Search results for "Biomolecules"
showing 10 items of 549 documents
Effect of low levels of dietary fish oil on fatty acid desaturation and tissue fatty acids in obese and lean rats
1995
The effect of very low levels of dietary long-chain n-3 fatty acids on delta 6 desaturation of linoleic acid (18:2n-6) and alpha-linolenic acid (18:3n-3), and on delta 5 desaturation of dihomo-gamma-linolenic acid (20:3n-6), in liver microsomes and its influence on tissue fatty acids were examined in obese and lean Zucker rats and in Wistar rats. Animals fed for 12 wk a balanced diet containing ca. 200 mg of long-chain polyunsaturated n-3 fatty acids per 100 g of diet were compared to those fed the same amount of alpha-linolenic acid. Low amounts of long-chain n-3 fatty acids greatly inhibited delta 6 desaturation of 18:2n-6 and delta 5 desaturation of 20:3n-6, while delta 6 desaturation of…
Regulation of lipid flux between liver and adipose tissue during transient hepatic steatosis in carnitine-depleted rats
2007
Rats with carnitine deficiency due to trimethylhydrazinium propionate (mildronate) administered at 80 mg/100 g body weight per day for 10 days developed liver steatosis only upon fasting. This study aimed to determine whether the transient steatosis resulted from triglyceride accumulation due to the amount of fatty acids preserved through impaired fatty acid oxidation and/or from up-regulation of lipid exchange between liver and adipose tissue. In liver, mildronate decreased the carnitine content by approximately 13-fold and, in fasted rats, lowered the palmitate oxidation rate by 50% in the perfused organ, increased 9-fold the triglyceride content, and doubled the hepatic very low density …
Algorithms for {K, s+1}-potent matrix constructions
2013
In this paper, we deal with {K, s + 1}-potent matrices. These matrices generalize all the following classes of matrices: k-potent matrices, periodic matrices, idempotent matrices, involutory matrices, centrosymmetric matrices, mirrorsymmetric matrices, circulant matrices, among others. Several applications of these classes of matrices can be found in the literature. We develop algorithms in order to compute {K, s + 1}-potent matrices and {K, s + 1}-potent linear combinations of {K, s + 1}-potent matrices. In addition, some examples are presented in order to show the numerical performance of the method. (C) 2012 Elsevier B.V. All rights reserved.
Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures
2016
We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromo…
Dynamical properties of myoglobin in an ultraviscous water-glycerol solvent investigated with elastic neutron scattering and FTIR spectroscopy
2018
Abstract Proteins have distinctive dynamical properties, characterized by the fluctuations of protein molecules among the different minima of their energy landscape. These fluctuations, progressively activated for temperature values larger than ~180 K, lead to a steep increase in the temperature dependence of all measurable dynamical properties. This phenomenon is known as Protein Dynamical Transition and, in spite of the intense studies due to its importance in protein function and to the relation with the fascinating fundamental thermodynamics of complex systems, many aspects of it are not yet clearly understood. Among these, the relationship with the properties of the external solvent an…
Vibrational spectroscopy of trans and cis deuterated formic acid (HCOOD): Anharmonic calculations and experiments in argon and neon matrices
2010
The absorption spectra of trans and cis conformers of deuterated formic acid (HCOOD) isolated in argon and neon matrices are analyzed in the mid-infrared and near-infrared spectral regions (7900–450 cm � 1 ). Vibrational excitation by narrow-band IR radiation is used to convert the lower-energy trans conformer to the higher-energy cis form. A large number of overtone and combination bands are identified. The results of anharmonic vibrational calculations (CC-VSCF) for both conformers are reported and compared to the experimental spectra.
Synthetic nanopores with fixed charges: An electrodiffusion model for ionic transport
2003
Synthetic nanopores with fixed charges exhibit ionic equilibrium and transport properties that resemble those displayed by biological ion channels. We present an electrodiffusion model based on the Nernst-Planck flux equations, which allows for a qualitative description of the steady state ionic transport through a nanopore when the membrane fixed charges and all mobile carriers (including the water ions) are properly taken into account. In particular, we study the current-voltage curve, the electrical conductance, the reversal potential (a measure of the nanopore ionic selectivity), as well as the flux inhibition by protons and divalent cations in the nanopore. The model clearly shows how …
Trapping of 27 bp–8 kbp DNA and immobilization of thiol-modified DNA using dielectrophoresis
2006
Dielectrophoretic trapping of six different DNA fragments, sizes varying from the 27 to 8416 bp, has been studied using confocal microscopy. The effect of the DNA length and the size of the constriction between nanoscale fingertip electrodes on the trapping efficiency have been investigated. Using finite element method simulations in conjunction with the analysis of the experimental data, the polarizabilities of the different size DNA fragments have been calculated for different frequencies. Also the immobilization of trapped hexanethiol- and DTPA-modified 140 nm long DNA to the end of gold nanoelectrodes was experimentally quantified and the observations were supported by density functiona…
Orientation of non-spherical protonated water clusters revealed by infrared absorption dichroism
2018
Infrared continuum bands that extend over a broad frequency range are a key spectral signature of protonated water clusters. They are observed for many membrane proteins that contain internal water molecules, but their microscopic mechanism has remained unclear. Here we compute infrared spectra for protonated and unprotonated water chains, discs, and droplets from ab initio molecular dynamics simulations. The continuum bands of the protonated clusters exhibit significant anisotropy for chains and discs, with increased absorption along the direction of maximal cluster extension. We show that the continuum band arises from the nuclei motion near the excess charge, with a long-ranged amplifica…
Force probe simulations using an adaptive resolution scheme
2021
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In force probe molecular dynamics (FPMD) simulations, one pulls one end of the molecule with a constant velocity in order to induce the relevant conformational transitions. Since the extended configuration of the system has to fit into the simulation box together with the solvent such simulations are very time consuming. Here, we apply a hybrid scheme in which the solute is treated with atomistic resolution and the solvent molecules far away from the solute a…