Cyclic nucleotide binding and structural changes in the isolated GAF domain of Anabaena adenylyl cyclase, CyaB2

GAF domains are a large family of regulatory domains, and a subset are found associated with enzymes involved in cyclic nucleotide (cNMP) metabolism such as adenylyl cyclases and phosphodiesterases. CyaB2, an adenylyl cyclase from Anabaena, contains two GAF domains in tandem at the N-terminus and an adenylyl cyclase domain at the C-terminus. Cyclic AMP, but not cGMP, binding to the GAF domains of CyaB2 increases the activity of the cyclase domain leading to enhanced synthesis of cAMP. Here we show that the isolated GAFb domain of CyaB2 can bind both cAMP and cGMP, and enhanced specificity for cAMP is observed only when both the GAFa and the GAFb domains are present in tandem(GAFab domain). In silico docking and mutational analysis identified distinct residues important for interaction with either cAMP or cGMP in the GAFb domain. Structural changes associated with ligand binding to the GAF domains could not be detected by bioluminescence resonance energy transfer (BRET) experiments. However, amide hydrogen-deuterium exchange mass spectrometry (HDXMS) experiments provided insights into the structural basis for cAMP-induced allosteric regulation of the GAF domains, and differences in the changes induced by cAMP and cGMP binding to the GAF domain. Thus, our findings could allow the development of molecules that modulate the allosteric regulation by GAF domains present in pharmacologically relevant proteins.

Contrasting Electronic Requirements for C-H Binding and C-H Activation in d(6) Half-Sandwich Complexes of Rhenium and Tungsten

A computational study of the interaction half-sandwich metal fragments (metal=Re/W, electron count=d(6)), containing linear nitrosyl (NO+), carbon monoxide (CO), trifluorophosphine (PF3), N-heterocyclic carbene (NHC) ligands with alkanes are conducted using density functional theory employing the hybrid meta-GGA functional (M06). Electron deficiency on the metal increases with the ligand in the order NHC < CO < PF3 < NO+. Electron-withdrawing ligands like NO+ lead to more stable alkane complexes than NHC, a strong electron donor. Energy decomposition analysis shows that stabilization is due to orbital interaction involving charge transfer from the alkane to the metal. Reactivity and dynamics of the alkane fragment are facilitated by electron donors on the metal. These results match most of the experimental results known for CO and PF3 complexes. The study suggests activation of alkane in metal complexes to be facile with strong donor ligands like NHC. (C) 2015 Wiley Periodicals, Inc.

Structurally engineered cytochromes c with novel ligand-binding properties

Semisynthesis of horse heart cytochrome c and site-directed mutagenesis of Saccharomyces cerevisiae (S. c.) iso-1-cytochrome c have been utilized to substitute Ala for the cytochrome c heme axial ligand Met80 to yield ligand-binding proteins (horse heart Ala80cyt c and S.c. Ala80cyt c) with spectroscopic properties remarkably similar to those of myoglobin. Both species of Fe(II)Ala80cyt c form exceptionally stable dioxygen complexes with autoxidation rates 10-30x smaller and O₂ binding constants ~ 3x greater than those of myoglobin. The resistance of O₂-Fe(II)Ala80cyt c to autoxidation is attributed in part to protection of the heme site from solvent as exhibited by the exceptionally slow rate of CO binding to the heme as well as the low quantum yield of CO photodissociation.

UV/vis, EPR, and paramagnetic NMR spectroscopy indicate that at pH 7 the Fe(III)Ala80cyt c heme is low-spin with axial His-OH^- coordination and that below pH ~6.5, Fe(III)Ala80cyt cis high-spin with His-H₂O heme ligation. Significant differences in the pH dependence of the ¹H NMR spectra of S.c. Fe(III)Ala80cyt c compared to wild-type demonstrate that the axial ligands influence the conformational energetics of cytochrome c.

