Helical Pores Research Articles

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

In the current report, we provide a quantitative analysis of the convergence of the sampling of conformational space accomplished in molecular dynamics simulations of membrane proteins of duration in the order of 10 nanoseconds. A set of proteins of diverse size and topology is considered, ranging from helical pores such as gramicidin and small beta-barrels such as OmpT, to larger and more complex structures such as rhodopsin and FepA. Principal component analysis of the C(alpha)-atom trajectories was employed to assess the convergence of the conformational sampling in both the transmembrane domains and the whole proteins, while the time-dependence of the average structure was analyzed to obtain single-domain information. The membrane-embedded regions, particularly those of small or structurally simple proteins, were found to achieve reasonable convergence. By contrast, extra-membranous domains lacking secondary structure are often markedly under-sampled, exhibiting a continuous structural drift. This drift results in a significant imprecision in the calculated B-factors, which detracts from any quantitative comparison to experimental data. In view of such limitations, we suggest that similar analyses may be valuable in simulation studies of membrane protein dynamics, in order to attach a level of confidence to any biologically relevant observations.

Self-assembly of amphiphilic dendritic dipeptides into helical pores

Natural pore-forming proteins act as viral helical coats and transmembrane channels, exhibit antibacterial activity and are used in synthetic systems, such as for reversible encapsulation or stochastic sensing. These diverse functions are intimately linked to protein structure. The close link between protein structure and protein function makes the design of synthetic mimics a formidable challenge, given that structure formation needs to be carefully controlled on all hierarchy levels, in solution and in the bulk. In fact, with few exceptions, synthetic pore structures capable of assembling into periodically ordered assemblies that are stable in solution and in the solid state have not yet been realized. In the case of dendrimers, covalent and non-covalent coating and assembly of a range of different structures has only yielded closed columns. Here we describe a library of amphiphilic dendritic dipeptides that self-assemble in solution and in bulk through a complex recognition process into helical pores. We find that the molecular recognition and self-assembly process is sufficiently robust to tolerate a range of modifications to the amphiphile structure, while preliminary proton transport measurements establish that the pores are functional. We expect that this class of self-assembling dendrimers will allow the design of a variety of biologically inspired systems with functional properties arising from their porous structure.

Simulation Studies of a Helical m-Phenylene Ethynylene Foldamer

The folded state of an oligo(m-phenylene ethynylene) foldamer solvated in water is examined using a 30 ns NpT molecular dynamics simulation. The 18-monomer oligomer with methyl ester exterior side groups maintains a helical structure, where turns of the helix are in close contact throughout the simulation. The structure exhibits large fluctuations in both the radius of the interior cylindrical pore and the effective dihedral angle between monomers. The radius fluctuations are correlated with the number of water molecules within the helical pore. The folded state is found to be surprisingly flexible while maintaining a helical structure.

Chiral Supramolecular Materials from Columnar Liquid Crystals

Chirality plays an integral role in the molecular organization of many liquid crystals and, consequently, in the design of liquid crystal-based supramolecular materials. Chiral columnar phases are of particular interest since they can serve as synthetic templates for polymer networks with helical channels or pores. Several β-diketonate ligands have been synthesized to contain a chiral directing element and/or a polymerizable moiety. Octahedral iron complexes of these ligands were crosslinked in the columnar hexagonal phase using acyclic diene metathesis (ADMET) polymerization. The resulting materials were chiral and retained the order of the mesophase.

Fabrication and optical characterization of template-constructed thin films with chiral nanostructure

We report the fabrication of thin films perforated by high aspect ratio helical or chevron pores by an extension of the glancing angle deposition (GLAD) technique. The perforated films were created by transferring the nanostructure of a GLAD template film into target materials such as polymers and spin-on-glasses and subsequently removing the template. The pore shapes are shown to be highly controllable and films designed to suit particular applications are discussed. By a double templating technique, we replicate the structure of the original film using alternate materials, which are typically less suited to the unmodified GLAD technique. Helical films of Cu and Ni were created by this method and the process should be transferable to additional electrodeposited materials. The optical rotatory power of perforated thin films formed on glass substrates was characterized and perforated films were shown to be effective in rotating the polarization plane of linearly polarized incident light by as much as 1.4/spl deg///spl mu/m.

The Position of Aib Residues Defines the Antimicrobial Activity of Aib-Containing Peptides

