1,721,050 research outputs found
Interaction Study of Bioactive Molecules with Fibrinogen and Human Platelets Determined by 1H-NMR Relaxation Experiments
No full textIn order to investigate the interaction processes between bioactive molecules and macromolecular receptors
NMR methodology based on the analysis of selective and non-selective spin–lattice relaxation rate
enhancements of ligand protons was used.
The contribution from the bound ligand fraction to the observed relaxation rate in relation to macromolecular
target concentration allowed the calculation of the normalized affinity index
in which the
effects of motional anisotropies and different proton densities have been removed.
In this paper, we applied this methodology to investigate the affinity of epinephrine and isoproterenol
towards two different systems: fibrinogen and platelets
Biopolymers and biomacromolecules solvent dynamics
No full textBiomacromolecules in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of biomolecules, in particular proteins, are extended for several angstroms. The role of the hydration shells around a protein has yet to be completely understood. Hydrated proteins maintain more dynamic flexibility with respect to the dried system, which is an important property in protein-protein and/or protein-ligand recognition processes. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. The water proton spin-lattice relaxation rate in protein solution is analyzed considering all possible dipolar contributions from coupled protons environments. The analysis of both selective and non-selective water spin-lattice relaxation rates allowed the calculation of the average effective correlation time for the water molecules at the protein interface and the evaluation of the long range ordering effect of the protein surface. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Fibrinogen-Catecholamine Interaction as Observed by NMR and Fourier Transform Infrared Spectroscopy
No full textIn this work, the interactions between the main catecholaminessepinephrine and norepinephrinesand fibrinogen
were investigated by NMR and Fourier transform infrared spectroscopies. The two hormones were found to interact
with fibrinogen and to affect the protein secondary structure to a different extent. In particular, the protein selectively
binds epinephrine at both the basal and stress concentrations, while it shows a weak nonspecific interaction with
norepinephrine. The interaction with the stress level of epinephrine leads to drastic protein conformational changes,
whereas norepinephrine does not affect fibrinogen secondary structure, even at stress concentration
Stacking interaction study of resveratrol (trans-3,5,4'-trihydroxystilbene) in solution by Nuclear Magnetic Resonance and Fourier Transform Infrared Spectroscopy
No full textInteractions between aromatic rings or other unsaturated systems, including p-stacking and face-to-edge complexes, are the origin of many phenomena in both organic and biological chemistry. It is well known that these interactions play an important role in the stabilization of the stereo-structure of DNA and the tertiary structure of many proteins.
Trans-resveratrol (trans-3,5,4-trihydroxystilbene, trans-RSV) is a phytoalexin found in Vitis sp. and in many other plants and food products and has received much attention because of its possible positive health benefits.
In this work, the p-stacking interaction of trans-RSV was studied by nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopy. In particular, the proton chemical shift dependence of the RSV concentration in the range2×10-2 - 1×10-5 M and temperature were analysed. Moreover, the dynamics of the supramolecular aggregates were studied by nuclear spin relaxation data
Simulating the active sites of copper-trafficking proteins. Density functional structural and spectroscopy studies on copper(I) complexes with thiols, carboxylato, amide and phenol ligands
No full textA series of mononuclear binary and ternary Cu(I) complexes with formato, formamide, methylphenol, and methanethiolato ligands were optimized at DFT-B3LYP/6-31G** (BS1) and DFT-B3LYP/6-311++G** (BS2) levels of theory. The solvent effect was taken into account via PCM method (BS1W and BS2W, respectively). The coordination arrangement for [Cu-I(SCH3/S(H)CH3)(OOCH)](-/0) and [Cu-I(SCH3/S(H)CH3)(O(H)(C6H4)CH3)](0/+) was pseudo-linear and for [Cu-I(SCH3/S(H)CH3)(OOCH)(OC(H)NH2)](-/0) was pseudo-trigonal. The [Cu-I(S-S(H)CH3/Cu-I(S-SCH3)](+/0) link even to amide carbonyl and to general O(H)R residues (R=C6H5CH3). [Cu-I(SCH3)(2)(O(H)(C6H4)CH3)](-) went towards dissociation of the O(H)(C6H4)CH3 ligand, whereas [Cu-I(S(H)CH3)(2)(O(H)(C6H4)CH3)](+) converged nicely, maintaining the hydroxy function linked to the metal. The trends of total electronic energies seemed to be significant, suggesting that linear (CuS2)-S-I coordination is more suitable than (CuS)-S-I, (CuS3)-S-I and (CuS4)-S-I arrangements. The formation energies of [Cu-I(S(H)CH3/SCH3)(OOCH)](0/-1) were higher than those of [Cu-I(S(H)CH3/SCH3)(2)](+/-) on starting from [Cu-I(S(H)CH3/Cu-I(SCH3)](+/0) by ca. 11-9kcalmol(-1) (BS2W). The structural arrangements, bond distances, and angles as well as computed spectroscopic parameters resulted in good agreement with experimental data for corresponding synthetic complexes and with metal site regions of several copper(I)-proteins. These data help in interpreting structural data of complex biological systems and in constructing reliable force fields for molecular mechanics computations. © 2016 Taylor and Francis
Solution Structure of Rifaximin and its Synthetic Derivative Rifaximin OR determined by Experimental NMR and Theoretical Simulation Methods
No full textThe solution structure of rifaximin and its derivative rifaximin OR (open ring) was determined by combining NMR
experimental results, theoretical simulation of two-dimensional NMR spectra by complete relaxation matrix analysis (CORMA), and
molecular dynamics calculations.
