Roberto Bogomolni | University of California, Santa Cruz (original) (raw)

Papers by Roberto Bogomolni

Proceedings of SPIE, Nov 3, 2003

In this study, gold nanoparticles (AuNPs) and ZnO-decorated zirconia (AuNPs/ZnO-ZrO 2) were synth... more In this study, gold nanoparticles (AuNPs) and ZnO-decorated zirconia (AuNPs/ZnO-ZrO 2) were synthesized through co-precipitation and hydrolysis coupled with heat treatment, and explored as a novel adsorbent for arsenic removal from aqueous solution. The effects of synthesis parameters were examined, such as support type, Zn/Zr mole ratio, co-precipitation method and calcination temperature. X-ray powder diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), high resolution transmission electron microscopy (HR-TEM), Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS) and N 2 adsorption were used to investigate the enhancement of arsenic adsorption on the hybrid composites. It was found that the adsorption property of AuNPs/ZnO-ZrO 2 was strongly dependent on support type, Zn/Zr mole ratio, co-precipitation method and calcination temperature. The optimized AuNPs/ZnO-ZrO 2 exhibited the best adsorption capacity for arsenic at lower concentrations (less than 8 mg L −1), compared with ZnO-decorated zirconia (ZnO-ZrO 2) and bare zirconia (ZrO 2). The enhanced adsorption of arsenic by AuNPs/ZnO-ZrO 2 was ascribed to the larger specific surface area, abundant hydroxyl groups and co-existance of ionic gold (Au(OH) 2 +) and gold clusters (Au δ+) highly dispersed on the surface which could act as smart scavengers for low-concentration arsenic from water. The adsorption equilibrium of arsenic on AuNPs/ZnO-ZrO 2 fitted to the Langmuir, Brunauer-Emmett-Teller (BET) and Gunary models well and the Gunary model gave the best fit. Isotherm analysis results showed that the adsorption of arsenic on AuNPs/ZnO-ZrO 2 occurred dominantly through monolayer formation but was a non-ideal Langmuir type adsorption. However, ZnO-ZrO 2 showed much higher adsorption capacity for arsenic than that of ZrO 2 , which was mainly attributed to the formation of basic zinc carbonate (BZC) with rich structural hydroxyl groups and to the improvement in surface properties of zirconia. Significant multilayer adsorption was able to proceed on the surface at higher arsenic concentrations (more than 8 mg L −1), obeying the BET isotherm.

Proceedings of the National Academy of Sciences of the United States of America, 1987

Spectroscopic evidence indicates the presence of a second sensory receptor sR-II in Halobacterium... more Spectroscopic evidence indicates the presence of a second sensory receptor sR-II in Halobacterium halobium, which causes a repellent response to blue-green light. Reactions with hydroxylamine and NaCNBH3 and reconstitution of the bleached pigment with retinal show that it is very similar to the other retinylidene pigments bacteriorhodopsin, halorhodopsin, and especially the earlier-discovered phototaxis receptor, sensory rhodopsin, renamed sR-I587. The second sensory receptor, sR-Ha9, has an absorbance maximum at 480 nm and undergoes a cyclic photoreaction with a half-time of w200 msec. Its predominant photocycle intermediate absorbs maximally near 360 nm. The receptor can be detected spectroscopically in the

Biochemistry, Oct 1, 1987

Time-resolved resonance Raman spectra of the hRL intermediate of halorhodopsin have been obtained... more Time-resolved resonance Raman spectra of the hRL intermediate of halorhodopsin have been obtained. The structurally sensitive fingerprint region of the hRL spectrum is very similar to that of bacteriorhodopsin's Lss0 intermediate, which is known to have a 13-cis configuration. This indicates that hRL contains a 13-cis chromophore and that an all-trans-13-cis isomerization occurs in the halorhodopsin photocycle. hRL exhibits a Schiff base stretching mode at 1644 cm-*, which shifts to 1620 cm-I in D20. This demonstrates that the Schiff base linkage to the protein is protonated. The insensitivity of the CC stretching mode frequencies to N-deuteriation suggests that the Schiff base configuration is anti. The 24 cm-' shift of the Schiff base mode in D20 indicates that the Schiff base proton in hRL has a stronger hydrogen-bonding interaction with the protein than does hRST8.

