associated with charge movement through the membrane. In contrast, at least some of the activation transitions leading to first opening are considerably voltage dependent and account for all of the voltage dependence seen in the macroscopic currents. This mechanism is similar in many ways to that of vertebrate neuronal voltage-sensitive sodium channels, and together with the sequence similarities in the S4 region suggests a conserved mechanism for voltage-dependent gating among channels with different selectivities. By testing independent and coupled models for activation and inactivation we have determined that the final opening transition and inactivation are not likely to arise from the independent action of multiple subunits, each with simple gating transitions, but rather come about through their aggregate properties. A partially coupled model accurately reproduces all of the single-channel and macroscopic data. This model will provide a framework on which to organize and understand alterations in gating that occur in Shaker variants and mutants.

Animals↗
PubMed2003

Segmentation of carpal bones from CT images using skeletally coupled deformable models.

The in vivo investigation of joint kinematics in normal and injured wrist requires the segmentation of carpal bones from 3D (CT) images, and their registration over time. The non-uniformity of bone tissue, ranging from dense cortical bone to textured spongy bone, the irregular shape of closely packed carpal bones, small inter-bone spaces compared to the resolution of CT images, along with the presence of blood vessels, and the inherent blurring of CT imaging render the segmentation of carpal bones a challenging task. We review the performance of statistical classification, deformable models (active contours), region growing, region competition, and morphological operations for this application. We then propose a model which combines several of these approaches in a unified framework. Specifically, our approach is to use a curve evolution implementation of region growing from initialized seeds, where growth is modulated by a skeletally-mediated competition between neighboring regions. The inter-seed skeleton, which we interpret as the predicted boundary of collision between two regions, is used to couple the growth of seeds and to mediate long-range competition between them. The implementation requires subpixel representations of each growing region as well as the inter-region skeleton. This method combines the advantages of active contour models, region growing, and both local and global region competition methods. We demonstrate the effectiveness of this approach for our application where many of the difficulties presented above are overcome as illustrated by synthetic and real examples. Since this segmentation method does not rely on domain-specific knowledge, it should be applicable to a range of other medical imaging segmentation tasks.

Algorithms↗
PubMed2005

Electronic Raman spectroscopy of the vanadium(III) hexaaqua cation in guanidinium vanadium sulphate: Quintessential manifestation of the dynamical Jahn-Teller effect.

Single-crystal Raman spectra are presented for the salt [C(NH2)3][V(OH2)6](SO4)2, displaying electronic transitions between the trigonal components of the vanadium(III) 3T1g(Oh) ground term. The 3A-->3E(C3) electronic Raman band is centered at approximately 2720 cm-1, and exhibits extensive structure, revealing the energies of the spinor components of the 3E(C3) term for the two crystallographically distinct [V(OH2)6]3+ cations. The data are interpreted in conjunction with parameters previously reported from an electron paramagnetic resonance study of the salt. A satisfactory reproduction of the electronic Raman profile and ground-state spin-Hamiltonian parameters is achieved by employing a (3A plus sign in circle3E)multiply sign in circle e vibronic coupling model, in which the spin-orbit splitting of the 3E(C3) is quenched significantly by the Ham effect, and the intensity of harmonics of the Jahn-Teller active vibration enhanced by their proximity to the electronic Raman bands. The model gives an excellent account of the intensities of the electronic Raman bands, which are shown to depend profoundly on both temperature and the selected component of the polarizability tensor. The electronic Raman profile changes notably upon deuteriation, a result that exposes deficiencies in the single-mode coupling model.

Journal Article↗
PubMed2001

Phase-coupled oscillator models can predict hippocampal inhibitory synaptic connections.

What factors are responsible for propagating electrical activity in the hippocampus? Using an intact, isolated hippocampus preparation, it is possible to observe spontaneous delta (< or = 4 Hz) waves of rhythmic field potentials. These rhythmic potentials are inhibitory in nature, mediated by GABAergic inhibitory potentials originating from a population of principal neurons. They start in the ventro-temporal region and move longitudinally towards the dorso-septal region with a phase lag of approximately 10% between the extracellular recordings. We use the mathematical framework of phase-coupled oscillators (PCO) to gain some insight into the underlying network system. A chain of 15 nearest-neighbour bidirectionally coupled PCOs is used where each oscillator refers to a segment of the CA1 region of the hippocampus that can generate these slow field potentials. We find that ventro-dorsal delta waves exist if there is a dominance in coupling strength in one direction. Without a one-way coupling dominance, ventro-dorsal waves can still exist, but then the coupling strengths need to be much larger. The relationship between entrained and intrinsic frequencies and the variation of propagation speeds along the longitudinal axis can be used to determine which case applies. Currently available experimental data supports one of the cases, predicting that there is a stronger ventral to dorsal inhibitory effect.

