Flip Rates Research Articles

Molecular Determinants Responsible for Differences in Desensitization Kinetics of AMPA Receptor Splice Variants

Flip (i) and flop (o) alternatively spliced variants of the four glutamate AMPA receptor subunits (GluR1-4) are differentially expressed in the CNS and can display distinct rates of desensitization that contribute to the heterogeneity of native AMPA receptor-dependent synaptic responses. In the present study, we initially compared the kinetics of desensitization in response to fast application of glutamate (1 mm) for the eight different homomeric recombinant human AMPA receptors (hGluR1-4i and o) heterologously expressed in mammalian cells. Consistent with previous reports on recombinant rat AMPA receptors, the time constants of desensitization between human GluR1i and GluR1o receptors were the same, whereas the flip isoforms for GluR2-4 receptors exhibited significantly slower rates of desensitization compared with the flop isoforms. To identify the molecular determinants responsible for these functional differences, the effects of exchanging amino acid residues in the flip-flop cassette of GluR2i and GluR2o were investigated. Three amino acid residues in the flip-flop region (Thr765, Pro766, and Ser775 in flip and Asn765, Ala766, and Asn775 in flop) were identified that contribute to splice-variant differences in the rate of desensitization. Recent structural data show that these three residues are located on helix J, which forms part of the intradimer interface of AMPA receptor ligand-binding cores, and that the stability of this interface may regulate desensitization. The present results suggest that these three residues may confer differences in flip and flop receptor desensitization rates by directly and/or indirectly influencing the stability of the interface between adjacent subunits.

Infrequent cavity‐forming fluctuations in HPr from Staphylococcus carnosus revealed by pressure‐ and temperature‐dependent tyrosine ring flips

Infrequent structural fluctuations of a globular protein is seldom detected and studied in detail. One tyrosine ring of HPr from Staphylococcus carnosus, an 88-residue phosphocarrier protein with no disulfide bonds, undergoes a very slow ring flip, the pressure and temperature dependence of which is studied in detail using the on-line cell high-pressure nuclear magnetic resonance technique in the pressure range from 3 MPa to 200 MPa and in the temperature range from 257 K to 313 K. The ring of Tyr6 is buried sandwiched between a beta-sheet and alpha-helices (the water-accessible area is less than 0.26 nm2), its hydroxyl proton being involved in an internal hydrogen bond. The ring flip rates 10(1)-10(5) s(-1) were determined from the line shape analysis of H(delta1, delta2) and H(epsilon1,epsilon2) of Tyr6, giving an activation volume DeltaV++ of 0.044 +/- 0.008 nm3 (27 mL mol(-1)), an activation enthalpy DeltaH++ of 89 +/- 10 kJ mol(-1), and an activation entropy DeltaS++ of 16 +/- 2 JK(-1) mol(-1). The DeltaV++) and DeltaH++ values for HPr found previously for Tyr and Phe ring flips of BPTI and cytochrome c fall within the range of DeltaV(double dagger) of 28 to 51 mL mol(-1) and DeltaH++ of 71 to 155 kJ mol(-1). The fairly common DeltaV++ and DeltaH++ values are considered to represent the extra space or cavity required for the ring flip and the extra energy required to create a cavity, respectively, in the core part of a globular protein. Nearly complete cold denaturation was found to take place at 200 MPa and 257 K independently from the ring reorientation process.

How Much π-Stacking Do DNA Termini Seek? Solution Structure of a Self-Complementary DNA Hexamer with Trimethoxystilbenes Capping the Terminal Base Pairs,

The exposed terminal base pairs of DNA duplexes are nonclassical binding sites for small molecules. Instead, small molecules usually prefer intercalation or minor groove binding. Here we report the solution structure of the DNA duplex (TMS-TGCGCA)(2), where TMS denotes trimethoxystilbene carboxamides that are 5'-tethered to the DNA. The stilbenes, for which intercalation is conformationally accessible, stack on the terminal T:A base pairs of an undisturbed B-form duplex. Two conformations, differing by the orientation of the stilbene relative to the terminal base pair, are observed, indicating that the flip rate is slow for the pi-stacked aromatic ring system. The trimethoxystilbene is known to greatly increase base pairing fidelity at the terminus. Here we show that it gauges the size of the T:A base pair by embracing the 2'-methylene group of the terminal dA residue of the unmodified terminus with its methoxy "arms", but that it does not engage the entire base pair in pi-stacking. Mismatched base pairs with their altered geometry will not allow for the same embracing interaction. On the basis of the current structure, a trimethoxychrysene carboxamide is proposed as a ligand with increased pi-stacking surface and possible applications as improved fidelity-enhancing element.

