Conformational preferences of the amylin nucleation site in SDS micelles: an NMR study

Human islet amyloid polypeptide (hIAPP), or amylin, is a 37 amino acid hormone secreted by pancreatic beta-cells. hIAPP constitutes approximately 90% of the amyloid deposits found in type II diabetic patients. It has been shown that the central region of the peptide (hIAPP(20-29)) constitutes the nucleation site for the amyloidogenic process with F23 playing a key role in the formation of the beta-pleated structures. In addition, it has been proposed that an important stage in the cytotoxicity of hIAPP is its interaction with the beta-cell membranes. As a first step toward the characterization of the interaction of hIAPP with cell membranes, we determined conformational preferences of hIAPP(20-29) in membrane-mimicking environments. We found that upon interacting with negatively charged micelles, the dominant conformation of hIAPP(20-29) is a distorted type I beta-turn centered on residues F23 and G24, with F23, A25, and I26 forming a small hydrophobic cluster that may facilitate the interaction of this peptide with the membrane bilayer. Moreover, we were able to elucidate the topological orientation of the peptide that is absorbed on the micelle surface, with the hydrophobic cluster oriented toward the hydrocarbon region of the micelles and both N- and C-termini exposed to the solvent.     

Molecular dynamics simulation studies of cytochrome b5 from outer mitochondrial and microsomal membrane

Two forms of cytochrome b(5) have been identified, associated with the outer membrane of liver mitochondria (OM cyt b(5)) and with the membrane of the endoplasmic reticulum (microsomal, Mc cyt b(5)). These proteins have very similar structures, but differ significantly in physical properties, with the OM cyt b(5) exhibiting a more negative reduction potential, higher stability, and stronger interactions with the heme. We perform molecular dynamics simulations to probe the structures and fluctuations of the two proteins in solution, to help explain the observed physical differences. We find that the structures of the two proteins, highly similar in the crystal, differ in position of a surface loop involving residues 49-51 in solution. Hydrophobic residues Ala-18, Ile-32, Leu-36, and Leu-47 tend to cluster together on the surface of rat OM cyt b(5), blocking water access to the protein interior. In bovine Mc cyt b(5), two of these positions, Ser-18 and Arg-47, are occupied by hydrophilic residues. This leads to breaking the hydrophobic cluster and allowing the protein to occupy a more open conformation. A measure of this structural transition is the opening of a cleft on the protein surface, which is 5 A wider in the OM cyt b(5) simulation compared to the Mc form. The OM protein also appears to have a more compact hydrophobic core in its beta-sheet region. These effects may be used to explain observed stability differences between the two proteins.     

Use of terrestrial chemical trails for nest orientation in an open nesting wasp, <Emphasis Type="Italic">Dolichovespula saxonica</Emphasis> F.

Summary The long-cheeked wasp Dolichovespula saxonica typically constructs exposed nests which can be reached by flying. Usually foragers do not walk on substrates in the close vicinity of the nests as cavity breeding wasps do (Steinmetz et al., 2002). Unexpectedly, when forced to walk outside the nest instead of flying in an artificial tunnel system, D. saxonica foragers lay a terrestrial trail and use it for orientation in the nest area in our experiments. 41% of the foragers followed the trail in a direction they were not accustomed to. We suggest that the foragers have employed the same orientation cues normally used for orientation in the close vicinity of the nest when approaching a free-hanging nest by flying, for example nest odour. Nest odour substances may have been transferred to the substrate as a trail as a consequence of foragers walking through the tunnels.Received 23 August 2002; revised 27 January 2003; accepted 30 April 2003.     

Relative lengths of fingers and toes in human males and females

Digital scans of the hands and feet were obtained from 62 heterosexual females and 60 heterosexual males. Scans only of the hands were obtained from 29 homosexual females and 35 homosexual males. The lengths of the individual fingers and toes were estimated from those images by two experienced judges, and length ratios were constructed for all possible pairs of fingers (or toes) on each hand (or foot). Thumbs were not measured, but the great toe was measured and used to construct length ratios. Past research had concentrated on the relative lengths of the index and ring fingers (the 2D:4D ratio). This ratio is close to 1.0 in females and smaller than 1.0 in males. Here 2D:4D did exhibit the largest sex difference, for both hands, followed by 2D:5D and 3D:4D. The sex differences were larger for the right hand than for the left. For both homosexual females and homosexual males, nearly all of the length ratios for fingers were intermediate to those for heterosexual females and heterosexual males; that is, the ratios of homosexual females were masculinized and those of homosexual males were hypomasculinized, but few of these differences were significant. Because many toes were substantially arched, acceptable estimates of length often could not be obtained from the two-dimensional scans, meaning that conclusions about toes are much less certain than those for fingers. Nevertheless, the length ratios were generally larger for toes than for fingers, and the sex differences were generally smaller for toes.     

Towards high-resolution solid-state NMR on large uniformly 15N- and [13C,15N]-labeled membrane proteins in oriented lipid bilayers

Based on exact numerical simulations, taking into account isotropic and conformation-dependent anisotropic nuclear spin interactions, we systematically analyse the prospects for high-resolution solid-state NMR on large isotope-labeled membrane proteins macroscopically oriented in phospholipid bilayers. Using the known X-ray structures of rhodopsin and porin as models for large membrane proteins with typical -helical and -barrel structural motifs, the analysis considers all possible one- to six-dimensional spectra comprised of frequency dimensions with evolution under any combination of amide ¹H, amide ¹⁵N, and carbonyl ¹³C chemical shifts as well as ¹H-¹⁵N dipole-dipole couplings. Under consideration of typical nuclear spin interaction and experimental line-shape parameters, the analysis provides new insight into the resolution capability and orientation-dependent transfer efficiency of existing experiments as well as guidelines as to improved experimental approaches for the study of large uniformly ¹⁵N- and [¹³C,¹⁵N]-labeled membrane proteins. On basis of these results and numerical optimizations of coherence-transfer efficiencies, we propose several new high-resolution experiments for sequential protein backbone assignment and structure determination.     

