Phi Values Research Articles

Crystallographic, Photophysical, NMR Spectroscopic and Reactivity Manifestations of the “8-Heteroaryl Effect” in 4,4-Difluoro-8-(C4H3X)-4-bora-3a,4a-diaza-s-indacene (X = O, S, Se) (BODIPY) Systems

We have synthesized and fully characterized three novel, yet closely related, heterocyclically meso-substituted (BODIPY) fluorophores 4,4-difluoro-8-(C(4)H(3)X)-4-bora-3a,4a-diaza-s-indacene (X = O, 2-/3-furyl (7/10); Se, 2-selenenyl (9)) through the use of 2-D NMR (COSY, HSQC, and HMBC), single crystal X-ray diffraction, mass spectrometry, elemental analysis, UV-vis spectroscopy, and fluorescent decay lifetimes, for comparison to the previously reported thienyl species (X = S, 2-/3-thienyl (8/11)). Specifically, 7-11 differ formally by chalcogen (O, S, or Se) or chalcogen placement. Solid state comparisons reveal major effects stemming from subtle structural differences which allows for insights into fluorescent crystal engineering. For the 2-heteroatom substitution, an increase in molecular weight (7 < 8 < 9) correlates with an increasing unit cell-volume, a greater orthogonality for the C(4)H(3)X group, and a lower value for Phi(F). Solution and density functional theory (DFT) results reveal interesting platforms for potential in fluorescent studies for neurology. 2-Heterocyclic species show larger lambda(abs,max/em,max) values relative to 3-heterocyclic ones, based on electron withdrawing effects. 10 has the greatest Phi(F) value herein (0.25, toluene). Fluorescence lifetimes were found to be 2.60 (7), 0.74 (8), 0.27 (9), 4.26 (10), and 1.86 ns (11); lambda(em,max) decay was studied for 8. Heterocyclic differences give rise to somewhat different pyrrolic NMR spectroscopic shifts as well. These compounds resist decomposition as seen from titrations with H(2)O(2), and uniformly undergo lambda(abs,max) red-shifting and lowered Phi(F) values as they become brominated with Br(2).

Experimental and theoretical dosimetry of a new polymer encapsulated iodine‐125 source—SmartSeed: Dosimetric impact of fluorescence x rays

The detailed study of a new permanent iodine-125 brachytherapy source, SmartSeed, is presented in this article. It is the first iodine seed made with biocompatible polymer and is manufactured by the IBt-Bebig group. Three dosimetric studies have been performed: The first one used thermoluminescent detectors in a solid water phantom with NIST (National Institute of Standards and Technology, USA) calibrated seeds, and two separate studies were of Monte Carlo photon transport calculations (MCNP5 code). The TG-43U1 protocol was applied to derive dosimetric parameters for clinical applications. The radial dose function g(r) was determined at different distances ranging from 0.5 to 10 cm; and the anisotropy function F(r, theta) at angles ranging from 0 degrees to 350 degrees in 10 degrees increments. Monte Carlo calculations were performed in liquid water to obtain values for lambda, g(r), F(r, theta), and phi(an)(r) as recommended by the TG-43U1 protocol for use in treatment planning system software. SmartSeed's biocompatible polymer capsule permits fluorescence x rays (3, 5, and 12 keV), generated by lead glass marker, to be present in the emission spectrum, influencing the dose rate constant. The impact on near field dosimetry in water from these x rays was also investigated and reported. The capsule also attenuates iodine-125 energies much less than typical titanium encased sources, resulting in a highly isotropic source. SmartSeed has a dose rate constant of 0.895 +/- 7.3% cGy h(-1) U(-1), a radial dose function nearly identical to the IBt-Bebig model I25.S06 seed, and a highly isotropic dose distribution. Fluorescence x rays account for the relatively low value of lambda, yet their variable contribution to dosimetry arising from seed dimensional uncertainties is estimated to be < 0.2%.

