Localizing and Quantifying Carotenoids in Intact Cells and Tissues

Raman spectroscopy provides detailed information about the molecular structure of carotenoids. Advances in detector sensitivity and acquisition speed have driven the expansion of Raman spectroscopy from a bulk analytical tool to a powerful method for mapping carotenoid abundance in cells and tissues. In many applications, the technique is compatible with living organisms, providing highly specific molecular structure information in intact cells and tissues with subcellular spatial resolution. This leads to spatial-temporal-chemical resolution critical to understanding the complex processes in the life cycle of carotenoids and other biomolecules

Dynamic elements and kinetics: Most favorable conformations of peptides in solution with measurements and simulations

This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared inJ. Chem. Phys. 151, 225102 (2019); doi: 10.1063/1.5131782 and may be found at https://aip.scitation.org/doi/10.1063/1.5131782.Small peptides in solution adopt a specific morphology as they function. It is of fundamental interest to examine the structural properties of these small biomolecules in solution and observe how they transition from one conformation to another and form functional structures. In this study, we have examined the structural properties of a simple dipeptide and a five-residue peptide with the application of far-UV circular dichroism (CD) spectroscopy as a function of temperature, fluorescence anisotropy, and all-atom molecular dynamics simulation. Analysis of the temperature dependent CD spectra shows that the simplest dipeptide N-acetyl-tryptophan-amide (NATA) adopts helical, beta sheet, and random coil conformations. At room temperature, NATA is found to have 5% alpha-helical, 37% beta sheet, and 58% random coil conformations. To our knowledge, this type of structural content in a simplest dipeptide has not been observed earlier. The pentapeptide (WK5) is found to have four major secondary structural elements with 8% 310 helix, 14% poly-L-proline II, 8% beta sheet, and 14% turns. A 56% unordered structural population is also present for WK5. The presence of a significant population of 310 helix in a simple pentapeptide is rarely observed. Fluorescence anisotropy decay (FAD) measurements yielded reorientation times of 45 ps for NATA and 120 ps for WK5. The fluorescence anisotropy decay measurements reveal the size differences between the two peptides, NATA and WK5, with possible contributions from differences in shape, interactions with the environment, and conformational dynamics. All-atom molecular dynamics simulations were used to model the structures and motions of these two systems in solution. The predicted structures sampled by both peptides qualitatively agree with the experimental findings. Kinetic modeling with optimal dimensionality reduction suggests that the slowest dynamic processes in the dipeptide involve sidechain transitions occurring on a 1 ns timescale. The kinetics in the pentapeptide monitors the formation of a distorted helical structure from an extended conformation on a timescale of 10 ns. Modeling of the fluorescence anisotropy decay is found to be in good agreement with the measured data and correlates with the main contributions of the measured reorientation times to individual conformers, which we define as dynamic elements. In NATA, the FAD can be well represented as a sum of contributions from representative conformers. This is not the case in WK5, where our analysis suggests the existence of coupling between conformational dynamics and global tumbling. The current study involving detailed experimental measurements and atomically detailed modeling reveals the existence of specific secondary structural elements and novel dynamical features even in the simplest peptide systems

Detection of High Energy Ionizing Radiation using Deeply Depleted Graphene-Oxide-Semiconductor Junctions

Graphene's linear bandstructure and two-dimensional density of states provide an implicit advantage for sensing charge. Here, these advantages are leveraged in a deeply depleted graphene-oxide-semiconductor (D2GOS) junction detector architecture to sense carriers created by ionizing radiation. Specifically, the room temperature response of the silicon-based D2GOS junction is analyzed during irradiation with 20 MeV Si4+ ions. Detection was demonstrated for doses ranging from 12-1200 ions with device functionality maintained with no substantive degradation. To understand the device response, D2GOS pixels were characterized post-irradiation via a combination of electrical characterization, Raman spectroscopy, and photocurrent mapping. This combined characterization methodology underscores the lack of discernible damage caused by irradiation to the graphene while highlighting the nature of interactions between the incident ions and the silicon absorber.Comment: 15 pages, 4 figure

Magnetotransport Properties of Quasi-Free Standing Epitaxial Graphene Bilayer on SiC: Evidence for Bernal Stacking

