Search results for " Biophysics"
showing 10 items of 136 documents
Glutamate 270 plays an essential role in K+-activation and domain closure ofThermus thermophilusisopropylmalate dehydrogenase
2014
The mutant E270A of Thermus thermophilus 3-isopropylmalate dehydrogenase exhibits largely reduced (∼1%) catalytic activity and negligible activation by K(+) compared to the wild-type enzyme. A 3-4 kcal/mol increase in the activation energy of the catalysed reaction upon this mutation could also be predicted by QM/MM calculations. In the X-ray structure of the E270A mutant a water molecule was observed to take the place of K(+). SAXS and FRET experiments revealed the essential role of E270 in stabilisation of the active domain-closed conformation of the enzyme. In addition, E270 seems to position K(+) into close proximity of the nicotinamide ring of NAD(+) and the electron-withdrawing effect…
Quenching of fluorescein-conjugated lipids by antibodies. Quantitative recognition and binding of lipid-bound haptens in biomembrane models, formatio…
1992
Three model biomembrane systems, monolayers, micelles, and vesicles, have been used to study the influence of chemical and physical variables of hapten presentation at membrane interfaces on antibody binding. Hapten recognition and binding were monitored for the anti-fluorescein monoclonal antibody 4–4-20 generated against the hapten, fluorescein, in these membrane models as a function of fluorescein-conjugated lipid architecture. Specific recognition and binding in this system are conveniently monitored by quenching of fluorescein emission upon penetration of fluorescein into the antibody's active site. Lipid structure was shown to play a large role in affecting antibody quenching. Interes…
Simple molecular model for the binding of antibiotic molecules to bacterial ion channels
2003
A molecular model aimed at explaining recent experimental data by Nestorovich et al. [Proc. Natl. Acad. Sci. USA 99, 9789 (2002)] on the interaction of ampicillin molecules with the constriction zone in a channel of the general bacterial porin, OmpF (outer membrane protein F), is presented. The model extends T. L. Hill’s theory for intermolecular interactions in a pair of binding sites [J. Am. Chem. Soc. 78, 3330 (1956)] by incorporating two binding ions and two pairs of interacting sites. The results provide new physical insights on the role of the complementary pattern of the charge distributions in the ampicillin molecule and the narrowest part of the channel pore. Charge matching of int…
Combining Pharmacokinetics and Vibrational Spectroscopy: MCR-ALS Hard-and-Soft Modelling of Drug Uptake In Vitro Using Tailored Kinetic Constraints
2022
Raman microspectroscopy is a label-free technique which is very suited for the investigation of pharmacokinetics of cellular uptake, mechanisms of interaction, and efficacies of drugs in vitro. However, the complexity of the spectra makes the identification of spectral patterns associated with the drug and subsequent cellular responses difficult. Indeed, multivariate methods that relate spectral features to the inoculation time do not normally take into account the kinetics involved, and important theoretical information which could assist in the elucidation of the relevant spectral signatures is excluded. Here, we propose the integration of kinetic equations in the modelling of drug uptake…
Endo-/exo- and halogen-bonded complexes of conformationally rigid C-ethyl-2-bromoresorcinarene and aromatic N-oxides
2017
The host-guest complexes of conformationally rigid C-ethyl-2-bromoresorcinarene with aromatic N-oxides were studied using single crystal X-ray crystallography. Unlike that of the conformationally more flexible C-ethyl-2-methylresorcinarene, the C-ethyl-2-bromoresorcinarene cavity forms endo-complexes only with the small pyridine-N-oxides, such as pyridine N-oxide, 2-methyl-, 3-methyl- and 4-methylpyrdine N-oxide, and quinoline N-oxide. The larger 2,4,6-trimethylpyridine, 4-phenylpyridine and isoquinoline N-oxide, and 4,4-bipyridine N,N′-dioxide and 1,3-bis(4-pyridyl)propane N,N′-dioxide do not fit into the host cavity. Instead endo-acetone complexes are formed. Remarkably, differing from th…
Highly selective detection of Epinephrine at oxidized Single-Wall Carbon Nanohorns modified Screen Printed Electrodes (SPEs)
2014
Oxidized Single-Wall Carbon Nanohorns (o-SWCNHs) were used, for the first time, to assemble chemically modified Screen Printed Electrodes (SPEs) selective towards the electrochemical detection of Epinephrine (Ep), in the presence of Serotonine-5-HT (S-5HT), Dopamine (DA), Nor-Epineprhine (Nor-Ep), Ascorbic Acid (AA), Acetaminophen (Ac) and Uric Acid (UA). The Ep neurotransmitter was detected by using Differential Pulse Voltammetry (DPV), in a wide linear range of concentration (2-2500 μM) with high sensitivity (55.77 A M(-1) cm(-2)), very good reproducibility (RSD% ranging from 2 to 10 for different SPEs), short response time for each measurement (only 2s) and low detection of limit (LOD=0.…
Recent advances in the development of high-resolution 3D cadmium-zinc-telluride drift strip detectors.
2020
In the last two decades, great efforts have been made in the development of 3D cadmium–zinc–telluride (CZT) detectors operating at room temperature for gamma-ray spectroscopic imaging. This work presents the spectroscopic performance of new high-resolution CZT drift strip detectors, recently developed at IMEM-CNR of Parma (Italy) in collaboration with due2lab (Italy). The detectors (19.4 mm × 19.4 mm × 6 mm) are organized into collecting anode strips (pitch of 1.6 mm) and drift strips (pitch of 0.4 mm) which are negatively biased to optimize electron charge collection. The cathode is divided into strips orthogonal to the anode strips with a pitch of 2 mm. Dedicated pulse processing analysis…
Modeling Changes for SHOIN(D) Ontologies: An Exhaustive Structural Model
2013
Ontology development starts with a rigorous ontological analysis that provides a conceptualization of the domain to model agreed by the community. An ontology, specified in a formal language, approximates the intended models of this conceptualization. It needs then to be revised and refined until an ontological commitment is found. Also ulterior updates, responding to changes in the domain and/or the conceptualization, are expected to occur throughout the ontology life cycle. To handle a consistent application of changes, a couple of ontology evolution methodologies have been proposed. Maintaining the structural consistency is one of the ontology evolution criteria. It implies modeling chan…
Characterization of antigenic epitopes of potato virus Y.
1993
Immunochemical analysis of overlapping synthetic hexapeptides covering the entire length of the coat protein of potato virus Y (PVY) revealed immunodominant regions both at the N-terminal and at the C-terminal end of the coat protein. Immunization of rabbits with synthetic peptides representing N- and C-terminal regions of the coat protein resulted in production of antibodies that reacted with PVY. Antigenicity of PVY peptides was found to correlate with predicted beta turns, with hydrophilicity and with predicted chain flexibility. Characterization of the immunochemical properties of PVY will facilitate the development of detection methods for potyviruses.
Tunable Optical Antennas Using Vanadium Dioxide Metal-Insulator Phase Transitions
2019
Here, we investigate the possibility of exploiting the insulator-to-metal transition in vanadium dioxide (VO2) to tune and optically control the resonances of dipole nanoantennas in the visible near-infrared region. We compare the results obtained in the case of antennas completely made by VO2 with those of previous works and highlight the key role of the substrate to perform dynamical tuning. We also present a highly efficient configuration composed of dipole gold antenna loaded with VO2 and give some general guidelines to optimally exploit phase transitions to tune nanodevices.