Abstract 748: Development and application of novel in silico methods in the discovery and characterization of integrins antagonists

Abstract Integrins play crucial roles in mediating tumour angiogenesis, therefore gaining increasing importance as drug targets in antiangiogenic cancer therapy. The peptide sequence Arg-Gly-Asp (RGD) is by far the most prominent ligand to promote specific cell adhesion through integrin stimulation and this sequence has been used as a lead for developing different integrin antagonists. Recent biochemical studies have shown that the deamidation of the NGR sequence gives rise to isoDGR, a new αvβ3-binding motif. To design low-molecular mass RGD or isoDGR-containing molecules, the determination of their biologically active conformation is a prerequisite. However, experimental measurements are usually insufficient to draw conclusions concerning the nature of all relevant conformers affecting binding affinity. As computational drug design becomes increasingly reliant on virtual screening and on high-throughput 3D modeling, the need for fast, robust, and reliable methods for sampling molecular conformations is warranted. We have successfully developed an innovative application of MetaDynamics (MtD), a fast computational method to efficiently sample the free energy of complex polyatomic systems in the space of a few course-grained quantities named collective variables (CVs). CVs allows to rapidly and exhaustively describe the whole conformational space accessible to these peptides. The method was applied to analyze a small library of RGD- and isoDGR-containing cyclopeptides to a) identify the highest populated conformations, b) predict their flexibility, and c) obtain reliable structural models that can be docked inside the receptor. Choosing the phi and psi angles of the central glycine as CV, we discriminated among αvβ3-binding and non-binding cyclopeptides. In addition, we demonstrated that the method is able to predict effect of chemical modifications, including metylation and acetylation, to affect flexibility and conformation of the peptides. To validate this approach and its prediction power, we search the whole protein data bank (PDB) using the RGD sequence, and then we mapped the phi and psi angle values of the central glycine for all RGD-containing structures. Remarkably, the natural distribution of glycine phi and psi angles reliably coincide with the one predicted by MtD. Furthermore, the distribution of phi and psi angles of the central glycine can be used as a descriptor to predict the receptor preference of αvβ3- and αIIbβ3-binding cyclopeptides and peptidomimetics. In conclusions, these findings may have an important impact on the discovery and characterization of new diagnostic and therapeutic agents based on the isoDGR motif, providing support for the rationale design and optimization of isoDGR peptidomimetics, for the fine-tuning of their conformations to increase receptor selectivity, and for selection of ligands for chemical synthesis. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 748.

Photoluminescent Properties of Chalcobromide−capped Octahedral Hexarhenium(III) Complexes [{Re6Q8−nBrn}Br6]n−4(Q = Se,n= 1−3; Q = S,n= 1, 2)

Photoluminescent properties of chalcobromide-capped octahedral hexarhenium(III) complexes with terminal bromide ligands [{Re(6)Q(8-n)Br(n)}Br(6)](n-4) (Q = Se, n = 1 ([1-Se](3-)), n = 2 ([2a-Se](2-) and [2b-Se](2-)), and n = 3 ([3-Se](-)); Q = S, n = 1 ([1-S](3-)), n = 2 ([2a-S](2-), [2b-S](2-), and [2c-S](2-)) were studied. The Q(7)Br capped complex [{Re(6)Q(7)Br}Br(6)](3-) and Q(6)Br(2) [{Re(6)Q(6)Br(2)}Br(6)](2-) (both D(3d) and C(2v) symmetric geometrical isomers) were successfully separated by column chromatography. All of the chalcobromide-capped complexes studied showed photoluminescence in both crystalline and solution phases. The emission maximum wavelength of the complexes at 296 K spans 853-915 or 868-968 nm in the crystalline phase or in acetonitrile, respectively. The selenobromide-capped complexes showed more intense emission as compared with the thiobromide analogues. The emission quantum yield (Phi(em)) and emission lifetime (tau(em)) became smaller and shorter, respectively, with an increase in the number of a capping bromide ligand in [{Re(6)Q(8-n)Br(n)}Br(6)](n-4). In the crystalline phase at 80 K, the emission maximum of the chalcobromide-capped complex shifted to the longer wavelength relative to that at 296 K. The emissive excited-state of the chalcobromide-capped hexarhenium(III) complexes was concluded to originate from the {Re(6)Q(8-n)Br(n)}(n+2) core with a spin-triplet type. The Phi(em) and tau(em) values of the {Re(6)Q(8-n)Br(n)}(n+2) complex were dependent significantly on the symmetry of the hexarhenium core, showing more intense emission for the complex with the higher symmetric core. A linear correlation between natural logarithm of the nonradiative decay rate constant and the emission maximum energy was observed for [{Re(6)Q(6)Br(2)}Br(6)](2-).

