Ns Time Scale Research Articles

A flexible x-ray imaging endstation for synchrotron radiation facilities

We present an endstation suited for high resolution x-ray imaging based on a modular concept. One to three cylindrical vacuum chambers can be placed on an external rail system in variable distances to each other, while an internal optical rail system can carry up to five x-y-z-motion stages per chamber, each having 50 mm travel range in x- and y- and virtually infinite in z-direction with a position accuracy better than 100 nm. The piezo-driven stages will for a particular experiment be equipped with optics, filters, detectors, specimen or other components needed. The endstation can be configured for full-field x-ray microscopy (TXM), scanning transmission x-ray microscopy (STXM), x-ray fluorescence microscopy, ptychographic and x-ray holographic setups and other experiments that may be of scientific value to the user. The STXM setup already allows imaging the specimen under investigation in different image modes, like bright field, phase contrast, differential phase contrast and dark field. In first experiments, a full-field transmission x-ray microscope was set up at beamline P04 at PETRA III . With this setup we demonstrated imaging of structures in the sub-50 nm range. Furthermore, the microscope was used for imaging the magnetic orientation of nano-structured materials utilizing the x-ray magnetic circular dichroism (XMCD) contrast with temporal resolution, allowing for observing the evolvement of magnetic domains on nm-space and ns-time scale [1, 2].

Cathodic Electrodeposition of Ni-Mo on Semiconducting NiFe2 O4 for Photoelectrochemical Hydrogen Evolution in Alkaline Media.

Photocathodes for hydrogen evolution from water were made by electrodeposition of Ni-Mo layers on NiFe2 O4 substrates, deposited by spin coating on F:SnO2 -glass. Analysis confirmed the formation of two separate layers, without significant reduction of NiFe2 O4 . Bare NiFe2 O4 was found to be unstable under alkaline conditions during (photo)electrochemistry. To improve the stability significantly, the deposition of a bifunctional Ni-Mo layer through a facile electrodeposition process was performed and the composite electrodes showed stable operation for at least 1 h. Moreover, photocurrents up to -2.1 mA cm-2 at -0.3 V vs. RHE were obtained for Ni-Mo/NiFe2 O4 under ambient conditions, showing that the new combination functions as both a stabilizing and catalytic layer for the photoelectrochemical evolution of hydrogen. The photoelectrochemical response of these composite electrodes decreased with increasing NiFe2 O4 layer thickness. Transient absorption spectroscopy showed that the lifetime of excited states is short and on the ns timescale. An increase in lifetime was observed for NiFe2 O4 of large layer thickness, likely explained by decreasing the defect density in the primary layer(s), as a result of repetitive annealing at elevated temperature. The photoelectrochemical and transient absorption spectroscopy results indicated that a short charge carrier lifetime limits the performance of Ni-Mo/NiFe2 O4 photocathodes.

The photoluminescence, ultrafast nonlinear optical properties and carrier dynamics of 1D In-doped ZnO nanostructures: Experiment and mechanism

1D In-doped ZnO (IZO) nanostructures with different morphologies, namely nanowires, nanoseries(serial), nanorods and nanoprisms, have been successfully synthesized by chemical vapour deposition method. The structural, morphology and optical properties of IZO nanowires have been characterized. The ultrafast nonlinear optical and carrier dynamics characteristics of IZO were studied using femtosecond Z-scan, time-resolved photoluminescence (TRPL) and two-color pump-probe (TCPP) technique, respectively. The TRPL showed that the luminescence decay lifetimes of about several 10 ps and nanoseconds time response scale can be attributed to the shallow trap (ST) state, and deep trap (DT) state emissions, respectively. The mechanisms of the TRPL behavior in the different emission band were analyzed. The result of TCPP experiment showed that the bleach recovery with lifetimes on the fast (100–200 ps), and slow (>1 ns) time scale, caused by the shallow donor mixed with donor bound recombination, and donor−acceptor pair recombination (DAP), respectively. The optical transition process in the IZO nanostructures has demonstrated that the energy transfer process from the host electron-hole pairs can efficiently excite the metal ions. Comparing with the results obtained from the TRPL experiment, we found the fast decay process was resulted from the exciton migration and the slow decay to the recombination process of the relaxed excitons. Our results show that IZO nanostructures are a promising candidate in further optoelectronic device applications.

