Search results for "molecular conformation"
showing 10 items of 376 documents
High speed X-ray analysis of plant enzymes at room temperature.
2013
X-ray measurements at room temperature (295 K) deliver high quality data sets with unprecedented speed (2 min), as shown for crystallized raucaffricine-O-β-D-glucosidase (RG), its mutant RG-Glu186Gln and several ligand complexes of the enzyme which participates in alkaloid biosynthesis in the plant Rauvolfia. The data obtained are compared with data sets measured under typical cryo conditions (100K). Under both conditions, density maps are highly comparable and favor the described protocol for room temperature measurements, potentially paving the way for future crystallographic studies capturing biosynthetic pathway intermediates.
Calculation of the Phase Behavior of Lipids
1998
The self-assembly of monoacyl lipids in solution is studied employing a model in which the lipid's hydrocarbon tail is described within the Rotational Isomeric State framework and is attached to a simple hydrophilic head. Mean-field theory is employed, and the necessary partition function of a single lipid is obtained via a partial enumeration over a large sample of molecular conformations. The influence of the lipid architecture on the transition between the lamellar and inverted-hexagonal phases is calculated, and qualitative agreement with experiment is found.
Counterion-mediated attraction and kinks on loops of semiflexible polyelectrolyte bundles.
2006
The formation of kinks in a loop of bundled polyelectrolyte filaments is analyzed in terms of the thermal fluctuations of charge density due to polyvalent counterions adsorbed on the polyelectrolyte filaments. It is found that the counterion-mediated attraction energy of filaments depends on their bending. By consideration of curvature elasticity energy and counterion-mediated attraction between polyelectrolyte filaments, the characteristic width of the kink and the number of kinks per loop is found to be in reasonable agreement with existing experimental data for rings of bundled actin filaments.
Influence of chain stiffness on knottedness in single polymers.
2013
In the present article, we investigate and review the influence of chain stiffness on self-entanglements and knots in a single polymer chain with Monte Carlo simulations spanning good solvent, theta and globular phases. The last-named are of particular importance as a model system for DNA in viral capsids. Intriguingly, the dependence of knot occurrence and complexity with increasing stiffness is non-trivial, but can be understood with a few simple concepts outlined in the present article.
Biomolecular-solvent stereodynamic coupling probed by deuteration.
1983
Thermodynamic interpretation of experiments with isotopically perturbed solvent supports the view that solvent stereodynamics is directly relevant to thermodynamic stability of biomolecules. According with the current understanding of the structure of the aqueous solvent, in any stereodynamic configuration of the latter, connectivity pathways are identifiable for their topologic and order properties. Perturbing the solvent by isotopic substitution or, e.g., by addition of co-solvents, can therefore be viewed as reinforcing or otherwise perturbing these topologic structures. This microscopic model readily visualizes thermodynamic interpretation. In conclusion, the topologic stereodynamic str…
Internal rotation of 1,2-dichloroethane in haloalkane dehalogenase. A test case for analyzing electrostatic effects in enzymes
2003
1,2-Dichoroethane (DCE) is a prototypical molecule for studying electrostatic solvent effects on molecular conformation as far as rotation around the carbon−carbon bond notably changes the electric...
Stereoselective synthesis of unsaturated and functionalized L-NHBoc amino acids, using Wittig reaction under mild phase-transfer conditions.
2012
The stereoselective synthesis of a new amino acid phosphonium salt was described by quaternization of melting triphenylphosphine with the γ-iodo NHBoc-amino ester, derived from L-aspartic acid. The deprotection of the carboxylic acid function to afford the phosphonium salt with a free carboxylic acid group was achieved by a palladium-catalyzed desallylation reaction. This phosphonium salt was used in the Wittig reaction with aromatic or aliphatic aldehydes and trifluoroacetophenone, under solid-liquid phase-transfer conditions in chlorobenzene and in the presence of K(3)PO(4) as weak base, to afford the corresponding unsaturated amino acids without racemization. Thus, the reaction with subs…
Conformation of tert-butoxycarbonylglycyl-dehydroalanyl-glycine methyl ester in the crystalline state and calculated in the gas phase.
2006
tert-Butoxycarbonylglycyl-dehydroalanyl-glycine methyl ester (systematic name: methyl {2-[(tert-butoxycarbonylamino)acetamido]prop-2-enamido}acetate) (Boc0-Gly1-ΔAla2-Gly3-OMe), C13H21N3O6, has been structurally characterized by single-crystal X-ray diffraction and by density functional theory (DFT) calculations at the B3LYP/6–311+G** level. The peptide chain in both the solid-state and calculated structures adopts neither β nor γ turns. All amino acid residues in the tripeptide sequence are linked trans to each other. The bond lengths and valence angles of the amino acid units in the crystal structure and gas phase are comparable. However, the conformation of the third glycyl residue (…
Increased conformational rigidity of humic substances by oxidative biomimetic catalysis
2005
A synthetic water-soluble meso-tetra(2,6-dichloro-3-sulfonatophenyl)porphyrinate of iron(III) chloride, Fe(TDCPPS)Cl, was employed as a biomimetic catalyst in the oxidative coupling of terrestrial humic materials. High-performance size-exclusion chromatography (HPSEC), solid-state nuclear magnetic resonance (CPMAS-(13)C NMR), electron paramagnetic resonance (EPR), and diffuse reflectance infrared spectroscopy (DRIFT) were used to follow conformational and structural changes brought about in different humic materials by the oxidative coupling. Increase in apparent weight-average molecular weight (Mw(a)) occurred invariably for all humic substances with the oxidative polymerization catalyzed …
Geometrical and conformational preferences of the 9‐fluorenylmethoxycarbonyl‐amino moiety
2004
Structural parameters, originating from x-ray crystallographic data, have been compiled for 13 derivatives of amino acids, peptides and related compounds, which contain a total of 14 Fmoc-NH- moieties. For these moieties, molecular geometries and conformations--described by the omegao, theta1, theta2 and theta3' torsion angles--were analysed and compared with the corresponding parameters for the Z-NH- and Boc-NH-moieties (290 and 553, respectively). To gain a deeper insight into the conformational features of the Fmoc-NH- moiety, ab initio free molecule calculations were performed for fully relaxed minima. Also the potential energy surface as a function of the torsion angles (theta3', theta…