Probing the Transition State for Nucleic Acid Hybridization Using Φ-Value Analysis

Genetic regulation by noncoding RNA elements such as microRNA and small interfering RNA (siRNA) involves hybridization of a short single-stranded RNA with a complementary segment in a target mRNA. The physical basis of the hybridization process between the structured nucleic acids is not well understood primarily because of the lack of information about the transition-state structure. Here we use transition-state theory, inspired by phi-value analysis in protein folding studies, to provide quantitative analysis of the relationship between changes in the secondary structure stability and the activation free energy. Time course monitoring of the hybridization reaction was performed under pseudo-steady-state conditions using a single fluorophore. The phi-value analysis indicates that the native secondary structure remains intact in the transition state. The nativelike transition state was confirmed via examination of the salt dependence of the hybridization kinetics, indicating that the number of sodium ions associated with the transition state was not substantially affected by changes in the native secondary structure. These results propose that hybridization between structured nucleic acids undergoes a transition state leading to formation of a nucleation complex and then is followed by sequential displacement of preexisting base pairings involving successive small energy barriers. The proposed mechanism might provide new insight into physical processes during small RNA-mediated gene silencing, which is essential to selection of a target mRNA segment for siRNA design.

Deciphering the folding transition state structure and denatured state properties of nucleophosmin C-terminal domain.

Nucleophosmin (NPM1), one of the most abundant nucleolar proteins, is a frequent target of oncogenic mutations in acute myeloid leukaemia (AML). Mutation-induced changes at the C-terminal domain of NPM1 (Cter-NPM1) compromise its stability and cause the aberrant translocation of NPM1 to the cytosol. Hence, this protein represents a suitable candidate to investigate the relations between folding and disease. Since Cter-NPM1 folds via a compact denatured state, stabilization of the folded state of the mutated variants demands detailed structural information on both the native and denatured states. Here, we present the characterization of the complete folding pathway of Cter-NPM1 and provide molecular details for both the transition and the denatured states. The structure of the transition state was assessed by Phi-value analysis, whereas residual structure in the denatured state was mapped by evaluating the effect of mutations as modulated by conditions promoting denatured state compaction. Data reveal that folding of Cter-NPM1 proceeds via an extended nucleus and that the denatured state retains significant malleable structure at the interface between the second and third helices. Our observations constitute the essential prerequisite for structure-based drug-design studies, aimed at identifying molecules that may rescue pathological NPM1 mutants by stabilizing the native-like state.

Novel Fluorophores as Building Blocks for Optical Probes for In Vivo Near Infrared Fluorescence (NIRF) Imaging

Aiming at the identification of new fluorescent reporters for targeted optical probes, we assessed the application-relevant features of a novel asymmetric cyanine, DY-681, in comparison to the only clinically approved dye indocyanine green (ICG), the golden imaging standard Cy5.5, and the asymmetric cyanine DY-676 successfully exploited by us for the design of different contrast agents. This comparison included the analysis of the spectroscopic properties of the free fluorophores and their thermal stability in aqueous solution as well as their cytotoxic potential. In addition, the absorption and emission features of IgG-conjugated DY-681 were examined. The trimethine DY-681 exhibited spectral features closely resembling that of the pentamethine Cy5.5. Its high thermal stability in phosphate buffer saline (PBS) solution in conjunction with its low cytotoxicity, reaching similar values as determined for Cy5.5 and DY-676, renders this dye more attractive as ICG and, due to its improved fluorescence quantum yield in PBS, also superior to DY-676. Although in PBS, Cy5.5 was still more fluorescent, the fluorescence quantum yields (Phi(f)) of DY-681 and Cy5.5 in PBS containing 5 mass-% bovine serum albumin (BSA) were comparable. Labeling experiments with DY-681 and the model antibody IgG revealed promisingly high Phi(f) values of the bioconjugated dye.

Prostate-Specific Antigen (PSA) Isoform p2PSA in Combination with Total PSA and Free PSA Improves Diagnostic Accuracy in Prostate Cancer Detection