¹H NMR spectroscopy has been utilized to determine the solution structure of the cyanide derivative of S.c. Fe(III)Ala80cyt c. 82% of the resonances in the ¹H NMR spectrum of S.c. CN-Fe(III)Ala80cyt c have been assigned through 1D and 2D experiments. The RMSD values after restrained energy minimization of the family of 17 structures obtained from distance geometry calculations are 0.68 ± 0.11 Å for the backbone and 1.32 ± 0.14 Å for all heavy atoms. The solution structure indicates that a tyrosine in the "distal" pocket of CN-Fe(III)Ala80cyt c forms a hydrogen bond with the Fe(III)-CN unit, suggesting that it may play a role analogous to that of the distal histidine in myoglobin in stabilizing the dioxygen adduct.

Computational Predictions of G Protein-Coupled Receptor Structures and Binding Sites

G protein-coupled receptors (GPCRs) are the largest family of proteins within the human genome. They consist of seven transmembrane (TM) helices, with a N-terminal region of varying length and structure on the extracellular side, and a C-terminus on the intracellular side. GPCRs are involved in transmitting extracellular signals to cells, and as such are crucial drug targets. Designing pharmaceuticals to target GPCRs is greatly aided by full-atom structural information of the proteins. In particular, the TM region of GPCRs is where small molecule ligands (much more bioavailable than peptide ligands) typically bind to the receptors. In recent years nearly thirty distinct GPCR TM regions have been crystallized. However, there are more than 1,000 GPCRs, leaving the vast majority of GPCRs with limited structural information. Additionally, GPCRs are known to exist in a myriad of conformational states in the body, rendering the static x-ray crystal structures an incomplete reflection of GPCR structures. In order to obtain an ensemble of GPCR structures, we have developed the GEnSeMBLE procedure to rapidly sample a large number of variations of GPCR helix rotations and tilts. The lowest energy GEnSeMBLE structures are then docked to small molecule ligands and optimized. The GPCR family consists of five subfamilies with little to no sequence homology between them: class A, B1, B2, C, and Frizzled/Taste2. Almost all of the GPCR crystal structures have been of class A GPCRs, and much is known about their conserved interactions and binding sites. In this work we particularly focus on class B1 GPCRs, and aim to understand that family’s interactions and binding sites both to small molecules and their native peptide ligands. Specifically, we predict the full atom structure and peptide binding site of the glucagon-like peptide receptor and the TM region and small molecule binding sites for eight other class B1 GPCRs: CALRL, CRFR1, GIPR, GLR, PACR, PTH1R, VIPR1, and VIPR2. Our class B1 work reveals multiple conserved interactions across the B1 subfamily as well as a consistent small molecule binding site centrally located in the TM bundle. Both the interactions and the binding sites are distinct from those seen in the more well-characterized class A GPCRs, and as such our work provides a strong starting point for drug design targeting class B1 proteins. We also predict the full structure of CXCR4 bound to a small molecule, a class A GPCR that was not closely related to any of the class A GPCRs at the time of the work.

Stability and molecular modeling of triplex DNA inhibiting DNA binding protein binding to the core promoter of hepatitis B virus.

Two three-dimensional structure models of the 21nt oligodeoxyribonucleotides, CPI (G3TG-2TGT2G5TG2TGT) and CP3 (TGTG2TGST2GTG2TG3), were constructed by InsightII (MSI) software in IRIS Indigo2 (SGI) workstation using the crystal structure of TAT tripler formation as the template. The initial structures subsequently were minimized by molecular mechanics. The final structures were believed as the dominant conformation. The results showed that the energy of CP1 is lower than that of CP3, and the former is more stable than the latter. Moreover, the results further proved that the 21nt oligodeoxyribo-nucleotide CP1 stably combines with the core promoter (Cp) fragment of hepatitis B virus (HBV) to form a tripler DNA, and CP1 specifically inhibits a specific cellular factor (DNA binding protein) binding to Cp fragment. These results indicated that specific repression of gene transcription of HBV DNA might be possible by tripler-formation DNA.

Donor-donor binding in In2O3: Engineering shallow donor levels

Using first-principles band structure methods, we investigate the interactions between different donors in In2O3. Through the formation energy and transition energy level calculations, we find that an oxygen-vacancy creates a deep donor level, while an indium-interstitial or a tin-dopant induces a shallow donor level. The coupling between these donor levels gives rise to even shallower donor levels and leads to a significant reduction in their formation energies. Based on the analysis of the PBE0-corrected band structure and the molecular-orbital bonding diagram, we demonstrate these effects of donor-donor binding. In addition, total energy calculations show that these defect pairs tend to be more stable with respect to the isolated defects due to their negative binding energies. Thus, we may design shallow donor levels to enhance the electrical conductivity via the donor donor binding.

