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Structural Preferences (structural + preference)

Distribution by Scientific Domains
Chemistry100%

Selected Abstracts

Structural Preferences of Single-Walled Silica Nanostructures: Nanospheres and Chemically Stable Nanotubes

CHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2006
Mikko Linnolahti Dr.
Abstract Structural preferences of single-walled and coordinatively saturated spherical and tubular nanostructures of silica have been determined by ab initio calculations. Two families of spherical (SiO2)n clusters derived from Platonic solids and Archimedean polyhedra are depicted, with n ranging from 4,120. The analogue of a truncated icosidodecahedron, Ih -symmetric Si120O240, is favored in energy, closely followed by the Ih -symmetric Si60O120 -truncated icosahedron. The silica nanotubes derived from spherical clusters are capped by Si2O2 rings, whereas the tubular section consists of single oxygen bridges. Periodic studies performed with open-ended silica nanotubes and the ,-quartz polymorph of silica, along with a comparisons to fullerenes and carbon nanotubes, suggest that tubes with diameters of approximately 1 nm should be chemically stable. [source]

Do Valine Side Chains Have an Influence on the Folding Behavior of , -Substituted , -Peptides?

HELVETICA CHIMICA ACTA, Issue 10 2004
Alice Glättli
The influence of valine side chains on the folding/unfolding equilibrium and, in particular, on the 314 -helical propensity of ,3 -peptides were investigated by means of molecular-dynamics (MD) simulation. To that end, the valine side chains in two different ,3 -peptides were substituted by leucine side chains. The resulting four peptides, of which three have never been synthesized, were simulated for 150 to 200,ns at 298 and 340,K, starting from a fully extended conformation. The simulation trajectories obtained were compared with respect to structural preferences and folding behavior. All four peptides showed a similar folding behavior and were found to predominantly adopt 314 -helical conformations, irrespective of the presence of valine side chains. No other well-defined conformation was observed at significant population in any of the simulations. Our results imply that ,3 -peptides show a structural preference for 314 -helices independent of the branching nature of the side chains, in contrast to what has been previously proposed on the basis of circular-dichroism (CD) measurements. [source]

The Alzheimer ,-peptide shows temperature-dependent transitions between left-handed 31 -helix, ,-strand and random coil secondary structures

FEBS JOURNAL, Issue 15 2005
Jens Danielsson
The temperature-induced structural transitions of the full length Alzheimer amyloid ,-peptide [A,(1,40) peptide] and fragments of it were studied using CD and 1H NMR spectroscopy. The full length peptide undergoes an overall transition from a state with a prominent population of left-handed 31 (polyproline II; PII)-helix at 0 °C to a random coil state at 60 °C, with an average ,H of 6.8 ± 1.4 kJ·mol,1 per residue, obtained by fitting a Zimm,Bragg model to the CD data. The transition is noncooperative for the shortest N-terminal fragment A,(1,9) and weakly cooperative for A,(1,40) and the longer fragments. By analysing the temperature-dependent 3JHNH, couplings and hydrodynamic radii obtained by NMR for A,(1,9) and A,(12,28), we found that the structure transition includes more than two states. The N-terminal hydrophilic A,(1,9) populates PII-like conformations at 0 °C, then when the temperature increases, conformations with dihedral angles moving towards ,-strand at 20 °C, and approaches random coil at 60 °C. The residues in the central hydrophobic (18,28) segment show varying behaviour, but there is a significant contribution of ,-strand-like conformations at all temperatures below 20 °C. The C-terminal (29,40) segment was not studied by NMR, but from CD difference spectra we concluded that it is mainly in a random coil conformation at all studied temperatures. These results on structural preferences and transitions of the segments in the monomeric form of A, may be related to the processes leading to the aggregation and formation of fibrils in the Alzheimer plaques. [source]

Do Valine Side Chains Have an Influence on the Folding Behavior of , -Substituted , -Peptides?

HELVETICA CHIMICA ACTA, Issue 10 2004
Alice Glättli
The influence of valine side chains on the folding/unfolding equilibrium and, in particular, on the 314 -helical propensity of ,3 -peptides were investigated by means of molecular-dynamics (MD) simulation. To that end, the valine side chains in two different ,3 -peptides were substituted by leucine side chains. The resulting four peptides, of which three have never been synthesized, were simulated for 150 to 200,ns at 298 and 340,K, starting from a fully extended conformation. The simulation trajectories obtained were compared with respect to structural preferences and folding behavior. All four peptides showed a similar folding behavior and were found to predominantly adopt 314 -helical conformations, irrespective of the presence of valine side chains. No other well-defined conformation was observed at significant population in any of the simulations. Our results imply that ,3 -peptides show a structural preference for 314 -helices independent of the branching nature of the side chains, in contrast to what has been previously proposed on the basis of circular-dichroism (CD) measurements. [source]

Determination of ,-helix N1 energies after addition of N1, N2, and N3 preferences to helix/coil theory

PROTEIN SCIENCE, Issue 4 2000
Jia Ke Sun
Abstract Surveys of protein crystal structures have revealed that amino acids show unique structural preferences for the N1, N2, and N3 positions in the first turn of the ,-helix. We have therefore extended helix-coil theory to include statistical weights for these locations. The helix content of a peptide in this model is a function of N-cap, C-cap, N1, N2, N3, C1, and helix interior (N4 to C2) preferences. The partition function for the system is calculated using a matrix incorporating the weights of the fourth residue in a hexamer of amino acids and is implemented using a FORTRAN program. We have applied the model to calculate the N1 preferences of Gln, Val, Ile, Ala, Met, Pro, Leu, Thr, Gly, Ser, and Asn, using our previous data on helix contents of peptides Ac-XAKAAAAKAAGY-CONH2. We find that Ala has the highest preference for the N1 position. Asn is the most unfavorable, destabilizing a helix at N1 by at least 1.4 kcal mol,1 compared to Ala. The remaining amino acids all have similar preferences, 0.5 kcal mol,1 less than Ala. Gln, Asn, and Ser, therefore, do not stabilize the helix when at N1. [source]