Interactions of adenine, thymine, and uracil with epinephrine: UV studies

Based upon UV absorption studies, charge transfer complex formations by the nucleic acid bases adenine, thymine, and uracil with epinephrine were demonstrated. The pertient equilibrium constants were calculated by assuming 1:1 complexes using the Benesi-Hildebrand equation and were found to decrease in the following order: uracil-epinephrine greater than thymine-epinephrine greater than adenine-epinephrine. The values of delta G degrees, delta H degrees, and delta S degrees were calculated for the various interactions. Theoretical arguments are presented as to the possible stoichiometries of the various complexes existing in aqueous solutions. The electron-donating or electron-accepting abilities of the interacting molecular species are discussed.     

Thermodynamics of oligoarginines binding to RNA and DNA

We have examined the equilibrium binding of a series of synthetic oligoarginines (net charge z = +2 to +6) containing tryptophan to poly(U), poly(A), poly(C), poly(I), and double-stranded (ds) DNA. Equilibrium association constants, K(obs), measured by monitoring tryptophan fluorescence quenching, were examined as functions of monovalent salt (MX) concentration and type, as well as temperature, from which deltaG(standard)obs, deltaH(obs), and deltaS(standard)obs were determined. For each peptide, K(obs) decreases with increasing [K+], and the magnitude of the dependence of K(obs) on [K+], delta log K(obs)/delta log[K+], increases with increasing net peptide charge. In fact, the values of delta log K(obs)/delta log[K+] are equivalent for oligolysines and oligoarginines possessing the same net positive charge. However, the values of K(obs) are systematically greater for oligoarginines binding to all polynucleotides, when compared to oligolysines with the same net charge. The origin of this difference is entirely enthalpic, with deltaH(obs), determined from van't Hoff analysis, being more exothermic for oligoarginine binding. The values of deltaH(obs) are also independent of [K+]; therefore, the salt concentration dependence of deltaG(standard)obs is entirely entropic in origin, reflecting the release of cations from the nucleic acid upon complex formation. These results suggest that hydrogen bonding of arginine to the phosphate backbone of the nucleic acids contributes to the increased stability of these complexes.     

Energy transfer and charge separation in photosystem I: P700 oxidation upon selective excitation of the long-wavelength antenna chlorophylls of Synechococcus elongatus

Photosystem I of the cyanobacterium Synechococcus elongatus contains two spectral pools of chlorophylls called C-708 and C-719 that absorb at longer wavelengths than the primary electron donor P700. We investigated the relative quantum yields of photochemical charge separation and fluorescence as a function of excitation wavelength and temperature in trimeric and monomeric photosystem I complexes of this cyanobacterium. The monomeric complexes are characterized by a reduced content of the C-719 spectral form. At room temperature, an analysis of the wavelength dependence of P700 oxidation indicated that all absorbed light, even of wavelengths of up to 750 nm, has the same probability of resulting in a stable P700 photooxidation. Upon cooling from 295 K to 5 K, the nonselectively excited steady-state emission increased by 11- and 16-fold in the trimeric and monomeric complexes, respectively, whereas the quantum yield of P700 oxidation decreased 2.2- and 1.7-fold. Fluorescence excitation spectra at 5 K indicate that the fluorescence quantum yield further increases upon scanning of the excitation wavelength from 690 nm to 710 nm, whereas the quantum yield of P700 oxidation decreases significantly upon excitation at wavelengths longer than 700 nm. Based on these findings, we conclude that at 5 K the excited state is not equilibrated over the antenna before charge separation occurs, and that approximately 50% of the excitations reach P700 before they become irreversibly trapped on one of the long-wavelength antenna pigments. Possible spatial organizations of the long-wavelength antenna pigments in the three-dimensional structure of photosystem I are discussed.     

Multiphoton fluorescence excitation: new spectral windows for biological nonlinear microscopy

Intrinsic, three-dimensionally resolved, microscopic imaging of dynamical structures and biochemical processes in living preparations has been realized by nonlinear laser scanning fluorescence microscopy. The search for useful two-photon and three-photon excitation spectra, motivated by the emergence of nonlinear microscopy as a powerful biophysical instrument, has now discovered a virtual artist's palette of chemical indicators, fluorescent markers, and native biological fluorophores, including NADH, flavins, and green fluorescent proteins, that are applicable to living biological preparations. More than 25 two-photon excitation spectra of ultraviolet and visible absorbing molecules reveal useful cross sections, some conveniently blue-shifted, for near-infrared absorption. Measurements of three-photon fluorophore excitation spectra now define alternative windows at relatively benign wavelengths to excite deeper ultraviolet fluorophores. The inherent optical sectioning capability of nonlinear excitation provides three-dimensional resolution for imaging and avoids out-of-focus background and photodamage. Here, the measured nonlinear excitation spectra and their photophysical characteristics that empower nonlinear laser microscopy for biological imaging are described.     

Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding

Denaturant m values, the dependence of the free energy of unfolding on denaturant concentration, have been collected for a large set of proteins. The m value correlates very strongly with the amount of protein surface exposed to solvent upon unfolding, with linear correlation coefficients of R = 0.84 for urea and R = 0.87 for guanidine hydrochloride. These correlations improve to R = 0.90 when the effect of disulfide bonds on the accessible area of the unfolded protein is included. A similar dependence on accessible surface area has been found previously for the heat capacity change (delta Cp), which is confirmed here for our set of proteins. Denaturant m values and heat capacity changes also correlate well with each other. For proteins that undergo a simple two-state unfolding mechanism, the amount of surface exposed to solvent upon unfolding is a main structural determinant for both m values and delta Cp.     

Domain structure of the Fib-1 and Fib-2 regions of human fibronectin. Thermodynamic properties of the type I finger module

The stability of the Fib-1 (29 kDa) and Fib-2 (19 kDa) fragments of human fibronectin as well as several different subfragments and isolated type I "finger" modules were studied under various solvent conditions by differential scanning calorimetry and fluorescence spectroscopy. It was established that all fibronectin fingers constitute independently folded domains whose melting temperatures range from 54 to 108 degrees C. The difference between heat capacities of the native and denatured states (delta Cp) is low, about 0.03 cal/K-g, which is consistent with the relatively low percentage of hydrophobic amino acids and the consequent small change in non-polar surface area exposed to the solvent upon denaturation. The free energy of unfolding at 25 degrees, as calculated from the calorimetric data or measured directly by titration with GdmSCN is also small, in the range of 2.4 to 6.7 kcal/mol. The small delta G value and its flat dependence on temperature (determined by delta Cp) translates the small variations in delta G between fingers into large variations in tm. The small value of delta G also indicates that finger modules are structurally rather fragile which may account for their sensitivity to proteolysis; almost any cleavage within either of the two disulfide loops destroys the cooperative structure and abolishes the corresponding melting transition. The fact that some fingers exhibit large decreases in tm upon separation from more stable neighbors with which they interact can also be viewed as a consequence of the low values of delta G and delta Cp.     

Excited states and trapping in reaction center complexes of the green sulfur bacterium Prosthecochloris aestuarii

The excited states of bacteriochlorophyll (BChl) a were studied by pump-probe transient absorption spectroscopy in reaction center core (RCC), Fenna-Matthews-Olson (FMO) and FMO-RCC complexes of the green sulfur bacterium Prosthecochloris aestuarii. Excitation at 790 or 835 nm resulted in rapid equilibration of the energy between the BChl a molecules of the RCC complex: within 1 ps, most of the excitations had relaxed to the lowest energy level (835 nm), as a result of strong interactions between the BChls. Excitation of chlorophyll a 670 resulted in energy transfer to BChl a with a time constant of 1.2 ps, followed by thermal equilibration. Independent of the wavelength of excitation, the decay at 835 nm could be fitted with a time constant of about 25 ps, comparable to the 30 ps measured earlier with membrane fragments, which is ascribed to trapping in the reaction centers. Similar results were obtained with the FMO-RCC complex upon excitation at 835 or 670 nm, but the results upon 790 nm excitation were quite different. Again an equilibrium was rapidly reached, but now most of the excitations remained within the FMO complex, with a maximum bleaching at 813 nm, the same as observed in the isolated FMO. Even after 100 ps there was no bleaching at 835 nm and no evidence for charge separation. We conclude that there is no equilibration of the energy between the FMO and the RCC complex and that the efficiency of energy transfer from FMO to the reaction center core is low.     

New time-resolved techniques in two-photon microscopy

Microscopy is traditionally a tool for determining biological structures. Many recent advances in optical microscopy involves the incorporation of spectroscopy techniques to monitor biochemical states of microscopic structures in living cells and tissues. By minimizing tissue photodamage, two-photon excitation microscopy provides a new opportunity to study the dynamics of biological systems on time scales from nanoseconds to hours. This review will focus on a number of these new methods: two-photon time-lapse microscopy, two-photon photoactivation, two-photon correlated spectroscopy, two-photon single particle tracking and two-photon lifetime microscopy.     

