Search results for "Models"
showing 10 items of 8211 documents
Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2.
2008
Recent, primarily structural observations indicate that related viruses, harboring no sequence similarity, infect hosts of different domains of life. One such clade of viruses, defined by common capsid architecture and coat protein fold, is the so-called PRD1-adenovirus lineage. Here we report the structure of the marine lipid-containing bacteriophage PM2 determined by crystallographic analyses of the entire approximately 45 MDa virion and of the outer coat proteins P1 and P2, revealing PM2 to be a primeval member of the PRD1-adenovirus lineage with an icosahedral shell and canonical double beta barrel major coat protein. The view of the lipid bilayer, richly decorated with membrane protein…
Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site.
2010
The protein structure-based virtual screening is typically accomplished using a molecular docking procedure. However, docking is a fairly slow process that is limited by the available scoring functions that cannot reliably distinguish between active and inactive ligands. In contrast, the ligand-based screening methods that are based on shape similarity identify the active ligands with high accuracy. Here, we show that the usage of negative images of the ligand-binding site, together with shape comparison tools, which are typically used in ligand-based virtual screening, improve the discrimination of active molecules from inactives. In contrast to ligand-based shape comparison, the negative …
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…
Accurate Treatment of Large Supramolecular Complexes by Double-Hybrid Density Functionals Coupled with Nonlocal van der Waals Corrections.
2015
In this work, we present a thorough assessment of the performance of some representative double-hybrid density functionals (revPBE0-DH-NL and B2PLYP-NL) as well as their parent hybrid and GGA counterparts, in combination with the most modern version of the nonlocal (NL) van der Waals correction to describe very large weakly interacting molecular systems dominated by noncovalent interactions. Prior to the assessment, an accurate and homogeneous set of reference interaction energies was computed for the supramolecular complexes constituting the L7 and S12L data sets by using the novel, precise, and efficient DLPNO-CCSD(T) method at the complete basis set limit (CBS). The correction of the bas…
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 …
Theoretical Study of Catalytic Efficiency of a Diels–Alderase Catalytic Antibody: An Indirect Effect Produced During the Maturation Process
2007
The Diels–Alder reaction is one of the most important and versatile transformations available to organic chemists for the construction of complex natural products, therapeutics agents, and synthetic materials. Given the lack of efficient enzymes capable of catalyzing this kind of reaction, it is of interest to ask whether a biological catalyst could be designed from an antibody-combining site. In the present work, a theoretical study of the different behavior of a germline catalytic antibody (CA) and its matured form, 39 A-11, that catalyze a Diels–Alder reaction has been carried out. A free-energy perturbation technique based on a hybrid quantum-mechanics/molecular-mechanics scheme, togeth…
Macrocyclic oligoureas with xanthene and diphenyl ether units
2009
Two cyclic oligoureas with 64- and 80-membered rings in which two sets of three or four rigid xanthene (X) units are connected via flexible diphenyl ether (D) units were synthesized by a stepwise fragment condensation. The compounds were characterized by (1)H NMR and ESI mass spectrometry. The structure of the cyclic octamer (XXXDXXXD) was additionally confirmed by single crystal X-ray analysis. The molecule assumes a strongly folded conformation with distorted C(2)-symmetry, stabilized by intramolecular hydrogen bonds. Surprisingly, intermolecular hydrogen bonds between the macrocycles were not observed. (1)H NMR spectra suggest a C(2) symmetrical conformation of the octamer in solution al…
Chemistry and Photochemistry of 2,6-Bis(2-hydroxybenzilidene)cyclohexanone. An Example of a Compound Following the Anthocyanins Network of Chemical R…
2014
The kinetics and thermodynamics of the 2,6-bis(2-hydroxybenzilidene)cyclohexanone chemical reactions network was studied at different pH values using NMR, UV-vis, continuous irradiation, and flash photolysis. The chemical behavior of the system partially resembles anthocyanins and their analogue compounds. 2,6-Bis(2-hydroxybenzilidene)cyclohexanone exhibits a slow color change from yellow to red styrylflavylium under extreme acidic conditions. The rate constant for this process (5 × 10(-5) s(-1)) is pH independent and controlled by the cis-trans isomerization barrier. However, the interesting feature is the appearance of the colorless compound, 7,8-dihydro-6H-chromeno[3,2-d]xanthene, isolat…
Osmium(III) Complexes with POP Pincer Ligands: Preparation from Commercially Available OsCl3·3H2O and Their X-ray Structures
2010
Complexes OsCl3{dbf(PiPr2)2} [1; dbf(PiPr2)2 = 4,6-bis(diisopropylphosphino)dibenzofuran], OsCl3{xant(PiPr2)2} [2; xant(PiPr2)2 = 9,9-dimethyl-4,5-bis(diisopropylphosphino)xanthene], and OsCl3{xant(PPh2)2} [3; xant(PPh2)2 = 9,9-dimethyl-4,5-bis(diphenylphosphino)xanthene] have been obtained in high yield by the reaction of the corresponding diphosphine with OsCl3·3H2O. The ruthenium(III) counterparts RuCl3{dbf(PiPr2)2} (4), RuCl3{xant(PiPr2)2} (5), and RuCl3{xant(PPh2)2} (6) are similarly obtained from RuCl3·3H2O in moderate yields. The X-ray structures of dbf(PiPr2)2 and complexes 1−3 are also reported.
Preparation of two sets of 5,6,7-trioxygenated dihydroflavonol derivatives as free radical scavengers and neuronal cell protectors to oxidative damag…
2009
An unusual class of 5,6,7-trioxygenated dihydroflavonols (3a-e and 4a-j) were designed and prepared. Their antioxidative properties were assessed by examining their capacities in several in vitro models, including superoxide anion and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging, rat liver homogenate lipid peroxidation inhibition, PC12 cells protection from oxidative damage, and xanthine oxidase inhibition. These dihydroflavonols displayed positive quenching abilities towards O(2)(-) and DPPH free radicals, in which the majority exhibited superior antioxidant properties to Vitamin C. cis-Configurated compound (+/-)-3e demonstrated remarkable inhibition to LPO with an IC(50) value…