BackgroundNovel markers for prostate cancer (PCa) detection are needed. Total prostate-specific antigen (tPSA) and percent free prostate-specific antigen (%fPSA=tPSA/fPSA) lack diagnostic specificity. ObjectiveTo evaluate the use of prostate-specific antigen (PSA) isoforms p2PSA and benign prostatic hyperplasia–associated PSA (BPHA). Design, setting, and participantsOur study included 405 serum samples from the Rotterdam arm of the European Randomised Study of Screening for Prostate Cancer and 351 samples from the Urology Department of Innsbruck Medical University. MeasurementsBPHA, tPSA, fPSA, and p2PSA levels were measured by Beckman-Coulter Access Immunoassay. In addition, the Beckman Coulter Prostate Health Index was calculated: phi=(p2PSA/fPSA)×√(tPSA). Results and limitationsThe p2PSA and phi levels differed significantly between men with and without PCa. No difference in BPHA levels was observed. The highest PCa predictive value in both cohorts was achieved by phi with areas under the curve (AUCs) of 0.750 and 0.709, a significant increase compared to tPSA (AUC: 0.585 and 0.534) and %fPSA (AUC: 0.675 and 0.576). Also, %p2PSA (p2PSA/fPSA) showed significantly higher AUCs compared to tPSA and %fPSA (AUC: 0.716 and 0.695, respectively). At 95% and 90% sensitivity, the specificities of phi were 23% and 31% compared to 10% and 8% for tPSA, respectively. In both cohorts, multivariate analysis showed a significant increase in PCa predictive value after addition of p2PSA to a model consisting of tPSA and fPSA (increase in AUC from 0.675 to 0.755 and from 0.581 to 0.697, respectively). Additionally, the specificity at 95% sensitivity increased from 8% to 24% and 7% to 23%, respectively. Furthermore, %p2PSA, phi, and the model consisting of tPSA and fPSA with or without the addition of p2PSA missed the least of the tumours with a biopsy or pathologic Gleason score ≥7 at 95% and 90% sensitivity. ConclusionsThis study shows significant increases in PCa predictive value and specificity of phi and %p2PSA compared to tPSA and %fPSA. p2PSA has limited additional value in identifying aggressive PCa (Gleason score ≥7).

Two pentadehydropeptides with different configurations of the ΔPhe residues

Comparison of the crystal structures of two pentadehydropeptides containing DeltaPhe residues, namely (Z,Z)-N-(tert-butoxycarbonyl)glycyl-alpha,beta-phenylalanylglycyl-alpha,beta-phenylalanylglycine (or Boc(0)-Gly(1)-Delta(Z)Phe(2)-Gly(3)-Delta(Z)Phe(4)-Gly(5)-OH) methanol solvate, C(29)H(33)N(5)O(8) x CH(4)O, (I), and (E,E)-N-(tert-butoxycarbonyl)glycyl-alpha,beta-phenylalanylglycyl-alpha,beta-phenylalanylglycine (or Boc(0)-Gly(1)-Delta(E)Phe(2)-Gly(3)-Delta(E)Phe(4)-Gly(5)-OH), C(29)H(33)N(5)O(8), (II), indicates that the Delta(Z)Phe residue is a more effective inducer of folded structures than the Delta(E)Phe residue. The values of the torsion angles phi and psi show the presence of two type-III' beta-turns at the Delta(Z)Phe residues and one type-II beta-turn at the Delta(E)Phe residue. All amino acids are linked trans to each other in both peptides. Beta-turns present in the peptides are stabilized by intramolecular 4-->1 hydrogen bonds. Molecules in both structures form two-dimensional hydrogen-bond networks parallel to the (100) plane.

Catching a protein in the act

Seeing is believing. This old saying sums up one of the main goals in biology and biophysics: to watch and ultimately understand the molecular processes that sustain life. Thanks to advances in both experimentation and simulation, we are rapidly gaining a molecular-level understanding of key biomolecular processes. Nevertheless, experiments remain largely limited to the identification and characterization of intermediates along a reaction path, requiring significant populations and sufficiently long lifetimes to be detectable. Ultimately, a full understanding of the molecular mechanisms will also require the characterization of the transitions between the intermediates. One might even argue that the molecular mechanism is contained in the transition state separating the intermediates. But despite much recent progress [e.g., with an upper bound determined for the transition time in protein folding from fluorescence spectroscopy (1)], our mechanistic understanding of biomolecular transitions is derived primarily from indirect measurements, such as phi-value analysis (2), leaving the transitions themselves largely in the dark. In this issue of the PNAS, Vreede et al. (3) show how modern molecular simulation techniques can be used to shed light on molecular transitions, even those occurring on a millisecond timescale far beyond that of standard molecular dynamics calculations.