Direct observation of excitonic polaron in InAs/GaAs quantum dots

We report a direct observation of excitonic polaron in InAs/GaAs quantum dots using the photoluminescence (PL) spectroscopy. We observe that a new peak s' emerges below the s-shell which has anomalous temperature dependence emission energy. The peak s' anticrosses with s at a certain temperature, with a large anticrossing gap up to 31 meV. The behavior of the new peak, which cannot be interpreted using Huang-Rhys model, provides a direct evidence for strong coupling between exciton and LO phonons, and the formation of the excitonic polaron. The strong coupling between exciton and phonons opens a way to coherently control the polaron states.

Sixfold symmetry of excitonic transition energies in c-plane for wurtzite GaN

The optical properties of the strained wurtzite GaN are investigated theoretically within the nearest neighbor tight-binding method. The piezoelectric effect is also taken into account. The empirical rule has been used in the strained band-structure calculation. The results show that the excitonic transition energies are anisotropic in the c-plane in a high electronic concentration system and have a 60 degrees periodicity, which is in agreement with experiment. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.3001937]

Tuning of energy levels and optical properties of graphene quantum dots

We investigate theoretically the magnetic levels and optical properties of zigzag- and armchair-edged hexagonal graphene quantum dots (GQDs) utilizing the tight-binding method. A bound edge state at zero energy appears for the zigzag GQDs in the absence of a magnetic field. The magnetic levels of GQDs exhibit a Hofstadter-butterfly spectrum and approach the Landau levels of two-dimensional graphene as the magnetic field increases. The optical properties are tuned by the size, the type of the edge, and the external magnetic field.

Energy Levels of Hydrogenic Impurities in InAs Quantum Ring

The distribution of energy levels of the ground state and the low-lying excited states of hydrogenic impurities in InAs quantum ring was investigated by applying the effective mass approximation and the perturbation method. In 2D polar coordinates, the exact solution to the Schrodinger equation was used to calculate the perturbation integral in a parabolic confinement potential. The numerical results show that the energy levels of electron are sensitively dependent on the radius of the quantum ring and a minimum exists on account of the parabolic confinement potential. With decreasing the radius, the energy spacing between energy levels increases. The degenerate energy levels of the first excited state for hydrogenic impurities are not relieved, and when the degenerate energy levels are split and the energy spacing will increase with the increase in the radius. The energy spacing between energy levels of electron is also sensitively dependent on the angular frequency and will increase with the increases in it. The degenerate energy levels of the first excited state are not relieved. The degenerate energy levels of the second excited state are relieved partially. The change in angular frequency will have a profound effect upon the calculation of the energy levels of the ground state and the low-lying excited states of hydrogenic impurities in InAs quantum ring. The conclusions of this paper will provide important guidance to investigating the optical transitions and spectral structures in quantum ring.

Observation of intershell and hybridized energy states in InAs/GaAs quantum dots

We have investigated the evolution of exciton state filling as a function of excitation power density in InAs/GaAs quantum dots (QDs). In addition to the emission bands of exciton recombination corresponding to the atom-like S, P, and D, etc. shells of quantum dots, it was observed that some extra states, P-' (between the S and P shells) and D-' (between the P and D shells), appear in the spectra with increasing number of excitons occupying the QDs. The emergence of these intershell excitonic levels is an experimental demonstration of strong exciton-exciton exchange interaction and coupling as well as state mixing and hybridization of a multiexciton system in quantum dots.