Journal of Biological Chemistry, Nov 1, 1989

Sensory rhodopsin I (SR-I) is a retinal-containing pigment which functions as a phototaxis recept... more Sensory rhodopsin I (SR-I) is a retinal-containing pigment which functions as a phototaxis receptor in Halobacterium halobium. We have obtained resonance Raman vibrational spectra of the native membranebound form of SRss7 and used these data to determine the structure of its retinal prosthetic group. The similar frequencies and intensities of the skeletal fingerprint modes in SRSs7, bacteriorhodopsin (BRses), and halorhodopsin (HR678) as well as the position of the dideuterio rocking mode when SR-I is regenerated with 12,14-D2 retinal (915 cm") demonstrate that the retinal chromophore has an all-trans configuration. The shift of the C=N stretching mode from 1628 cm" in HzO to 1620 cm" in DzO demonstrates that the chromophore in SRsa7 is bound to the protein by a protonated Schiff base linkage. The small shift of the 1195 cm" Cl4-C16 stretching mode in D20 establishes that the protonated Schiff base bond has an anti configuration. The low value of the Schiff base stretching frequency together with its small 8 cm" shift in D20 indicates that the Schiff base proton is weakly hydrogen bonded to its protein counterion. This suggests that the red shift in the absorption maximum of SR-I (587 nm) compared with HR (578 nm) and BR (568 nm) is due to a reduction of the electrostatic interaction between the protonated Schiff base group and its protein counterion. Sensory rhodopsin I (SR-I),' halorhodopsin (HR), and bacteriorhodopsin (BR) are retinal proteins found in the cytoplasmic membrane of the bacterium Halobacterium halobium

Journal of Physical Chemistry B, Nov 17, 2004

A unique gold nanoparticle aggregate (GNA) system has been shown to be an excellent substrate for... more A unique gold nanoparticle aggregate (GNA) system has been shown to be an excellent substrate for surfaceenhanced Raman scattering (SERS) applications. Rhodamine 6G (R6G), a common molecule used for testing SERS activity on silver, but generally difficult to detect on gold substrates, has been found to readily bind to the GNA and exhibit strong SERS activity due to the unique surface chemistry afforded by sulfur species on the surface. This GNA system has yielded a large SERS enhancement of 10 7-10 9 in bulk solution for R6G, on par with or greater than any previously reported gold SERS substrate. SERS activity has also been successfully demonstrated for several biological molecules including adenine, L-cysteine, L-lysine, and L-histidine for the first time on a gold SERS substrate, showing the potential of this GNA as a convenient and powerful SERS substrate for biomolecular detection. In addition, the SERS spectrum of R6G on single aggregates has been measured. We have shown that the special surface properties of the GNA, in conjunction with strong near-IR absorption, make it useful for SERS analysis of a wide variety of molecules.

The Journal of Physical Chemistry, 2004

Springer eBooks, 1975

Halobacteria depend on high concentrations of NaC1 for growth and survival. They occur naturally ... more Halobacteria depend on high concentrations of NaC1 for growth and survival. They occur naturally in environments such as salt lakes, where the salt concentration due to evaporation is near or at saturation. Typically, the temperature and solar radiation density are high in such locations, at least during the day, and the O2 concentration in the brine must be low unless O2-producing halophilic algae are present. Most halobacteria do not contain chlorophyll, and it was rather puzzling to observe that many of them do not ferment sugars either and appear to rely entirely on oxidative phosphorylation as their energy source (for a review, see LARSEN, 1963, 1967). The solution to this puzzle has been provided by the observation that halobacteria can use light energy to drive metabolic processes through a chlorophyll-independent mechanism.

