Search results for "conformation"
showing 10 items of 1414 documents
Structure-dynamics-function relationships in Asian elephant (Elephas maximus) myoglobin. An optical spectroscopy and flash photolysis study on functi…
1993
In this work we report the thermal behavior (10–300 K) of the Soret band lineshape of deoxy and carbonmonoxy derivatives of Asian elephant (Elephas maximus) and horse myoglobins together with their carbon monoxide recombination kinetics after flash photolysis; the results are compared to analogous data relative to sperm whale myoglobin. The Soret band profile is modeled as a Voigt function that accounts for the coupling with high and low frequency vibrational modes, while inhomogeneous broadening is taken into account with suitable distributions of purely electronic transition frequencies. This analysis makes it possible to isolate the various contributions to the overall lineshape that; in…
Interactions between aroma compounds and beta-lactoglobulin in the heat-induced molten globule state
2010
; he present study aims to elucidate the binding of small hydrophobic ligands onto the molten globule state of β-lactoglobulin (BLG). The conversion of the native BLG into a molten globule state was induced by heat treatment at acidic pH. The molten globule state was evidenced by far and near-UV circular dichroism spectra. β-Ionone and guaiacol exhibited a higher binding ability to BLG in the heat-induced molten globule state compared to unheated BLG, as assessed by protein surface hydrophobicity measurements, using 6-propionyl-2-(dimethylamino)naphthalene (PRODAN) fluorescent probe. The binding sites of the two aroma compounds were determined by 2D nuclear magnetic resonance (NMR) spectro…
One- and Two-Dimensional Diffusion of Metal Atoms in Graphene
2008
In the present work, individual Au or Pt atoms in layersconsisting of one or twographene planes have been monitoredin real time at high temperature by high-resolution TEM. Weobtain information about the location of metal atoms ingrapheneandthediffusionmechanisms.Activationenergiesfordiffusion are obtained in a temperature range close to thetemperature of the technically important metal-assisted CVDprocess.Thematerialwassynthesizedinanarcdischarge
Characteristics of the polymer transport in ratchet systems
2010
Molecules with complex internal structure in time-dependent periodic potentials are studied by using short Rubinstein-Duke model polymers as an example. We extend our earlier work on transport in stochastically varying potentials to cover also deterministic potential switching mechanisms, energetic efficiency and non-uniform charge distributions. We also use currents in the non-equilibrium steady state to identify the dominating mechanisms that lead to polymer transportation and analyze the evolution of the macroscopic state (e.g., total and head-to-head lengths) of the polymers. Several numerical methods are used to solve the master equations and nonlinear optimization problems. The domina…
Formation of nanostructures in Eu3+ doped glass-ceramics: an XAS study.
2012
We describe the results of x-ray absorption experiments carried out to deduce structural and chemical information in Eu(3+) doped, transparent, oxyfluoride glass and nanostructured glass-ceramic samples. The spectra were measured at the Pb and Eu-L(III) edges. The Eu environment in the glass samples is observed to be similar to that of EuF(3). Complementary x-ray diffraction experiments show that thermal annealing creates β-PbF(2) type nanocrystals. X-ray absorption indicates that Eu ions act as seeds in the nanocrystal formation. There is evidence of interstitial fluorine atoms around Eu ions as well as Eu dimers. X-ray absorption at the Pb-L(III) edge shows that after the thermal treatmen…
Structural basis for the potential antitumour activity of DNA-interacting benzo[kl]xanthene lignans
2010
The biological properties and possible pharmacological applications of benzo[kl]xanthene lignans, rare among natural products and synthetic compounds, are almost unexplored. In the present contribution, the possible interaction of six synthetic benzo[kl]xanthene lignans and the natural metabolite rufescidride with DNA has been investigated through a combined STD-NMR and molecular docking approach, paralleled by in vitro biological assays on their antiproliferative activity towards two different cancer cell lines: SW 480 and HepG2. Our data suggest that the benzo[kl]xanthene lignans are suitable lead compounds for the design of DNA selective ligands with potential antitumour properties.
Xanthine oxidase catalyzes the synthesis of retinoic acid
2001
Milk xanthine oxidase (xanthine: oxygen oxidoreductase; XO; EC 1.1.3.22) was found to catalyze the conversion of retinaldehyde to retinoic acid. The ability of XO to synthesize all trans-retinoic acid efficiently was assessed by its turnover number of 31.56 min-1, determined at pH 7.0 with 1 nM XO and all trans-retinaldehyde varying between 0.05 to 2 microM. The determination of both retinoid and purine content in milk was also considered in order to correlate their concentrations with kinetic parameters of retinaldehyde oxidase activity. The velocity of the reaction was dependent on the isomeric form of the substrate, the all trans- and 9-cis-forms being the preferred substrates rather tha…
Thermodynamics and kinetics of ion permeation in wild-type and mutated open active conformation of the human α7 nicotinic receptor
2020
Molecular studies of human pentameric ligand-gated ion channels (LGICs) expressed in neurons and at neuromuscular junctions are of utmost importance in the development of therapeutic strategies for neurological disorders. We focus here on the nicotinic acetylcholine receptor nAChR-α7, a homopentameric channel widely expressed in the human brain, with a proven role in a wide spectrum of disorders including schizophrenia and Alzheimer's disease. By exploiting an all-atom structural model of the full (transmembrane and extracellular) protein in the open, agonist-bound conformation we recently developed, we evaluate the free energy and the mean first passage time of single-ion permeation using …
Thermal aggregation of proteins in presence of metal ions.
2008
The study of the aggregation processes in presence of metal ions is an essential step for understanding the key role of metals in protein-protein and protein-solvent interactions. Indeed, the presence of metal ions can radically change the main features of the standard denaturation/aggregation processes and such effects result to be strongly dependent on the kind of metal and on its concentration. Metal ions have an active role in thermal aggregation and cold set gelation processes. These processes are intrinsically different, but both are based on the proteins ability to form aggregates.
Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case.
2003
In this paper a deeper insight into the chorismate-to prephenate-rearrangement, catalyzed by Bacillus subtilis chorismate mutase, is provided by means of a combination of statistical quantum mechanics/molecular mechanics simulation methods and hybrid potential energy surface exploration techniques. The main aim of this work is to present an estimation of the preorganization and reorganization terms of the enzyme catalytic rate enhancement. To analyze the first of these, we have studied different conformational equilibria of chorismate in aqueous solution and in the enzyme active site. Our conclusion is that chorismate mutase preferentially binds the reactive conformer of the substrate--that…