Abstract 2-Aminoisobutyric acid (Aib,1 2-amino-2-methylpropionic acid) is an unusual amino acid, which is present in some antimicrobial peptides. To elucidate the impact of Aib residues on the conformation and biological activity of ion channel forming peptides, Aib residues in Ac-(Aib-Lys-Aib-Ala)5-NH2 were partially and fully replaced by Ala residues. A total of three analogs were thus synthesized. Two of these analogs, Ac-(Aib-Lys-Ala-Ala)5-NH2 (BKAA-20) and Ac-(Ala-Lys-Aib-Ala)5-NH2 (AKBA-20), had similar amino acid composition and were not hemolytic. BKAA-20 exhibited comparable antimicrobial activity to gramicidin S against Gram-positive bacteria (minimum inhibitory concentration: ∼3.13 µg ml-1), whereas AKBA-20 was not active. Single-channel measurements showed that there was a clear correlation between the antimicrobial activity and the ion channel activity in these analogs. The third analog, Ac-(Ala-Lys-Ala-Ala)5-NH2, was biologically inactive. Circular dichroism spectroscopy revealed that the helix forming propensities of BKAA-20 and AKBA-20 were independent of the position of Aib residues in negatively charged phospholipid vesicles, as mimics of external cell membranes of bacteria. However, different positions of Aib residues in BKAA-20 and AKBA-20 affected their antimicrobial activity. It is indicated that the introduction of Aib residues into the peptide backbone not only promotes the generation of stable helical conformations, but also modulates the antimicrobial activity. The results of this study can implicate a deeper understanding of the role of Aib residues in the structure-activity relationships of helical pore forming peptides, which in turn promotes the rational design of effective antimicrobial peptides.

Fabrication of Perforated Film Nanostructures

ABSTRACTWe have demonstrated the fabrication of perforated thin films (PTFs), comprised of thin coatings perforated with unusual pore shapes such as helices or chevrons. PTFs are fabricated using a template of nanohelices or nanochevrons produced using the Glancing Angle Deposition (GLAD) technique. PTFs can be produced by filling GLAD films with a variety of substances, etching back the coating to reveal the tips of the helices or chevrons, and etching out the template film. A process for fabricating nickel PTFs has been developed, and a nickel PTF of helical pores with nominal diameters of 100nm has been produced.

Fabrication of Perforated Thin Films with Helical and Chevron Pore Shapes

Fabrication of Perforated Thin Films with Helical and Chevron Pore Shapes

Collagen fiber arrangement in canine hepatic venules.

Cell-maceration/scanning electron microscopy, serial sections and scanning electron microscopy of vascular resin casts were employed to demonstrate the arrangement of collagen fibers in the terminal hepatic venules, involving the central, intercalated and collecting veins in dog liver. In cell-maceration specimens, each collagen fiber was observed to run in various directions, forming a sheath with a compact meshwork of collagen fibers. The collagenous meshwork in the hepatic venules was looser than those of the terminal portal venules and hepatic arterioles. Some collagen fibers formed bundles with an elongated spiral arrangement encircling the wall of the terminal hepatic venules. In resin casts, these venules were observed as a twisted configuration caused by spiral collagen bundles. A helical modification of such connective tissue bundles might provide a mechanically stable vascular structure and permit reversible changes in linear and circumferential vascular dimensions at the terminal tributaries of veins. Round or oval pores with diameters of approximately 9 microns were also observed in the sheath of collagen fibers. These pores, together with the relatively loose collagenous meshwork in the hepatic venules, might play a role in lymphocyte migration from these venules into the surrounding tissue and provide high permeability to the venule walls. No such helical configuration and pores were observed in either the portal venules or the hepatic arterioles.

ChemInform Abstract: Synthesis and Organization of Zeolite‐Like Materials with Three‐Dimensional Helical Pores.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Synthesis and organization of zeolite-like materials with three-dimensional helical pores

The increasing demand for enantiomerically pure chemicals has stimulated extensive research into the preparation of heterogeneous chiral catalysts or separation media that combine both shape selectivity and enantioselectivity1. Helical pores in inorganic materials might be able to perform such functions, but their occurrence is rare1. Attempts have been reported to synthesize a specific enantiomorph of the chiral zeolite beta2, and chiral metal complexes have been used to assemble inorganic precursors into chiral frameworks3,4. Materials with a fully three-dimensional array of helical structural units are particularly rare, because helical structures (such as quartz) are commonly generated by a uni-dimensional symmetry element acting on an achiral structural subunit5,6. Here we report on a family of zeolite-type materials (which we call UCSB-7) that possess two independent sets of three-dimensional crosslinked helical pores, separated by a gyroid periodic minimal surface13. We have synthesized the UCSB-7 framework for various compositions (zinc and beryllium arsenates, gallium germanate) using either inorganic cations or amines as structure-directing agents. The helical-ribbon motif that we identify might be exploited more widely for developing useful chiral solid-state structures.

Recent Advances in the High Resolution Structures of Bacterial Channels: Gramicidin A

Gramicidin is a polypeptide antibiotic which forms dimeric channels specific for the transport of monovalent cations across membranes. It adopts several different conformations, most notably double helical (pore) and helical dimer (channels) forms, which have very different structural and functional characteristics. This review focuses on recent high resolution structure determinations of both the pore and channel forms of the molecule by X-ray crystallographic and/or NMR spectroscopic techniques. It discusses the structural consequences of binding ions and the location of ion binding sites and how the structures are related to the conductance properties of the molecule. This relatively simple molecule is probably the best characterized ion channel (both structurally and functionally) and has, to date, been the principal proving-ground for many of our ideas about the molecular nature of ion conduction in membranes.