Biochemistry, Dec 2, 2010

Light-induced activation of the LOV2-JR domain of the photoreceptor phototropin from oat is belie... more Light-induced activation of the LOV2-JR domain of the photoreceptor phototropin from oat is believed to involve the detachment of the JR helix from the central β-sheet and its subsequent unfolding. The dynamics of these conformational changes were monitored by time-resolved emission spectroscopy with 100 ns time resolution. Three transitions were detected during the LOV2-JR photocycle with time constants of 3.4 μs, 500 μs, and 4.3 ms. The fastest transition is due to the decay of the flavin phosphorescence in the transition of the triplet LOV L 660 state to the singlet LOV S 390 signaling state. The 500 μs and 4.3 ms transitions are due to changes in tryptophan fluorescence and may be associated with the dissociation and unfolding of the JR helix, respectively. They are absent in the transient absorption signal of the flavin chromophore. The tryptophan fluorescence signal monitors structural changes outside the chromophore binding pocket and indicates that there are at least three LOV S 390 intermediates. Since the 500 μs and 4.3 ms components are absent in a construct without the JR helix and in the mutant W557S, the fluorescence signal is mainly due to tryptophan 557. The kinetics of the main 500 μs component is strongly temperature dependent with activation energy of 18.2 kcal/mol suggesting its association with a major structural change. In the structurally related PAS domain protein PYP the N-terminal cap dissociates from the central β-sheet and unfolds upon signaling state formation with a similar time constant of ∼1 ms. Using transient fluorescence we obtained a nearly identical activation energy of 18.5 kcal/mol for this transition.

Biophysical Journal, 2001

Sensory rhodopsin-I (SRI), a phototaxis receptor of archaebacteria, is a retinal-binding protein ... more Sensory rhodopsin-I (SRI), a phototaxis receptor of archaebacteria, is a retinal-binding protein that exists in the cell membrane intimately associated with a signal-transducing protein (HtrI) homologous to eubacterial chemotaxis receptors. Transducer-free sensory rhodopsin-I (fSRI), from cells devoid of HtrI, undergoes a photochemical cycle kinetically different from that of native SRI. We report here on the measurement and analysis of the photochemical kinetics of fSRI reactions in the 350-750-nm spectral range and in a 10 Ϫ7 s to 1 s time window. The lack of specific intermolecular interactions between SRI and HtrI results in early return of the ground form via distinct branching reactions in fSRI, not evident in the photocycle of native SRI. The chromophore transitions are loosely coupled to protein structural transitions. The coexistence of multiple spectral forms within kinetic intermediates is interpreted within the concept of multicolored protein conformational states.

Journal of Chemical Physics, Mar 1, 1983

In order to explore the feasibility of microwave absorption techniques as a tool for the study of... more In order to explore the feasibility of microwave absorption techniques as a tool for the study of interfaces and electrode reactions we have measured the electrochemical and photochemical properties of ZnO in contact with an aqueous electrolyte by conventional electrochemical procedures and simultaneously by electrodeless detection of microwave absorption at 9.5 GHz in a resonant cavity. Pronounced potential dependent microwave absorption signals were found which proved to be influenced by illumination and electrochemical surface reactions. The comparison of microwave absorption with the electrochemically measured electrode behavior indicates, that microwave absorption data can provide interesting complementary information on the nature and reactivity of charge carriers and dipoles in the electrode/electrolyte interface. The proposed method is so sensitive that signals arising from fractions of monolayers will be detectable. A comprehensive interpretation of the results is not yet attempted. Further experimental studies on simple electrode systems are needed to clarify the mechanism. Because of its nondestructive nature, the microwave method could develop into a valuable new technique in surface chemistry.