The mesoscopic chiral metal-insulator transition

Sharp localization transitions of chiral edge states in disordered quantum wires subject to a strong magnetic field are shown to be driven by crossovers from two-to one-dimensional localization of bulk states. As a result, the two-terminal conductance is found to exhibit discontinuous transitions at zero temperature between exactly integer plateau values and zero, reminiscent of first-order phase transitions. We discuss the corresponding phase diagram. The spin of the electrons is shown to result in a multitude of phases when the spin degeneracy is raised by the Zeeman energy. The width of conductance plateaus is found to depend sensitively on the spin flip rate 1/τs.

On the mechanism of drug-induced acceleration of phospholipid translocation in the human erythrocyte membrane

Small amphiphilic compounds (M(r)<200 Da) such as anaesthetics and hexane derivatives with different polar groups produced a concentration-dependent acceleration of the slow passive transbilayer movement of NBD-labelled phosphatidylcholine in the human erythrocyte membrane. Above a threshold concentration characteristic for each compound, the flip rate gradually increased at increasing concentrations in the medium. For compound concentrations required to produce a defined flip acceleration, corresponding membrane concentrations were estimated using reported octanol/water partition coefficients. The effective threshold membrane concentrations (50-150 mmol l(-1)) varied in the order: hexylamine>isoflurane=hexanoic acid>hexanol=chloroform>hexanethiol=1,1,2,2-tetrachloroethane>chlorohexane. Apolar hexane, which mainly distributes in the apolar membrane core, was much less effective and supersaturating concentrations were required to enhance flip. Localization of the drug at the lipid-water interface seems to be required for flip acceleration. Such a localization may increase the lateral pressure in this region and the bilayer curvature stress with concomitant decrease of order and rigidity at the interface. This unspecific bilayer perturbation is proposed to enhance the probability of formation of hydrophobic defects in the bilayer, facilitating penetration of the polar head group of the phospholipid into the apolar membrane core.

Hydrogen states in CuInSe2—a μSR study

Implanted positive muons, used to mimic protons, are observed to form a diamagnetic state in the chalcopyrite semiconductor CuInSe2. A shift of the muon precession frequency is observed at a high transverse magnetic field (1600G) and is interpreted as being associated to the presence of a transient neutral state. A high charge or spin flip rate of the electron bound to the muon is suggested to be the cause for the absence of a hyperfine splitting, i.e., a direct signature of a neutral state. This observation is consistent with the presence of a hydrogen donor level close to or above the conduction band minimum.

Permeability investigations of phospholipid liposomes by adding cholesterol

Abstract The sublytic changes caused by sodium dodecyl sulfate (SDS) in egg phosphatidylcholine (PC) liposomes with rising concentrations of cholesterol (CH) (PC:CH mole ratios from 9:1 to 7:3) were investigated. The effective molar ratios Re of membrane-bound surfactant to lipid and the bilayer/aqueous phase partition coefficients (K) were determined. A linear increase and decrease in Re and K, respectively, take place as the CH proportion increase. Given that the surfactant capacity to interact with liposomes is inversely related to the Re value, the rise of CH reduces linearly both the SDS activity against vesicles (increase in Re) and its affinity with these structures (decrease in K). These linear variations may be due to the linear increase of hydrophobicity in the interfacial region of bilayers and to their reduced translational fluidity by changes in the bilayer packing and ordering. The increase in Re always results in two opposite effects on K. At low Re, K firstly increases because only the outer vesicle leaflet is available for interaction with SDS. The following abrupt fall in K is due to the fact that the binding of additional SDS molecules to bilayer is hampered. The K peaks obtained are correlated in all cases with the saturation of the outer vesicle leaflet by SDS. Increasing Re values, lead to an increased rate of flip–flop of the surfactant molecules (or permeabilization of the bilayers to SDS), thus also making the inner monolayer available for interaction with added SDS. The free SDS concentrations are always lower than its critical micelle concentration indicating that the SDS–liposome interaction is mainly ruled by the action of surfactant monomers regardless of the CH concentration in bilayers.

