Biomedical subjects

David Zanuy

Publications and source records attributed to David Zanuy.

10 recordsLinked to original sources

PubMed2003

EVEBAT: a fast strategy for the examination of the empty space in polymer matrices.

A very efficient strategy to evaluate the "free volume" and the "unoccupied volume" in polymer matrices is proposed. The method, which has been denoted EVEBAT (Empty Volume Evaluation Based on Atom-Types), emerges from the concept of atom type, which is the basis of a force field. Accordingly, the numerical treatment is minimized by analyzing the atom types used to describe the polymer matrix, which are always a few, rather than all the explicit, atoms involved in it. The performance of the new method has been pointed out by a detailed comparison with the classical insertion algorithms.

Journal Article↗

PubMed2003

The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29.

Amyloid fiber formation and the possible polymorphism of molecular arrangements depend on the polypeptide length and composition. Here, we seek the chemical clues underlying these processes. Our starting point is based on the experimental observation that some short peptide segments are able to develop fibers that are very similar to those of their original parent proteins. We focus our study on the NFGAILSS peptide, derived from the human islet amyloid polypeptide (residues 22-29). This peptide turned out to be a perfect example, illustrating the fact that the amyloid microscopic organization is highly complex, rather than simply involving hydrogen bond formation. Furthermore, obtaining a reliable molecular model has allowed us to analyze the differences between the amyloid structure we have obtained for this peptide and that obtained for the previously studied, two residues shorter, segment (residues 22-27, NFGAIL). This comparative study yields some clues about chemical events that govern the aggregation of proteins into oriented fibers, such as molecular packing between sheets and the degree of interaction specificity. We characterize the important role played by the hydrophobic and aromatic residues in the inter-sheet association and present new approaches toward the understanding of the nature of events that are likely to take place during fibril formation. These include analysis of interaction patterns derived from specific sheet-associated packing.

Amino Acid Sequence↗

PubMed2003

Thermally induced phase transition in helical comblike poly(beta-peptide)s: an atomistic simulation.

Atomistic Monte Carlo (MC) simulations have been used to study a thermally induced phase transition in poly(alpha-octadecyl-beta,L-aspartate). Simulations were performed by using the parallelized version of Configurational Bias MC algorithm adapted to study comblike polymers. A total of 1.15. 10(6) steps were carried out for a molecular system constituted by 6240 atoms/pseudoatoms. Results were consistent with available experimental observations. The limitations of atomistic simulations to study large length-scale phenomena are discussed.

Algorithms↗

PubMed2003

Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL.

Experimentally, short peptides have been shown to form amyloids similar to those of their parent proteins. Consequently, they present useful systems for studies of amyloid conformation. Here we simulate extensively the NFGAIL peptide, derived from the human islet amyloid polypeptide (residues 22-27). We simulate different possible strand/sheet organizations, from dimers to nonamers. Our simulations indicate that the most stable conformation is an antiparallel strand orientation within the sheets and parallel between sheets. Consistent with the alanine mutagenesis, we find that the driving force is the hydrophobic effect. Whereas the NFGAIL forms stable oligomers, the NAGAIL oligomer is unstable, and disintegrates very quickly after the beginning of the simulation. The simulations further identify a minimal seed size. Combined with our previous simulations of the prion-derived AGAAAAGA peptide, AAAAAAAA, and the Alzheimer Abeta fragments 16-22, 24-36, 16-35, and 10-35, and the solid-state NMR data for Abeta fragments 16-22, 10-35, and 1-40, some insight into the length and the sequence matching effects may be obtained.

Amino Acid Sequence↗

PubMed2003

Extended disordered proteins: targeting function with less scaffold.

It has been estimated that a large fraction of cellular proteins are natively disordered. Current opinion largely holds that natively disordered proteins are more 'adaptive', leading to advantages in regulation and in binding diverse ligands. Here, we argue for another, simple, physically based reason. Disordered proteins often have large intermolecular interfaces, the size of which is dictated by protein function. For proteins to be stable as monomers with extensive interfaces, protein size would need to be 2-3 times larger. This would either increase cellular crowding or enlarge the size of the cell by 15-30%, owing to the increase in the sequence length. Smaller sizes of cells, proteins, DNA and RNA conserve energy. Thus, disordered proteins provide a simple yet elegant solution to having large intermolecular interfaces, but with smaller protein, genome and cell sizes.

