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Faraday Discussions

Elena Lesca, Valérie Panneels, Gebhard F X Schertler
G protein coupled receptors (GPCRs) are a key family of membrane proteins in all eukaryotes and also very important drug targets for medical intervention. The extensively studied visual pigment rhodopsin is a prime example of a family A GPCR. Its chromophore ligand retinal is covalently linked to a lysine in helix seven forming a protonated Schiff base. Interestingly, this is the same situation in other-non-GPCR-retinal proteins, like the prototype light-driven microbial proton pump bacteriorhodopsin, albeit there is no (or only a very remote) phylogenetical link...
February 7, 2018: Faraday Discussions
Veniamin A Borin, Christian Wiebeler, Igor Schapiro
The primary photochemical reaction of the green-absorbing proteorhodopsin is studied by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The simulations are based on a homology model derived from the blue-absorbing proteorhodopsin crystal structure. The geometry of retinal and the surrounding sidechains in the protein binding pocket were optimized using the QM/MM method. Starting from this geometry the isomerization was studied with a relaxed scan along the C13[double bond, length as m-dash]C14 dihedral...
February 2, 2018: Faraday Discussions
D Agathangelou, Y Orozco-Gonzalez, M Del Carmen Marín, P P Roy, J Brazard, H Kandori, K-H Jung, J Léonard, T Buckup, N Ferré, M Olivucci, S Haacke
Anabaena sensory rhodopsin (ASR) is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR photo-isomerization reaction, ASR is a model system allowing to study, within the same protein, the protein-PSBR interactions for two different PSBR conformers at the same time...
February 1, 2018: Faraday Discussions
Subhas C Bera, Tapas Paul, A N Sekar Iyengar, Padmaja P Mishra
We have investigated the isomerization dynamics and plausible energy landscape of 4-way Holliday junctions (4WHJs) bound to integration host factor (IHF, a DNA binding protein), considering the effect of applied external force, by single-molecule FRET methods. A slowing down of the forward as well as the backward rates of the isomerization process of the protein bound 4WHJ has been observed under the influence of an external force, which indicates an imposed restriction on the conformational switching. This has also been reflected by an increase in rigidity, as observed from the increase in the single-molecule FRET (smFRET)-anisotropy values (0...
January 31, 2018: Faraday Discussions
Yuyuan Zhang, Kimberly de La Harpe, Mahesh Hariharan, Bern Kohler
The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs...
January 31, 2018: Faraday Discussions
Shaina Dhamija, Bhisham Thakur, Purnananda Guptasarma, Arijit K De
Fluorescent proteins exhibit interesting excited state photochemistry, leading to bright fluorescence emission that renders their versatile biological role and wide use as biomarkers. A molecular-level mechanism of the excited state dynamics is desirable to pinpoint the origin of the bright fluorescence of these proteins. Here we present studies on a yellow fluorescent protein variant, Venus, and investigate the photophysics behind the dual fluorescence emission upon UV excitation. Based on our studies, we propose that the unique nature of the potential energy surface is responsible for the observation of minor fluorescence in Venus which is not seen in wild type GFP...
January 30, 2018: Faraday Discussions
Akos Banyasz, Tiia Ketola, Lara Martínez-Fernández, Roberto Improta, Dimitra Markovitsi
There is increasing evidence that the direct absorption of photons with energies that are lower than the ionization potential of nucleobases may result in oxidative damage to DNA. The present work, which combines nanosecond transient absorption spectroscopy and quantum mechanical calculations, studies this process in alternating adenine-thymine duplexes (AT)n. We show that the one-photon ionization quantum yield of (AT)10 at 266 nm (4.66 eV) is (1.5 ± 0.3) × 10-3. According to our PCM/TD-DFT calculations carried out on model duplexes composed of two base pairs, (AT)1 and (TA)1, simultaneous base pairing and stacking does not induce important changes in the absorption spectra of the adenine radical cation and deprotonated radical...
January 26, 2018: Faraday Discussions
Brennan Ashwood, Luis A Ortiz-Rodríguez, Carlos E Crespo-Hernández
S6-Methylthioinosine and O6-methylguanosine are byproducts resulting from the enzymatic reactions of sulfur-substituted prodrugs in cells and from the interaction of alkylating agents with cellular DNA, respectively. Their photochemistry has not been investigated, and it is currently unknown whether light absorption by these byproducts may pose any threat to the cell. In this contribution, their photoinduced processes upon absorption of UVB radiation are reported using broadband transient absorption spectroscopy...