A general module for RNA crystallization

Crystallization of RNA molecules other than simple oligonucleotide duplexes remains a challenging step in structure determination by X-ray crystallography. Subjecting biochemically, covalently and conformationally homogeneous target molecules to an exhaustive array of crystallization conditions is often insufficient to yield crystals large enough for X-ray data collection. Even when large RNA crystals are obtained, they often do not diffract X-rays to resolutions that would lead to biochemically informative structures. We reasoned that a well-folded RNA molecule would typically present a largely undifferentiated molecular surface dominated by the phosphate backbone. During crystal nucleation and growth, this might result in neighboring molecules packing subtly out of register, leading to premature crystal growth cessation and disorder. To overcome this problem, we have developed a crystallization module consisting of a normally intramolecular RNA-RNA interaction that is recruited to make an intermolecular crystal contact. The target RNA molecule is engineered to contain this module at sites that do not affect biochemical activity. The presence of the crystallization module appears to drive crystal growth, in the course of which other, non-designed contacts are made. We have employed the GAAA tetraloop/tetraloop receptor interaction successfully to crystallize numerous group II intron domain 5-domain 6, and hepatitis delta virus (HDV) ribozyme RNA constructs. The use of the module allows facile growth of large crystals, making it practical to screen a large number of crystal forms for favorable diffraction properties. The method has led to group II intron domain crystals that diffract X-radiation to 3.5 A resolution.     

Simplified Modeling of Bridge Response on Soft Soil to Nonuniform Seismic Excitation

Simple modeling is developed for the response of bridges on soft soil to spatially nonuniform seismic excitation. The bridges are modeled as single- and multispan elastic frames founded on a homogeneous soil layer over rigid rock. Three different excitation types are considered: (1) general harmonic excitation with different amplitude and phase at each support; (2) oblique harmonic SH waves traveling within the soil layer (“wave-passage effect”); and (3) vertically propagating SH waves in conjunction with different soil conditions at the supports (“site-response effect”). Response of a single-span symmetric bridge is obtained by decomposing the excitation into symmetric and antisymmetric components. The analysis is then extended to a multispan integral bridge subjected to translational and rotational input. Harmonic and transient responses are considered and analytical expressions for various response parameters are obtained. Soil-structure interaction (SSI) effects are studied by considering long, drilled shaft foundations. To compare the effects of uniform and nonuniform input, pertinent response ratios are introduced. It is shown that when the amplitude of ground motion varies among the supports, defining a reference uniform excitation is not straightforward.     

Suppressor mutation analysis of the sensory rhodopsin I-transducer complex: insights into the color-sensing mechanism

The molecular complex containing the phototaxis receptor sensory rhodopsin I (SRI) and transducer protein HtrI (halobacterial transducer for SRI) mediates color-sensitive phototaxis responses in the archaeon Halobacterium salinarum. One-photon excitation of the complex by orange light elicits attractant responses, while two-photon excitation (orange followed by near-UV light) elicits repellent responses in swimming cells. Several mutations in SRI and HtrI cause an unusual mutant phenotype, called orange-light-inverted signaling, in which the cell produces a repellent response to normally attractant light. We applied a selection procedure for intragenic and extragenic suppressors of orange-light-inverted mutants and identified 15 distinct second-site mutations that restore the attractant response. Two of the 3 suppressor mutations in SRI are positioned at the cytoplasmic ends of helices F and G, and 12 suppressor mutations in HtrI cluster at the cytoplasmic end of the second HtrI transmembrane helix (TM2). Nearly all suppressors invert the normally repellent response to two-photon stimulation to an attractant response when they are expressed with their suppressible mutant alleles or in an otherwise wild-type strain. The results lead to a model for control of flagellar reversal by the SRI-HtrI complex. The model invokes an equilibrium between the A (reversal-inhibiting) and R (reversal-stimulating) conformers of the signaling complex. Attractant light and repellent light shift the equilibrium toward the A and R conformers, respectively, and mutations are proposed to cause intrinsic shifts in the equilibrium in the dark form of the complex. Differences in the strength of the two-photon signal inversion and in the allele specificity of suppression are correlated, and this correlation can be explained in terms of different values of the equilibrium constant (Keq) for the conformational transition in different mutants and mutant-suppressor pairs.     

Adiabatic electron transfer: comparison of modified theory with experiment

The radical cations of properly designed bishydrazines allow comparison of observed and calculated electron transfer rate constants. These compounds have rate constants small enough to be measured by dynamic electron spin resonance spectroscopy and show charge transfer bands corresponding to vertical excitation from the energy well for the charge occurring upon one hydrazine unit to that for the electron-transferred species. Analysis of the data for all six compounds studied indicates that the shape of the adiabatic surface on which electron transfer occurs can be obtained from the charge transfer band accurately enough to successfully predict the electron transfer rate constant and that explicit tunneling corrections are not required for these compounds.     