Solution structure determination of the two DNA-binding domains in the Schizosaccharomyces pombe Abp1 protein by a combination of dipolar coupling and diffusion anisotropy restraints

We have solved the solution structure of the N-terminal region of the fission yeast centromere protein, Abp1, bound to a 21-base pair DNA fragment bearing its recognition site (Mw = 30 kDa). Although the two DNA-binding domains in the Abp1 protein were defined well by a conventional NOE-based NMR methodology, the overall structure of the Abp1 protein was poorly defined, due to the lack of interdomain distance restraints. Therefore, we additionally used residual dipolar couplings measured in a weakly aligned state, and rotational diffusion anisotropies. Neither the NH residual dipolar couplings nor the backbone ¹⁵N T ₁/T ₂ data were sufficient to determine the overall structure of the Abp1 protein, due to spectral overlap. We used a combination of these two orientational restraints (residual dipolar coupling and rotational diffusion anisotropy), which significantly improved the convergence of the overall structures. The range of the observed T ₁/T ₂ ratios was wider (20–50 for the secondary structure regions of Abp1) than the previously reported data for several globular proteins, indicating that the overall shape of the Abp1DNA complex is ellipsoid. This extended form would facilitate the recognition of the two separate sites in the relatively long DNA sequence by the DNA-binding domains of Apb1.     

Cellulose orientation at the surface of the Arabidopsis seedling. Implications for the biomechanics in plant development

In diffuse growing cells the orientation of cellulose fibrils determines mechanical anisotropy in the cell wall and hence also the direction of plant and organ growth. This paper reports on the mean or net orientation of cellulose fibrils in the outer epidermal wall of the whole Arabidopsis plant. This outer epidermal wall is considered as the growth-limiting boundary between plant and environment. In the root a net transverse orientation of the cellulose fibrils occurs in the elongation zone, while net random and longitudinal orientations are found in subsequent older parts of the differentiation zone. The position and the size of the transverse zone is related with root growth rate. In the shoot the net orientation of cellulose fibrils is transverse in the elongating apical part of the hypocotyl, and longitudinal in the fully elongated basal part. Leaf primordia and very young leaves have a transverse orientation. Throughout further development the leaf epidermis builds a very complex pattern of cells with a random orientation and cells with a transverse or a longitudinal orientation of the cellulose fibrils. The patterns of net cellulose orientation correlate well with the cylindrical growth of roots and shoots and with the typical planar growth of the leaf blade. On both the shoot and the root surface very specific patterns of cellulose orientation occur at sites of specific cell differentiation: trichome-socket cells complexes on the shoot and root hairs on the root.     

A new group-selection model for the evolution of homosexuality

Abstract. Scientists have long puzzled over how homosexual orientation has evolved, given the assumed low relative fitness of homosexual individuals compared to heterosexual individuals. A number of theoretical models for the evolution of homosexuality have been postulated including balance polymorphism, "Fertile females", hypervariability of DNA sequences, kin selection, and "parental manipulation". In this paper, I propose a new group-selection model for the evolution of homosexuality which offers two advantages over existing models: (1) its non-assumption of genetic determinism, and (2) its lack of dependency on an inefficient altruism relation and family dynamics theory.     

A cooperation and competition based simple cell receptive field model and study of feed-forward linear and nonlinear contributions to orientation selectivity

We present a model for development of orientation selectivity in layer IV simple cells. Receptive field (RF) development in the model, is determined by diffusive cooperation and resource limited competition guided axonal growth and retraction in geniculocortical pathway. The simulated cortical RFs resemble experimental RFs. The receptive field model is incorporated in a three-layer visual pathway model consisting of retina, LGN and cortex. We have studied the effect of activity dependent synaptic scaling on orientation tuning of cortical cells. The mean value of hwhh (half width at half the height of maximum response) in simulated cortical cells is 58° when we consider only the linear excitatory contribution from LGN. We observe a mean improvement of 22.8° in tuning response due to the non-linear spiking mechanisms that include effects of threshold voltage and synaptic scaling factor.     

Micromechanics and anatomical changes during early ontogeny of two lianescent Aristolochia species

 The mechanical properties of young stems of Aristolochia macrophylla Lam. and Aristolochia brasiliensis Mart. et Zucc. were studied during elongation growth and primary differentiation. Data for the modulus of elasticity, for the viscoelastic behaviour caused by longitudinal tension and for the shear modulus resulting from torsion around a longitudinal axis were related to the underlying structural changes by quantitative analysis of stem anatomy, tissue distribution, ultrastructure, and cell wall biochemistry. The orientation of cellulose microfibrils was determined by light microscopy and small-angle X-ray diffraction, and the lignin content was determined by thioglycolic acid derivatization and spectroscopic quantification. It was demonstrated that the increase in stability during early development is due to the complementary effects of increase in cell wall material, lignification, and cellulose microfibril alignment. A detailed micromechanical model, considering internal prestresses, is proposed to explain the characteristic biphasic stress-strain behaviour as well as the strain-hardening observed. Received: 22 March 1999 / Accepted 9 September 1999