Biochemistry, Mar 20, 2007

Light-, oxygen-, or voltage-regulated (LOV1 and LOV2) domains bind flavin mononucleotide (FMN) an... more Light-, oxygen-, or voltage-regulated (LOV1 and LOV2) domains bind flavin mononucleotide (FMN) and activate the phototropism photoreceptors phototropin 1 (phot1) and phototropin 2 (phot2) by using energy from absorbed blue light. Upon absorption of blue light, chromophore and protein conformational changes trigger the kinase domain for subsequent autophosphorylation and presumed downstream signal transduction. To date, the light-induced photocycle of the phot1 LOV2 protein is known to involve formation of a triplet flavin mononucleotide (FMN) chromophore followed by the appearance of a FMN adduct within 4 µs [

Journal of Integrative Plant Biology, 2007

The phototropins phot1 and phot2 are plant blue-light receptors that mediate phototropism, chloro... more The phototropins phot1 and phot2 are plant blue-light receptors that mediate phototropism, chloroplast movements, stomatal opening, leaf expansion, the rapid inhibition of hypocotyl growth in etiolated seedlings, and possibly solar tracking by leaves in those species in which it occurs. The phototropins are plasma membrane-associated hydrophilic proteins with two chromophore domains (designated LOV1 and LOV2 for their resemblance to domains in other signaling proteins that detect light, oxygen, or voltage) in their Nterminal half and a classic serine/threonine kinase domain in their C-terminal half. Both chromophore domains bind flavin mononucleotide (FMN) and both undergo light-activated formation of a covalent bond between a nearby cysteine and the C(4a) carbon of the FMN to form the signaling state. LOV2-cysteinyl adduct formation leads to the release downstream of a tightly bound amphipathic α α α α α-helix, a step required for activation of the kinase function. This cysteinyl adduct then slowly decays over a matter of seconds or minutes to return the photoreceptor chromophore modules to their ground state. Functional LOV2 is required for light-activated phosphorylation and for various blue-light responses mediated by the phototropins. The function of LOV1 is still unknown, although it may serve to modulate the signal generated by LOV2. The LOV domain is an ancient chromophore module found in a wide range of otherwise unrelated proteins in fungi and prokaryotes, the latter including cyanobacteria, eubacteria, and archaea. Further general reviews on the phototropins are those by Celaya and Liscum (2005) and Christie and Briggs (2005).

Biophysical Journal, Aug 1, 1985

Dark and light adaptation of bacteriorhodopsin in purple membrane multilayers at <100% relative h... more Dark and light adaptation of bacteriorhodopsin in purple membrane multilayers at <100% relative humidity differs from that seen in suspensions. Equilibrium between the two bacteriorhodopsin isomers (bR55'0 and bR'") in the light-adapted state becomes dependent on the wavelength of actinic light. Excitation at the red edge of the visible absorption band causes dark adaptation in a light-adapted sample. Using polarized actinic and measuring light, we show that acceleration of the dark adaptation through heating by actinic light cannot explain this observation. A light-driven bR5'70 to bR5^^r eaction that competes with the well-known 13 cis-to-all-trans light adaptation reaction must exist under our experimental conditions. Trans-to-cis conversion is a one-photon process distinct from the two photon process observed by others in purple membrane suspensions (Sperling, W., C. N. Rafferty, K. D. Kohl, and N. A. Dencher, 1978, FEBS (Fed. Eur. Biochem. Soc.) Lett. 97:129-132). Its quantum efficiency increases monotonously on reducing the hydration level, and is paralleled by an increase in the lifetime of the M410 intermediate of the trans photocycle. We suggest that at this point a branch leads from the all-trans into the 1 3-cis photocycle. It is probably the same reaction that causes the reduced light adaptation in monomeric bacteriorhodopsin (Casadio, R., H.