The gramicidin pore: Selective tryptophan replacement with aspartic acid

The chemoselective transformation of Trp 9 and Trp 11, located at the hydrophobic core of the antiparallel, double helical pore of O-acetyl gramicidin A(HCO-ValGlyAlaLeu oAlaVal oValVal o TrpLeu o TrpLeu oTrpLeu oTrpNHCH 2CH 2OAc; o = D isomer) to Asp 9 gramicidin and Asp 9 Asp 11 gramicidin has been demonstrated by oxidation with 0.25 eq. of in situ generated Ru(VIII), HPLC isolation, amino acid analysis and peptide sequencing.

Protein electrophoresis in polyacrylamide gels with templated pores.

An approach is described for the synthesis of nanostructured hydrogels with defined size channels or pores for separations of biological macromolecules. Polyacrylamide gels (15-20% acrylamide) were cast in the presence of high concentrations (5%-28%) of hydrophilic, macromolecular cosolutes either semirigid, rod-like polyelectrolytes (short fragments of DNA or xanthan) or spherical micelles of sodium dodecyl sulfate (SDS). Polyanionic cosolutes were then removed by a combination of diffusion and electrophoresis. These processes are expected to yield gels with 'templated' channels having dimensions near those of the double helical polymers (diameters approximately 2-3 nm, lengths of 50-200 nm) or pores near the size of the spherical SDS micelles (approximately 4-5 nm). This hypothesis was tested by comparing the relative electrophoretic mobilities of proteins (3400 to 43,000 Da) complexed with SDS on templated and conventional gels. Differences in electrophoretic mobilities were observed between all templated gels and control normal gels, demonstrating that the templating process altered the polyacrylamide network. No evidence was found for phase separation of cosolutes from the polyacrylamide network during polymerization. Templated pores are expected to enhance the mobilities of molecules in a particular size range relative to smaller and larger molecules. Gels templated with DNA or xanthan (8-10% final concentration) exhibited little size selectivity, but selectivity was observed for gels templated with SDS varied with polyacrylamide concentration in a manner consistent with the creation of templated pores approximately the size of SDS micelles and larger than the average pore size in a surrounding polyacrylamide network.

Synthesis and Structure of NaGaSn2. A Zintl Phase with a Helical Framework Structure

A new Zintl phase NaGaSn2 is obtained pure from stoichiometric reactions of the elements in sealed Ta at ∼450 °C. Its orthorhombic framework structure (space group C2221, 6.309(3) × 10.986(4) × 6.162(4) Å) contains one-dimensional helical pores ∼6 Å in diameter along c⃗ (6 atoms/turn) that bind relatively well-ordered sodium countercations at 50% occupancy. The structure can also be described in terms of interlinked puckered double layers normal to b⃗ and parallel to the channels. Gallium is disordered over both tetrahedral framework sites, the gallium-richer and more negative site having closer sodium neighbors. The potassium compound cannot be made. Among analogous phases reported by others, NaInSn2 has a lower symmetry and ordered cations, while NaGaSn5 cannot be reproduced.

Ion pair binding of Ca 2+ and Cl − ions in micellar-packaged gramicidin A

The two independent NMR experiments were performed to investigate the interaction between CaCl 2 and the gramicidin A (GA) ion transport channel, using 13C-enriched GA and GA molecules incorporated into dodecylphosphocholine (DPC) micelles. The chemicals shifts of C-13 labeled carbonyl carbons vs. CaCl 2 concentration demonstrate that Ca 2+ and Cl − ions interact as an ion pair within the GA structure with the Cl − ion located near the position of the carbonyl group of the Trp 11 residue some 5.5 Å from the mouth of the GA helix, and the Ca 2+ ion bound at the position of the carbonyl group of the Trp 15 residue some 2.5 Å from the entrance to the helical pore. The measurements of the 35Cl line-widths and transverse relaxation times illustrate that the interaction occurs between Cl − ions and GA in DPC when in CaCl 2 solution, that no interaction is detected between Cl − ions and GA in DPC when in NaCl solution, and that the interaction between Cl − ions and GA in DPC when in MgCl 2 solution is much weaker than in CaCl 2 solution. In short, a Cl − ion can enter the GA when it is paired with a divalent Ca 2+ ion; and Ca 2+ and Cl − ions as a pair exchange rapidly with sites of the GA dimer.

Transverse cuticular structures arise above actin filament bundles in the epidermis of Calpodes ethlius (Stöll) (Lepidoptera : Hesperiidae)

Rhodaminyl phalloin labelling of larval epidermal cells in Calpodes ethlius (Stöll) (Lepidoptera : Hesperiidae) shows dorsal areas with apical bundles of F-actin. The bundles are present only during the first 36 hr of the 5th stadium. Most cells have only one or 2, rarely 3, 4 or 5. The bundles extend into the overlying cuticle as the cores of large helical microvilli that continue on as transverse cuticle components, resembling very large helical pore canals. The transverse structures are like those seen in extensible insect cuticles that may allow cuticular stretching during larval growth. Neither the bundles nor the transverse structures are easily resolvable by conventional stains for LM or EM. The results suggest that transverse fibrillar structures may be a more common component of soft cuticles than has been generally realized.