Dynamics in molecular crystals: An application of proton NMR to selectively protonated biphenyl. Do the rings flip together or independently?

The synthesis of a specific isotopomer, C6D4H(ortho)-H(ortho)D4C6 of biphenyl is reported. The intramolecular dipolar coupling of the protons leads to a well-resolved single-crystal proton nuclear magnetic resonance (NMR) spectrum and allows one to study the dynamics of the phenyl rings in a unique way. At room temperature and above, the most conspicuous dynamical mode consists of 180° ring flips. The present data together with previous measurements of the total flip rate allow us to conclude that the rings flip almost exclusively independently of each other. Between the incommensurate (IC) phase transition of biphenyl at 38 K andT=250 K, the prominent namical mode consists of oscillatory twists ϕ(t) of the two rings. The data allow us to infer the mean square, (φ2), of these twists. (φ2) is found to grow linearly withT for 50<T<200 K. From the slope of (φ2) vs.T the frequency (the wave number\(\tilde v\)) is derived. The result is\(\tilde v = 20\) cm−1. ForT<38 K, the spectra give direct evidence of the IC phase transition and its nature (stripelike rather than quiltlike). The temperature dependence of the magnitude of the order parameter of the IC phase is obtained.

Inhomogeneous Voter Models in One Dimension

We establish conditions for survival and extinction of types of one-dimensional voter models, and show that increasing the flip rates at a finite number of sites typically does not affect survival, unless the flipping mechanism is altered. We provide an example of a modified voter model that does not survive but can be made to survive simply by altering the flip mechanism at one site. We also show that a rather general class of such models have clustering behavior.

A Flashing Model for Transport of Brownian Motors

A flashing coloured noise model is proposed to describe the motion ofa molecular motor. In this model, the overdamped Brownian particlemoves in an asymmetric periodic potential with a flashingOrnstein-Ulenbeck coloured noise. The relationship between thecurrent and the parameters - such as the intensity, the correlationtime of coloured noise and the flip rate of the noise - is discussedusing the Monte Carlo simulation method. Current reversal occurs withthe change of the correlation time and the flip rate of colourednoise, which may be related to the directed motion and the currentreversal of molecular motors.

Dynamical phase transition of a one-dimensional kinetic Ising model with boundaries.

The Glauber model on a one-dimensional lattice with boundaries (for the ferromagnetic and antiferromagnetic cases) is considered. The large-time behavior of the one-point function is studied. It is shown that at any temperature, the system shows a dynamical phase transition. The dynamical phase transition is controlled by the rate of spin flip at the boundaries, and is a discontinuous change of the derivative of the relaxation time towards the stationary configuration.

Suppressed Electron-Hole Exchange Spin Flip in Cavity Polaritons

We consider theoretically the spin relaxation of exciton–polaritons in semiconductor microcavities in the strong coupling regime. The dominant quantum well exciton polarization relaxation mechanism is typically due to the long-range intra-exciton electron–hole exchange. We estimate perturbatively the corresponding contribution for the lower polaritons as a function of the elastic scattering time in analogy to the Dyakonov-Perel model for electron spin relaxation. We find a strong suppression of the polariton spin flip rate due to the electron–hole exchange with respect to the quantum well exciton case.

Glauber dynamics for fermion point processes

AbstractWe construct a Glauber dynamics on {0, 1}ℛ, ℛ a discrete space, with infinite range flip rates, for which a fermion point process is reversible. We also discuss the ergodicity of the corresponding Markov process and the log-Sobolev inequality.

