Expanding the Topological Landscape by a G-Column Flip of a Parallel G-Quadruplex

Canonical G-quadruplexes can adopt a variety of different topologies depending on the arrangement of propeller, lateral, or diagonal loops connecting the four G-columns. A novel intramolecular G-quadruplex structure is derived through inversion of the last G-tract of a three-layered parallel fold, associated with the transition of a single propeller into a lateral loop. The resulting (3+1) hybrid fold features three syn⋅anti⋅anti⋅anti G-tetrads with a 3’-terminal all-syn G-column. Although the ability of forming a duplex stem-loop between G-tracts seems beneficial for a propeller-to-lateral loop rearrangement, unmodified G-rich sequences resist folding into the new (3+1) topology. However, refolding can be driven by the incorporation of syn-favoring guanosine analogues into positions of the fourth G-stretch. The presented hybrid-type G-quadruplex structure as determined by NMR spectroscopy may provide for an additional scaffold in quadruplex-based technologies.     

A Thermodynamic Perspective on Potential G-Quadruplex Structures as Silencer Elements in the MYC Promoter

Multiple G-tracts within the promoter region of the c-myc oncogene may fold into various G-quadruplexes with the recruitment of different tracts and guanosine residues for the G-core assembly. Thermodynamic profiles for the folding of wild-type and representative truncated as well as mutated sequences were extracted by comprehensive DSC experiments. The unique G-quadruplex involving consecutive G-tracts II–V with formation of two one-nucleotide and one central two-nucleotide propeller loop, previously proposed to be the biologically most relevant species, was found to be the most stable fold in terms of its Gibbs free energy of formation at ambient temperatures. Its stability derives from its short propeller loops but also from the favorable type of loop residues. Whereas quadruplex folds with long propeller loops are significantly disfavored, a snap-back loop structure formed by incorporating a 3’-terminal guanosine into the empty position of a tetrad seems highly competitive based on its thermodynamic stability. However, its destabilization by extending the 3’-terminus questions the significance of such a species under in vivo conditions.     

Rapid Separation of Proteins by Capillary HPLC on a Short Polymethacrylate-based Strong Cation-exchange Monolithic Column

A polymethacrylate‐based strong cation‐exchange capillary monolithic column was prepared by in‐situ copolymerization for the fast separation of proteins. Glycidyl methacrylate (GMA) was used as monomer, ethylenedimethacrylate (EDMA) as cross link agent and the mixture of 1‐propanol, 1,4‐butanediol and water as porogen solvent. The monolith was sulfonated using 1 mol/L Na₂SO₃ based on a ring opening of epoxides. The influences of the contents of the porogen solvent and GMA and the various concentration ratios of 1‐propanol to 1,4‐butanediol in the polymerization mixture on the morphology, porosity, globule size, stability and column efficiency were investigated. The morphology and pore size distribution of the monolith were characterized by SEM and mercury intrusion porosimetry, respectively. Using only 1.5 cm length of this monolithic capillary column, four kinds of proteins, trypsin, cytochrome C, lysozyme (egg white) and egg albumin, were successfully separated from each other in 5 min at a high flow rate of 110 mm/s.     

Exchange and Delocalization Effects in [Fe6S6]2+ Superclusters

A theoretical study of Heisenberg exchange and double exchange (delocalization) effects in the iron-sulphur supercluster is presented. Such clusters can play important role in biological systems (proteins and enzymes) acting as so-called active centres. The cluster with valence 2+ can be modelled by two Fe(III) and four Fe(II) ions. An idealized structure of double cubane has been considered instead of a more realistic defected double cubane structure of lower symmetry. Energies of the lowest spin states have been calculated numerically depending on the Heisenberg exchange J _i and double exchange b parameters. Possible spin ground states (S=0, 1, 2, 3, 4, 5) have been predicted. The ground state of a given total spin Sis usually achieved for the intermediate spin value of S ₅₆=4 in the case of fully antiferromagnetic as well as partially ferromagnetic spin interactions. In the case of no double exchange, the ground state with the total spin S=3 should always be observed, while a nonzero hopping effect results in narrowing a parameter region of the ground state. If the double exchange is taken into account, then the spin values depend on the Heisenberg integrals. The model results can be applied in order to interpret many structural and magnetic properties of proteins and enzymes possessing the Fe-S active centres.     

