Search results for "Biomolecule"
showing 10 items of 666 documents
Can multiscale simulations unravel the function of metallo-enzymes to improve knowledge-based drug discovery?
2019
Metallo-enzymes are a large class of biomolecules promoting specialized chemical reactions. Quantum-classical quantum mechanics/molecular mechanics molecular dynamics, describing the metal site at quantum mechanics level, while accounting for the rest of system at molecular mechanics level, has an accessible time-scale limited by its computational cost. Hence, it must be integrated with classical molecular dynamics and enhanced sampling simulations to disentangle the functions of metallo-enzymes. In this review, we provide an overview of these computational methods and their capabilities. In particular, we will focus on some systems such as CYP19A1 a Fe-dependent enzyme involved in estroge…
5-(3,4-Dimethoxybenzyl)-7-isopropyl-1,3,5-triazepane-2,6-dione acetonitrile solvate refined using a multipolar atom model
2010
International audience; The crystal structure of the title compound, C16H23N3O4·CH3CN, was refined using a multipolar atom model transferred from an experimental electron-density database. The refinement showed some improvement in crystallographic statistical indices compared with the independent atom model. The triazepane ring adopts a twist-boat conformation. In the crystal structure, the molecule forms intermolecular contacts with 14 different neighbours. There are two N-H...O and one C-H...O intermolecular hydrogen bond.
String kernels and high-quality data set for improved prediction of kinked helices in α-helical membrane proteins.
2011
The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. For the particular case of kink prediction, we generated a data set of 132 membrane proteins containing 1014 manually labeled helices and examined the environment of kinks. Our sequence analysis confirms the great relevance of proline and reveals disproportionately high occurrences of glycine and serine at kink positions. The structural analysis shows significantly different solvent accessible surface area mean values for kinked and nonkinked helices. More important, …
Characterization of Iron−Carbonyl-Protected Gold Clusters
2009
Ligand-stabilized nanometer-sized gold particles are interesting building blocks for molecular electronics, precursors for catalysts, optical labels for biomolecules and diagnosis, and potential nontoxic carriers for therapeutics. In this work we characterize for the first time, by means of near-infrared and Raman spectroscopy and time-dependent density functional calculations, gold clusters protected with iron-carbonyl ligands, such as {Au(22)[Fe(CO)(4)](12)}(6-) shown in the figure. Surprisingly, our results show that these novel compounds bear many analogues to another, well-studied, class of gold clusters, namely those of thiolate-monolayer-protected gold clusters. Our work adds a new d…
Protein knot server: detection of knots in protein structures
2007
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…
Density functional theory fragment descriptors to quantify the reactivity of a molecular family: Application to amino acids
2007
By using the exact density functional theory, one demonstrates that the value of the local electronic softness of a molecular fragment is directly related to the polarization charge (Coulomb hole) induced by a test electron removed (or added) from (at) the fragment. Our finding generalizes to a chemical group a formal relation between these molecular descriptors recently obtained for an atom in a molecule using an approximate atomistic model [P. Senet and M. Yang, J. Chem. Sci. 117, 411 (2005)]. In addition, a practical ab initio computational scheme of the Coulomb hole and related local descriptors of reactivity of a molecular family having in common a similar fragment is presented. As a b…
Collective properties of hydration: long range and specificity of hydrophobic interactions
1997
We report results of molecular dynamics (MD) simulations of composite model solutes in explicit molecular water solvent, eliciting novel aspects of the recently demonstrated, strong many-body character of hydration. Our solutes consist of identical apolar (hydrophobic) elements in fixed configurations. Results show that the many-body character of PMF is sufficiently strong to cause 1) a remarkable extension of the range of hydrophobic interactions between pairs of solute elements, up to distances large enough to rule out pairwise interactions of any type, and 2) a SIF that drives one of the hydrophobic solute elements toward the solvent rather than away from it. These findings complement re…
Rapid hyperpolarization and purification of the metabolite fumarate in aqueous solution
2020
Significance Magnetic resonance imaging is hindered by inherently low sensitivity, which limits the method for the most part to observing water molecules in the body. Hyperpolarized molecules exhibit strongly enhanced MRI signals which opens the door for imaging low-concentration species in vivo. Biomolecules can be hyperpolarized and injected into a patient allowing for metabolism to be tracked in real time, greatly expanding the information available to the radiologist. Parahydrogen-induced polarization (PHIP) is a hyperpolarization method renowned for its low cost and accessibility, but is generally limited by low polarization levels, modest molecular concentrations, and contamination by…
Synthesis and molecular properties of donor–π-spacer–acceptor ynamides with up to four conjugated alkyne units
2010
A set of push-pull ynamides with up to four conjugated triple bonds has been synthesized and the molecular properties of these new carbon rods have been characterised showing effective intramolecular charge transfers and high values for the change of the electrical dipole moment after transition from the ground to the Franck-Condon excited state.
Regulation of cholesterol metabolism in the retina under experimental conditions associated with glaucoma
2019
Cholesterol is a lipid found in every animal cell and is necessary for its survival. Among its multiple roles in the body, it is a component of cell membranes that is crucial for the maintenance of their structure and fluidity and is thus implicated in the modulation of many signalling pathways. Neurons are especially dependant on cholesterol input since the proper composition of their plasma membrane is required for vesicular exocytosis of neurotransmitters and transduction of the post-synaptic signal. It has been shown that both an excess and a lack of cholesterol is neurotoxic. Moreover, many neurodegenerative diseases, such as Alzheimer’s or Huntington’s disease, have been associated wi…