An elementary proof of the uniqueness of invariant product measures for some infinite dimensional processes

Consider an infinite dimensional diffusion process with state space T Z d , where T is the circle, and defined by an infinitesimal generator L which acts on local functions f as Lf(η)=∑ i∈ Z d ( a i 2(η i) 2 ∂ 2f ∂η i 2 +b i(η) ∂f ∂η i ) . Suppose that the coefficients a i and b i are smooth, bounded, of finite range, have uniformly bounded second order partial derivatives, that a i are uniformly bounded from below by some strictly positive constant, and that a i is a function only of η i . Suppose that there is a product measure ν which is invariant. Then if ν is the Lebesgue measure or if d=1,2, it is the unique invariant measure. Furthermore, if ν is translation invariant, it is the unique invariant, translation invariant measure. The proofs are elementary. Similar results can be proved in the context of an interacting particle system with state space {0,1} Z d , with uniformly positive bounded flip rates which are finite range. To cite this article: A.F. Ramı́rez, C. R. Acad. Sci. Paris, Ser. I 334 (2002) 139–144

Space–time large deviation lower bounds for spin particle systems

Abstract In this Letter we study large deviation lower bounds for space–time empirical processes of spin particle systems with possibly vanishing spin flip rates. We present an approach for obtaining such lower bounds for systems starting from almost all configurations w.r.t. an translation invariant and extremal invariant measure of the systems, so that in such cases we have full large deviation principle.

Polarization resolved intensity noise in vertical-cavity surface-emitting lasers

We report explicit analytical and numerical results for the polarization resolved intensity noise of vertical-cavity surface-emitting lasers operating in the fundamental transverse mode. We describe the fluctuations of the linear and circular polarization components of linearly polarized states on both sides of a nonthermal polarization switching. Our description is valid for small and large birefringence and arbitrary values of the spin flip rate, giving a complete description of the role of these parameters. Normalized cross-correlation functions for both linear and circular components are discussed in detail. They show different degrees of anticorrelated fluctuations in different frequency ranges.

The ins(ide) and out(side) of dolichyl phosphate biosynthesis and recycling in the endoplasmic reticulum.

The precursor oligosaccharide donor for protein N-glycosylation in eukaryotes, Glc3Man9GlcNAc(2)-P-P-dolichol, is synthesized in two stages on both leaflets of the rough endoplasmic reticulum (ER). There is good evidence that the level of dolichyl monophosphate (Dol-P) is one rate-controlling factor in the first stage of the assembly process. In the current topological model it is proposed that ER proteins (flippases) then mediate the transbilayer movement of Man-P-Dol, Glc-P-Dol, and Man5GlcNAc(2)-P-P-Dol from the cytoplasmic leaflet to the lumenal leaflet. The rate of flipping of the three intermediates could plausibly influence the conversion of Man5GlcNAc(2)-P-P-Dol to Glc3Man(9)GlcNAc(2)-P-P-Dol in the second stage on the lumenal side of the rough ER. This article reviews the current understanding of the enzymes involved in the de novo biosynthesis of Dol-P and other polyisoprenoid glycosyl carrier lipids and speculates about the role of membrane proteins and enzymes that could be involved in the transbilayer movement of the lipid intermediates and the recycling of Dol-P and Dol-P-P discharged during glycosylphosphatidylinositol anchor biosynthesis, N-glycosylation, and O- and C-mannosylation reactions on the lumenal surface of the rough ER.

Energy-dependent Flip of Fluorescence-labeled Phospholipids Is Regulated by Nutrient Starvation and Transcription Factors, PDR1 and PDR3

The yeast Saccharomyces cerevisiae readily accumulates short-chain, fluorescent 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD)-labeled phosphatidylcholine and phosphatidylethanolamine at the nuclear envelope/endoplasmic reticulum and mitochondria. The net intracellular accumulation reflects the sum of their inwardly and outwardly directed transbilayer translocation across the plasma membrane (flip and flop, respectively). The rate of flop is negligible in energy-depleted cells as well as at low temperature (2 degrees C). Although flip is reduced at 2 degrees C, it can still be measured by flow cytometry, allowing the rate of flip, independent of flop, to be characterized at this temperature. Flip requires the energy of the plasma membrane proton electrochemical gradient and is down-regulated as cells pass through the diauxic shift and enter stationary phase. Furthermore, drug-resistant, gain-of-function mutations in the transcription factors, PDR1 and PDR3, result in a dramatic down-regulation of flip in addition to their already established up-regulation of flop. These results imply that down-regulation of the NBD-phospholipid flip pathway is a physiological response to environmental stress.