Time-resolved infrared studies of the unfolding of a light triggered β-hairpin peptide

The light triggered unfolding reaction of the azobenzene peptide AzoTrpZip2 is investigated from 1 ps to 100 µs. Absorption changes show that the unfolding is a multistep process with the initial breaking of the hydrogen bonds in the vicinity of the AMPP chromophore on the 1 ns time scale followed by the disappearance of the remaining interstrand hydrogen bonds of the native hairpin structure with a 1.9 µs process. Subsequently, the hydrophobic core structure still stabilising a hairpin-like pattern rearranges in a 17 µs process. The strong slowing down of this reaction at lower temperature points to a barrier height in the range of 60 kJ/mol.

Vibrational energy relaxation dynamics of diatomic molecules inside superfluid helium nanodroplets. The case of the I2 molecule.

The vibrational energy relaxation (VER) of a homonuclear diatomic molecule (X2) in a 4He superfluid nanodroplet (HeND; T = 0.37 K) was studied adapting appropriately a hybrid theoretical quantum approach recently proposed by us. In the first application the interesting case of the I2(X) molecule was examined and, as far as we know, this corresponds to the first theoretical investigation on the VER of molecules embedded in HeND. Vibrational relaxation of I2 takes place according to a cascade mechanism [sequential transitions between two consecutive vibrational levels (ν → ν - 1; ν - 1 → ν - 2; …; 2 → 1; 1 → 0), where an arbitrary relaxation, e.g., ν - 1 → ν - 2, can only occur once the previous relaxation has taken place, and so on]. The global relaxation from the initial excited state ν down to the ground state (ν = 0) happens on the nanosecond scale. Data on the VER of molecules in HeND are very scarce and a vibrational lifetime not far from the I2 one for ν = 1 has been estimated experimentally for Na3(24E') on HeND (a qualitatively similar 0 → 1 vibrational energy gap occurs in both species), but metastability has not been reported in the second case. The cascade mechanism was understood once the values of the coupling matrix elements were examined, and the time evolution of the populations of two consecutive vibrational levels was adequately described using a non-linear two-state Hamiltonian model for I2 in the HeND. According to the calculations, superfluid liquid helium is very efficient in releasing the excess of energy arising from the I2 vibrational de-excitation, as it should be. However, the number of He atoms evaporated is small compared to what is expected. We hope that this first theoretical work on the molecular VER dynamics in HeND will encourage researchers to investigate this important process about which we still know very little.

NMR investigation of the isolated second voltage-sensing domain of human Nav1.4 channel

Voltage-gated Na+ channels are essential for the functioning of cardiovascular, muscular, and nervous systems. The α-subunit of eukaryotic Na+ channel consists of ~2000 amino acid residues and encloses 24 transmembrane (TM) helices, which form five membrane domains: four voltage-sensing (VSD) and one pore domain. The structural complexity significantly impedes recombinant production and structural studies of full-sized Na+ channels. Modular organization of voltage-gated channels gives an idea for studying of the isolated second VSD of human skeletal muscle Nav1.4 channel (VSD-II). Several variants of VSD-II (~150a.a., four TM helices) with different N- and C-termini were produced by cell-free expression. Screening of membrane mimetics revealed low stability of VSD-II samples in media containing phospholipids (bicelles, nanodiscs) associated with the aggregation of electrically neutral domain molecules. The almost complete resonance assignment of 13C,15N-labeled VSD-II was obtained in LPPG micelles. The secondary structure of VSD-II showed similarity with the structures of bacterial Na+ channels. The fragment of S4 TM helix between the first and second conserved Arg residues probably adopts 310-helical conformation. Water accessibility of S3 helix, observed by the Mn2+ titration, pointed to the formation of water-filled crevices in the micelle embedded VSD-II. 15N relaxation data revealed characteristic pattern of μs–ms time scale motions in the VSD-II regions sharing expected interhelical contacts. VSD-II demonstrated enhanced mobility at ps–ns time scale as compared to isolated VSDs of K+ channels. These results validate structural studies of isolated VSDs of Na+ channels and show possible pitfalls in application of this ‘divide and conquer’ approach.

