Search results for "hydrophobic"
showing 10 items of 332 documents
Polynucleotide differentiation using hybrid solid-state nanopore functionalizing with α-hemolysin
2019
We report results from full atomistic molecular dynamics simulations on the properties of biomimetic nanopores. This latter result was obtained through the direct insertion of an α-hemolysin protein inside a hydrophobic solid-state nanopore. Upon translocation of different DNA strands, we demonstrate here that the theoretical system presents the same discrimination properties as the experimental one obtained previously. This opens an interesting way to promote the stability of a specific protein inside a solid nanopore to develop further biomimetic applications for DNA or protein sequencing.
Profiling of lipid species by normal-phase liquid chromatography, nanoelectrospray ionization, and ion trap–orbitrap mass spectrometry
2013
Detailed analysis of lipid species can be challenging due to their structural diversity and wide concentration range in cells, tissues, and biofluids. To address these analytical challenges, we devised a reproducible, sensitive, and integrated lipidomics workflow based on normal-phase liquid chromatography-Fourier transform mass spectrometry (LC-FTMS) and LC-ITMS(2) (ion trap tandem mass spectrometry) for profiling and structural analysis of lipid species. The workflow uses a normal-phase LC system for efficient separation of apolar and polar lipid species combined with sensitive and specific analysis powered by a chip-based nanoelectrospray ion source and a hybrid ion trap-orbitrap mass sp…
Molecular mechanism of T-cell protein tyrosine phosphatase (TCPTP) activation by mitoxantrone.
2013
T-cell protein tyrosine phosphatase (TCPTP) is a ubiquitously expressed non-receptor protein tyrosine phosphatase. It is involved in the negative regulation of many cellular signaling pathways. Thus, activation of TCPTP could have important therapeutic applications in diseases such as cancer and inflammation. We have previously shown that the α-cytoplasmic tail of integrin α1β1 directly binds and activates TCPTP. In addition, we have identified in a large-scale high-throughput screen six small molecules that activate TCPTP. These small molecule activators include mitoxantrone and spermidine. In this study, we have investigated the molecular mechanism behind agonist-induced TCPTP activation.…
Effect of T-R conformational change on sickle-cell hemoglobin interactions and aggregation
2004
We compare the role of a conformational switch and that of a point mutation in the thermodynamic stability of a protein solution and in the consequent propensity toward aggregation. We study sickle-cell hemoglobin (HbS), the beta6 Glu-Val point mutant of adult human hemoglobin (HbA), in its R (CO-liganded) conformation, and compare its aggregation properties to those of both HbS and HbA in their T (unliganded) conformation. Static and dynamic light scattering measurements performed for various hemoglobin concentrations showed critical divergences with mean field exponents as temperature was increased. This allowed determining spinodal data points T(S)(c) by extrapolation. These points were …
Low density lipoproteins and human serum albumin as the carriers of squalenoylated drugs: insights from molecular simulations
2018
We have studied the interaction of three clinically promising squalenoylated drugs (gemcitabine-squalene, adenine-squalene, and doxorubicin-squalene) with low-density lipoproteins (LDL) by means of atomistic molecular dynamics simulations. It is shown that all studied squalenoylated drugs accumulate inside the LDL particles. This effect is promoted by the squalene moiety, which acts as an anchor and drives the hydrophilic drugs into the hydrophobic core of the LDL lipid droplet. Our data suggest that LDL particles could be a universal carriers of squalenoylated drugs in the bloodstream. Interaction of gemcitabine-squalene with human serum albumin (HSA) was also studied by ensemble of dockin…
Interactions between flavor compounds and food ingredients and their influence on flavor perception
2002
Interactions between flavor compounds and food ingredients are reviewed and their influence on flavor perception is discussed. Proteins are known to bind flavor compounds. For β-lactoglobulin, the most-studied example, hydrophobic interactions with volatiles are described. The effect of the medium on the conformation of the protein and its ability to bind flavor compounds is discussed. In general, the retention of volatiles by protein is much lower than that by fat. In emulsions, however, the presence of protein at the oil/water interface induces a significant effect on flavor release and flavor perception of hydrophobic flavor compounds. For starch, an extensively studied hydrocolloid, amy…
Binding isotope effects as a tool for distinguishing hydrophobic and hydrophilic binding sites of HIV-1 RT.
2014
The current treatment for HIV-1 infected patients consists of a cocktail of inhibitors, in an attempt to improve the potency of the drugs by adding the possible effects of each supplied compound. In this contribution, nine different inhibitors of HIV-1 RT, one of the three key proteins responsible for the virus replication, have been selected to develop and test a computational protocol that allows getting a deep insight into the inhibitors’ binding mechanism. The interaction between the inhibitors and the protein have been quantified by computing binding free energies through FEP calculations, while a more detailed characterization of the kind of inhibitor–protein interactions is based on …
The introduction of fluorine atoms or trifluoromethyl groups in short cationic peptides enhances their antimicrobial activity
2006
The effect of introducing fluorine atoms or trifluoromethyl groups in either the peptidic chain or the C-terminal end of cationic pentapeptides is reported. Three series of amide and ester peptides were synthesised and their antimicrobial properties evaluated. An enhanced activity was found in those derivatives whose structure contained fluorine, suggesting an increase in their hydrophobicity.
Modeling Supramolecular Polymerization: The Role of Steric Effects and Hydrophobic Interactions
2019
We present a combined experimental–simulation study of self-assembly into one-dimensional filaments. Experimentally, we study amphiphilic AuI-metallopeptides in neutral aqueous media. Our model foc...
Mononuclear rearrangement of heterocycles in zwitterionic micelles of amine oxide surfactants.
2012
Abstract Rate constants for the mononuclear rearrangement (MRH) of Z -phenylhydrazones of some 5-substituted-3-benzoyl-1,2,4-oxadiazoles in water have been measured in the presence of zwitterionic micelles. The use of micellized N -tetradecyl- N , N -dimethylamineoxide (C 14 DMAO) as the reaction medium allowed to solubilize the otherwise water-insoluble oxadiazoles. Micellar rate effects were analyzed by using a simple pseudo-phase model and compared with those obtained in non-ionic micelles (Triton X-100). Evidence that both the rate of the rearrangement reaction and the binding of the substrates to the micelles are mainly governed by substrate hydrophobicity is obtained. The disagreement…