Search results for " Biophysics"
showing 10 items of 136 documents
Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser
2014
We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions. peerReviewed
Taming conformational heterogeneity in and with vibrational circular dichroism spectroscopy
2019
Chemical science 10, 7680 -7689 (2019). doi:10.1039/C9SC02866H
A fast solver for nonlocal electrostatic theory in biomolecular science and engineering
2011
Biological molecules perform their functions surrounded by water and mobile ions, which strongly influence molecular structure and behavior. The electrostatic interactions between a molecule and solvent are particularly difficult to model theoretically, due to the forces' long range and the collective response of many thousands of solvent molecules. The dominant modeling approaches represent the two extremes of the trade-off between molecular realism and computational efficiency: all-atom molecular dynamics in explicit solvent, and macroscopic continuum theory (the Poisson or Poisson--Boltzmann equation). We present the first fast-solver implementation of an advanced nonlocal continuum theo…
Comparison of complex fractionated atrial electrograms at cellular scale using numerical and experimental models.
2010
This study investigates the existence of the pseudo complex fractionated atrial electrogram (CFAE) at cellular level. Our assumptions are based on the fact that CFAEs are linked to the generation of the spiral waves. These are created using a numerical model and an experimental model of in vitro culture of neonatal rats cardiac cells. Pseudo bipolar electrograms resulting from these two models are compared qualitatively and some patterns could be identified as CFAE signature.
Energy Recovery of Multiple Charge Sharing Events in Room Temperature Semiconductor Pixel Detectors
2021
Multiple coincidence events from charge-sharing and fluorescent cross-talk are typical drawbacks in room-temperature semiconductor pixel detectors. The mitigation of these distortions in the measured energy spectra, using charge-sharing discrimination (CSD) and charge-sharing addition (CSA) techniques, is always a trade-off between counting efficiency and energy resolution. The energy recovery of multiple coincidence events is still challenging due to the presence of charge losses after CSA. In this work, we will present original techniques able to correct charge losses after CSA even when multiple pixels are involved. Sub-millimeter cadmium–zinc–telluride (CdZnTe or CZT) pixel detectors we…
A novel pro-apoptotic role of zinc octacarboxyphthalocyanine in melanoma me45 cancer cell's photodynamic therapy (PDT)
2018
Abstract Zn-based phthalocyanine acts as drug or photosensitizer in photodynamic therapy (PDT) for the treatment of cancer cells. The activated zinc octacarboxyphthalocyanine (ZnPcOC) reacts with oxygen, to generate reactive oxygen species for the damage of melanoma cancer cells, Me45. This in vitro study aimed at investigating the cytotoxic effects of different concentrations of ZnPcOC activated with a diode laser (λ = 685 nm) on Me45, and normal human fibroblast cells, NHDF. To perform this study 104 cells/ml were seeded in 96-well plates and allowed to attach overnight, after which cells were treated with different concentrations of ZnPcOC (10, 20 and 30 μM). After 4 h, cells were irradi…
According to the CPLL proteome sheriffs, not all aperitifs are created equal!
2014
Combinatorial peptide ligand libraries (CPLLs) have been adopted for investigating the proteome of a popular aperitif in Northern Italy, called "Amaro Branzi", stated to be an infusion of a secret herbal mixture, of which some ingredients are declared on the label, namely Angelica officinalis, Gentiana lutea and orange peel, sweetened by a final addition of honey. In order to assess the genuineness of this commercial liqueur, we have prepared extracts of the three vegetable ingredients, assessed their proteomes, and compared them to the one found in the aperitif. The amaro's proteome was identified via prior capture with CPLLs at two different pH values (2.2 and 4.8). Via mass spectrometry …
Molecular determinants of large cargo transport into the nucleus
2020
Nucleocytoplasmic transport is tightly regulated by the nuclear pore complex (NPC). Among the thousands of molecules that cross the NPC, even very large (>15 nm) cargoes such as pathogens, mRNAs and pre-ribosomes can pass the NPC intact. For these cargoes, there is little quantitative understanding of the requirements for their nuclear import, especially the role of multivalent binding to transport receptors via nuclear localisation sequences (NLSs) and the effect of size on import efficiency. Here, we assayed nuclear import kinetics of 30 large cargo models based on four capsid-like particles in the size range of 17–36 nm, with tuneable numbers of up to 240 NLSs. We show that the requireme…
In silico molecular investigations of pyridine N-Oxide compounds as potential inhibitors of SARS-CoV-2: 3D QSAR, molecular docking modeling, and ADME…
2020
The new coronavirus SARS-CoV-2 virus is causing a severe pneumonia in human, provoking the serious outbreak epidemic CoV-2. Since its appearance in Wuhan, China on December 2019, CoV-2 becomes the biggest challenge the world is facing today, including the discovery of antiviral drug for SARS-CoV-2. In this study, the potential inhibitory of a class of human SARS inhibitors, namely pyridine N-oxide derivatives, against CoV-2 was addressed by quantitative structure-activity relationship 3 D-QSAR. The reliable CoMSIA developed model of 110 pyridine N-oxide based-antiviral compounds, showed Q
The membrane anchor of microsomal epoxide hydrolase from human, rat, and rabbit displays an unexpected membrane topology.
1997
The microsomal epoxide hydrolase (mEH) and cytochrome P450s catalyze the sequential formation of carcinogenic metabolites. According to one algorithm for predicting the membrane topology of proteins, the human, the rabbit, and the rat mEH should adopt a type II topology. The type II topology is also predicted by a recently established neuronal network which is trained to recognize signal peptides with very high accuracy. In contrast to these predictions we find, based on N-glycosylation analysis in a cell-free and in a cellular system, that the membrane anchor of human, rat, and rabbit mEH displays a type I topology. This result is correctly predicted by the positive inside rule in which ne…