Manipulating adenoviral vector ion‐exchange chromatography: Hexon versus fiber

The serotype specificity of adenovirus ion‐exchange chromatography has previously been studied using standard particle‐based columns, and the hexon protein has been reported to determine retention time. In this study, we have submitted Adenovirus type 5 recombinants to anion‐exchange chromatography using methacrylate monolithic supports. Our experiments with hexon‐modified adenoviral vectors show more precisely that the retention time is affected by the substitution of amino acids in hypervariable region 5, which lies within the hexon DE1 loop. By exploring the recombinants modified in the fiber protein, we have proven the previously predicted chromatographic potential of this surface constituent. Modifications that preserve the net charge of the hexon protein, or those that cause only a small charge difference in the fiber protein, in addition to shortening the fiber shaft, did not change the chromatographic behavior of the adenovirus particles. However, modifications that include the deletion of just two negatively charged amino acids in the hexon protein, or the introduction of a heterologous fiber protein, derived from another serotype, revealed recognizable changes in anion‐exchange chromatography. This could be useful in facilitating chromatography‐approach purification by creating targeted capsid modifications, thereby shifting adenovirus particles away from particular interfering substances present in the crude lysate.     

Control of the Conductance of Engineered Protein Nanopores through Concerted Loop Motions

Protein nanopores have attracted much interest for nucleic acid sequencing, chemical sensing, and protein folding at the single molecule level. The outer membrane protein OmpG from E. coli stands out because it forms a nanopore from a single polypeptide chain. This property allows the separate engineering of each of the seven extracellular loops that control access to the pore. The longest of these loops, loop 6, has been recognized as the main gating loop that closes the pore at low pH values and opens it at high pH values. A method was devised to pin each of the loops to the embedding membrane and measure the single‐pore conductances of the resulting constructs. The electrophysiological and complementary NMR measurements show that the pinning of individual loops alters the structure and dynamics of neighboring and distant loops in a correlated fashion. Pinning loop 6 generates a constitutively open pore and patterns of concerted loop motions control access to the OmpG nanopore.     

Spatial geometric arrangements of disulfide-crosslinked loops in proteins

The classification of patterns of the three-dimensional folding of a covalently crosslinked polypeptide chain can be used to introduce long-range interactions into the theoretical search for the native conformation of a protein. This classification into Spatial Geometric Arrangements of Loops (SGAL) had been proposed earlier (H. Meirovitch and H. A. Scheraga, Macromolecules 14 , 1250, 1981). It is based on the subdivision of the protein molecule into closed loops, defined by covalent crosslinks (such as disulfide bonds). Various SGAL classes correspond to the presence or absence of mutual penetration of loops, called entanglements or thrustings. A systematic and objective method is developed here to enumerate all theoretically possible SGAL's for a protein, based only on its covalent structure, i.e., the pattern of disulfide bonds or other crosslinks, regardless of whether the three-dimensional structure is known or unknown. This information can be of use in structural predictions of folding patterns. Using a modification of the method, it is also possible to determine the SGAL class to which a protein of known structure belongs. Out of 18 proteins with known three-dimensional structure and containing more than two disulfide bonds, five have a native structure with at least one entanglement or thrusting. Thus, threaded SGAL's represent a significant structural feature of native proteins. All five involve neighboring loops in the sequences. Their presence in a protein can suggest restrictions on the possible ways of folding the protein.     

Exact electronic properties in the classically forbidden region of a metal surface

We derive exact properties of the inhomogeneous electron gas in the asymptotic classically forbidden region at a metal–vacuum interface within the framework of local effective potential energy theory. We derive a new expression for the asymptotic structure of the Kohn–Sham density functional theory (KS‐DFT) exchange‐correlation potential energy v_xc(r) in terms of the irreducible electron self‐energy. We also derive the exact asymptotic structure of the orbitals, density, the Dirac density matrix, the kinetic energy density, and KS exchange energy density. We further obtain the exact expression for the Fermi hole and demonstrate its structure in this asymptotic limit. The exchange‐correlation potential energy is derived to be v_xc(z → ∞) = ?α_KS,xc/z, and its exchange and correlation components to be v_x(z → ∞) = ?α_KS,x/z and v_c(z → ∞) = ?α_KS,c/z, respectively. The analytical expressions for the coefficients α_KS,xc and α_KS,x show them to be dependent on the bulk‐metal Wigner–Seitz radius and the barrier height at the surface. The coefficient α_KS,c = 1/4 is determined in the plasmon‐pole approximation and is independent of these metal parameters. Thus, the asymptotic structure of v_xc(z) in the vacuum region is image‐potential‐like but not the commonly accepted one of ?1/4z. Furthermore, this structure depends on the properties of the metal. Additionally, an analysis of these results via quantal density functional theory (Q‐DFT) shows that both the Pauli W_x(z → ∞) and lowest‐order correlation‐kinetic W(z → ∞) components of the exchange potential energy v_x(z → ∞), and the Coulomb W_c(z → ∞) and higher‐order correlation‐kinetic components of the correlation potential energy v_c(z → ∞), all contribute terms of O(1/z) to the structure. Hence correlations attributable to the Pauli exclusion principle, Coulomb repulsion, and correlation‐kinetic effects all contribute to the asymptotic structure of the effective potential energy at a metal surface. The relevance of the results derived to the theory of image states and to KS‐DFT is also discussed. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Near‐IR Absorbing Solar Cell Sensitized With Bacterial Photosynthetic Membranes