We investigate the magnetotransport properties of quasi-free standing epitaxial graphene bilayer on SiC, grown by atmospheric pressure graphitization in Ar, followed by H$_2$ intercalation. At the charge neutrality point the longitudinal resistance shows an insulating behavior, which follows a temperature dependence consistent with variable range hopping transport in a gapped state. In a perpendicular magnetic field, we observe quantum Hall states (QHSs) both at filling factors ($\nu$) multiple of four ($\nu=4, 8, 12$), as well as broken valley symmetry QHSs at $\nu=0$ and $\nu=6$. These results unambiguously show that the quasi-free standing graphene bilayer grown on the Si-face of SiC exhibits Bernal stacking.Comment: 12 pages, 5 figure

Photo-physics and electronic structure of lateral graphene/MoS2 and metal/MoS2 junctions

Integration of semiconducting transition metal dichalcogenides (TMDs) into functional optoelectronic circuitries requires an understanding of the charge transfer across the interface between the TMD and the contacting material. Here, we use spatially resolved photocurrent microscopy to demonstrate electronic uniformity at the epitaxial graphene/molybdenum disulfide (EG/MoS2) interface. A 10x larger photocurrent is extracted at the EG/MoS2 interface when compared to metal (Ti/Au) /MoS2 interface. This is supported by semi-local density-functional theory (DFT), which predicts the Schottky barrier at the EG/MoS2 interface to be ~2x lower than Ti/MoS2. We provide a direct visualization of a 2D material Schottky barrier through combination of angle resolved photoemission spectroscopy with spatial resolution selected to be ~300 nm (nano-ARPES) and DFT calculations. A bending of ~500 meV over a length scale of ~2-3 micrometer in the valence band maximum of MoS2 is observed via nano-ARPES. We explicate a correlation between experimental demonstration and theoretical predictions of barriers at graphene/TMD interfaces. Spatially resolved photocurrent mapping allows for directly visualizing the uniformity of built-in electric fields at heterostructure interfaces, providing a guide for microscopic engineering of charge transport across heterointerfaces. This simple probe-based technique also speaks directly to the 2D synthesis community to elucidate electronic uniformity at domain boundaries alongside morphological uniformity over large areas

Stereodifferentiation in the intramolecular singlet excited state quenching of hydroxybiphenyl-tryptophan dyads