Long-range energy transport in photosystem II.

We simulate the long-range inter-complex electronic energy transfer in photosystem II-from the antenna complex, via a core complex, to the reaction center-using a non-Markovian (ZOFE) quantum master equation description that allows the electronic coherence involved in the energy transfer to be explicitly included at all length scales. This allows us to identify all locations where coherence is manifested and to further identify the pathways of the energy transfer in the full network of coupled chromophores using a description based on excitation probability currents. We investigate how the energy transfer depends on the initial excitation-localized, coherent initial excitation versus delocalized, incoherent initial excitation-and find that the overall energy transfer is remarkably robust with respect to such strong variations of the initial condition. To explore the importance of vibrationally enhanced transfer and to address the question of optimization in the system parameters, we systematically vary the strength of the coupling between the electronic and the vibrational degrees of freedom. We find that the natural parameters lie in a (broad) region that enables optimal transfer efficiency and that the overall long-range energy transfer on a ns time scale appears to be very robust with respect to variations in the vibronic coupling of up to an order of magnitude. Nevertheless, vibrationally enhanced transfer appears to be crucial to obtain a high transfer efficiency, with the latter falling sharply for couplings outside the optimal range. Comparison of our full quantum simulations to results obtained with a "classical" rate equation based on a modified-Redfield/generalized-Förster description previously used to simulate energy transfer dynamics in the entire photosystem II complex shows good agreement for the overall time scales of excitation energy transport.

MULTI-IFE—A one-dimensional computer code for Inertial Fusion Energy (IFE) target simulations

The code MULTI-IFE is a numerical tool devoted to the study of Inertial Fusion Energy (IFE) microcapsules. It includes the relevant physics for the implosion and thermonuclear ignition and burning: hydrodynamics of two component plasmas (ions and electrons), three-dimensional laser light ray-tracing, thermal diffusion, multigroup radiation transport, deuterium–tritium burning, and alpha particle diffusion. The corresponding differential equations are discretized in spherical one-dimensional Lagrangian coordinates. Two typical application examples, a high gain laser driven capsule and a low gain radiation driven marginally igniting capsule are discussed. In addition to phenomena relevant for IFE, the code includes also components (planar and cylindrical geometries, transport coefficients at low temperature, explicit treatment of Maxwell’s equations) that extend its range of applicability to laser–matter interaction at moderate intensities (<1016 W cm−2). The source code design has been kept simple and structured with the aim to encourage user’s modifications for specialized purposes. Program summaryProgram title: MULTI-IFECatalogue identifier: AEZR_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEZR_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 267428No. of bytes in distributed program, including test data, etc.: 3798542Distribution format: tar.gzProgramming language: Fortran 95.Computer: Any.Operating system: Any.RAM: 1.8 MBClassification: 19.7.Nature of problem: The implosion and ignition of inertial energy fusion capsules driven either directly by laser beams or indirectly by thermal radiation.Solution method: The one-dimensional equations of hydrodynamic motion, laser propagation, energy transport by thermal conduction and radiative transfer, deuterium–tritium thermonuclear burning, and α-particle diffusion are discretized on a Lagrangian grid, and advanced in time by a fractional step scheme. An implicit conservative method is used to treat hydrodynamics. Thermal and electrical conductivities as well as coefficients for laser absorption and electron–ion energy exchange are obtained from a two temperature (for electrons and ions) model. Laser propagation is treated by 3D tracing of the laser rays in the geometrical optics approximation. Radiation transfer is solved by using the forward–reverse method for a discrete number of frequency groups. Matter properties are interpolated from tables (equations-of-state, ionization, and opacities) generated by external codes.Restrictions: The code has been designed for typical conditions prevailing in inertial confinement fusion (ps–ns time scale, matter states close to local thermodynamic equilibrium, and negligible radiation pressure). A wider range of situations can be treated, as long as the above conditions are fulfilled. This includes, in particular, laser plasma experiments at moderate intensities (≤1016W cm−2).Unusual features: An optional graphical post-processing package is included in the distribution. This option requires a Linux/Unix operating system with the essential developing tools (C compiler; X11 libraries and include files; and the xterm command). Most of the figures in this paper have been created using this software.Additional comments: The source code design has been kept simple and structured, with the aim to encourage user’s modifications for specialized purposes. A technical manual is included in the package.Running time: 13–18 s for the examples discussed in the paper.

