Search results for "Quantitative"
showing 10 items of 2409 documents
The Role of Adenine Excimers in the Photophysics of Oligonucleotides
2009
Energies and structures of different arrangements of the stacked adenine homodimer have been computed at the ab initio CASPT2 level of theory in isolation and in an aqueous environment. Adenine dimers are shown to form excimer singlet states with different degrees of stacking and interaction. A model for a 2-fold decay dynamics of adenine oligomers can be supported in which, after initial excitation in the middle UV range, unstacked or slightly stacked pairs of nucleobases will relax by an ultrafast internal conversion to the ground state, localizing the excitation in the monomer and through the corresponding conical intersection with the ground state. On the other hand, long-lifetime intra…
Irreversible gelation of thermally unfolded proteins:structural and mechanical properties of lysozyme aggregates
2010
The formation of protein aggregates is important in many fields of life science and technology. The morphological and mechanical properties of protein solutions depend upon the molecular conformation and thermodynamic and environmental conditions. Non-native or unfolded proteins may be kinetically trapped into irreversible aggregates and undergo precipitation or gelation. Here, we study the thermal aggregation of lysozyme in neutral solutions. We characterise the irreversible unfolding of lysozyme by differential scanning calorimetry. The structural properties of aggregates and their mechanisms of formation with the eventual gelation are studied at high temperature by spectroscopic, rheolog…
Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes
2015
In the present study, we introduce novel 3D protein descriptors based on the bilinear algebraic form in the ℝn space on the coulombic matrix. For the calculation of these descriptors, macromolecular vectors belonging to ℝn space, whose components represent certain amino acid side-chain properties, were used as weighting schemes. Generalization approaches for the calculation of inter-amino acidic residue spatial distances based on Minkowski metrics are proposed. The simple- and double-stochastic schemes were defined as approaches to normalize the coulombic matrix. The local-fragment indices for both amino acid-types and amino acid-groups are presented in order to permit characterizing fragme…
Protein search for multiple targets on DNA
2016
Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the molecular description of these phenomena, but many aspects of the mechanisms of protein search for the targets on DNA remain not well understood. One of the most intriguing problems is the role of multiple targets in protein search dynamics. Using a recently developed theoretical framework we analyze this question in detail. Our method is based on a discrete-state stochastic appro…
Monolayer curvature stabilizes nanoscale raft domains in mixed lipid bilayers
2013
According to the lipid raft hypothesis, biological lipid membranes are laterally heterogeneous and filled with nanoscale ordered "raft" domains, which are believed to play an important role for the organization of proteins in membranes. However, the mechanisms stabilizing such small rafts are not clear, and even their existence is sometimes questioned. Here we report the observation of raft-like structures in a coarse-grained molecular model for multicomponent lipid bilayers. On small scales, our membranes demix into a liquid ordered (lo) and a liquid disordered (ld) phase. On large scales, phase separation is suppressed and gives way to a microemulsion-type state that contains nanometer si…
Calculation of partition coefficient and hydrophobic moment of the secondary structure of lysozyme
2001
A method that permits a semiquantitative estimate of the partitioning of any solute between any two media is presented. As an example, the partition coefficients and hydrophobic moment of the secondary structure of lysozyme are calculated. Program GSCAP is written as a version of Pascal's solvent-dependent conformational analysis (SCAP) program. The dipole moments calculated for the helices are trebled with respect to that for the sheet. For helices, the main contribution to the water-accessible surface area is the hydrophobic term, while the hydrophilic part dominates in the sheet. Molecular globularity and the three studied partition coefficients differentiate between helices and sheet.
Canonical azimuthal rotations and flanking residues constrain the orientation of transmembrane helices.
2013
AbstractIn biological membranes the alignment of embedded proteins provides crucial structural information. The transmembrane (TM) parts have well-defined secondary structures, in most cases α-helices and their orientation is given by a tilt angle and an azimuthal rotation angle around the main axis. The tilt angle is readily visualized and has been found to be functionally relevant. However, there exist no general concepts on the corresponding azimuthal rotation. Here, we show that TM helices prefer discrete rotation angles. They arise from a combination of intrinsic properties of the helix geometry plus the influence of the position and type of flanking residues at both ends of the hydrop…
3D-Chiral quadratic indices of the ‘molecular pseudograph’s atom adjacency matrix’ and their application to central chirality codification: classific…
2004
Quadratic indices of the 'molecular pseudograph's atom adjacency matrix' have been generalized to codify chemical structure information for chiral drugs. These 3D-chiral quadratic indices make use of a trigonometric 3D-chirality correction factor. These indices are nonsymmetric and reduced to classical (2D) descriptors when symmetry is not codified. By this reason, it is expected that they will be useful to predict symmetry-dependent properties. 3D-Chirality quadratic indices are real numbers and thus, can be easily calculated in TOMOCOMD-CARDD software. These descriptors circumvent the inability of conventional 2D quadratic indices (Molecules 2003, 8, 687-726. http://www.mdpi.org) and othe…
Receptor-guided 3D-QSAR approach for the discovery of c-kit tyrosine kinase inhibitors
2012
Studies of the the three-dimensional quantitative structure–activity relationships for ninety-five c-kit tyrosine kinase inhibitors were performed. Based on a co-crystallized compound (1 T46), known inhibitors were aligned with c-kit by induced-fit docking, and multiple training/test set splitting was performed to validate the selected pharmacophore model. The best pharmacophore model consisted of five features: one hydrogen-bond donor and four aromatic rings. Reliable statistics were obtained (R 2 = 0.95, R pred 2 = 0.75), and the model was validated by using it to select c-kit inhibitors from a database; 82.1% of the hits it retrieved were active. Accordingly, our model can be reliably u…
QSPR prediction of retention times of phenylurea herbicides by biological plastic evolution.
2012
A simple/sensitive high-performance liquid chromatographic method, with ultraviolet (UV) detection, was developed for phenylurea-herbicide analysis, which involves preconcentration using solid-phase extraction. Mobile phase was acetonitrile/water at flow-rate of 1 mL.min-1 with direct UV absorbance detection at 210 nm. Analyte separation studied on a C18 column was applied successfully to herbicide analysis in soft drink's brands and tap water. Good linearity/repeatability was observed for all pesticides. Retention times increase as: metoxuron < monuron < diuron < matazachlor < linuron. They are modelled by structure-property relations. The effect of different types of features is analyzed:…