Models, Molecular↗

PubMed2002

The conformation of dehydroalanine in short homopeptides: molecular dynamics simulations of a 6-residue chain.

A molecular dynamics study about the conformational preferences in a chloroform solution of a homo-oligomer constituted by six residues of dehydroalanine is presented. For this purpose, two sets of force-field parameters and explicit solvent molecules have been used. Furthermore, ab initio calculations have been performed in order to estimate 1[H]-NMR chemical shifts. Results have been compared with experimental data.

Alanine↗

PubMed2002

A molecular dynamics study of the stoichiometric complex formed by poly (alpha, L-glutamate) and octyltrimethylammonium ions in chloroform solution.

We present a molecular dynamics simulation at 300 K in explicit solvent environment of chloroform of the stoichiometric complex formed by poly(alpha,L-glutamate) and octyltrimethylammonium ions. We observed that the alpha-helix conformation of the polypeptide chain remains stable during a 2-ns run. The surfactant ions predominantly adopted an extended conformation that is stabilized by favorable interactions with the organic solvent. Analysis of the organization of the surfactant with respect to the polypeptide chain indicated that each octyltrimethylammonium cation was preferentially bound to more than one carboxylate group. It was found that the most populated arrangement was that with the surfactant cations interacting with two carboxylate groups simultaneously.

Cations↗

PubMed2002

Influence of the presence of small gas molecules in the structure of comblike polyacrylates: a Monte Carlo study.

A theoretical strategy has been developed to study the motion of small molecules through ordered polymeric systems. The strategy, which has been incorporated into a computer program denoted MCDP/2, is especially useful to study comblike polymers organized in biphasic arrangements. This is because it is based on a configurational bias Monte Carlo algorithm, which is more efficient than conventional methods to study dense systems. The MCDP/2 program has been used to investigate the influence of CH(4) and CO(2) gas molecules in the structure of isotactic poly(octadecyl acrylate), a typical comblike polymer. For this purpose, the pure polymer and different molecular systems constituted by several gas molecules dissolved in the polymer matrix have been simulated. Results indicated that the structural relaxation of the polymer is not coupled to the motion of gas molecules. The importance of these results in the field of molecular modeling of transport properties in comblike polymers is discussed.

Journal Article↗

PubMed2002

On the protonation equilibrium for the benzimidazole derivative Hoechst 33258: an electronic molecular orbital study.

Hoechst 33258 and its deprotonated forms have been examined in the gas-phase and in solution using quantum mechanical methods. Ab initio calculations at the HF level have been used to investigate the more relevant geometrical trends of such species, while proton affinities and gas-phase basicities were derived from B3LYP and MP2 electronic energies. Solvation energies were calculated using a dielectric continuum model: MST. The Delta(p)K(a) values were estimated by combining the gas-phase basicities and the free energies of solvation. Comparison of these Delta(p)K(a) values with experimentally reported data have been used to highlight the advantages and limitations of this strategy.

Benzimidazoles↗

PubMedDate not supplied

Comblike poly(alpha-alkyl gamma-glutamate)s: computer simulation studies of an intermediate thermal phase.

Monte Carlo (MC) simulations have been used to study the structure of an intermediate thermal phase of poly(alpha-octadecyl gamma,D-glutamate). This is a comblike poly(gamma-peptide) able to adopt a biphasic structure that has been described as a layered arrangement of backbone helical rods immersed in a paraffinic pool of polymethylene side chains. Simulations were performed at two different temperatures (348 and 363 K), both of them above the melting point of the paraffinic phase, using the configurational bias MC algorithm. Results indicate that layers are constituted by a side-by-side packing of 17/5 helices. The organization of the interlayer paraffinic region is described in atomistic terms by examining the torsional angles and the end-to-end distances for the octadecyl side chains. Comparison with previously reported comblike poly(beta-peptide)s revealed significant differences in the organization of the alkyl side chains.

Calorimetry↗