Search results for "interaction [dark matter]"
showing 10 items of 363 documents
A Computational Study of the Protein-Ligand Interactions in CDK2 Inhibitors: Using Quantum Mechanics/Molecular Mechanics Interaction Energy as a Pred…
2006
ABSTRACT: We report a combined quantum mechanics/molecular mechanics (QM/MM) study to determine the protein-ligand interaction energy between CDK2 (cyclin-dependent kinase 2) and five inhibitors with the N2 -substituted 6-cyclohexylmethoxypurine scaffold. The computational results in this work show that the QM/MM interaction energy is strongly correlated to the biological activity and can be used as a predictor, at least within a family of substrates. A detailed analysis of the protein-ligand structures obtained from molecular dynamics simulations shows specific interactions within the active site that, in some cases, have not been reported before to our knowledge. The computed interaction …
Structure of the human filamin A actin-binding domain.
2009
Filamin A (FLNa) is a large dimeric protein that binds to actin filaments via its actin-binding domain (ABD). The crystal structure of this domain was solved at 3.2 A resolution. The domain adopts a closed conformation typical of other ABDs, but also forms a dimer both in crystallization conditions and in solution. The structure shows the localization of the residues mutated in patients with periventricular nodular heterotopia or otopalatodigital syndrome. Structural analysis predicts that mutations in both types of disorder may affect actin binding.
Interaction of Circadian Clock Proteins CRY1 and PER2 Is Modulated by Zinc Binding and Disulfide Bond Formation
2014
SummaryPeriod (PER) proteins are essential components of the mammalian circadian clock. They form complexes with cryptochromes (CRY), which negatively regulate CLOCK/BMAL1-dependent transactivation of clock and clock-controlled genes. To define the roles of mammalian CRY/PER complexes in the circadian clock, we have determined the crystal structure of a complex comprising the photolyase homology region of mouse CRY1 (mCRY1) and a C-terminal mouse PER2 (mPER2) fragment. mPER2 winds around the helical mCRY1 domain covering the binding sites of FBXL3 and CLOCK/BMAL1, but not the FAD binding pocket. Our structure revealed an unexpected zinc ion in one interface, which stabilizes mCRY1-mPER2 int…
The C-terminal rod 2 fragment of filamin A forms a compact structure that can be extended
2012
Filamins are large proteins that cross-link actin filaments and connect to other cellular components. The C-terminal rod 2 region of FLNa (filamin A) mediates dimerization and interacts with several transmembrane receptors and intracellular signalling adaptors. SAXS (small-angle X-ray scattering) experiments were used to make a model of a six immunoglobulin-like domain fragment of the FLNa rod 2 (domains 16–21). This fragment had a surprising three-branched structural arrangement, where each branch was made of a tightly packed two-domain pair. Peptides derived from transmembrane receptors and intracellular signalling proteins induced a more open structure of the six domain fragment. Mutagen…
The Modular X- and Gamma-Ray Sensor (MXGS)of the ASIM Payload on the International Space Station
2019
The Modular X- and Gamma-ray Sensor (MXGS) is an imaging and spectral X- and Gamma-ray instrument mounted on the starboard side of the Columbus module on the International Space Station. Together with the Modular Multi-Spectral Imaging Assembly (MMIA) (Chanrion et al. this issue) MXGS constitutes the instruments of the Atmosphere-Space Interactions Monitor (ASIM) (Neubert et al. this issue). The main objectives of MXGS are to image and measure the spectrum of X- and γ-rays from lightning discharges, known as Terrestrial Gamma-ray Flashes (TGFs), and for MMIA to image and perform high speed photometry of Transient Luminous Events (TLEs) and lightning discharges. With these two instruments sp…
Toward an Understanding of the Catalytic Role of Hydrogen-Bond Donor Solvents in the Hetero-Diels−Alder Reaction between Acetone and Butadiene Deriva…
2006
A detailed theoretical investigation of the catalytic role of hydrogen-bond- (HB-) donor molecules (water, methanol, chloroform, dichloromethane, and chloromethane) in the hetero-Diels-Alder reaction between acetone and N,N-dimethyl-1-amino-3-methoxy-1,3-butadiene is presented. This work extends a previous study (Domingo, L. R.; Andres, J. J. Org. Chem. 2003, 68, 8662) in which the importance of weak HB-donor solvents to catalyze more effectively than solvents with a higher dielectric constant but no HB-donor capability was analyzed. Now, based on density functional theory (DFT) at B3LYP/6-31+G(d) level calculations, different techniques for analyzing the nature of HB interaction, namely, n…
Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues.
2007
Abstract Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. S-1360 is a potent and selective inhibitor of HIV-1 IN. In this work, we have carried out molecular dynamics (MD) simulations using a hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approach, to determine the protein–ligand interaction energy for S-1360 and two analogues. Analysis of the MD trajectories reveals that the strongest protein–inhibitor interactions, observed in the three studied complexes, are established with Lys-159 residue and Mg 2+ cation. Calculations of binding energy using BLYP/MM level of theory reveal that there is a direct rela…
Using Prototyping in Authentic Learning of Human-Centred Design of Mobile Apps
2017
Recent advances in mobile technology have seen a sharp increase in the number of mobile applications across various application domains. The challenge remains that many software development teams may lack appropriate competences to design usable and human-centred interactive systems. This can negatively affect the usability and the user experience. In this article, we present how to learn the human-centred design process using an authentic learning approach. Students need to investigate, discuss, construct new knowledge and apply theoretical concepts to address real world problems. The main purpose of authentic learning as a pedagogical approach is to position the subject of study into a re…
Optical biosensors based on ZnO nanostructures: advantages and perspectives. A review
2016
This review article highlights the application of beneficial physico-chemical properties of ZnO nanostructures for the detection of wide range of biological compounds. As the medical diagnostics require accurate, fast and inexpensive biosensors, the advantages inherent optical methods of detection are considered. The crucial points of the immobilization process, responsible for biosensor performance (biomolecule adsorption, surface properties, surface defects role, surface functionalization etc.) along with the interaction mechanism between biomolecules and ZnO are disclosed. The latest achievements in surface plasmon resonance (SPR), surface enhanced Raman spectroscopy (SERS) and photolumi…
Modelling of natural and synthetic polyelectrolyte interactions in natural waters.
2006
In this paper SIT and Pitzer models are used for the first time to describe the interactions of natural and synthetic polyelectrolytes in natural waters. Measurements were made potentiometrically at 25 °C in single electrolyte media, such as Et4NI and NaCl (for fulvic acid 0.1 < I /mol L− 1 < 0.75), and in a multi-component medium simulating the composition of natural waters at a wide range of salinities (for fulvic and alginic acids: 5 < S < 45) with particular reference to sea water [Synthetic Sea Water for Equilibrium studies, SSWE]. In order to simplify calculations, SSWE was considered to be a “single salt” BA, with cation B and anion A representing all the major cations (Na+, K+, Mg2+…