The μCF Experiments at PSI – A Conclusive Review

During 25 years pioneering μCF experiments were performed at PSI. After initial study of the Wolfenstein–Gershtein effect in H/D, an intense research program on dμd fusion led to the early discovery of resonant dμd formation at low temperature and to the first direct observation of μd spin flip. With the Gatchina ionisation chamber absolute precisions of ∼1% on the determination of dμd formation and spin flip rates were recently obtained in good agreement with the theory.

Aromatic ring-flipping in supercooled water: implications for NMR-based structural biology of proteins.

We have characterized, for the first time, motional modes of a protein dissolved in supercooled water: the flipping kinetics of phenylalanyl and tyrosinyl rings of the 6 kDa protein BPTI have been investigated by NMR at temperatures between -3 and -16.5 degrees C. At T = -15 degrees C, the ring-flipping rate constants of Tyr 23, Tyr 35, and Phe 45 are smaller than 2 s(-1), i.e., flip-broadening of aromatic NMR lines is reduced beyond detection and averaging of NOEs through ring-flipping is abolished. This allows neat detection of distinct NOE sets for the individual aromatic (1)H spins. In contrast, the rings of Phe 4, Tyr 10, Tyr 21, Phe 22, and Phe 33 are flipping rapidly on the chemical shift time scale with rate constants being in the range from approximately 10(2) to 10(5) s(-1) even at T = -15 degrees C. Line width measurements in 2D [(1)H,(1)H]-NOESY showed that flipping of the Phe 4 and Phe 33 rings is, however, slowed to an extent that the onset of associated line broadening in the fast exchange limit is registered. The reduced ring-flipping rate constant of Phe 45 in supercooled water allowed very precise determination of Eyring activation enthalpy and entropy from cross relaxation suppressed 2D [(1)H,(1)H]-exchange spectroscopy. This yielded DeltaH = 14 +/- 0.5 kcal.mol(-1) and DeltaS = -4 +/- 1 cal.mol(-1).K(-1), i.e., values close to those previously derived by Wagner and Wüthrich for the temperature range from 4 to 72 degrees C (DeltaH = 16 +/- 1 kcal.mol(-1) and DeltaS = 6 +/- 2 cal.mol(-1).K(-1)). The preservation of the so far uniquely low value for DeltaS indicates that the distribution of internal motional modes associated with the ring flip of Phe 45 is hardly affected by lowering T well below 0 degrees C. Hence, if a globular protein does not cold denature, aromatic flipping rates, and thus likely also the rates of other conformational and/or chemical exchange processes occurring in supercooled water, can be expected to be well estimated from activation parameters obtained at ambient T. This is of keen interest to predict the impact of supercooling for future studies of biological macromolecules, and shows that our approach enables one to conduct NMR-based structural biology at below 0 degrees C in an unperturbed aqueous environment. A search of the BioMagResBank indicated that the overwhelming majority of the Phe and Tyr rings (>95%) are flipping rapidly on the chemical shift time scale at ambient T, while our data for BPTI and activation parameters available for ring-flipping in Iso-2-cytochrome c reveal that in these smaller proteins a total of six out of seventeen rings ( approximately 35%) are "frozen in" at T = -15 degrees C. This suggests that a large fraction of Tyr and Phe rings in globular proteins that are flipping rapidly on the chemical shift time scale at ambient T can be effectively slowed in supercooled water. The present investigation demonstrates that supercooling of protein solutions appears to be an effective means to (i) harvest potential benefits of stalled ring-flipping for refining NMR solution structures, (ii) recruit additional aromatic rings for investigating protein dynamics, and (iii) use multiple slowly flipping rings to probe cold denaturation. The implications for NMR-based structural biology in supercooled water are addressed.