Search results for "conformation"

Role of THAP11 in the transcriptional regulation and chromatin structure of the human MYC locus

C-MYC è uno dei geni più frequentemente deregolati nei tumori umani. Una comprensione dettagliata della regolazione trascrizionale di questo gene è essenziale per comprendere meglio gli aspetti molecolari delle sue diverse funzioni. Usando diversi tipi di analisi (EMSA, 2D-IPG e analisi MALDI), nei nostri laboratori abbiamo caratterizzato un elemento con funzione di enhancer blocker (HB2.8) situato 32Kb valle del gene c-MYC . Saggi di trasfezione transiente e stabile hanno dimostrato che l'attività dell’elemento enhancer-blocker può essere attribuita esclusivamente ad un sub-regione di DNA di circa 400 bp chiamato AA0.4. Ulteriori test per valutare l'attività enhancer blocker di questa sequ…

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.

2019

Abstract Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues. Results While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are…

Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering (vol 5, pg 881, 2008)

2008

Tracking Ca2+ ATPase intermediates in real time by x-ray solution scattering

2020

Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) transporters regulate calcium signaling by active calcium ion reuptake to internal stores. Structural transitions associated with transport have been characterized by x-ray crystallography, but critical intermediates involved in the accessibility switch across the membrane are missing. We combined time-resolved x-ray solution scattering (TR-XSS) experiments and molecular dynamics (MD) simulations for real-time tracking of concerted SERCA reaction cycle dynamics in the native membrane. The equilibrium [Ca2] E1 state before laser activation differed in the domain arrangement compared with crystal structures, and following laser-induced release o…

Influence of metal ions on thermal aggregation of bovine serum albumin: aggregation kinetics and structural changes

2009

Metal ions are implicated in protein aggregation processes of several neurodegenerative pathologies. In this work the effects of Cu(II) and Zn(II) ions on heat-induced structural modifications of bovine serum albumin (BSA) were studied, with the aim of delineating the role of these ions in the early stages of proteins aggregation kinetics. A joint application of different techniques was used. The aggregate growth was followed by dynamic light scattering measurements, whereas the conformational changes occurring in the protein structure were monitored by Raman and IR spectroscopy. Both in absence and in presence of metal ions, heating treatment gave rise to b-structures to the detriment of a…

Lower rim arylation of calix[n]arenes with extended perfluorinated domains

2006

Abstract Exhaustive O-arylation of p-tert -butylcalix[ n ]arenes 2 ( n  = 4–8) with an excess of 3-pentadecafluoroheptyl-5-pentafluorophenyl-1,2,4-oxadiazole 3 and K 2 CO 3 in refluxing acetonitrile provides an easy entry to a new family of perfluorinated calix[ n ]arenes 1 . The cyclic tetramer furnishes a mixture of cone , partial cone , and 1,2-alternate conformers, while the larger macrocycles afford single products. The structures of all new compounds are substantiated by NMR techniques and MALDI-TOF mass spectral data. Single-crystal X-ray diffraction studies on the pentamer derivative 1b reveal a distorted cone-in conformation of the calixarene cup.

Activity of the dietary flavonoid, apigenin, against multidrug-resistant tumor cells as determined by pharmacogenomics and molecular docking

2015

Apigenin is a common dietary flavonoid with considerable cytotoxic activity in vitro and in vivo. Despite many mechanistic studies, less is known about resistance factors hampering apigenin's activity. We investigated the ATP-binding cassette (ABC) transporters BCRP/ABCG2, P-glycoprotein/ABCB1 and its close relative ABCB5. Multidrug-resistant cells overexpressing these ABC transporters were not cross-resistant toward apigenin. Moreover, apigenin inhibited not only P-glycoprotein but also BCRP by increasing cellular uptake of doxorubicin and synergistic inhibition of cell viability in combination with doxorubicin or docetaxel in multidrug-resistant cells. To perform in silico molecular docki…

A blend of polyphenolic compounds explains the stimulatory effect of red wine on human endothelial NO synthase

2005

A high intake of polyphenolic compounds is likely to have beneficial effects on the cardiovascular system. Especially red wine is a rich source of polyphenols, and we have previously shown that French red wine upregulates eNOS, a protective enzyme in the cardiovascular system. The current study tested (poly)phenolic constituents of red wine for their ability to enhance eNOS expression (and the activity of a 3.5-kb human eNOS promoter) in human EA.hy 926 endothelial cells. Of the compounds tested, we found 3,4',5-trihydroxy-trans-stilbene (trans-resveratrol) to be the most efficacious stimulator of eNOS expression (and eNOS transcription), but this compound alone could not explain the total …

Complete 1H and 13C NMR assignments of clerodane diterpenoids of Salvia splendens.

2006

Unambiguous and complete assignments of 1H and 13C NMR chemical shifts for five clerodane diterpenes, four of them isolated from Salvia splendens (salviarin, splendidin and splenolides A and B) and one obtained by acetylation of splenolide A, are presented. The assignments are based on 2D shift-correlated [1H,1H–COSY, 1H,13C-gHSQC–1J(C,H) and 1H,13C-gHMBC-nJ(C,H) (n = 2 and 3)] and nuclear Overhauser effect (NOE) experiments. The conformation of the rings of these compounds is supported by the 3J(H,H) values and NOE results. Copyright © 2006 John Wiley & Sons, Ltd.

Reversible switching of the electronic ground state in a pentacoordinated Cu(ii) complex.

2013

International audience; An easy reversible switching of the electronic ground state in a pentacoordinated copper(ii) complex is reported for the first time. The simple protonation of a carboxylic group in a Cu(ii) complex with a {dx(2)-y(2)}(1) electronic configuration leads to a flip of the ground electronic configuration from {dx(2)-y(2)}(1) to {dz(2)}(1) in the metal ion.