Search results for "molecular dynamics"
showing 10 items of 1075 documents
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 …
Do dynamic effects play a significant role in enzymatic catalysis? A theoretical analysis of formate dehydrogenase.
2010
A theoretical study of the protein dynamic effects on the hydride transfer between the formate anion and nicotinamide adenine dinucleotide (NAD + ), catalyzed by formate dehydrogenase (FDH), is presented in this paper. The analysis of free downhill molecular dynamic trajectories, performed in the enzyme and compared with the reaction in aqueous solution, has allowed the study of the dynamic coupling between the reacting fragments and the protein or the solvent water molecules, as well as an estimation of the dynamic effect contribution to the catalytic effect from calculation of the transmission coefficient in the enzyme and in solution. The obtained transmission coefficients for the enzyme…
Molecular topology applied to the discovery of 1-benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a non-ligand-binding-p…
2014
We report the discovery of 1-benzyl-2-(3- fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole- 5-one as a novel non-ligand binding pocket (non-LBP) antagonist of the androgen receptor (AR) through the application of molecular topology techniques. This compound, validated through time-resolved fluorescence resonance energy transfer and fluorescence polarization biological assays, provides the basis for lead optimization and structure−activity relationship analysis of a new series of non-LBP AR antagonists. Induced-fit docking and molecular dynamics studies have been performed to establish a consistent hypothesis for the interaction of the new active molecule on the AR surface. Refereed/…
Molecular recognition of naphthalene diimide ligands by telomeric quadruplex-DNA: the importance of the protonation state and mediated hydrogen bonds.
2016
In depth Monte Carlo conformational scans in combination with molecular dynamics (MD) simulations and electronic structure calculations were applied in order to study the molecular recognition process between tetrasubstituted naphthalene diimide (ND) guests and G-quadruplex (G4) DNA receptors. ND guests are a promising class of telomere stabilizers due to which they are used in novel anticancer therapeutics. Though several ND guests have been studied experimentally in the past, the protonation state under physiological conditions is still unclear. Based on chemical intuition, in the case of N-methyl-piperazine substitution, different protonation states are possible and might play a crucial …
Potassium Triggers a Reversible Specific Stiffness Transition of Polyethylene Glycol
2017
We use plasmon rulers made from two connected gold nanoparticles to monitor the conformation and stiffness of single PEG molecules and their response to cations. By observing equilibrium fluctuations of the interparticle distance, we obtain the spring constants or stiffness of the connecting single-molecule tether with pico-Newton sensitivity. We observe a transition of the PEG molecules’ extension and stiffness above about 1.2 mM K+ ion concentration which is specific to potassium ions. Molecular dynamics simulations reveal the formation of crown-like structures as the most likely molecular mechanism responsible for this specific effect.
Hydrolysis of Phosphotriesters: A Theoretical Analysis of the Enzymatic and Solution Mechanisms
2012
A theoretical study on the alkaline hydrolysis of paraoxon, one of the most popular organophosphorus pesticides, in aqueous solution and in the active site of Pseudomonas diminuta phosphotriesterase (PTE) is presented. Simulations by means of hybrid quantum mechanics/molecular mechanics (QM/MM) potentials show that the hydrolysis of paraoxon takes place through an A(N)D(N) or associative mechanism both in solution and in the active site of PTE. The results correctly reproduce the magnitude of the activation free energies and can be used to rationalize the observed kinetic isotope effects (KIEs) for the hydrolysis of paraoxon in both media. Enzymatic hydrolysis of O,O-diethyl p-chlorophenyl …
Peptide Metal–Organic Frameworks for Enantioselective Separation of Chiral Drugs
2017
We report the ability of a chiral Cu(II) 3D MOF based on the tripeptide Gly-L-His-Gly (GHG) for the enantioselective separation of metamphetamine and ephedrine. Monte Carlo simulations suggest that chiral recognition is linked to preferential binding of one of the enantiomers as result of either stronger or additional H-bonds with the framework that lead to energetically more stable diastereomeric adducts. Solid phase extraction (SPE) of a racemic mixture by using Cu(GHG) as extractive phase permits isolating more than 50% of the (+)-ephedrine enantiomer as target compound in only four minutes. To the best of our knowledge, this represents the first example of a MOF capable of separating ch…
(Z)- und (E)-Enole von diarylsubstituierten β-Ketocarbonsäurederivativen
2006
(Z) and (E) Enols of Diaryl-Substituted β-Ketocarboxylic Acid Derivatives Thermolysis of the 1,3-diaryl-2-diazo-1,3-propanediones 4 in the presence of alcohols or amines yielded the compounds 7–11 which exist as chelated (Z) enols or as tautomeric ketones. Contrary to the steric interaction of two mesityl groups the steric interaction between two naphthyl or two anthryl groups or between naphthyl and mesityl is not sufficient to stabilize the corresponding (E) enols. The latter isomers were generated in irradiation processes of some (Z) enols. Detailed NMR studies were performed in order to characterize the enols and their molecular dynamics.
Sticking Probability on Zeolites
2006
The sticking coefficient, i.e., the probability that, on hitting the surface of a nanoporous particle (zeolite), a molecule shall be able to enter the intracrystalline space, is a key quantity for the application of such materials in heterogeneous catalysis and molecular sieving. On the basis of pulsed field gradient NMR diffusion measurements and molecular dynamics simulations, typical values of this probability are found to be close to one. They exceed previous estimates on the basis of IR uptake measurements by many orders of magnitude.
Physics of the nuclear pore complex: Theory, modeling and experiment
2021
Abstract The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular “nanomachine” known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the…