Dynamics of ionic liquids in bulk and in confinement by means of1H NMR relaxometry – BMIM-OcSO4in an SiO2matrix as an example

(1)H nuclear magnetic resonance relaxometry is applied to reveal information on the translational and rotational dynamics of the ionic liquid: 1-butyl-3-methyl imidazoliumoctyl sulfate (BMIM-OcSO4) in bulk and in a confinement formed by a nanoporous SiO2 matrix. The experimental studies were performed in a very broad frequency range, from 8 kHz to 40 MHz (referring to the (1)H resonance frequency), in order to probe motional processes at very different time scales using a single experiment, and in the temperature range of 243-303 K. The relaxation results for BMIM-OcSO4 in bulk are interpreted in terms of three relaxation contributions: a term associated with the translational dynamics of the ions (it has been assumed that the translational dynamics of cations and anions can be described by one diffusion coefficient) and two terms associated with the rotational motion of the anion and the cation, respectively. The relationships between the obtained dynamic parameters (rotational correlation times and translational diffusion coefficients) are thoroughly discussed and used as a "reference" for the dynamics of BMIM-OcSO4 confined in an SiO2 matrix. Analysis of the corresponding relaxation data for the confined liquid shows that the confinement does not significantly affect the rotational dynamics, but it has a considerable impact on the translational motion. It is demonstrated that the relaxation term associated with the translational dynamics stems from two contributions: a contribution from a core (bulk-like) fraction of the liquid and from a fraction moving near the pore surface and therefore being for some time adsorbed on the pore walls. The translational diffusion coefficient for the last fraction is determined and several conclusions regarding the residence lifetime of the ions on the surface are drawn. Moreover, an additional motional process on the timescale of ns or shorter is revealed in the confinement.

High-resolution structures of the d-alanyl carrier protein (Dcp) DltC from Bacillus subtilis reveal equivalent conformations of apo- and holo-forms

d-Alanylation of lipoteichoic acids plays an important role in modulating the properties of Gram-positive bacteria cell walls. The d-alanyl carrier protein DltC from Bacillus subtilis has been solved in apo- and two cofactor-modified holo-forms, whereby the entire phosphopantetheine moiety is defined in one. The atomic resolution of the apo-structure allows delineation of alternative conformations within the hydrophobic core of the 78 residue four helix bundle. In contrast to previous reports for a peptidyl carrier protein from a non-ribosomal peptide synthetase, no obvious structural differences between apo- and holo-DltC forms are observed. Solution NMR spectroscopy confirms these findings and demonstrates in addition that the two forms exhibit similar backbone dynamics on the ps–ns and ms timescales.

