Special Pair Research Articles

Crystal structure of the novel haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 reveals a special halide-stabilizing pair and enantioselectivity mechanism

A novel haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 belongs to the HLD-II subfamily and hydrolyzes brominated and iodinated compounds, leading to the generation of the corresponding alcohol, a halide ion, and a proton. Because DatA possesses a unique Asn-Tyr pair instead of the Asn-Trp pair conserved among the subfamily members, which was proposed to keep the released halide ion stable, the structural basis for its reaction mechanism should be elucidated. Here, we determined the crystal structures of DatA and its Y109W mutant at 1.70 and 1.95 Å, respectively, and confirmed the location of the active site by using its novel competitive inhibitor. The structural information from these two crystal structures and the docking simulation suggested that (i) the replacement of the Asn-Tyr pair with the Asn-Trp pair increases the binding affinity for some halogenated compounds, such as 1,3-dibromopropane, mainly due to the electrostatic interaction between Trp109 and halogenated compounds and the change of substrate-binding mode caused by the interaction and (ii) the primary halide-stabilizing residue is only Asn43 in the wild-type DatA, while Tyr109 is a secondary halide-stabilizing residue. Furthermore, docking simulation using the crystal structures of DatA indicated that its enantioselectivity is determined by the large and small spaces around the halogen-binding site.

The Primitive Exponent of a Class of Special Nonnegative Matrix Pairs

There is a one-to-one relationship between nonnegative matrix pairs and two-colored digraph, so the problem of matrices can be changed into that of graphics to be solved. With the knowledge of graph theory, by studying the associated directed digraph of a class of special nonnegative matrix pairs, that is a class of two-colored digraphs whose uncolored digraph have vertices and consists of one-cycle and one-cycle are considered. The exponent and characteristic of extreme two-colored digraphs are given.

Explicit proton transfer in classical molecular dynamics simulations

We present Hydrogen Dynamics (HYDYN), a method that allows explicit proton transfer in classical force field molecular dynamics simulations at thermodynamic equilibrium. HYDYN reproduces the characteristic properties of the excess proton in water, from the special pair dance, to the continuous fluctuation between the limiting Eigen and Zundel complexes, and the water reorientation beyond the first solvation layer. Advantages of HYDYN with respect to existing methods are computational efficiency, microscopic reversibility, and easy parameterization for any force field.

Role of Electronic-Vibrational Mixing in Enhancing Vibrational Coherences in the Ground Electronic States of Photosynthetic Bacterial Reaction Center

We describe polarization controlled two-color coherence photon echo studies of the reaction center complex from a purple bacterium Rhodobacter sphaeroides. Long-lived oscillatory signals that persist up to 2 ps are observed in neutral, oxidized, and mutant (lacking the special pair) reaction centers, for both (0°,0°,0°,0°) and (45°,-45°,90°,0°) polarization sequences. We show that the long-lived signals arise via vibronic coupling of the bacteriopheophytin (H) and accessory bacteriochlorophyll (B) pigments that leads to vibrational wavepackets in the B ground electronic state. Fourier analysis of the data suggests that the 685 cm(-1) mode of B may play a key role in the H to B energy transfer.

Unsupervised quality estimation model for English to German translation and its application in extensive supervised evaluation.

With the rapid development of machine translation (MT), the MT evaluation becomes very important to timely tell us whether the MT system makes any progress. The conventional MT evaluation methods tend to calculate the similarity between hypothesis translations offered by automatic translation systems and reference translations offered by professional translators. There are several weaknesses in existing evaluation metrics. Firstly, the designed incomprehensive factors result in language-bias problem, which means they perform well on some special language pairs but weak on other language pairs. Secondly, they tend to use no linguistic features or too many linguistic features, of which no usage of linguistic feature draws a lot of criticism from the linguists and too many linguistic features make the model weak in repeatability. Thirdly, the employed reference translations are very expensive and sometimes not available in the practice. In this paper, the authors propose an unsupervised MT evaluation metric using universal part-of-speech tagset without relying on reference translations. The authors also explore the performances of the designed metric on traditional supervised evaluation tasks. Both the supervised and unsupervised experiments show that the designed methods yield higher correlation scores with human judgments.