January 26, 2018: Faraday Discussions
Lara Martinez-Fernandez, Roberto Improta
The energetics of the two main proton coupled electron transfer processes that could occur in DNA are determined by means of time dependent-DFT calculations, using the M052X functional and the polarizable continuum model to include solvent effect. This approach has been applied to fragments of GC and AT alternated duplexes containing up to 4 base pairs. In GC DNA, intra-strand G → C charge transfer (CT) can trigger inter-strand Proton Transfer (PT) involving the C anion, since the reaction is exothermic and the related energy barrier is <0...
January 25, 2018: Faraday Discussions
Juntai Liu, Vincent M Friebe, David J K Swainsbury, Lucy I Crouch, David A Szabo, Raoul N Frese, Michael R Jones
Reaction centre/light harvesting proteins such as the RCLH1X complex from Rhodobacter sphaeroides carry out highly quantum-efficient conversion of solar energy through ultrafast energy transfer and charge separation, and these pigment-proteins have been incorporated into biohybrid photoelectrochemical cells for a variety of applications. In this work we demonstrate that, despite not being able to support normal photosynthetic growth of Rhodobacter sphaeroides, an engineered variant of this RCLH1X complex lacking the PufX protein and with an enlarged light harvesting antenna is unimpaired in its capacity for photocurrent generation in two types of bio-photoelectrochemical cells...
January 24, 2018: Faraday Discussions
Pratip Chakraborty, Tolga N V Karsili, Barbara Marchetti, Spiridoula Matsika
DNA/RNA photohydrates represent a class of well-known biomolecular lesions formed by the absorption of near- to mid-UV light. They are formed via a photoinduced nucleophilic hydrolysis reaction in which water is split (via nucleobase sensitisation) into H + OH radicals. These nascent radicals can then add across C5[double bond, length as m-dash]C6, saturating the preexisting double bond. If unrepaired, such lesions can lead to mutagenic carcinogenesis, which is responsible for several forms of cancer. Using high-level electronic structure theory (CASPT2), we map the key excited-state reaction paths associated with the reactivity of DNA (guanine and thymine) and RNA (uracil) nucleobases with water...
January 24, 2018: Faraday Discussions
Samsuzzoha Mondal, Amitava Chandra, Ravindra Venkatramani, Ankona Datta
We present a systematic experimental and computational study of phospholipid induced peptide coil-helix transitions which are relevant in the context of proteins mediating cytoskeletal rearrangement via membrane binding. We developed a sensitive Förster resonance energy transfer (FRET) based assay to address whether coil-helix transitions in phospholipid binding motifs of actin-binding proteins can be induced by physiologically-relevant concentrations (1-20 μM) of phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) phospholipids...
January 24, 2018: Faraday Discussions
Mohd Ziauddin Ansari, Amrendra Kumar, Dileep Ahari, Anurag Priyadarshi, Padmavathi Lolla, Rashna Bhandari, Rajaram Swaminathan
Protein Charge Transfer Spectra (ProCharTS) originate when charged amino/carboxylate groups in the side chains of Lys/Glu act as electronic charge acceptors/donors for photoinduced charge transfer either from/to the polypeptide backbone or to each other. The absorption band intensities in ProCharTS at wavelengths of 250-800 nm are dependent on the 3D spatial proximity of these charged functional groups across the protein. Intrinsically disordered proteins (IDPs) are an important class of proteins involved in signalling and regulatory functions in the eukaryotic cell...
January 24, 2018: Faraday Discussions
Kristen E Brown, Arunoday P N Singh, Yi-Lin Wu, Lin Ma, Ashutosh K Mishra, Brian T Phelan, Ryan M Young, Frederick D Lewis, Michael R Wasielewski
The ground- and excited-state electronic interactions between the nucleobase analog 8-(4'-phenylethynyl)deoxyguanosine, EG, with natural nucleobases and 7-deazaguanine, as well as between adjacent EG base analogs, have been characterized using a combination of steady-state spectroscopy and time-resolved fluorescence, absorption, and stimulated Raman spectroscopies. The properties of the nucleoside EG-H2 are only weakly perturbed upon incorporation into synthetic DNA hairpins in which thymine, cytosine or adenine are the bases flanking EG...