Growth estimation of mangrove cockle Anadara tuberculosa (Mollusca: Bivalvia): application and evaluation of length-based methods

Growth is one of the key processes in the dynamic of exploited resources, since it provides part of the information required for structured population models. Growth of mangrove cockle, Anadara tuberculosa was estimated through length-based methods (ELEFAN I y NSLCA) and using diverse shell length intervals (SLI). The variability of L(infinity), k and phi prime (phi') estimates and the effect of each sample were quantified by jackknife techniques. Results showed the same L(infinity) estimates from ELEFAN I and NSLCA across each SLI used, and all L(infinity) were within the expected range. On the contrary, k estimates differed between methods. Jackknife estimations uncovered the tendency of ELEFAN I to overestimate k with increases in SLI, and allowed the identification of differences in uncertainty (PE and CV) between both methods. The average values of phi' derived from NSCLA1.5 and length-age sources were similar and corresponded to ranges reported by other authors. Estimates of L(infinity), k and (phi' from NSCLA1.5 were 85.97 mm, 0.124/year and 2.953 with jackknife and 86.36mm de L(infinity), 0.110/year de k and 2.914 de phi' without jackknife, respectively. Based on the observed evidence and according to the biology of the species, NSCLA is suggested to be used with jackknife and a SLI of 1.5 mm as an ad hoc approach to estimate the growth parameters of mangrove cockle.

Colloidal Dispersion Stability of CuPc Aqueous Dispersions and Comparisons to Predictions of the DLVO Theory for Spheres and Parallel Face-to-Face Cubes

The dispersion stability and the zeta potentials of nonspherical crystalline (beta-form) copper phthalocyanine (CuPc) particles of hydrodynamic diameter d(h) approximately = 90 nm were investigated at 25 degrees C in water and in aqueous solutions of NaNO(3). The electrolyte concentrations c ranged from 1 to 500 mM and the particle concentrations ranged from 50 to 10,000 ppm (0.005 to 1 wt %). In each case, the Fuchs-Smoluchowski stability ratio W was determined from dynamic light scattering (DLS) data and the Rayleigh-Debye-Gans (RDG) scattering theory. The data suggest that electrostatic effects play a major role in the stability of CuPc-based dispersions. The calculated particle charge z per CuPc particle based on the zeta potential data and the area of the particles (assumed to be cubical) suggests that there is preferential adsorption of NO(3)(-) ions on the uncharged CuPc surface, and the surface charge increases with increasing electrolyte concentration. Furthermore, two new models of the DLVO theory, for spheres and for parallel face-to-face cubes, were reformulated in dimensionless form. The Hamaker constant of CuPc particles was calculated by the same authors on the basis of theoretical models in J. Chem. Theory Comput. (2010, in press). The key dimensionless group is the ratio N of the electrostatic double layer energy to the Hamaker constant. The two DLVO models were used to predict the value of a dimensionless maximum potential energy Phi(max), the conditions when it may exist, and then the value of W. In water, the DLVO model for spheres overpredicted the stability, while the model for cubes underpredicted the stability. At c = 1 mM, both models overpredicted the stability. At c = 10 mM, the model for spheres underpredicted the stability, whereas the model for cubes overpredicted the stability. Hence, there seems to be some significant shape effects on the electrostatic stabilization of CuPc particle dispersions. At c = 100 and 500 mM, both models underpredicted the stability substantially, suggesting the existence of additional short-range repulsive forces, which may primarily control the stability. Simple sensitivity analysis on the calculations supported these conclusions.

Dehydroindigo, the Forgotten Indigo and Its Contribution to the Color of Maya Blue