Current interest in natural photosynthesis as a blueprint for solar energy conversion has led to the development of a biohybrid photovoltaic cell in which bacterial photosynthetic membrane vesicles (chromatophores) have been adsorbed to a gold electrode surface in conjunction with biological electrolytes (quinone [Q] and cytochrome c; Magis et al. [2010] Biochim. Biophys. Acta 1798 , 637–645). Since light‐driven current generation was dependent on an open circuit potential, we have tested whether this external potential could be replaced in an appropriately designed dye‐sensitized solar cell (DSSC). Herein, we show that a DSSC system in which the organic light‐harvesting dye is replaced by robust chromatophores from Rhodospirillum rubrum, together with Q and cytochrome c as electrolytes, provides band energies between consecutive interfaces that facilitate a unidirectional flow of electrons. Solar I–V testing revealed a relatively high I _sc (short‐circuit current) of 25 μA cm^?2 and the cell was capable of generating a current utilizing abundant near‐IR photons (maximum at ca 880 nm) with greater than eight‐fold higher energy conversion efficiency than white light. These studies represent a powerful demonstration of the photoexcitation properties of a biological system in a closed solid‐state device and its successful implementation in a functioning solar cell.     

Kinetic partitioning mechanism as a unifying theme in the folding of biomolecules

We describe a unified approach to describe the kinetics of protein and RNA folding. The underlying conceptual basis for this framework relies on the notion that biomolecules are topologically frustrated due to their polymeric nature and due to the presence of conflicting energies. As a result, the free energy surface (FES) has, in addition to the native basin of attraction (NBA), several competing basins of attraction. A rough FES results in direct and indirect pathways to the NBA, i.e., a kinetic partitioning mechanism (KPM). The KPM leads to a foldability principle according to which fast folding sequences are characterized by the folding transition temperature T _F being close to the collapse transition temperature T _θ, at which a transition from the random coil to the compact structure takes place. Biomolecules with T _θ ≈ T _F , such as small proteins and tRNAs, are expected to fold rapidly with two-state kinetics. Estimates for the multiple time scales in KPM are also given. We show that experiments on proteins and RNA can be understood semi-quantitatively in terms of the KPM. Received: 14 January 1997 / Accepted: 23 January 1997     

The heisenberg exchange integral in a non-orthogonal basis for antiferromagnetic and ferromagnetic systems

The Dirac-Van Vleck-Serber permutation degeneracy method is used to demonstrate that the Heisenberg spin exchange Hamiltonian, –2J ₁₂s₁·s₂, is a good approximate Hamiltonian for the theoretical interpretation of antiferromagnetic and ferromagnetic systems. The approach does not neglect double or higher-order permutations and covers the general case of a singleN-electron configuration as well as that of configuration interaction. An analogy between antiferromagnetic and hydrogen-molecule-like systems is established, and a formula for the estimation of the Heisenberg exchange integral is derived.     

A molecular approach to chain entanglement in linear polymers

The phenomenon of chain entanglement in undiluted linear amorphous polymers is treated by calculating the probability of forming closed intramolecular loops. Adoption of the rotational isomeric state model of polymer chains permits an appropriate accounting of the detailed molecular structure to be made through the configurational characteristics of the polymer. The second (〈r〉₀) and fourth (〈r〉₀) moments of the vector r_hk connecting groups h and k in the isolated polymer chain and averaged over all chain conformations are calculated and used to evaluate the probability W_x(0) that r_hk is 0, or that an intramolecular loop of x = k ? h bonds is formed. Several linear polymers with widely differing molecular structures are treated. An attempt is made to correlate the degree of chain entanglement they manifest in the bulk with their ability to fold back upon themselves to form closed intramolecular loops.     

