1,721,138 research outputs found
Site specificity in cycloadditions of diphenylnitrile imine with 8-substituted-8-azaheptafulvenes and tricarbonyl(8-azaheptafulvene)iron complexes
No full textFolding simulation of protein models on the structure-based cubo-octahedral lattice with the Contact Interactions algorithm
No full textComputer simulations of protein models on lattices have been widely used as an aid in the study of protein folding process. Following the suggestion of Raghunathan and Jernigan (1997, Protein Sci 6:2072-2083) that the cubooctahedral lattice can allow a more realistic representation of proteins than other lattices, we propose here the use of a new set of internal coordinates theta for the description of a protein model on this lattice. An easy procedure for the conversion of the theta coordinates to the Cartesian coordinates is also described. When the Contact Interaction approach, already proposed by us for simulations on square or cubic lattices, was applied to the cube-octahedral lattice, the system obeyed the correct thermodynamics derived from the definition of energy. Thus, lattice simulations of protein models, in which secondary structure elements such as alpha-helices or beta-strands can be easily identifiable, can be performed
A lattice study of multimolecular ensembles of protein models. Effect of sequence on the final state: Globules, aggregates, dimers, fibrillae
No full textThree sequences of simple protein models on the two-dimensional square lattice have been chosen for a study of the behavior of different classes of proteins as a function of temperature and concentration using multimolecular systems under periodic boundary conditions. The results of the dynamic simulations have shown the profound influence that the intermolecular contacts can have on the accessibility of the states the various sequences can reach: this makes possible the formation of different kinds of structures under the control not only of sequence and temperature but also of concentration that can become the main driving force for the formation of ordered lamellar structures for sequences properly designed
Contact interactions method: A new algorithm for protein folding simulations
No full textComputer simulations of simple exact lattice models are an aid in the study of protein folding process; they have sometimes resulted in predictions experimentally proved. The contact interactions (CI) method is here proposed as a new algorithm for the conformational search in the low-energy regions of protein chains modeled as copolymers of hydrophobic and polar monomers configured as self-avoiding walks on square or cubic lattices. It may be regarded as an extension of the standard Monte Carlo method improved by the concept of cooperativity deriving from nonlocal contact interactions. A major difference with respect to other algorithms is that criteria for the acceptance of new conformations generated during the simulations are not based on the energy of the entire molecule, but cooling factors associated with each residue define regions of the model protein with higher or lower mobility. Nine sequences of length ranging from 20 to 64 residues were used on the square lattice and 15 sequences of length ranging from 46 to 136 residues were used on the cubic lattice. The CI algorithm proved very efficient both in two and three dimensions, and allowed us to localize energy minima nor localized by other searching algorithms described in the literature. Use of this algorithm is not limited to the conformational search, because it allows the exploration of thermodynamic and kinetic behavior of model protein chains
Simulation of melting transitions in crystalline polymers
No full textWe have used a very simple dynamic Monte Carlo approach to simulate polymer behavior in a 2-dimensional lattice. In this paper we show that the model is able to simulate all the basic features of crystallization and melting of real polymer crystals. Crystals of large polymer molecules can be obtained with a thickness which depends on the temperature of crystallization. We also demonstrate that the crystals melt in agreement with the Gibbs-Thompson equation, showing a strong influence of the rate of heating on the melting process. Furthermore thin crystals may thicken upon annealing: in adequate conditions. The results obtained may be used in the interpretation of scattering experiments on the crystallization of polymers
Classical and non-classical secondary orbital interactions and Coulombic attraction in regiospecific dimerization of acrolein
No full textNon-classical (bridging) and classical (Woodward-Hoffmann) secondary orbital interactions as well as a favourable electrostatic interaction are involved in the stabilization of the two lowest transition passes of the acrolein dimerization. The heteroatoms provide anchimeric assistance to the hetero Diels-Alder reaction through a neighbouring-group mechanism
An unexpected bispericyclic transition structure leading to 4+2 and 2+4 cycloadducts in the endo dimerization of cyclopentadiene
No full textThe stereospecific endo dimerization of cyclopentadiene takes place through an asynchronous and symmetrical bispericyclic transition structure, which shows a merging of the 4+2 and 2+4 cycloaddition paths. The shape of the transition structure testifies to the presence of attractive Salem/Houk secondary orbital interactions assisting the endo approach
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