Actinic light density dependence of the bacteriorhodopsin protocycle

The photocycle of bacteriorhodopsin (BR) was studied in the 0.3 microsecond to 10 s time interval after excitation, using a wide range of actinic light intensities (10 ns half-duration, 0.06-60 mJ/cm2), at neutral and alkaline pH values. The relative weights of the rapidly and the slowly decaying components of the M intermediate (Mf and M(s), respectively) and the yield of the third millisecond component, N(R,P), are the function of the exciting light intensity (density), while their lifetimes are not. The relative weight of M(s) is found to be a linear function of the portion of the BR molecules undergoing the photocycle. This suggests the existence of a cooperative interaction of the BR molecules arranged in the crystalline purple membrane sheets. Another source of M(s) is also found, which results a nonvanishing relative weight of M(s) even at very weak actinic light density values. The explanation for this may be a branching, or the heterogeneity of BR itself or with its environment. It is shown that the relative weights of the rising and decaying components of the M form(s) do not correlate directly with each other.     

Continuous wave two-photon scanning near-field optical microscopy

We have implemented continuous-wave two-photon excitation of near-UV absorbing fluorophores in a scanning near-field optical microscope (SNOM). The 647-nm emission of an Ar-Kr mixed gas laser was used to excite the UV-absorbing DNA dyes DAPI, the bisbenzimidazole Hoechst 33342, and ethidium bromide in a shared aperture SNOM with uncoated fiber tips. Polytene chromosomes of Drosophila melanogaster and the nuclei of 3T3 Balb/c cells labeled with these dyes were readily imaged. The fluorescence intensity showed the expected nonlinear (second order) dependence on the excitation power in the range of 8-180 mW. We measured the fluorescence intensity as a function of the tip-sample displacement in the direction normal to the sample surface in the single- and two-photon excitation modes (SPE, TPE). The fluorescence intensity decayed faster in TPE than in SPE.     

Effect of high pressure on the association of melittin to membranes

To determine the underlying basis for the sensitivity of peripheral peptides to lipid packing, we monitored the change in association of melittin to different membranes under hydrostatic pressure by fluorescence polarization and by fluorescence intensity in the presence of aqueous quenchers. Association to lysophosphatidylcholine micelles or to membranes composed of dimyristoylphosphatidylcholine, dipalmitoylphosphatidylcholine, palmitoyloleoylphosphatidylcholine, or dioleoylphosphatidylcholine was found to be stable from 1 to 2000 atm. Similar results were obtained using multilamellar vesicles, small unilamellar vesicles, or large unilamellar vesicles. Thus, the increase in lipid chain packing induced by pressure does not alter the association of bound complexes. This result indicates similar compressibilities of the peptide and the head group binding region. Increasing the ionic strength to increase the charge of the free peptide also resulted in a pressure-insensitive complex showing that the hydration does not change upon binding. This conclusion is substantiated by a lack of van't Hoff delta H to dioleoylphosphatidylcholine large unilamellar vesicles. To gain a more molecular picture of these associations, the rotational properties of the tryptophan side chain of bound melittin as a function of lipid packing was also studied. These data indicate subtle differences in peptide orientation in different lipids.     

Control of self-reactive cytotoxic T lymphocytes expressing gamma delta T cell receptors by natural killer inhibitory receptors

The majority of peripheral blood gamma delta T cells in human adults expresses T cell receptors (TCR) with identical V regions (V gamma 9 and V delta 2). These V gamma 9 V delta 2 T cells recognize the major histocompatibility complex (MHC) class I-deficient B cell line Daudi and broadly distributed nonpeptidic antigens present in bacteria and parasites. Here we show that unlike alpha beta or V gamma 9- gamma delta T cells, the majority of V gamma 9V delta 2 T cells harbor natural killer inhibitory receptors (KIR) (mainly CD94/NKG2A heterodimers), which are known to deliver inhibitory signals upon interaction with MHC class I molecules. Within V gamma 9V delta 2 T cells, KIR were mainly expressed by clones exhibiting a strong lytic activity against Daudi cells. In stark contrast, almost all V gamma 9V delta 2 T cell clones devoid of killing activity were KIR-, thus suggesting a coordinate acquisition of KIR and cytotoxic activity within V gamma 9V delta 2 T cells. In functional terms, KIR inhibited lysis of MHC class I-positive tumor B cell lines by V gamma 9V delta 2 cytotoxic T lymphocytes (CTL) and raised their threshold of activation by microbial antigens presented by MHC class I-positive cells. Furthermore, masking KIR or MHC class I molecules revealed a TCR-dependent recognition by V gamma 9V delta 2 CTL of ligands expressed by activated T lymphocytes, including the effector cells themselves. Taken together, these results suggest a general implication of V gamma 9V delta 2 T cells in immune response regulation and a central role of KIR in the control of self-reactive gamma delta CTL.     

