Helix

Abstract: A novel method to model and predict the location and orientation of alpha helices in membrane- spanning proteins is presented. It is based on a hidden Markov model (HMM) with an architecture that corresponds closely to the biological system. The model is cyclic with 7 types of states for helix core, helix caps on either side, loop on the cytoplasmic side, two loops for the non-cytoplasmic side, and a globular domain state in the middle of each loop. The two loop paths on the non-cytoplasmic side are used to model short and long loops separately, which corresponds biologically to the two known different membrane insertions mechanisms. The close mapping between the biological and computational states allows us to infer which parts of the model architecture are important to capture the information that encodes the membrane topology, and to gain a better understanding of the mechanisms and constraints involved. Models were estimated both by maximum likelihood and a discriminative method, and a method for reassignment of the membrane helix boundaries were developed. In a cross validated test on single sequences, our transmembrane HMM, TMHMM, correctly predicts the entire topology for 77% of the sequences in a standard dataset of 83 proteins with known topology. The same accuracy was achieved on a larger dataset of 160 proteins. These results compare favourably with existing methods.

Abstract: An algorithm has been developed which identifies alpha-helices involved in the interactions of membrane proteins with lipid bilayers and which distinguishes them from helices in soluble proteins. The membrane-associated helices are then classified with the aid of the hydrophobic moment plot, on which the hydrophobic moment of each helix is plotted as a function of its hydrophobicity. The magnitude of hydrophobic moment measures the amphiphilicity of the helix (and hence its tendency to seek a surface between hydrophobic and hydrophilic phases), and the hydrophobicity measures its affinity for the membrane interior. Segments of membrane proteins in alpha-helices tend to fall in one of three regions of a hydrophobic moment plot: (1) monomeric transmembrane anchors (class I HLA transmembrane sequences) lie in the region of highest hydrophobicity and smallest hydrophobic moment; (2) helices presumed to be paired (such as the transmembrane M segments of surface immunoglobulins) and helices which are bundled together in membranes (such as bacteriorhodopsin) fall in the adjacent region with higher hydrophobic moment and smaller hydrophobicity; and (3) helices from surface-seeking proteins (such as melittin) fall in the region with still higher hydrophobic moment. alpha-Helices from globular proteins mainly fall in a region of lower mean hydrophobicity and hydrophobic moment. Application of these methods to the sequence of diphtheria toxin suggests four transmembrane helices and a surface-seeking helix in fragment B, the moiety known to have transmembrane function.

Abstract: We investigated propagation of light through a uniaxial photonic metamaterial composed of three-dimensional gold helices arranged on a two-dimensional square lattice. These nanostructures are fabricated via an approach based on direct laser writing into a positive-tone photoresist followed by electrochemical deposition of gold. For propagation of light along the helix axis, the structure blocks the circular polarization with the same handedness as the helices, whereas it transmits the other, for a frequency range exceeding one octave. The structure is scalable to other frequency ranges and can be used as a compact broadband circular polarizer.

Abstract: The transition between the helical and randomly coiled forms of a polypeptide chain is discussed by reference to a simple model that allows bonding only between each group and the third preceding Two principal parameters are introduced, a statistical parameter that is essentially an equilibrium constant for the bonding of segments to a portion of the chain that is already in helical form, and a special correction factor for the initiation of a helix A third parameter which specifies the minimum number of segments in a random section between two helical portions has only a minor effect on the results The partition function for this model is handled in two alternative ways, either as a summation suitable for short chains, or in terms of the eigenvalues and eigenvectors of a characteristic matrix; the latter is more suitable for long chains A transition from the random to the helical form is encountered as either the bonding parameter or the chain length is increased The critical value of the bonding pa