The structural parameters of rare-earth oxides lanthania (La2O3) and ytterbia (YbO), and of transition-metal oxides yttria (Y2O3) and lutetia (Lu2O3), candidate replacements of silica as gate insulators in nanometric Si electronics, are determined via ab initio calculations. The stability against formation of silica, silicides, and silicates for these oxides in contact with silicon is also investigated: we find stability against silica and silicide formation, but not against silicates

Motivation: Proteins with solenoid repeats evolve more quickly than non-repetitive ones and their periodicity may be rapidly hidden at sequence level, while still evident in structure. In order to identify these repeats, we propose here a novel method based on a metric characterizing amino-acid properties (polarity, secondary structure, molecular volume, codon diversity, electric charge) using five previously derived numerical functions.Results: The five spectra of the candidate sequences coding for structural repeats, obtained by Discrete Fourier Transform (DFT), show common features allowing determination of repeat periodicity with excellent results. Moreover it is possible to introduce a phase space parameterized by two quantities related to the Fourier spectra which allow for a clear distinction between a non-homologous set of globular proteins and proteins with solenoid repeats. The DFT method is shown to be competitive with other state of the art methods in the detection of solenoid structures, while improving its performance especially in the identification of periodicities, since it is able to recognize the actual repeat length in most cases. Moreover it highlights the relevance of local structural propensities in determining solenoid repeats.Availability: A web tool implementing the algorithm presented in the article (REPETITA) is available with additional details on the data sets at the URL: http://protein.bio.unipd.it/repetita/.Contact: silvio.tosatto@unipd.it

We show that a framework derived from the common character of globular proteins can be used to understand the design of protein sequences, the behavior of intrinsically unstructured proteins, and the formation of amyloid fibrils in a unified manner. Our studies provide compelling support for the idea that protein native-state structures, the structures adopted by intrinsically unstructured proteins on binding as well as those of amyloid aggregates, all reside in a physical state of matter in which the free energy landscape is sculpted not by the specific sequence of amino acids, but rather by considerations of geometry and symmetry. We elucidate the key role played by sequence design in selecting the structure of choice from the predetermined menu of putative native-state structures.amyloid formation ͉ presculpted free energy landscape ͉ protein design ͉ protein folding I t is well known that the sequence of amino acids comprising a protein encodes its native-state structure. The protein folding problem, the determination of the native-state structure given a sequence of amino acids, however, has remained unsolved, in part because of the sheer complexity of the problem: the huge number of degrees of freedom associated with the protein atoms and the surrounding water molecules as well as the history dependence implicit in an evolutionary process. It was recently proposed (1, 2) that considerations of symmetry and geometry determine the limited menu of folded conformations from which a protein can choose for its native-state structure (3). Protein structures belong to a novel phase of matter associated with the marginally compact phase of short tubes with a thickness specially self-tuned to be comparable with the range of attractive interactions promoting the compaction. This phase is a finite size effect and exists only for relatively short tubes. That it is poised near a phase transition provides a simple explanation for the flexibility of native-state structures. The marginally compact phase is stabilized by the interplay of the hydrophobic (H) effect and hydrogen-bond formation. The structures that one finds in it are modular in construction, being made up of two principal building blocks, helices and planar sheets; the degeneracy is greatly reduced so that the number of the resulting energy minima is relatively small.The principal theme of our work is to present a unification of several seemingly distinct aspects of proteins within the unified framework sketched above, which is derived from the common characteristics of all proteins. We will tackle three issues: (i) protein design (4-12); (ii) intrinsically unstructured proteins (IUPs), which interact with different molecular partners and adopt relatively rigid conformations in the presence of natural ligands (13-19); and (iii) the propensity of proteins to misfold and aggregate leading to the formation of amyloid fibrils, which are implicated in debilitating human diseases (20-30) such as Alzheimer's, light-chain amyloidosis, type II diabetes, and spongiform...

We propose a computational framework to study the lipid-mediated clustering of integral membrane proteins. Our method employs a hierarchical approach. The potential of mean force (PMF) of two interacting proteins is computed under a coarse-grained 3-D model that successfully describes the structural properties of reconstituted lipid bilayers of dymiristoylphophatidylcholine (DMPC) molecules. Subsequently, a 2-D model is adopted, where proteins represented as self-avoiding disks interact through the previously computed PMF, which is modified to take into account three body corrections. The aggregation of the proteins is extensively studied under the condition of negative hydrophobic mismatch: the formation of clusters with increasing size agrees with previous computational and experimental findings.