Optimal Treatment Strategies for HIV with Antibody Response

Numerical analysis and optimization tools are used to suggest improved therapies to try and cure HIV infection. An HIV model of ordinary differential equation, which includes immune response, neutralizing antibodies, and multidrug effects, is improved. For a fixed time, single-drug and two-drug treatment strategies are explored based on Pontryagin’s maximum principle. Using different combinations of weight factor pairs combining with special upper-bound pairs for controls, nine types of treatment policies are determined and different therapy effects are numerically simulated with a gradient projection method. Some strategies are effective, but some strategies are not particularly helpful for the therapy of HIV/AIDS. Comparing the effective treatment strategies, we find a more appropriate strategy with maximizing the number of uninfected CD4+T-cells and minimizing the number of active virus.

Preorder Information Based Attributes' Weights Learning in Multi-attribute Decision Making

Choquet integral, as an adequate aggregation operator, extends the weighted mean operator by considering interactions among attributes. Choquet integral has been widely used in many real multi-attribute decision making. Weights (fuzzy measures) of attribute sets directly affect the decision results in multi-attribute decision making. In this paper, we aim to propose an objective method based on granular computing for determining the weights of the attribute sets. To address this issue, we first analyze the implied preorder relations under four evaluation forms and construct the corresponding preorder granular structures. Then, we define fuzzy measure of an attribute set by the similarity degree between a special preorder pairs. Finally, we employ two numerical examples for illustrating the feasibility and effectiveness of the proposed method. It is deserved to point out that the weight of each attribute subset can be learned from a given data set by the proposed method, not but be given subjectively by the decision maker. This idea provides a new perspective for multi-attribute decision making.

Efficient Error Analysis of a Real-Time Vision-Based Pointing Systems *

In this paper, an efficient error analysis of a real-time vision-based pointing system is proposed. We use two cameras to implement the pointing system according to a simplified 3D reconstruction scheme which is based on image feature extraction, homography, and 3D geometry. To that end, we study the relationship between image noises and the ultimate reconstruction errors, and develop efficient methods to find the error range of the latter given a range of the former. Experimental results show that the proposed approach can find the error range satisfactorily. Accordingly, users of similar pointing systems can get more robust pointing results by selecting a special pointer location, or possibly a special pair of cameras, that will result in minimal range of pointing error.

Midpoint Potential of the Interpolypeptide [4Fe-4S] Cluster FX in Reaction Centers from Heliobacterium Modesticaldum

Heliobacteria are members of a class of poorly characterized phototrophic bacteria that utilize a photosynthetic reaction center (RC) containing Fe/S clusters to convert light into chemical energy. The homodimeric RC of heliobacteria contains ∼22 light harvesting bacteriochlorophyll g (BChl g) pigments, the primary donor P800 (a special pair of BChl g') and the electron transfer cofactors A0 (81-OH ChlaF) and FX (an interpolypeptide [4Fe-4S] cluster). This terminal Fe/S cluster has been characterized by electron paramagnetic resonance (EPR) and mossbauer spectroscopies as being in the [4Fe-4S]1+ oxidation state with S = 3/2 in isolated RCs. To further characterize this cluster isolated RCs were titrated with sodium dithionite and analyzed by low temperature, transient, and field-modulated time-resolved EPR. Titration of the S = 3/2 signal with low temperature EPR revealed a midpoint potential of −504 mV (v. SHE). These results were confirmed by analysis of the one-and-the same samples by both transient and field-modulated time-resolved EPR.Altogether these three techniques reveal a midpoint potential of −500 mV ± 5 mV (v. SHE) for the FX cluster at pH 11. In agreement with previously published work, the lifetime of the flash-induced field-modulated EPR signal of P800+ was ∼ 2 ms at 90 K. These experiments suggest that the midpoint potential of FX in heliobacteria is ∼ 200 mV more positive than the counterpart FX cluster in Photosystem I, and show recombination kinetics with the primary donor that are faster at 90 K (∼ 2 ms) than at room temperature (∼ 15 ms). Funded by the Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences of the U.S. Department of Energy, under Grant DE-FG02-08ER15989.