Dynamics of the Peripheral Membrane Protein P2 from Human Myelin Measured by Neutron Scattering—A Comparison between Wild-Type Protein and a Hinge Mutant

Myelin protein P2 is a fatty acid-binding structural component of the myelin sheath in the peripheral nervous system, and its function is related to its membrane binding capacity. Here, the link between P2 protein dynamics and structure and function was studied using elastic incoherent neutron scattering (EINS). The P38G mutation, at the hinge between the β barrel and the α-helical lid, increased the lipid stacking capacity of human P2 in vitro, and the mutated protein was also functional in cultured cells. The P38G mutation did not change the overall structure of the protein. For a deeper insight into P2 structure-function relationships, information on protein dynamics in the 10 ps to 1 ns time scale was obtained using EINS. Values of mean square displacements mainly from protein H atoms were extracted for wild-type P2 and the P38G mutant and compared. Our results show that at physiological temperatures, the P38G mutant is more dynamic than the wild-type P2 protein, especially on a slow 1-ns time scale. Molecular dynamics simulations confirmed the enhanced dynamics of the mutant variant, especially within the portal region in the presence of bound fatty acid. The increased softness of the hinge mutant of human myelin P2 protein is likely related to an enhanced flexibility of the portal region of this fatty acid-binding protein, as well as to its interactions with the lipid bilayer surface requiring conformational adaptations.

Consequences of Hydrocarbon Contamination for Wettability and Protein Adsorption on Graphite Surfaces

We present results from molecular dynamics simulations and contact angle measurements on graphite showing that this surface is indeed intrinsically mildly hydrophilic contrary to the common belief. Hydrocarbon contamination, known to be the source for the usually observed hydrophobic property of graphite, also affects protein adsorption processes as shown in this study. In the computational part of this work ethane was used as a model hydrocarbon which acts on the surface by reducing the water–surface and protein–surface interactions. This contamination then results in higher water contact angles. The process of protein adsorption is studied for the example of insulin revealing a reduction in adsorption strength despite the surface being more hydrophobic when contaminated. Although the proteins did not denature on the contaminated surfaces, further processes, such as the displacement of hydrocarbons by the protein, may occur on a longer time scale. In conclusion, we argue that proteins adsorb faster on pure than on contaminated surfaces with respect to the molecular dynamics time scale of ns.

Efficient autoionization following intense laser-cluster interactions.

Electron emission as a result of the interaction of clusters with intense laser pulses is commonly understood in terms of direct and evaporative ionization processes. In contrast, we provide evidence here of an important role played by autoionization in intense field ionization of molecular oxygen clusters. Superexcited states are populated during the cluster expansion, and their autoionization is observed on a ns time scale. Decay processes on fs to ps time scales are obscured by energy exchange of the emitted electrons with the environment.

Production and Diagnostics of Dense Matter

AbstractHigh energy lasers are a unique tool to create high pressure states above 10 Mbar at ns time scales, which allow to study material properties under these extreme conditions. These conditions are, for example, comparable with planetary cores, where material properties play an important role for the properties and evolution of a planet. The rapid compression allows also to study dynamic effects of phase transitions as compression times are comparable to relaxation times. We will present recent results of laser compression of iron reaching conditions of so called “super‐Earth” cores. A description of the compression schemes as well as present and future diagnostics is presented. (© 2015 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Implementing Solution X-Ray Scattering Data as Active Constraints in MD Simulations

X-ray and neutron solution scattering are powerful techniques that provide a measure of biomolecular structure and its diversity. The techniques are highly sensitive to conformational change - however, the measured intensities represent a single global average over all conformations and obscures the extent of structural variations as well as their relative frequency. Thus, the utility of scattering data in molecular simulations depend on the ability to generate the underlying conformational ensemble, guided by only the average values. To resolve this, we recently implemented an explicit-solvent approach to predict the ensemble SWAXS pattern of a biomolecule using molecular dynamics [Chen and Hub, Biophys. J. 107:435-447 (2014)]. By relying upon MD to explicitly sample fast degrees of freedoms in both solvent and solute, accurate predictions were computed for relatively stable proteins. The approach adopted also enables the use of SWAXS data as constraints that provide forces to guide the simulation trajectory, which permits the interpretation of experimental data by directing simulated proteins into compatible conformations. The application of SWAXS-driven MD to biological examples is given in an accompanying talk.Here, we will address the derivation of such constraints, taking into account the sampling of different degrees of freedom and sources of uncertainty. We find that conformation-dependant SWAXS patterns can be derived over ∼1 ns timescales, permitting fast equilibration in constrained-simulations. Uncertainty due to buffer subtraction dominates at low angles q, while experimental and statistical errors dominate at large q. Inclusion of these errors in the constraints do not affect the qualitative behaviour of resulting trajectories. The application of SWAXS-based constraints in the context of both single-state and heterogenous ensembles will also be discussed.

Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant.

Catalysis by dihydrofolate reductase from the moderately thermophilic bacterium Geobacillus stearothermophilus (BsDHFR) was investigated by isotope substitution of the enzyme. The enzyme kinetic isotope effect for hydride transfer was close to unity at physiological temperatures but increased with decreasing temperatures to a value of 1.65 at 5 °C. This behavior is opposite to that observed for DHFR from Escherichia coli (EcDHFR), where the enzyme kinetic isotope effect increased slightly with increasing temperature. These experimental results were reproduced in the framework of variational transition-state theory that includes a dynamical recrossing coefficient that varies with the mass of the protein. Our simulations indicate that BsDHFR has greater flexibility than EcDHFR on the ps-ns time scale, which affects the coupling of the environmental motions of the protein to the chemical coordinate and consequently to the recrossing trajectories on the reaction barrier. The intensity of the dynamic coupling in DHFRs is influenced by compensatory temperature-dependent factors, namely the enthalpic barrier needed to achieve an ideal transition-state configuration with minimal nonproductive trajectories and the protein disorder that disrupts the electrostatic preorganization required to stabilize the transition state. Together with our previous studies of other DHFRs, the results presented here provide a general explanation why protein dynamic effects vary between enzymes. Our theoretical treatment demonstrates that these effects can be satisfactorily reproduced by including a transmission coefficient in the rate constant calculation, whose dependence on temperature is affected by the protein flexibility.

Ultrafast Photoinduced Electron Transfer in a π-Conjugated Oligomer/Porphyrin Complex.

Controlling charge transfer (CT), charge separation (CS), and charge recombination (CR) at the donor-acceptor interface is extremely important to optimize the conversion efficiency in solar cell devices. In general, ultrafast CT and slow CR are desirable for optimal device performance. In this Letter, the ultrafast excited-state CT between platinum oligomer (DPP-Pt(acac)) as a new electron donor and porphyrin as an electron acceptor is monitored for the first time using femtosecond (fs) transient absorption (TA) spectroscopy with broad-band capability and 120 fs temporal resolution. Turning the CT on/off has been shown to be possible either by switching from an organometallic oligomer to a metal-free oligomer or by controlling the charge density on the nitrogen atom of the porphyrin meso unit. Our time-resolved data show that the CT and CS between DPP-Pt(acac) and cationic porphyrin are ultrafast (approximately 1.5 ps), and the CR is slow (ns time scale), as inferred from the formation and the decay of the cationic and anionic species. We also found that the metallic center in the DPP-Pt(acac) oligomer and the positive charge on the porphyrin are the keys to switching on/off the ultrafast CT process.

Symmetrized photoinitiated electron flow within the [myoglobin:cytochrome b₅] complex on singlet and triplet time scales: energetics vs dynamics.

We report here that photoinitiated electron flow involving a metal-substituted (M = Mg, Zn) myoglobin (Mb) and its physiological partner protein, cytochrome b5 (cyt b5) can be “symmetrized”: the [Mb:cyt b5] complex stabilized by three D/E → K mutations on Mb (D44K/D60K/E85K, denoted MMb) exhibits both oxidative and reductive ET quenching of both the singlet and triplet photoexcited MMb states, the direction of flow being determined by the oxidation state of the cyt b5 partner. The first-excited singlet state of MMb (1MMb) undergoes ns-time scale reductive ET quenching by Fe2+cyt b5 as well as ns-time scale oxidative ET quenching by Fe3+cyt b5, both processes involving an ensemble of structures that do not interconvert on this time scale. Despite a large disparity in driving force favoring photooxidation of 1MMb relative to photoreduction (δ(−ΔG0) ≈ 0.4 eV, M = Mg; ≈ 0.2 eV, M = Zn), for each M the average rate constants for the two reactions are the same within error, 1kf > 108 s–1. This surprising observation is explained by considering the driving-force dependence of the Franck–Condon factor in the Marcus equation. The triplet state of the myoglobin (3MMb) created by intersystem crossing from 1MMb likewise undergoes reductive ET quenching by Fe2+cyt b5 as well as oxidative ET quenching by Fe3+cyt b5. As with singlet ET, the rate constants for oxidative ET quenching and reductive ET quenching on the triplet time scale are the same within error, 3kf ≈ 105 s–1, but here the equivalence is attributable to gating by intracomplex conversion among a conformational ensemble.