An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.     

A New Family of Trinuclear Nickel(II) Complexes as Single‐Molecule Magnets

Three new trinuclear nickel (II) complexes with the general composition [Ni₃L₃(OH)(X)](ClO₄) have been prepared in which X=Cl^? ( 1 ), OCN^? ( 2 ), or N₃^? ( 3 ) and HL is the tridentate N,N,O donor Schiff base ligand 2‐[(3‐dimethylaminopropylimino)methyl]phenol. Single‐crystal structural analyses revealed that all three complexes have a similar Ni₃ core motif with three different types of bridging, namely phenoxido (μ₂ and μ₃), hydroxido (μ₃), and μ₂‐Cl ( 1 ), μ_1,1‐NCO ( 2 ), or μ_1,1‐N₃ ( 3 ). The nickel(II) ions adopt a compressed octahedron geometry. Single‐crystal magnetization measurements on complex 1 revealed that the pseudo‐three‐fold axis of Ni₃ corresponds to a magnetic easy axis, being consistent with the magnetic anisotropy expected from the coordination structure of each nickel ion. Temperature‐dependent magnetic measurements indicated ferromagnetic coupling leading to an S=3 ground state with 2J/k=17, 17, and 28 K for 1 , 2 , and 3 , respectively, with the nickel atoms in an approximate equilateral triangle. The high‐frequency EPR spectra in combination with spin Hamiltonian simulations that include zero‐field splitting parameters D_Ni/k=?5, ?4, and ?4 K for 1 , 2 , and 3 , respectively, reproduced the EPR spectra well after a anisotropic exchange term was introduced. Anisotropic exchange was identified as D_i,j/k=?0.9, ?0.8, and ?0.8 K for 1 , 2 , and 3 , respectively, whereas no evidence of single‐ion rhombic anisotropy was observed spectroscopically. Slow relaxation of the magnetization at low temperatures is evident from the frequency‐dependence of the out‐of‐phase ac susceptibilities. Pulsed‐field magnetization recorded at 0.5 K shows clear steps in the hysteresis loop at 0.5–1 T, which has been assigned to quantum tunneling, and is characteristic of single‐molecule magnets.     

Formation of a Ligand‐Assisted Complex of Two RNA Hairpin Loops

The hairpin structure is one of the most common secondary structures in RNA and holds a central position in the stream of RNA folding from a non‐structured RNA to structurally complex and functional ribonucleoproteins. Since the RNA secondary structure is strongly correlated to the function and can be modulated by the binding of small molecules, we have investigated the modulation of RNA folding by a ligand‐assisted formation of loop–loop complexes of two RNA hairpin loops. With a ligand (NCT6), designed based on the ligand binding to the G–G mismatches in double‐stranded DNA, we successfully demonstrated the formation of both inter‐ and intra‐molecular NCT6‐assisted complex of two RNA hairpin loops. NCT6 selectively bound to the two hairpin loops containing (CGG)₃ in the loop region. Native polyacrylamide gel electrophoresis analysis of two doubly‐labeled RNA hairpin loops clearly showed the formation of intermolecular NCT6‐assisted loop–loop complex. Förster resonance energy‐transfer studies of RNA constructs containing two hairpin loops, in which each hairpin was labeled with Alexa488 and Cy3 fluorophores, showed the conformational change of the RNA constructs upon binding of NCT6. These experimental data showed that NCT6 simultaneously bound to two hairpin RNAs at the loop region, and can induce the conformational change of the RNA molecule. These data strongly support that NCT6 functions as molecular glue for two hairpin RNAs.     

A Closed‐Loop Control Strategy for Producing Nitrile Rubber of Uniform Chemical Composition in a Semibatch Reactor: A Simulation Study

To improve the quality of industrial nitrile rubbers, the copolymer chemical composition, p_A(t), should ideally be kept constant along the reaction. This work proposes a closed‐loop control strategy for the semibatch operation of the reactor with the aim of regulating p_A(t) within a reduced range of variability. The proposed strategy is evaluated by simulating a mathematical model of the process. To this effect, a simplified mathematical model of the reaction is first derived and then utilized to obtain a suboptimal control law and a soft‐sensor that estimates the polymerization rates. The suboptimal control law is compensated by adding a term proportional to errors in p_A(t). The simulated example considers the production of the low‐composition AJLT grade, with the copolymerization reaction represented by a detailed mathematical model adjusted to an industrial plant. Due to the high performance of the soft‐sensor, the simulation results suggest that the proposed closed‐loop strategy is efficient to adequately regulate p_A(t) in spite of structural and parametric uncertainties, while other quality variables remained practically unaffected.     