Resonance Raman studies of the protocatechuate 3,4-dioxygenase from Brevibacterium fuscum

Resonance Raman studies of the protocatechuate 3,4-dioxygenase (PCD) from Brevibacterium fuscum have been carried out to take advantage of the high iron-site homogeneity of this enzyme. Native uncomplexed PCD exhibits individual resonance-enhanced nu CO and delta CH vibrations for the two tyrosinates coordinated to the active site iron center, which can be assigned to a particular residue by their excitation profiles. Of the two nu CO features observed at 1254 and 1266 cm-1, only the latter is upshifted (to 1272 cm-1) when H2O is replaced by D2O. Similarly the 1254-cm-1 feature is unaffected, while the 1266-cm-1 feature is shifted to approximately 1290 cm-1 when inhibitors such as phenolates or terephthalate bind to the active site. These observed shifts can be rationalized by the presence of hydrogen-bonding interactions with solvent in the active site cavity, which are modulated by D2O and eliminated upon inhibitor binding. Examination of the PCD crystal structure suggests that the axial tyrosine can be hydrogen bonded in the uncomplexed enzyme to water molecules present in the substrate binding pocket. The equatorial tyrosine may also be hydrogen bonded but to solvent molecules which are trapped in a pocket inaccessible to bulk solvent. These studies allow for the first time the association of particular Raman spectroscopic features, i.e., the nu CO's at 1254 and 1266 cm-1, with the equatorial and axial tyrosine residues in the PCD active site, respectively; they lay the groundwork for further Raman studies on catalytically important species to determine the roles these tyrosine residues may play in the PCD reaction cycle.     

Regional Alfalfa Yield, ETc, and Water Value in Western States

Alfalfa hay yield, yield-consumptive use ratio (Y∕ETc), and hay price across a range of rainfall and evapotranspiration conditions of the western states is evaluated to determine alfalfa hay water value or benefit. Included is a determination of long-term mean values and variability of yield, Y∕ETc ratios, and associated irrigation water values. These are compared with published hay water-use efficiencies, production, and water costs. Available rainfall, reference evapotranspiration ET0, hay yields, and prices for counties in Arizona (1987–1999), California (1998–1999), and Idaho (1993–1999) were used. Alfalfa hay Y∕ETc ratios decrease with increasing ETc, although their variability increases with increasing ETc. The greatest Y∕ETc ratios (16–17 kg∕ha-mm) and irrigation water values IW$ (IW$ = $2,800–$3,000∕ha-m), with relatively moderate variability, are associated with an irrigation water IW requirement of ～800 mm, reflecting a combination of relatively high hay values, ETc, and beneficial rain. Although this IW$ is twice that of water delivery prices below the California delta and is comparable with average municipal water costs of $4,000∕ha-m for large western cities, the average is nearly 1∕3.     

Lyme arthritis synovial gamma delta T cells respond to Borrelia burgdorferi lipoproteins and lipidated hexapeptides

Lyme arthritis synovial fluid contains a large proportion of gamma delta T cells that proliferates upon stimulation with the causative spirochete, Borrelia burgdorferi. A panel of Borrelia-reactive gamma delta T cell clones was derived from synovial fluid of two patients with Lyme arthritis. Each of six gamma delta clones from one patient used the V delta 1 TCR segment but had otherwise unique CDR3 sequences and diverse V gamma segment usage. Stimulation of the V delta 1 clones was optimal in the presence of Borrelia, dendritic cells, and exogenous IL-2, which was reflected by proliferation, TCR down-modulation, as well as induction of CD25 and Fas ligand expression. Stimulation by B. burgdorferi-pulsed dendritic cells withstood chemical fixation and was not restricted to class I or class II MHC, CD1a, CD1b, or CD1c. In contrast, anti-gamma delta antibody potently inhibited proliferation. Extraction of B. burgdorferi lipoproteins with Triton X-114 enriched for the stimulatory component. This was confirmed using lipidated vs nonlipidated hexapeptides of Borrelia outer surface proteins. These observations suggest that synovial V delta 1 T cells may mediate an innate immune response to common lipoprotein products of spirochetes.