Temperature and Detection-Wavelength Dependence of the Electron Transfer Rates in Initial Stages of Photosynthesis

Unusual temperature behavior, observed in the initial electron transfer stages in the photosynthetic reaction centers of the purple bacteria, and a strong probing pulse wavelength dependence of transfer rates, determined in transient absorption spectroscopy, can easily be explained on assuming that the transfer takes place from dynamically unrelaxed states of protein environment. The transitions from the primary special pair (P) to a single bacteriochlorophyll (B) and next to a bacteriopheophytin (H) are controlled by diffusion down the energy value of underdamped vibrational modes of frequency 200 K, probably determining distances between the succeeding cofactors. The subsequent transition to the quinone A (Q) is controlled by diffusion in the position value of an overdamped conformational mode, probably corresponding to the local polarization. From the fit of available experimental data to simple theoretical formulas, the important physical conclusion arises that the very electronic transitions are fast as compared to the relaxation processes and, in the first approximation, only the latter contribute to the overall times of the initial electron transfer stages in photosynthesis.

Asymptotic Solutions of nth Order Dynamic Equation and Oscillations

We establish a new asymptotic theorem for the nth order nonautonomous dynamic equation by its transformation to the almost diagonal system and applying Levinson's asymptotic theorem. Our transformation is given in the terms of unknown phase functions and is chosen in such a way that the entries of the perturbation matrix are the weighted characteristic functions. The characteristic function is defined in the terms of the phase functions and their choice is exible. Further applying this asymptotic theorem we prove the new oscillation and nonoscillation theorems for the solutions of the nth order linear nonautonomous differential equation with complex-valued coefficients. We show that the existence of the oscillatory solutions is connected with the existence of the special pairs of phase functions.

A Briefest Feature Subset Selection Algorithm Based on Preference Attribute

Concept lattice is the core data structure of formal concept analysis and represents the order relationship between the concepts iconically. Feature selection has been the focus of research in machine learning.And feature selection has been shown very effective in removing irrelevant and redundant features,also increasing efficiency in learning process and obtaining more intelligible learned results.This paper proposes a new briefest feature subset selection algorithm based on preference attribute on the basis of study of concept lattice theory. User can put forward a preference attribute according to their subjective experiences, all the briefest feature subsets containing the given attribute can be discovered by the algorithm. It firstly find some special concept pairs and calculate their waned-value hypergraph, then obtain the minimal transversal of the hypergraph as a result. A practical example proves the method is cogent and effective.

Hearts of twin cotorsion pairs on exact categories

In the papers of Nakaoka, he introduced the notion of hearts of (twin) cotorsion pairs on triangulated categories and showed that they have structures of (semi-) abelian categories. We study in this article a twin cotorsion pair (S,T), (U,V) on an exact category B with enough projectives and injectives and introduce a notion of the heart. First we show that its heart is preabelian. Moreover we show the heart of a single cotorsion pair is abelian. These results are analog of Nakaokaʼs results in triangulated categories. We also consider special cases where the heart has nicer structure. By our results, the heart of a special twin cotorsion pair (S,T), (T,V), is integral and almost abelian. Finally we show that the Gabriel–Zisman localization of the heart at the class of regular morphisms is abelian, and moreover it is equivalent to the category of finitely presented modules over a stable subcategory of B.