January 24, 2018: Faraday Discussions
Sherin Joy, Vommina V Sureshbabu, Ganga Periyasamy
Chemical modifications at various peptide positions result in peptidomimetics with unique physical and chemical properties that can be used for a range of applications. Among many peptidomimetics, ureidopeptides are interesting due to their ability to act as donor-bridge-acceptor systems through which charge transfer occurs in one direction and can be triggered by an electrochemical pulse without perturbing the nuclear position. In this regard, some UP mimetics with different chromophoric units are studied in this work to understand their role using DFT based methods...
January 23, 2018: Faraday Discussions
I Mandal, S Paul, R Venkatramani
The absorption of light by proteins can induce charge transfer (CT) transitions in the UV-visible range of the electromagnetic spectrum. Metal-ligand complexes or active site prosthetic groups which absorb in the visible region exhibit prominent CT transitions. Furthermore, the protein backbone also exhibits CT transitions in the far UV range. In this manuscript, we present a detailed computational study of new near UV-visible CT transitions that involve amino acids with charged side chains. Specifically, using time dependent density functional theory calculations, we examine the absorption spectra of naturally charged amino acids (Lys, Glu, Arg, Asp and His), extracted from solution phase protein structures generated by classical molecular dynamics simulations, and phosphorylated amino acids (Tyr, Thr and Ser) from experimentally determined protein structures...
January 23, 2018: Faraday Discussions
Sandeepa Kulala Vittala, Joshy Joseph
Herein we discuss the differential interaction of three monosubstituted fullerene derivatives possessing pyridinium, aniline or phenothiazine end groups (F-Py, F-An and F-PTz, respectively) with calf thymus DNA (CT-DNA), probed via spectroscopic and imaging techniques. The pyridinium derivative, F-Py becomes molecularly dissolved in 10% DMSO-PBS and interacts with CT-DNA via groove binding and electrostatic interactions, leading to the initial condensation of CT-DNA into micrometer sized aggregates and subsequent precipitation...
January 23, 2018: Faraday Discussions
Angelo Giussani, Irene Conti, Artur Nenov, Marco Garavelli
The UVB-induced photomechanism leading the carbonyl group of a thymine nucleobase to react with the carbon-carbon double bond of a consecutive thymine nucleobase in a DNA strand to form the thymine-thymine (6-4) photodamage adduct remains poorly understood. Key questions remain unanswered, concerning both the intrinsic features of the photoreaction (such as the contribution (or not) of triplet states, the nature of the involved states and the time-scale of the photoprocess) and the role played by the non-reactive surroundings of the two reactive pyrimidine nucleobases (such as the nature of the flanked nucleobases and the flexibility of the whole DNA molecule)...
January 23, 2018: Faraday Discussions
Javier Segarra-Martí, Vishal K Jaiswal, Ana Julieta Pepino, Angelo Giussani, Artur Nenov, Shaul Mukamel, Marco Garavelli, Ivan Rivalta
A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows us to analyse ground state dynamics and to sample and measure different conformations attained by flexible molecular systems in solution. An explicit mixed quantum mechanics/molecular mechanics (QM/MM) approach is employed for the evaluation of the necessary electronic excited state energies and transition dipole moments. The method is applied towards a study of the highly flexible water-solvated adenine-adenine monophosphate (ApA), a system featuring two interacting adenine moieties that display various intermolecular arrangements, known to deeply affect their photochemical outcome...
January 23, 2018: Faraday Discussions
Hirak Chakraborty, Md Jafurulla, Andrew H A Clayton, Amitabha Chattopadhyay
The oligomerization of G protein-coupled receptors (GPCRs) represents an important process in GPCR function and drug discovery. We have addressed cholesterol-dependent oligomerization state of the serotonin1A receptor, a representative GPCR and an important drug target, utilizing photobleaching image correlation spectroscopy (pbICS). pbICS allows determination of oligomeric state of membrane receptors since change in cluster density upon photobleaching is dependent on the oligomeric state. Our results show that oligomeric state of the serotonin1A receptor is modulated by cell membrane cholesterol and a trimeric population of the receptor prevails in control (normal) cholesterol conditions...
January 23, 2018: Faraday Discussions
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