American Journal of Botany, Nov 1, 2003

Stomatal opening exhibits two main peaks of activity in the visible range-a red peak, mediated by... more Stomatal opening exhibits two main peaks of activity in the visible range-a red peak, mediated by photosynthesis, and a blue peak, mediated by one or more blue light (BL) photoreceptors. In addition, a pronounced peak in the UV-B region has been characterized, as has a smaller UV-A peak. The BL-induced stomatal opening can be reversed by green light (GL). Here we report that UV-Binduced opening is also antagonized by GL. To determine whether UV-B is being absorbed by the BL photoreceptor or by a separate UV-B receptor, the UV-B responses of two different Arabidopsis mutants, npq1 and phot1/phot2, were tested. Both putative BLphotoreceptor mutants exhibited normal stomatal opening in response to UV-B, consistent with the existence of a separate UV-B photoreceptor. Moreover, GL failed to antagonize UV-B-induced stomatal opening in the phot1/phot2 double mutant and only partially antagonized UV-B opening in npq1. Thus, both phot1 and phot 2, as well as zeaxanthin, are required for the normal GL inhibition of UV-B. A model for a photoreceptor network that regulates stomatal opening is presented. Unlike the situation in guard cells, the UV-B bending response of Arabidopsis hypocotyls during phototropism appears to be mediated by phototropins.

Journal of Biological Chemistry, 2003

The phototropins are a family of membrane-associated flavoproteins that function as the primary b... more The phototropins are a family of membrane-associated flavoproteins that function as the primary blue light receptors regulating phototropism, chloroplast movements, stomatal opening, and leaf expansion in plants. Phot1, a member of this family, contains two FMN-binding domains, LOV1 and LOV2, within the Nterminal region and a C-terminal serine-threonine protein kinase domain. Light irradiation of oat phot1 LOV2 produces a cysteinyl adduct (Cys-39) at the flavin C(4a) position, which decays thermally back to the dark state. We measured pH and isotope effects on the photocycle. Between pH 3.7 and 9.5, adduct formation showed minimal pH dependence, and adduct decay showed only slight pH dependence, indicating that the pK values of mechanistically relevant groups are outside this range. LOV2 showed a nearly 5-fold slowing of adduct formation in D 2 O relative to H 2 O, indicating that the ratelimiting step involves proton transfer(s). Light-induced changes in the far UV CD spectrum of LOV2 revealed putative protein structural perturbations. The light minus dark CD difference spectrum resembles an inverted ␣-helix spectrum, suggesting that ␣-helicity is reversibly lost upon light irradiation. Decay kinetics for CD spectral changes in the far UV region occur at the same rate as those in the visible region, indicating synchronous relaxation of protein and chromophore structures.

Proceedings of the National Academy of Sciences of the United States of America, May 23, 2011

Biochimica Et Biophysica Acta - Bioenergetics, Jul 1, 1976

The purple membrane of Halobacterium halobium acts as a light-driven proton pump, ejecting proton... more The purple membrane of Halobacterium halobium acts as a light-driven proton pump, ejecting protons from the cell interior into the medium and generating an electrochemical proton gradient across the cell membrane. However, the typical response of cells to light as measured with a pH electrode in the medium consists of an initial net inflow of protons which subsides and is then replaced by a net outflow which exponentially approaches a new lower steady state pH level. When the light is turned off a small transient acidification occurs before the pH returns to the original dark level. We present experiments suggesting that the initial inflow of protons is triggered by the beginning ejection of protons through the purple membrane and that the initial inflow rate is larger than the continuing light-driven outflow. When the initial inflow has decreased exponentially to a small value, the outflow dominates and causes the net acidification of the medium. The initial inflow is apparently driven by a pre-existing electrochemical gradient across the membrane, which the cells can maintain for extended times in the absence of light and oxygen. Treatments which collapse this gradient such as addition of small concentrations of uncouplers abolish the initial inflow. The triggered inflow occurs through the ATPase and is accompanied by ATP synthesis. Inhibitors of the ATPase such as N,N'-dicyclohexylcarbodiimide (DCCD) inhibit ATP synthesis and abolish tb.e inflow. They also abolish the transient light-off acidification, which is apparently caused by a short burst of ATP hydrolysis before the enzyme is blocked by its endogenous inhibitor. Similar transient inflows and outflows of protons are also observed when anaerobic cells are exposed to short oxygen pulses.