A comprehensive investigation of the electronic spectral and photophysical properties of the oxidized form of indigo, dehydroindigo (DHI), has been carried out in solution at 293 K. It is shown that dehydroindigo readily converts into its neutral keto form, the blue indigo, in a process which depends on the solvent and water content of the medium. DHI was investigated in toluene, in benzene, and in methanol and it was found that both the oxidized and the keto indigo forms are present in solution. In marked contrast to what has been found for keto-indigo, where the internal conversion channel dominates >99% of the excited state deactivation, or with the fully reduced leuco-indigo, where fluorescence, internal conversion, and singlet-to-triplet intersystem crossing coexist, in the case of DHI in toluene and benzene, the dominant excited state deactivation channel involves the triplet state. Triplet state yields (phi(T)) of 70-80%, with negligible fluorescence (< or = 0.01%) are observed in these solvents. In methanol the phi(T) value decreases to approximately 15%, with an increase of the fluorescence quantum yield to 2%, which makes these processes competitive with the S(1) --> S(0) internal conversion deactivation process. The data are experimentally compatible with the existence of a lowest lying singlet excited state of n,pi* origin in toluene and of pi,pi* origin in methanol. A time-resolved investigation in the picosecond time domain suggests that the emission of DHI involves three interconnected species (involving rotational isomerism), with relative contributions depending on the emission wavelength. DFT calculations (B3LYP 6-31G** level) were performed in order to characterize the electronic ground (S(0)) and excited singlet (S(1)) and triplet (T(1)) states of DHI. The HOMO-LUMO transition was found to accompany an n --> pi* transition of the oxygen nonbonding orbitals to the central CC and adjacent C-N bonds. Calculations also revealed that in S(0) the two indole-like moieties deviate from planarity from ca. 20 degrees, whereas in S(1) and T(1) the predicted structure is basically planar; a gradual decrease of the carbon-carbon central bond distance is seen in the order S(0), S(1), T(1). An additional study on the blue pigment Maya Blue was made, and the comparison between the solid-state spectra of indigo, DHI, and Maya Blue suggests that, in line with recent investigations, DHI is present together with indigo in Maya Blue. These results are relevant to the discussion of the involvement of dehydroindigo in the palette of colors of the ancient Maya Blue pigment.

Equilibrium Population of the Folding Intermediate of RNase H and its Importance in the Folding Trajectory

Proteins can sample a variety of partially folded conformations during the transition between the unfolded and native states. Some proteins never significantly populate these high-energy states and fold by an apparently two-state process. What factors govern which conformations are accessible to a protein as it folds? We have attempted to re-route the folding of ribonuclease H from E. coli by manipulating its regional stability. Using phi-value analysis, we compare the structures of the transition states for folding of RNases H that fold with and without a detectable partially folded intermediate and find that both versions of RNase H fold through a similar trajectory with similar high energy conformations. In light of the general importance of this species on the folding pathway, we attempted to populate the intermediate at equilibrium by destabilizing the region of the protein that is unfolded in this form. Surprisingly, a single change at Ile 25 (I25A) resulted in the equilibrium population of the intermediate under near-native conditions. The intermediate was undetectable in a series of HSQC's, revealing the dynamic nature of this partially unfolded form on the timescale of NMR detection. The dynamic nature of the RNase H intermediate may be important for its role as an on-pathway, productive species that promotes efficient folding.

Triplet formation of 6-azauridine and singlet oxygen sensitization with UV light irradiation

Excited state characteristics of 6-azauridine (6AUd), which is known as a medicine against psoriasis and neoplastic, were investigated with laser plash photolysis, time-resolved thermal lensing, and near IR single photon counting method. The triplet-triplet absorption spectrum of 6AUd was observed for the first time. The formation quantum yield of excited triplet 6AUd (Phi(ISC)) was estimated by acetone triplet sensitization and actinometry with benzophenone to be 1.00 +/- 0.07 (248 nm excitation) and 0.78 +/- 0.05 (308 nm excitation). This excitation wavelength effect could be explained by intersystem crossing (ISC) to the excited triplet manifolds occurring during the relaxation on the potential energy surface (PES) of the S(1)(npi*) state and be in competition with internal conversion to the S(0) state after the relaxation to the minimum of the S(1)(npi*) state. 6AUd had a lower Phi(ISC) value than 6-azauracil (6AU) with the 308 nm excitation (Phi(ISC) = 0.93 +/- 0.04 for 6AU). The nucleoside has more vibrational modes than 6AU, and therefore the ribose would accelerate intramolecular vibrational energy redistribution and the relaxation to the minimum of the PES of the S(1)(npi*) state. Sensitized singlet oxygen formation of 6AUd was also detected in the O(2)-saturated condition with quantum yields of 0.49 +/- 0.01 with the 248 nm excitation, indicating the high phototoxicity of 6AUd.

Is there a Au–S bond dipole in self-assembled monolayers on gold?

Self-assembled monolayers (SAMs) of functionalized thiols are widely used in organic (opto)electronic devices to tune the work function, Phi, of noble-metal electrodes and, thereby, to optimize the barriers for charge-carrier injection. The achievable Phi values not only depend on the intrinsic molecular dipole moment of the thiols but, importantly, also on the bond dipole at the Au-S interface. Here, on the basis of extensive density-functional theory calculations, we clarify the ongoing controversy regarding the existence, the magnitude, and the nature of that bond dipole.

