Restraint-based comparative modeling was used for calculation and visualization of the H4-H5-loop of Na+/K+-ATPase from mouse brain (Mus musculus, adult male brain, α2-isoform) between the amino acid residues Cys336 and Arg758 in the E1 conformation The structure consists of two well separated parts. The N-domain is formed by a seven-stranded antiparallel β-sheet with two additional β-strands and five α-helices sandwiching it, the P-domain is composed of a typical Rossman fold. The ATP-binding site was found on the N-domain to be identical in both α2- and α1-isoforms. The phosphorylation Asp369 residue was found in the central part of the P-domain, located at the C-terminal end of the central β-sheet. The distance between the α-carbon of Phe475 at the ATP-binding site and the α-carbon of Asp369 at the phosphorylation site is 3.22 nm. A hydrogen bond between the oxygen atom of Asp369 and the nitrogen atom of Lys690 was clearly detected and assumed to play a key role in maintaining the proper structure of the physphorylaton site in E1 conformation., G. Tejral, L. Koláčná, A. Kotyk, E. Amler., and Obsahuje bibliografii
The article presents the construction of an agent-based model of segregation step by step. The article is intended as a tutorial for the reader’s first steps with agent-based modeling. The model is programmed in the NetLogo software and provided in two versions: first as an online executable version, for first-impression purposes, and second as NetLogo code, for serious experiments and further model improvements by the reader. The article describes the user interface and source code of the model in close detail. Most of the article is dedicated to careful, in-depth explanation of the NetLogo code. The model aims to answer Schelling’s classical question: "Is it possible to obtain an ethnically segregated structure of a town with relatively tolerant inhabitants?" The model also aims to answer the question: "Does size of recognized neighbourhood suppress tendency to segregation?" Analysis of the data produced by the model informs us that the tendency to segregation decreased with larger recognized neighbourhood - the larger the neighbourhood the lower the number of inhabitants living in an ethnically homogenous neighbourhood. However, size of recognized neighbourhood did not moderate the relationship between intolerance and tendency to segregation - the slope of the relationship was still the same (or even steeper for larger neighbourhoods)., František Kalvas., and Obsahuje bibliografické odkazy
Počítačové modelování biomolekul je zaměřeno na studium struktury, dynamiky a vzájemných interakcí nukleových kyselin, proteinů a buněčných membrán, zkoumání katalytického účinku enzymů, racionální návrh struktury nových léků atd. K dispozici je celá škála metod - bioinformatika, klasické molekulárně-dynamické (MD) simulace, kvantově-chemické ab initio výpočty, popř. kombinované QM/MM přístupy. Mezi softwarovými balíky většinou existuje i víceméně plnohodnotná freewarová alternativa., Computer modeling of biomolecules is aimed at studying the structure, dynamics and interaction of nucleic acids, proteins and cell membranes, examining the catalytic effect of enzymes, rational drug design etc. There is a whole range of methods - bioinformatics, classical molecular dynamic (MD) simulations, quantum-chemical ab initio calculations, or combined QM/MM approaches. Among the software packages there is usually more of less full-featured freeware alternatives., Ivan Barvík., and Obsahuje bibliografii
Tento příspěvek představuje výsledky mé disertační práce na téma remodelace tkání s důrazem na tkáň kostní. Pro studium a modelování tohoto procesu jsme vyvinuli biotermodynamický koncept remodelace, který umožňuje zahrnutí obou zásadních vlivů: mechanické stimulace i biochemických podmínek. Na typických onemocněních spojených s remodelací dokumentujeme použitelnost modelu., This article presents key results from the author's Ph.D. thesis on tissue remodelling with focus on bone tissue. We have developed a biothermodynamic concept of remodeling, for studying and modelling, of this process which enables to inclusion of two crucial factors: mechanical stimulation and biochemical conditions. We use typical diseases related to remodelling to show the apllicability of the model., Václav Klika., and Obsahuje bibliografii
Molecular modeling of the H4-H5-loop of the α2 isoform of Na+/K+-ATPase in the E1 and E2 conformations revealed that twisting of the nucleotide (N) domain toward the phosphorylation (P) domain is connected with the formation of a short π-helix between Asp369 and Thr375. This conformational change close to the hinge region between the N-domain and the P-domain could be an important event leading to a bending of the N-domain by 64.7° and to a shortening of the distance between the ATP binding site and the phosphorylation site (Asp369) by 1.22 nm from 3.22 nm to 2.00 nm. It is hypothesized that this shortening mechanism is involved in the Na+-dependent formation of the Asp369 phospho-intermediate as part of the overall Na+/K+-ATPase activity., G. Tejral ... [et al.]., and Obsahuje seznam literatury