The photochemical processes occurring in diastereomeric dyads (S, S)-1 and (S, R)-1, prepared by conjugation of (S)-2-(2-hydroxy-1,1'-biphenyl-4-yl) propanoic acid ((S)-BPOH) with (S)- and (R)-Trp, have been investigated. In acetonitrile, the fluorescence spectra of (S, S)-1 and (S, R)-1 were coincident in shape and position with that of (S)-BPOH, although they revealed a markedly stereoselective quenching. Since singlet energy transfer from BPOH to Trp is forbidden (5 kcal mol(-1) uphill), the quenching was attributed to thermodynamically favoured (according to Rehm-Weller) electron transfer or exciplex formation. Upon addition of 20% water, the fluorescence quantum yield of (S)-BPOH decreased, while only minor changes were observed for the dyads. This can be explained by an enhancement of the excited state acidity of (S)-BPOH, associated with bridging of the carboxy and hydroxy groups by water, in agreement with the presence of water molecules in the X-ray structure of (S)-BPOH. When the carboxy group was not available for coordination with water, as in the methyl ester (S)-BPOHMe or in the dyads, this effect was prevented; accordingly, the fluorescence quantum yields did not depend on the presence or absence of water. The fluorescence lifetimes in dry acetonitrile were 1.67, 0.95 and 0.46 ns for (S)-BPOH, (S, S)-1 and (S, R)-1, respectively, indicating that the observed quenching is indeed dynamic. In line with the steady-state and time-resolved observations, molecular modelling pointed to a more favourable geometric arrangement of the two interacting chromophores in (S, R)-1. Interestingly, this dyad exhibited a folded conformation in the solid state.Financial support from the Spanish Government (CTQ2010-14882, BES-2008-003314, JCI-2011-09926, PR2011-0581), from the Generalitat Valenciana (Prometeo 2008/090) and from the Universitat Politecnica de Valencia (PAID 05-11, 2766) is gratefully acknowledged.Bonancía Roca, P.; Vayá Pérez, I.; Markovitsi, D.; Gustavsson, T.; Jiménez Molero, MC.; Miranda Alonso, MÁ. (2013). Stereodifferentiation in the intramolecular singlet excited state quenching of hydroxybiphenyl-tryptophan dyads. Organic and Biomolecular Chemistry. 11(12):1958-1963. https://doi.org/10.1039/c3ob27278hS195819631112Jiménez, M. C., Pischel, U., & Miranda, M. A. (2007). Photoinduced processes in naproxen-based chiral dyads. Journal of Photochemistry and Photobiology C: Photochemistry Reviews, 8(3), 128-142. doi:10.1016/j.jphotochemrev.2007.10.001Abad, S., Pischel, U., & Miranda, M. A. (2005). Wavelength-Dependent Stereodifferentiation in the Fluorescence Quenching of Asymmetric Naphthalene-Based Dyads by Amines. The Journal of Physical Chemistry A, 109(12), 2711-2717. doi:10.1021/jp047996aAbad, S., Vayá, I., Jiménez, M. C., Pischel, U., & Miranda, M. A. (2006). Diastereodifferentiation of Novel Naphthalene Dyads by Fluorescence Quenching and Excimer Formation. ChemPhysChem, 7(10), 2175-2183. doi:10.1002/cphc.200600337Bonancía, P., Vayá, I., Climent, M. J., Gustavsson, T., Markovitsi, D., Jiménez, M. C., & Miranda, M. A. (2012). Excited-State Interactions in Diastereomeric Flurbiprofen–Thymine Dyads. The Journal of Physical Chemistry A, 116(35), 8807-8814. doi:10.1021/jp3063838Paris, C., Encinas, S., Belmadoui, N., Climent, M. J., & Miranda, M. A. (2008). Photogeneration of 2-Deoxyribonolactone in Benzophenone−Purine Dyads. Formation of Ketyl−C1′ Biradicals. Organic Letters, 10(20), 4409-4412. doi:10.1021/ol801514vBelmadoui, N., Encinas, S., Climent, M. J., Gil, S., & Miranda, M. A. (2006). Intramolecular Interactions in the Triplet Excited States of Benzophenone–Thymine Dyads. Chemistry - A European Journal, 12(2), 553-561. doi:10.1002/chem.200500345Lhiaubet-Vallet, V., Boscá, F., & Miranda, M. A. (2007). Stereodifferentiating Drug−Biomolecule Interactions in the Triplet Excited State:  Studies on Supramolecular Carprofen/Protein Systems and on Carprofen−Tryptophan Model Dyads. The Journal of Physical Chemistry B, 111(2), 423-431. doi:10.1021/jp066968kVayá, I., Pérez-Ruiz, R., Lhiaubet-Vallet, V., Jiménez, M. C., & Miranda, M. A. (2010). Drug–protein interactions assessed by fluorescence measurements in the real complexes and in model dyads. Chemical Physics Letters, 486(4-6), 147-153. doi:10.1016/j.cplett.2009.12.091Seedher, N., & Bhatia, S. (2005). Mechanism of interaction of the non-steroidal antiinflammatory drugs meloxicam and nimesulide with serum albumin. Journal of Pharmaceutical and Biomedical Analysis, 39(1-2), 257-262. doi:10.1016/j.jpba.2005.02.031SEEDHER, N., & BHATIA, S. (2006). Reversible binding of celecoxib and valdecoxib with human serum albumin using fluorescence spectroscopic technique. Pharmacological Research, 54(2), 77-84. doi:10.1016/j.phrs.2006.02.008Nanda, R. K., Sarkar, N., & Banerjee, R. (2007). Probing the interaction of ellagic acid with human serum albumin: A fluorescence spectroscopic study. Journal of Photochemistry and Photobiology A: Chemistry, 192(2-3), 152-158. doi:10.1016/j.jphotochem.2007.05.018Zhou, B., Li, R., Zhang, Y., & Liu, Y. (2008). Kinetic