Structure-based modeling of energy transfer in photosynthesis

We provide a minimal model for a structure-based simulation of excitation energy transfer in pigment-protein complexes (PPCs). In our treatment, the PPC is assembled from its building blocks. The latter are defined such that electron exchange occurs only within, but not between these units. The variational principle is applied to investigate how the Coulomb interaction between building blocks changes the character of the electronic states of the PPC. In this way, the standard exciton Hamiltonian is obtained from first principles and a hierarchy of calculation schemes for the parameters of this Hamiltonian arises. Possible extensions of this approach are discussed concerning (i) the inclusion of dispersive site energy shifts and (ii) the inclusion of electron exchange between pigments. First results on electron exchange within the special pair of photosystem II of cyanobacteria and higher plants are presented and compared with earlier results on purple bacteria. In the last part of this mini-review, the coupling of electronic and nuclear degrees of freedom is considered. First, the standard exciton-vibrational Hamiltonian is parameterized with the help of a normal mode analysis of the PPC. Second, dynamical theories are discussed that exploit this Hamiltonian in the study of dissipative exciton motion.

Surface-Enhanced Infrared Absorption Spectroscopy (SEIRAS) of Light-Activated Photosynthetic Reaction Centers from Rhodobacter sphaeroides Reconstituted in a Biomimetic Membrane System

Surface-enhanced IR absorption spectroscopy (SEIRAS) in the ATR configuration has been performed on reaction centers (RCs) from R. sphaeroides. Surface-enhancement is achieved by a thin, structured gold film present on the surface of an ATR crystal. Purified RCs are immobilized as a monolayer on top of the gold film via a poly his-tag engineered to the C-terminal end of the M subunit. Subsequently, the RCs are reconstituted into a lipid bilayer by in situ dialysis. Light-minus-dark absorbance spectra were recorded under continuous illumination using the spectrum in the dark as the reference. A number of strong bands have been observed indicating the excitation of the special pair as well as alterations of quinone/quinol species. Spectra were recorded at different time intervals with and without liposoluble Q10 coreconstituted into the lipid phase. A steady (photostationary) state was approached slowly and bands were found to increase or decrease reversibly on illumination and relaxation. Tentative assignments were made for some bands, based on previous FTIR measurements. The long time scale of these processes was tentatively explained in terms of interprotein reactions of RC molecules.

Evidence for reverse pathways and equilibrium in singlet energy transfers between an artificial special pair and an antenna

A dyad, 1, built on an artificial special pair (bis(meso-nonyl)zinc(II)porphyrin), [Zn2], a spacer (biphenylene), a bridge (1,4-benzene), and an antenna (di-meso-(3,5-di(t-butyl)phenyl)porphyrin free base), FB, is prepared by Suzuki coupling and is analyzed by absorption and steady state, and time-resolved emission spectroscopy at 298 and 77 K. Using bases from the Förster theory, evidence for two pathways for S 1 energy transfer, FB* → [Zn2], and [Zn2]* → FB, along with their respective rates, k ET ( S 1)1 and k ET ( S 1)-1, are extracted from the comparison of the fluorescence decays monitored at the emission maximum. At 77 K, the unquenched (1.79 ([Zn2]) and 10.6 ns (FB)) and quenched components (<100 ps; i.e. k ET ( S 1) > 10 (ns)-1), are observed, hence, demonstrating the bidirectional paths with no back energy transfer. A 298 K, only two components are detected (0.44 ([Zn2]) and 2.64 ns (FB)) and the resulting reduced τFs indicates back energy transfer, therefore cycling and equilibrium. Their global rates are 0.31 and 1.8 (ns)-1 for k ET ( S 1)1 and k ET ( S 1)-1 at 298 K. This large temperature dependence on k ET ( S 1) is fully consistent with the participation of thermal activation. Finally, DFT calculations (B3LYP) were used to illustrate a clear correlation between the relative k ET ( S 1) s and the amplitude of the MO couplings between the artificial special pair and the antenna.

Sampling approximation by framelets in Sobolev space and its application in modifying interpolating error

Motivated by [B. Han, Z. Shen, Dual wavelet frames and Riesz bases in Sobolev spaces, Constr. Approx. 29 (2009) 369–406], we establish a sampling theorem in Hs(Rd), s>1/2,d≥1, using a special pair of dual frames. The converging rate of the corresponding sampling series is investigated, and then sampling approximation to a signal in Sobolev space is established. If a signal to be reconstructed satisfies a mild condition in Fourier transform, then its sampling series converges exponentially fast. As an application, the sampling approximation is used to modify interpolating error, which arises when using an interpolating refinable function to reconstruct f∈Hs(Rd), such that f can be arbitrarily approximated by its samples.

