Mitochondrial carriers are nuclear-encoded proteins, which translocate solutes across the inner mitochondrial membrane. functional as monomers and have six TM alpha-helices termini in intermembrane space.

We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges-regions situated between any of two major elements of secondary structure (alpha helices and beta strands)-containing a pure random coil were compared with connecting bridges containing 3/10 helices. We included discovered trends in the or...

Low-resolution experiments suggest that most membrane helices span over 17-25 residues and that most loops between two helices are longer than 15 residues. Both constraints have been used explicitly in the development of prediction methods. Here, we compared the largest possible sequence-unique data sets from high- and low-resolution experiments. For the high-resolution data, we found that only...

We compute the group of Morita self-equivalences (the Picard group) of a Poisson structure on an orientable surface, under the assumption that the degeneracies of the Poisson tensor are linear. The answer involves mapping class groups of surfaces, i.e., groups of isotopy classes of diffeomorphisms. We also show that the Picard group of these structures coincides with the group of outer Poisson ...

The topological structure of scalar, vector, and second-order tensor fields provides an important mathematical basis for data analysis and visualization. In this paper, we extend this framework towards higher-order tensors. First, we establish formal uniqueness properties for a geometrically constrained tensor decomposition. This allows us to define and visualize topological structures in symme...

Understanding the sequence-structure relationships in globular proteins is important for reliable protein structure prediction and de novo design. Using a database of 1131 alpha-helices with nonidentical sequences from 205 nonhomologous globular protein chains, we have analyzed structural and sequence characteristics of alpha-helices. We find that geometries of more than 99% of all the alpha-he...

All naturally occurring amino acids with the exception of glycine contain one or more chiral carbon atoms and can therefore occur in two different configurations, L (levo, left-handed) and D (dextro, right-handed). Proteins are almost exclusively built from L-amino acids. The stereochemical bias of nature is further reflected at the secondary structure level where right-handed helices are stron...

The problem of explicit generation of unitary operators for atomic systems with degenerate energy levels is considered. The Lie algebra structure is used to derive constructive control schemes for the creation of arbitrary superposition states and selective population interchanges for a transition between two three-fold degenerate energy levels.

Helix kinks are a common feature of α-helical membrane proteins, but are thought to be rare in soluble proteins. In this study we find that kinks are a feature of long α-helices in both soluble and membrane proteins, rather than just transmembrane α-helices. The apparent rarity of kinks in soluble proteins is due to the relative infrequency of long helices (≥20 residues) in these proteins. We c...

Identical objects, regularly assembled, form a helix, which is the principal motif of nucleic acids, proteins, and viral capsids.