Action Potentials↗
PubMed2002

Gelation of aqueous pectin solutions: a dynamic light scattering study.

We report the dynamic light scattering study of the gelation of aqueous solutions of the biopolymer, pectin, induced by the addition of calcium chloride. The time correlation function data are analyzed under the framework of the coupling model. As the solution enters the semidilute regime where gelation sets in, the relaxation process shows a stretched exponential behavior. The stretching exponent decreases and the characteristic time of the stretched exponential diverges as the system evolves to a gel. Aqueous pectin solutions in the presence of 0.1 M NaCl show similar behavior. Thus, the molecular relaxation modes of pectin solutions can be well described by the coupling model.

Journal Article↗
PubMed2001

The coupled oscillator model of between-hand coordination in alternate-hand tapping: a reappraisal.

Single and alternating hand tapping were compared to test the hypothesis that coordination during rhythmic movements is mediated by the control of specific time intervals. In Experiment 1, an auditory metronome was used to indicate a set of timing patterns in which a 1-s interval was divided into 2 subintervals. Performance, measured in terms of the deviation from the target patterns and variability, was similar under conditions in which the finger taps were made with 1 hand or alternated between the 2 hands. In Experiment 2, the modality of the metronome (auditory or visual) was found to influence the manner in which the produced intervals deviated from the target patterns. These results challenge the notion that bimanual coordination emerges from coupling constraints intrinsic to the 2-hand system. They are in accord with a framework that emphasizes the control of specific time intervals to form a series of well-defined motor events.

Analysis of Variance↗
PubMed1999

Detection and classification of hyperfine-shifted 1H, 2H, and 15N resonances of the Rieske ferredoxin component of toluene 4-monooxygenase.

T4MOC is a 12.3 kDa soluble Rieske ferredoxin that is obligately required for electron transfer between the oxidoreductase and diiron hydroxylase components of toluene 4-monooxygenase from Pseudomonas mendocina KR1. Our preliminary 1H NMR studies of oxidized and reduced T4MOC [Markley, J. L., Xia, B., Chae, Y. K., Cheng, H., Westler, W. M., Pikus, J. D., and Fox, B. G. (1996) in Protein Structure Function Relationships (Zaidi, Z., and Smith, D., Eds.) pp 135-146, Plenum Press, London] revealed the presence of hyperfine-shifted 1H resonances whose short relaxation times made it impractical to use nuclear Overhauser effect (NOE) measurements for assignment purposes. We report here the use of selective isotopic labeling to analyze the hyperfine-shifted 1H, 2H, and 15N signals from T4MOC. Selective deuteration led to identification of signals from the four Hbeta atoms of cluster ligands C45 and C64 in the oxidized and reduced forms of T4MOC. In the reduced state, the Curie temperature dependence of the Hbeta protons corresponded to that predicted from the simple vector spin-coupling model for nuclei associated with the localized ferric site. The signal at 25.5 ppm in the 1H spectrum of reduced T4MOC was assigned on the basis of selective 2H labeling to the His Hepsilon1 atom of one of the cluster ligands (H47 or H67). This assignment was corroborated by a one bond 1H-13C correlation (at 25.39 ppm 1H and 136.11 ppm 13C) observed in spectra of [U-13C]T4MOC with a 1H-13C coupling constant of approximately 192 Hz. The carbon chemical shift and one bond coupling constant are those expected for 1Hepsilon1-13Cepsilon1 in the imidazolium ring of histidine and are inconsistent with values expected for cysteine 1Halpha-13Calpha. The His Hepsilon1 proton exhibited weak Curie temperature dependence from 283 to 303 K, contrary to the anti-Curie temperature dependence predicted from the spin coupling model for nuclei associated with the localized ferrous site. A 1H peak at -12.3 ppm was observed in spectra of reduced T4MOC; this signal was found to correspond to a hydrogen (probably in an H-bond to the cluster) that exchanged with solvent with a half-time of about 2 days in the oxidized state but with a much longer (undetectable) half-time in the reduced state. These results with T4MOC call into question certain 1H assignments recently reported on the basis of NOE measurements for the comparable Rieske ferredoxin component of an evolutionarily related alkene monooxygenase from Xanthobacter sp. Py2 [Holz, R. C., Small, F. J., and Ensign, S. A, (1997) Biochemistry 36, 14690-14696]. Selective 15N labeling was used to identify hyperfine-shifted 15N NMR signals from the backbone nitrogens of all four cluster ligands (C45, H47, C64, and H67), from the Nepsilon2 atoms of the two histidine ligands (H47 and H67), and from nonligand Gln and Ala residues (Q48 and A66) present in the cluster-binding motif of T4MOC in the oxidized and reduced states. The results indicate that the Ndelta1 of each of the two ligand histidines of T4MOC are ligated to an iron atom and reveal a pattern of H-bonding to the Rieske [2Fe-2S] center involving four (H47, Q48, A66, and H67 of T4MOC) of the five backbone amide H-bonds expected on the basis of comparison with the crystal structures of other related Rieske proteins; the fifth backbone amide (I50 of T4MOC) failed to exhibit a hyperfine shift. This anomaly may arise from the lack of an associated disulfide in T4MOC, a fundamental structural difference between the three types of Rieske proteins that may be related to functional diversity in this protein family.