Symmetry Break of Special Pair: Photochemically Induced Dynamic Nuclear Polarization NMR Confirms Control by Nonaromatic Substituents

Despite the high structural symmetry of cofactor arrangement and protein environment, light-induced electron transfer in photosynthetic reaction centers (RCs) of the purple bacterium Rhodobacter sphaeroides runs selectively over one of the two branches of cofactors. The origin of this functional symmetry break has been debated for several decades. Recently, a crucial role of the substituents has been proposed by theoretical studies [Yamasaki, H.; Takano, Y.; Nakamura, H. J. Phys. Chem. B 2008, 112, 13923-13933]. Photo-CIDNP (photochemically induced dynamic nuclear polarization) MAS (magic angle spinning) NMR demonstrates that indeed the peripheral atoms show opposite electronic effects on both sides of the special pair. While the aromatic system of P(L) receives electron density from its periphery, the electron density of the aromatic ring of P(M) is decreased.

Completion of biosynthetic pathways for bacteriochlorophyll g in Heliobacterium modesticaldum: The C8-ethylidene group formation

Heliobacteria have the simplest photosynthetic apparatus, i.e., a type-I reaction center lacking a peripheral light-harvesting complex. Bacteriochlorophyll (BChl) g molecules are bound to the reaction center complex and work both as special-pair and antenna pigments. The C8-ethylidene group formation for BChl g is the last missing link in biosynthetic pathways for bacterial special-pair pigments, which include BChls a and b as well. Here, we report that chlorophyllide a oxidoreductase (COR) of Heliobacterium modesticaldum catalyzes the C8-ethylidene formation from 8-vinyl-chlorophyllide a, producing bacteriochlorophyllide g, the direct precursor for BChl g without the farnesyl tail. The finding led to plausible biosynthetic pathways for 81-hydroxy-chlorophyll a, a primary electron acceptor from the special pair in heliobacterial reaction centers. Proposed catalytic mechanisms on hydrogenation reaction of the ethylidene synthase-type CORs are also discussed.

Proton Displacements Coupled to Primary Electron Transfer in the Rhodobacter sphaeroides Reaction Center

Using first-principles molecular dynamics (AIMD) and constrained density functional theory (CDFT) we identify the pathway of primary electron transfer in the R. Sphaeroides reaction center from the special pair excited state (P*) to the accessory bacteriochlorophyll (BA). Previous AIMD simulations on the special pair (PLPM) predicted a charge-transfer intermediate formation through the excited-state relaxation along a reaction coordinate characterized by the rotation of an axial histidine (HisM202). To account for the full electron transfer we extend the model to include the primary acceptor BA. In this extended model, the LUMO is primarily localized on the acceptor BA and extends over an interstitial water (water A) that is known to influence the rate of electron transfer (Potter et al. Biochemistry 2005 280, 27155-27164). A vibrational analysis of the dynamical trajectories gives a frequency of 30-35 cm(-1) for a molecular motion involving the hydrogen-bond network around water A, in good agreement with experimental findings (Yakovlev et al. Biochemistry, 2003, 68, 603-610). In its binding pocket water A can act as a switch by breaking and forming hydrogen bonds. With CDFT we calculate the energy required to the formation of the charge-separated state and find it to decrease along the predicted anisotropic reaction coordinate. Furthermore, we observe an increased coupling between the ground and charge-separated state. Water A adapts its hydrogen-bonding network along this reaction coordinate and weakens the hydrogen bond with HisM202. We also present AIMD simulations on the radical cation (P(•+)) showing a weakening of the hydrogen bond between HisL168 and the 3(1)-acetyl of PL. This work demonstrates how proton displacements are crucially coupled to the primary electron transfer and characterizes the reaction coordinate of the initial photoproduct formation.