Electronic states in InAs quantum spheres and ellipsoids

The eight-band effective-mass Hamiltonian of the free-standing narrow-gap InAs quantum ellipsoids is developed, and the electron and hole electronic structures as well as optical properties are calculated by using the model. The energies, wave functions and transition probabilities of quantum spheres as functions of the radius of quantum sphere R is presented. It is found that the energy levels do not vary as 1/R-2, which is caused by the coupling between the conduction and valence bands, and by the constant terms correspond to the spin-orbit splitting energy. The blueshifts of hole states depend strongly on the coupling from electron states, so that the order of hole states changes as has been predicted in experiment. The exciton binding energies are calculated, the calculated excitonic gaps as functions of the ground exciton transition energy are in good agreement with the photoluminescence measured spectra in details. Finally, the hole energy levels and the linear polarization factors in InAs quantum ellipsoids as functions of the aspect ratio are presented. The state 1S(Z up arrow)((1/2)) becomes the hole ground state when e is larger than 2.4. The saturation value of the linear polarization factors of the InAs long ellipsoids of diameter 2.0 nm is 0.86, in agreement with the experimental results.

Temperature and power-density-dependent inter-shell energy states in InAs/GaAs quantum dots

We have investigated the evolution of exciton state filling in InAs/GaAs quantum dot (QD) structures as a function of the excitation power density by using rnicro-photoluminescence spectroscopy at different temperatures. In addition to the emission bands of exciton recombination corresponding to the atom-like S, P and D, etc. shells of QDs, it was observed that some extra states V between the S and P shells, and D' between the P and D shells appear in the spectra with increasing number of excitons occupying the QDs at a certain temperature. The emergence of these inter-shell excitonic levels is power density and temperature dependent, which is an experimental demonstration of strong exciton-exciton exchange interaction, state hybridization, and coupling of a multi-exciton system in QDs. (c) 2006 Elsevier B.V. All rights reserved.

Impact of polarization on quasi-two-dimensional exciton and barrier-width dependence of the exciton associated transition in wurtzite III-V nitride quantum wells

Excitonic states in AlxGa1-xN/GaN quantum wells (QWs) are studied within the framework of effective-mass theory. Spontaneous and piezoelectric polarizations are included and their impact on the excitonic states and optical properties are studied. We witnessed a significant blue shift in transition energy when the barrier width decreases and we attributed this to the redistribution of the built-in electric field between well layers and barrier layers. For the exciton the binding energies, we found in narrow QWs that there exists a critical value for barrier width, which demarcates the borderline for quantum confinement effect and the quantum confined Stark effect. Exciton and free carrier radiative lifetimes are estimated by simple argumentation. The calculated results suggest that there are efficient non-radiative mechanisms in narrow barrier QWs. (C) 2002 Elsevier Science Ltd. All rights reserved.

Degenerate four-wave-mixing signals from dc- and ac-driven semiconductor superlattice

Within the one-dimensional tight-binding model;rnd chi-3 approximation, we have calculated four-wave-mixing (FWM) signals for a semiconductor superlattice in the presence of both static and high-frequency electric fields. When the exciton effect is negligible, the time-periodic field dynamically delocalizes the otherwise localized Wannier-Stark states, and accordingly quasienergy band structures are formed, and manifest in the FWM spectra as a series of equally separated continua. The width of each continuum is proportional to the joint width of the valence and conduction minibands and is independent of the Wannier-Stark index. The realistic homogeneous broadening blurs the continua into broad peaks, whose line shapes, far from the Lorentzian, vary with the delay time in the FWM spectra. The swinging range of the peaks is just the quasienergy bandwidth. The dynamical delocalization (DDL) also induces significant FWM signals well beyond the excitation energy window. When the Coulomb interaction is taken into account, the unequal spacing between the excitonic Wannier-Stark levels weakens the DDL effect, and the FWM spectrum is transformed into groups of discrete lines. Strikingly, the groups are evenly spaced by the ac field frequency, reflecting the characteristic of the quasienergy states. The homogeneous broadening again smears out the line structures, leading to the excitonic FWM spectra quite similar to those without the exciton effect. However, all these features predicted by the dynamical theory do not appear in a recent experiment [Phys. Rev. Lett. 79, 301 (1997)], in which, by using the static approximation the observed Wannier-Stark ladder with delay-time-dependent spacing in the FWM spectra is attributed to a temporally periodic dipole field, produced by the Bloch oscillation of electrons in real space. The contradiction between the dynamical theory and the experiments is discussed. In addition, our calculation indicates that the dynamical localization coherently enhances the time-integrated FWM signals. The feasibility of using such a technique to study the dynamical localization phenomena is shown. [S0163-1829(99)10607-6].