Evidence that histidine forms a coordination bond to the A0A and A0B chlorophylls and a second H-bond to the A1A and A1B phylloquinones in M688HPsaA and M668HPsaB variants of Synechocystis sp. PCC 6803

The axial ligands of the acceptor chlorophylls, A0A and A0B, in Photosystem I are the Met sulfur atoms of M688PsaA and M668PsaB. To determine the role of the Met, His variants were generated in Synechocystis sp. PCC 6803. Molecular dynamics simulations on M688HPsaA show that there exist low energy conformations with the His coordinated to A0A and possibly H-bonded to A1A. Transient EPR studies on M688HPsaA indicate a more symmetrical electron spin distribution in the A1A phyllosemiquinone ring consistent with the presence of an H-bond to the C1 carbonyl. Ultrafast optical studies on the variants show that the 150fs charge separation between P700 and A0 remains unaffected. Studies on the ns timescale show that 57% of the electrons are transferred from A0A− to A1A in M688HPsaA and 48% from A0B− to A1B in M668HPsaB; the remainder recombine with P700+ with 1/e times of 25ns and 37ns, respectively. Those electrons that reach A1A and A1B in the branch carrying the mutation are not transferred to FX, but recombine with P700+ with 1/e times of ~15μs and ~5μs, respectively. Hence, the His is coordinated to A0 in all populations, but in a second population, the His may be additionally H-bonded to A1. Electron transfer from A0 to A1 occurs only in the latter, but the higher redox potentials of A0 and A1 as a result of the stronger coordination bond to A0 and the proposed second H-bond to A1 preclude electron transfer to the Fe/S clusters.

Transcription Factor Binding and Sliding Studied using Microscopic and Mesoscopic Models

In vitro experiments in the early 70s suggested that the time it takes for LacI to bind to the operator site is ∼100 times faster than what would be expected for a pure 3D diffusion-controlled binding reaction. This discrepancy between theory and observations was resolved by introducing the theory of facilitated diffusion where the operator search problem is viewed as a coupled 1D-3D diffusion process. Since then, numerous theoretical studies have been made to elucidate the details of the search process. In this work we have used fully atomistic molecular dynamics simulations for the complete LacI dimer (666 aa) and a stretch of nonspecific DNA (30 bp) to help unravel these details. In particular we find that LacI slides along DNA in a helical trajectory with fast hydrogen-bond dynamics, displacing water molecules and sodium atoms in its path. Using the umbrella sampling technique we also quantify the free energy variation of LacI sliding and dissociation. We then use this energy landscape to deduce the 1D diffusion constant, D1=0.14 μm2s−1, and a microscopic residence time, τmicro= 69 μs. Given that τmicro is not accessible on experimental timescales we employ Brownian dynamic simulations to estimate the average number of times LacI rebinds to DNA before macroscopically dissociating (∼700). Then, by connecting Brownian dynamics and molecular dynamics, we get a macroscopic residence time (τmacro= 48 ms). Finally, we estimate a sliding length of 240+-105 bp, which compares well to the experimental value of 150 bp. As such, we connect structural dynamics at the ns timescales and atomistic lengthscales with meso- and macroscopic information to unravel hitherto unknown apects of the search process.