Search results for "molecular model"

9 Å cryo-EM structure and molecular model of a gastropod hemocyanin didecamer (KLH1) reveals the architecture of the asymmetric collar

2008

Hemocyanins are blue copper proteins that transport oxygen in the hemolymph of many arthropods and molluscs. Molluscan hemocyanins are decamers, didecamers or multidecamers of a 350–400 kDa polypeptide subunit that is subdivided into seven or eight different functional units (FUs, each with a single copper active site). The quaternary structure is a semi-hollow cylinder consisting of a wall and a collar. Recently, we published a 9 A cryo-EM structure and molecular model of a cephalopod hemocyanin decamer (NpH, from Nautilus pompilius) that answered many hitherto unsolved questions concerning the quaternary structure of molluscan hemocyanin. Notably, it revealed the twisted pathway of the 10…

Molecular modeling studies on dopamine-amino acid conjugates as potential dopaminergic modulators

2015

Local aromaticity in polyacenes manifested by individual proton and carbon shieldings: DFT mapping of aromaticity

2019

Exponential dependencies between locally calculated geometric and magnetic indexes of aromaticity, harmonic oscillator model of aromaticity (HOMA) and nucleus independent chemical shifts (NICS)(0), NICS(1) and NICS(1)zz, and the number of conjugated benzene rings in linear acenes, from benzene to decacene were observed at B3LYP/6-311+G** level of theory. Correlations between HOMA and NICS indexes showed exponential dependencies and were fitted with simple three-parameter function. Similar correlations between both indexes of aromaticity and proton and carbon nuclear isotropic shieldings of individual acene rings were observed. Contrary to proton data, the predicted 13 C nuclear isotropic sh…

3He NMR studies on helium–pyrrole, helium–indole, and helium–carbazole systems: a new tool for following chemistry of heterocyclic compounds

2015

The 3He nuclear magnetic shieldings were calculated for free helium atom and He–pyrrole, He–indole, and He–carbazole complexes. Several levels of theory, including Hartree–Fock (HF), Second-order Møller-Plesset Perturbation Theory (MP2), and Density Functional Theory (DFT) (VSXC, M062X, APFD, BHandHLYP, and mPW1PW91), combined with polarization-consistent pcS-2 and aug-pcS-2 basis sets were employed. Gauge-including atomic orbital (GIAO) calculated 3He nuclear magnetic shieldings reproduced accurately previously reported theoretical values for helium gas. 3He nuclear magnetic shieldings and energy changes as result of single helium atom approaching to the five-membered ring of pyrrole, indo…

BANΔIT: B’‐factor Analysis for Drug Design and Structural Biology

2020

The analysis of B‐factor profiles from X‐ray protein structures can be utilized for structure‐based drug design since protein mobility changes have been associated with the quality of protein‐ligand interactions. With the BANΔIT (B’‐factor analysis and ΔB’ interpretation toolkit), we have developed a JavaScript‐based browser application that provides a graphical user interface for the normalization and analysis of B’‐factor profiles. To emphasize the usability for rational drug design applications, we have analyzed a selection of crystallographic protein‐ligand complexes and have given exemplary conclusions for further drug optimization including the development of a B’‐factor‐supported pha…

H−ZSM-5 Modified Zeolite:  Quantum Chemical Models of Acidic Sites

2007

A ZSM-5 fragment, containing 52 tetrahedral moieties, each of them formed by one silicon or one aluminum atom surrounded by four oxygen atoms, was employed to model (52T systems) by quantum chemical calculations (i) the influence of the positions of the acidic sites on the energetics of 22 aluminum monosubstituted and bisubstituted 52T acidic zeolite (H-ZSM-5) systems and (ii) the local adsorption properties and acidic strength of the corresponding -OH sites. The energetics and the structural properties of simpler acid H-ZSM-5 systems containing only five Tetrahedral moieties (5T systems) were also modeled for comparison. B3LYP/6-31G(d,p) partial geometry optimization routines were performe…

Statistical characterization of self-assembled charged nanoparticle structures

2013

We propose a novel approach for description of dynamics of nanostructure formation for a system consisting of oppositely charged particles. The combination of numerical solution of analytical Bogolyubov–Born–Green–Kirkwood–Yvon (BBGKY) type equation set with reverse Monte Carlo (RMC) method allows us to overcome difficulties of standard approaches, such as kinetic Monte Carlo or Molecular Dynamics, to describe effects of long-range Coulomb interactions. Moreover, this allows one to study the system dynamics on realistic time and length scales. We applied this method to a simple short-range Lenard–Jones (LJ)-like three- (3D) and two-dimensional (2D) system combining the long-range Coulomb an…

IDEA: interface dynamics and energetics algorithm.

2007

IDEA, interface dynamics and energetics algorithm, was implemented, in FORTRAN, under different operating systems to mimic dynamics and energetics of elementary events involved in interfacial processes. The code included a parallel elaboration scheme in which both the stochastic and the deterministic components, involved in the developed physical model, worked simultaneously. IDEA also embodied an optionally running VISUAL subroutine, showing the dynamic energy changes caused by the surface events, e.g., occurring at the gas-solid interface. Monte Carlo and ordinary differential equation system subroutines were employed in a synergistic way to drive the occurrence of the elementary events a…

Pyrrolo[1,2-f]phenanthridines and related non-rigid analogues as antiviral agents.

2002

Abstract The pyrrolo[1,2- f ]phenanthridines 8 – 22 and the corresponding non-rigid analogues 23 – 41 were synthesised and their ability to inhibit the replication of HIV-1 was tested. Only the polycyclic derivatives 10 , 11 , and 13 showed a weak anti -HIV activity, whereas several pyrrolo-phenanthridines ( 8 , 10 , 16 – 18 ) were found to stimulate the multiplication of MT-4 cells at low concentrations. Derivative 10 demonstrated to possess the unique property of stimulating the multiplication of lymphocytes joined to HIV inhibition.

3D-QSAR pharmacophore modeling and in silico screening of new Bcl-xl inhibitors.

2010

Bcl-2 proteins family members play several roles in tumoral proliferation: they inhibit proapoptotic activity during oncogenesis, support tumor cells survival, induce chemoresistance. The discovery of new small inhibitors of Bcl-xl represents a new frontier for cancer treatment. In this study, a 3D-QSAR pharmacophore model was developed, based on 42 biarylacylsulfonamides, and used to understand the structural factors affecting the inhibitory potency of these derivatives. Aromatic, negative charge, and hydrogen bond acceptor effects contribute to the inhibitory activity. The model was then employed as 3D search query to screen ZINC drug-like database in order to select new scaffolds. Finall…