ϕ-Value Analysis for Ultrafast Folding Proteins by NMR Relaxation Dispersion

Proteins that fold rapidly, on the (sub-) microsecond time scale, offer the prospect of direct comparison between experimental data and molecular dynamics simulations. However, experimental studies for such proteins frequently are hindered because folding rates are too fast to measure using conventional stopped-flow methods. To overcome this impediment, NMR spin relaxation dispersion experiments are used to quantify mutational effects on kinetics (DeltaDeltaG(o)), stability (DeltaDeltaG(o)), and phi-values (DeltaDeltaG(dagger)/DeltaDeltaG(o)) for proteins exhibiting chemical exchange line broadening that is fast on the NMR chemical shift time scale. The accuracy of phi-value analysis is enhanced because mutational effects on denatured or intermediate states can be detected through changes in line broadening. The transition and intermediate states of the villin headpiece domain, HP67, are characterized in varying solvent conditions to validate the method.

Self-Organized Criticality in Sheared Suspensions

Recent studies reveal that suspensions of neutrally buoyant non-brownian particles driven by slow periodic shear can undergo a dynamical phase transition between a fluctuating irreversible steady state and an absorbing reversible state. Using a computer model, we show that such systems exhibit self-organized criticality when a finite particle sedimentation velocity v(s) is introduced. Under periodic shear, these systems evolve, without external intervention, towards the shear-dependent critical concentration phi(c) as v(s) is reduced. This state is characterized by power-law distributions in the lifetime and size of fluctuating clusters. Experiments exhibit similar behavior and, as v(s) is reduced, yield steady-state values of phi that tend towards the phi(c) corresponding to the applied shear.

Na+/H+ exchanger blockade inhibits the expression of vascular endothelial growth factor in SGC7901 cells

Vascular endothelial growth factor (VEGF) overexpression is critically involved in tumor formation. Na+/H+ exchanger isoform (NHE) is elevated in cancer cells. We explored the effect of NHE inhibition on VEGF expression in human gastric cancer SGC7901 cells. VEGF mRNA expression was detected by real-time RT-PCR. VEGF protein expression was measured by western blotting and immunocytochemistry. For determination of viable cells the MTT colorimetric assay was used. Treatment of SGC7901 cells with NHE inhibitors resulted in significant decrease of VEGF mRNA and protein expression. NHE inhibition decreased intracellular pH (pHi) values and VEGF mRNA expression. These data demonstrate that NHE blockade inhibits VEGF expression in SGC7901 cells.

Effect of penehyclidine hydrochloride on gastric mucous membrane impairment during orthotopic liver transplantation

Objective To evaluate the effect of penehyclidine hydrochloride on gastric mucous membrane impairment during orthotopic liver transplantation (OLT) .Methods Thirty-eight ASA Ⅲ or Ⅳ patients aged 38-59 yr weighing 50-75 kg were randomly divided into 2 groups ( n = 19 each) : control group (C) and penehyclidine hydrochloride group (PH) . Penehyclidine hydrochloride 0.04 mg/kg in 50 ml of nomal saline (NS) was infused iv over 1 h after skin incision in group PH. Anesthesia was induced with midazolam, fentanyl, propofol and atracurium and maintained with isoflurane inhalation and infusion of propofol and atracurium. Radial artery was cannulated for blood sampling and BP monitoring. Swan-Ganz catheter was placed via right internal jugular vein. Gastric intramucosal tonometry catheter was inserted into the stomach. Gastric intramural pH and PCO_2 (pHi, PgCO_2) and arterial pH and PCO_2 ( pHa, PaCO_2 ) were measured immediately before operation (T_0, baseline) , 30 min before anhepatic phase (T_1 ) , 5, and 30 min of anhepatic phase (T_2 , T_3 ), 5, 30 and 60 min of neohepatic phase (T_4 , T_5 , T_6 ) and at the end of the operation (T_7 ) . Pg-aCO_2 was calculated. Results pHi and pHa significantly decreased while Pg-aCO_2 significantly increased at T_(2～5) as compared with the baseline values at T_0 in both groups. pHi and pHa values were significantly larger while Pg-aCO_2 was significantly smaller at T_(2～5) in group PH than in group C. Conclusion Intravenous penehyclidine hydrochloride 0.04 mg/kg can raise gastric intramural pH and protect gastric mucous membrane against injury. Key words: Cholinergic antagonists; liver transplantation; Gastric mucosa