analysis of the interaction between amphotericin B and human serum albumin using surface plasmon resonance and fluorescence spectroscopy. Photochemical & Photobiological Sciences, 7(4), 453. doi:10.1039/b717897bVahedian-Movahed, H., Saberi, M. R., & Chamani, J. (2011). Comparison of Binding Interactions of Lomefloxacin to Serum Albumin and Serum Transferrin by Resonance Light Scattering and Fluorescence Quenching Methods. Journal of Biomolecular Structure and Dynamics, 28(4), 483-502. doi:10.1080/07391102.2011.10508590Katrahalli, U., Kalalbandi, V. K. A., & Jaldappagari, S. (2012). The effect of anti-tubercular drug, ethionamide on the secondary structure of serum albumins: A biophysical study. Journal of Pharmaceutical and Biomedical Analysis, 59, 102-108. doi:10.1016/j.jpba.2011.09.013El-Kemary, M., Gil, M., & Douhal, A. (2007). Relaxation Dynamics of Piroxicam Structures within Human Serum Albumin Protein. Journal of Medicinal Chemistry, 50(12), 2896-2902. doi:10.1021/jm061421fTormo, L., Organero, J. A., Cohen, B., Martin, C., Santos, L., & Douhal, A. (2008). Dynamical and Structural Changes of an Anesthetic Analogue in Chemical and Biological Nanocavities. The Journal of Physical Chemistry B, 112(43), 13641-13647. doi:10.1021/jp803083yTardioli, S., Lammers, I., Hooijschuur, J.-H., Ariese, F., van der Zwan, G., & Gooijer, C. (2012). Complementary Fluorescence and Phosphorescence Study of the Interaction of Brompheniramine with Human Serum Albumin. The Journal of Physical Chemistry B, 116(24), 7033-7039. doi:10.1021/jp300055cVayá, I., Jiménez, M. C., & Miranda, M. A. (2007). Excited-State Interactions in Flurbiprofen−Tryptophan Dyads. The Journal of Physical Chemistry B, 111(31), 9363-9371. doi:10.1021/jp071301zCallis, P. R., & Burgess, B. K. (1997). Tryptophan Fluorescence Shifts in Proteins from Hybrid Simulations:  An Electrostatic Approach. The Journal of Physical Chemistry B, 101(46), 9429-9432. doi:10.1021/jp972436fLakowicz, J. R. (2000). On Spectral Relaxation in Proteins†¶‖. Photochemistry and Photobiology, 72(4), 421. doi:10.1562/0031-8655(2000)0722.0.co;2Schuler, B., & Eaton, W. A. (2008). Protein folding studied by single-molecule FRET. Current Opinion in Structural Biology, 18(1), 16-26. doi:10.1016/j.sbi.2007.12.003Shen, X., & Knutson, J. R. (2001). Subpicosecond Fluorescence Spectra of Tryptophan in Water. The Journal of Physical Chemistry B, 105(26), 6260-6265. doi:10.1021/jp010384vBeechem, J. M., & Brand, L. (1985). Time-Resolved Fluorescence of Proteins. Annual Review of Biochemistry, 54(1), 43-71. doi:10.1146/annurev.bi.54.070185.000355Callis, P. R. (1997). [7] 1La and 1Lb transitions of tryptophan: Applications of theory and experimental observations to fluorescence of proteins. Flourescence Spectroscopy, 113-150. doi:10.1016/s0076-6879(97)78009-1Basarić, N., & Wan, P. (2006). Competing Excited State Intramolecular Proton Transfer Pathways from Phenol to Anthracene Moieties. The Journal of Organic Chemistry, 71(7), 2677-2686. doi:10.1021/jo0524728Lukeman, M., & Wan, P. (2003). Excited-State Intramolecular Proton Transfer ino-Hydroxybiaryls:  A New Route to Dihydroaromatic Compounds. Journal of the American Chemical Society, 125(5), 1164-1165. doi:10.1021/ja029376yKeck, J., Kramer, H. E. A., Port, H., Hirsch, T., Fischer, P., & Rytz, G. (1996). Investigations on Polymeric and Monomeric Intramolecularly Hydrogen-Bridged UV Absorbers of the Benzotriazole and Triazine Class. The Journal of Physical Chemistry, 100(34), 14468-14475. doi:10.1021/jp961081hVollmer, F., & Rettig, W. (1996). Fluorescence loss mechanism due to large-amplitude motions in derivatives of 2,2′-bipyridyl exhibiting excited-state intramolecular proton transfer and perspectives of luminescence solar concentrators. Journal of Photochemistry and Photobiology A: Chemistry, 95(2), 143-155. doi:10.1016/1010-6030(95)04252-0Lukeman, M., & Wan, P. (2002). A New Type of Excited-State Intramolecular Proton Transfer:  Proton Transfer from Phenol OH to a Carbon Atom of an Aromatic Ring Observed for 2-Phenylphenol1. Journal of the American Chemical Society, 124(32), 9458-9464. doi:10.1021/ja0267831Jiménez, M. C., Miranda, M. A., Tormos, R., & Vayá, I. (2004). Characterisation of the lowest singlet and triplet excited states of S-flurbiprofen. Photochem. Photobiol. Sci., 3(11-12), 1038-1041. doi:10.1039/b408530bWeller, A. (1982). Photoinduced Electron Transfer in Solution: Exciplex and Radical Ion Pair Formation Free Enthalpies and their Solvent Dependence. Zeitschrift für Physikalische Chemie, 133(1), 93-98. doi:10.1524/zpch.1982.133.1.093Winget, P., Cramer, C. J., & Truhlar, D. G. (2004). Computation of equilibrium oxidation and reduction potentials for reversible and dissociative electron-transfer reactions in solution. Theoretical Chemistry Accounts, 112(4). doi:10.1007/s00214-004-0577-0ÇAKIR, S., & BÇER, E. (2010). SYNTHESIS, SPECTRAL CHARACTERIZATION AND ELECTROCHEMISTRY OF VANADIUM(V) COMPLEX WITH TRYPTOPHAN. Journal of the Chilean Chemical Society, 55(2). doi:10.4067/s0717-9707201000020002