Chemical hysteresis in phase transitions in the terbium oxide-oxygen system

A thermogravimetric study of hysteresis in the TbO_xO₂ system has provided insight into phase transitions occurring among the fluorite-related rare earth oxides. A series of isobaric scanning loops at 380 Torr have been made. The scans were between TbO_1.5(?) and TbO_1.714(ι) at higher temperatures and between TbO_1.714(ι) and TbO_1.818(δ) at lower temperatures. Corresponding isobaric studies were made utilizing high temperature X-ray powder diffraction to augment the TGA experiments.It was confirmed that sections of the lower temperature loop were dependent on the rate of temperature change while the higher temperature loop was entirely reproducible. Interior scanning loops made within the lower hysteresis loop showed univariant behavior typical of a single phase when reversed in the δ′δ pseudophase region, otherwise it exhibited bivariant behavior. The upper hysteresis loop showed bivariant behavior throughout the interior of the loop. Some thermodynamic aspects and the microdomain concept as applied to hysteresis are also considered.     

Extending the Sensitivity of CEST NMR Spectroscopy to Micro-to-Millisecond Dynamics in Nucleic Acids Using High-Power Radio-Frequency Fields

Biomolecules undergo motions on the micro-to-millisecond timescale to adopt low-populated transient states that play important roles in folding, recognition, and catalysis. NMR techniques, such as Carr–Purcell–Meiboom–Gill (CPMG), chemical exchange saturation transfer (CEST), and R_1ρ are the most commonly used methods for characterizing such transitions at atomic resolution under solution conditions. CPMG and CEST are most effective at characterizing motions on the millisecond timescale. While some implementations of the R_1ρ experiment are more broadly sensitive to motions on the micro-to-millisecond timescale, they entail the use of selective irradiation schemes and inefficient 1D data acquisition methods. Herein, we show that high-power radio-frequency fields can be used in CEST experiments to extend the sensitivity to faster motions on the micro-to-millisecond timescale. Given the ease of implementing high-power fields in CEST, this should make it easier to characterize micro-to-millisecond dynamics in biomolecules.     

Micellar Exchange Kinetics of Quaternary Ammonium Type Gemini Surfactants Monitored by Nuclear Magnetic Resonance

The dynamic NMR (DNMR) method was used to detect kinetic parameters of the molecular exchange process between monomers in bulk solution and those in the micelle for Gemini surfactants, 12-s-12 and 14-s-14(s=2, 3 and 4).The escape rate constant, k^-, was derived based on the simplified equations of DNMR theory, and the apparent activation energy of escape, E_a^-, was obtained based on the Arrhenius equation through temperature variation experiments.Results show that the orders of magnitude of k^- for 14-s-14 and 12-s-12 are respectively 10 and 10³ s^-1, E_a^- of 14-s-14 and 12-s-12 are respectively 54.04-73.64 and 33.42-47.09 kJ/mol.Furthermore, increases and E_a^- decreases with the spacer length growing.In combination with the micro-polarity measurements, it was revealed that molecules of 14-s-14 and 12-s-12 have to experience conformation changes when escaping from the micelles.The two-step molecular exchange mechanism for Gemini surfactants was therefore supported.     

Fragmentation pathways of metopimazine and its metabolite using ESI‐MSn,HR‐MS and H/D exchange

Metopimazine (MPZ) is a phenothiazine derivative used to prevent emesis during chemotherapy where few structural analysis of the aforementioned compound have been described in the literature. Thus, this work reports, for the first time, the detailed study of fragmentation pathways of MPZ and its metabolite (AMPZ) using electrospray ionization (EI) with multistage mass spectrometry (ESI‐MSⁿ) in positive‐ion mode. The structures of 21 product ions were identified and their accurate masses were determined using high resolution mass spectrometry (HRMS) experiments. Characteristic product ions of these two phenothiazine derivatives are more particularly displayed along with differences between their relative abundances and their structures checked by H/D exchange experiments. Copyright © 2010 John Wiley & Sons, Ltd.