Amino Acid Sequence↗
PubMed1998

Neuronal innervation, intracellular signal transduction and intercellular coupling: a model for syncytial tissue responses in the steady state.

A model tissue is proposed in which chemically responsive cells are interconnected by gap junctions and innervated by the autonomic nervous system. The model is explicitly dependent on the following physiologically relevant assumptions: (1) a fraction of the cells are directly innervated, and these cells respond to a periodic neuronal stimulus (i.e. the release of neurotransmitter) by production of an intracellular substance (i.e. second messenger molecule); (2) production of second messenger molecules modulates the amplitude of a cellular response, such as contraction or secretion; (3) intracellular formation of second messenger molecules in innervated cells is proportional to the periodicity of the neuronal stimulus, while the intracellular concentration in non-innervated cells is governed by the half-life of the second messenger molecule and the extent of cell-to-cell coupling; (4) the amplitude of the graded response of the individual cell is related to the intracellular second messenger concentration by a Michaelis-Menten function; (5) the amplitude of the graded tissue response is a function of the innervation density, the frequency of stimulation, and the extent of intercellular coupling. Thus, a stimulus-response relationship was developed, where the magnitude of the tissue response was described as a function of the total tissue stimulus. The predicted stimulus-response curve was encapsulated by two parameters: (1) the Hill-exponent, which reflects the steepness of the stimulus-response curve; and (2) the location of the stimulus-response curve, or the half-maximally effective stimulus. Both random and uniform neuronal innervation patterns were considered in model tissues with various effective dimensions. The simulations were also applied to a realistic model of vascular tissue. The shape of the stimulus-response curve is critically dependent on the geometry of innervation. For physiologically relevant (10-90% over 2-3 orders of magnitude) dose-response curves, the model yields an implicit relationship between three different dimensionless parameters. If, in a system, two of these parameters are known, the model can be used to bracket the possible range of the third parameter.

Animals↗
PubMed2006

A detailed analysis of vibrational excitations in x-ray photoelectron spectra of adsorbed small hydrocarbons.

The vibrational fine structure of x-ray photoelectron (XP) spectra of a number of different small hydrocarbon molecules and reaction intermediates adsorbed on Pt(111) and Ni(111) has been investigated in detail. The data for methyl, methylidyne, acetylene, and ethylene can consistently be analyzed within the linear coupling model. The S factor, i.e., the intensity ratio of the first vibrationally excited to the adiabatic transition, is obtained to be 0.17+/-0.02 per C-H bond; for the deuterated species a value of 0.23+/-0.02 is obtained. Therefore, the vibrational fine structure can be used for fingerprinting in the analysis of XP spectra and for identifying unknown reaction intermediates. From the data, Deltar, the change of the minimum in the potential energy curve upon core ionization, is calculated within the linear coupling model using a first order correction. For all adsorbates, including the deuterated ones, a value of Deltar=0.060+/-0.004 A is obtained. Furthermore, from the binding energy of the adiabatic peak and from the energy of the vibrational excitation in the ionic final state some information on the adsorbate/substrate bond and the adsorption site can be derived.

Journal Article↗