Mechanism of the Very Efficient Quenching of Tryptophan Fluorescence in Human γD- and γS-Crystallins: The γ-Crystallin Fold May Have Evolved To Protect Tryptophan Residues from Ultraviolet Photodamage†

Proteins exposed to UV radiation are subject to irreversible photodamage through covalent modification of tryptophans (Trps) and other UV-absorbing amino acids. Crystallins, the major protein components of the vertebrate eye lens that maintain lens transparency, are exposed to ambient UV radiation throughout life. The duplicated β-sheet Greek key domains of β- and γ-crystallins in humans and all other vertebrates each have two conserved buried Trps. Experiments and computation showed that the fluorescence of these Trps in human γD-crystallin is very efficiently quenched in the native state by electrostatically enabled electron transfer to a backbone amide [Chen et al. (2006) Biochemistry 45, 11552−11563]. This dispersal of the excited state energy would be expected to minimize protein damage from covalent scission of the excited Trp ring. We report here both experiments and computation showing that the same fast electron transfer mechanism is operating in a different crystallin, human γS-crystallin. Examination of solved structures of other crystallins reveals that the Trp conformation, as well as favorably oriented bound waters, and the proximity of the backbone carbonyl oxygen of the n − 3 residues before the quenched Trps (residue n), are conserved in most crystallins. These results indicate that fast charge transfer quenching is an evolved property of this protein fold, probably protecting it from UV-induced photodamage. This UV resistance may have contributed to the selection of the Greek key fold as the major lens protein in all vertebrates.National Eye Institute (Grant EY 015834

Low-fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerase ζ

To probe Pol ζ functions in vivo via its error signature, here we report the properties of Saccharomyces cerevisiae Pol ζ in which phenyalanine was substituted for the conserved Leu-979 in the catalytic (Rev3) subunit. We show that purified L979F Pol ζ is 30% as active as wild-type Pol ζ when replicating undamaged DNA. L979F Pol ζ shares with wild-type Pol ζ the ability to perform moderately processive DNA synthesis. When copying undamaged DNA, L979F Pol ζ is error-prone compared to wild-type Pol ζ, providing a biochemical rationale for the observed mutator phenotype of rev3-L979F yeast strains. Errors generated by L979F Pol ζ in vitro include single-base insertions, deletions and substitutions, with the highest error rates involving stable misincorporation of dAMP and dGMP. L979F Pol ζ also generates multiple errors in close proximity to each other. The frequency of these events far exceeds that expected for independent single changes, indicating that the first error increases the probability of additional errors within 10 nucleotides. Thus L979F Pol ζ, and perhaps wild-type Pol ζ, which also generates clustered mutations at a lower but significant rate, performs short patches of processive, error-prone DNA synthesis. This may explain the origin of some multiple clustered mutations observed in vivo

Carotenoid Distribution in Living Cells of Haematococcus pluvialis (Chlorophyceae)

Haematococcus pluvialis is a freshwater unicellular green microalga belonging to the class Chlorophyceae and is of commercial interest for its ability to accumulate massive amounts of the red ketocarotenoid astaxanthin (3,3′-dihydroxy-β,β-carotene-4,4′-dione). Using confocal Raman microscopy and multivariate analysis, we demonstrate the ability to spectrally resolve resonance–enhanced Raman signatures associated with astaxanthin and β-carotene along with chlorophyll fluorescence. By mathematically isolating these spectral signatures, in turn, it is possible to locate these species independent of each other in living cells of H. pluvialis in various stages of the life cycle. Chlorophyll emission was found only in the chloroplast whereas astaxanthin was identified within globular and punctate regions of the cytoplasmic space. Moreover, we found evidence for β-carotene to be co-located with both the chloroplast and astaxanthin in the cytosol. These observations imply that β-carotene is a precursor for astaxanthin and the synthesis of astaxanthin occurs outside the chloroplast. Our work demonstrates the broad utility of confocal Raman microscopy to resolve spectral signatures of highly similar chromophores in living cells