In this study the structural rearrangements due to the opening of the aliphatic chain of rifaximin after the reduction process to
form rifaximin OR were investigated.
Close spatial proximity of CH(14) and H28b protons detected by 2D-ROESY spectrum of rifaximin OR, which was not present
in rifaximin and the down-field shift of CH3(34) protons in rifaximin OR
1H spectrum were crucial to understand the structuralmodifications, which occurred within the system. The aliphatic chain of rifaximin OR was found to be no longer symmetrical withrespect to the aromatic moiety. Although no dramatic structural rearrangements were detected, the aliphatic chain moved toward CH3(14), causing a reduction of the aromatic shielding contribution in particular on CH(34)
Solution structure of hyaluronic acid oligomers by experimental and theoretical NMR, and molecular dynamics simulation.
No full textThe conformational properties of hyaluronic acid (HA) oligomers in aqueous solution were investigated by combining high-resolution NMR experimental results, theoretical simulation of NMR two-dimensional (2D) spectra by Complete Relaxation Matrix Analysis (CORMA), and molecular dynamics calculations. New experimental findings recorded for the tetra- and hexasaccharides enabled the stiffness of the HA and its viscoelastic properties to be interpreted. In particular, rotating frame nuclear Overhauser effect spectroscopy spectra provided new information about the arrangement of the glycosidic linkage. From C-13 NMR relaxation the rotational correlation time (tau (c)) were determined. The tau (c) were employed in the calculation of geometrical constraints, by using the MARDIGRAS algorithm. Restrained simulated annealing and I ns of unrestrained molecular dynamic simulations were performed on the hexasaccharide in a box of 1215 water molecules.
The beta (1 --> 3) and beta (1 --> 4) glycosidic links were found to be rigid. The lack of rotational degree of freedom is due to direct and/or water-mediated interresidue hydrogen bonding. Both single or tandem water bridges were found between carboxylate group and N-acetil group. The carboxylate group of glucuronic acid is, not involved in a direct link with the amide group of N-acetyl glucosamine and this facilitated bonding, between the residue and the water molecules
Interaction of Quercetin and its conjugate Quercetin 3-b-D-glucoside with Albumin Determined by NMR Relaxation Data
No full textNMR methodology has been developed in order to study phytochemical-macromolecular receptor interactions. This
approach is based on the analysis of proton selective spin–lattice relaxation rate enhancements of the ligand in the
presence of the macromolecule, to calculate an affinity index, [A]
, related to the strength of the interaction process.
This index has been modified by normalization to the relaxation rate of the free ligand, in order to take into account the
effects of motional anisotropies and different proton densities. The normalized affinity index, [A
L
T
N
]
, isolates the contribution
due to a decrease in the ligand dynamics caused by the binding with the protein. This methodology has been applied
to the interaction between two flavonoids (quercetin, 1, and quercetin 3-O-D-glucopyranoside,
2) and bovine serum
albumin (BSA). The calculated values of the affinity indexes and thermodynamic equilibrium constants suggested a
much stronger capacity of 1 to interact with BSA when compared with its glucosylated derivative, 2
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